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Hou Z, Fang C, Liu B, Yang H, Kong F. Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:36. [PMID: 37309391 PMCID: PMC10248697 DOI: 10.1007/s11032-023-01382-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 06/14/2023]
Abstract
Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.
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Affiliation(s)
- Zhihong Hou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Hui Yang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
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52
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Zhu Z, Esche F, Babben S, Trenner J, Serfling A, Pillen K, Maurer A, Quint M. An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2912-2931. [PMID: 36449391 DOI: 10.1093/jxb/erac470] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/28/2022] [Indexed: 06/06/2023]
Abstract
Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele of Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate-resilient crops.
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Affiliation(s)
- Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Finn Esche
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Steve Babben
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Str. 27, D-06484, Quedlinburg, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Puschstrasse 4, D-04103, Leipzig, Germany
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Yang Y, Li Y, Cheng Z, Su Q, Jin X, Song Y, Wang J. Genetic analysis and exploration of major effect QTLs underlying oil content in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:97. [PMID: 37027047 DOI: 10.1007/s00122-023-04328-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/20/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE AhyHOF1, likely encoding a WRI1 transcription factor, plays critical roles in peanut oil synthesis. Although increasing the oil content of peanut to meet growing demand has long been a primary aim of breeding programs worldwide, the mining of genetic resources to achieve this objective has obviously lagged behind that of other oil crops. In the present study, we developed an advanced recombinant inbred line population containing 192 F9:11 families derived from parents JH5 and KX01-6. We then constructed a high-resolution genetic map covering 3,706.382 cM, with an average length of 185.32 cM per linkage group, using 2840 polymorphic SNPs. Two stable QTLs, qCOA08_1 and qCOA08_2 having the highest contributions to genetic variation (16.1% and 20.7%, respectively), were simultaneously detected in multiple environments and closely mapped within physical intervals of approximately 2.9 Mb and 1.7 Mb, respectively, on chromosome A08. In addition, combined analysis of whole-genome and transcriptome resequencing data uncovered a strong candidate gene encoding a WRI1 transcription factor and differentially expressed between the two parents. This gene, designated as High Oil Favorable gene 1 in Arachis hypogaea (AhyHOF1), was hypothesized to play roles in oil accumulation. Examination of near-inbred lines of #AhyHOF1/#Ahyhof1 provided further evidence that AhyHOF1 increases oil content, mainly by affecting the contents of several fatty acids. Taken together, our results provide valuable information for cloning the favorable allele for oil content in peanut. In addition, the closely linked polymorphic SNP markers within qCOA08_1 and qCOA08_2 loci may be useful for accelerating marker-assisted selection breeding of peanut.
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Affiliation(s)
- Yongqing Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yurong Li
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Zengshu Cheng
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Qiao Su
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Xinxin Jin
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yahui Song
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China
| | - Jin Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, The Key Laboratory of Crop Genetics and Breeding of Hebei, Shijiazhuang, 050035, Hebei, China.
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Tang Y, Lu S, Fang C, Liu H, Dong L, Li H, Su T, Li S, Wang L, Cheng Q, Liu B, Lin X, Kong F. Diverse flowering responses subjecting to ambient high temperature in soybean under short-day conditions. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:782-791. [PMID: 36578141 PMCID: PMC10037154 DOI: 10.1111/pbi.13996] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/06/2022] [Accepted: 12/17/2022] [Indexed: 06/14/2023]
Abstract
Flowering time is one of important agronomic traits determining the crop yield and affected by high temperature. When facing high ambient temperature, plants often initiate early flowering as an adaptive strategy to escape the stress and ensure successful reproduction. However, here we find opposing ways in the short-day crop soybean to respond to different levels of high temperatures, in which flowering accelerates when temperature changes from 25 to 30 °C, but delays when temperature reaches 35 °C under short day. phyA-E1, possibly photoperiodic pathway, is crucial for 35 °C-mediated late flowering, however, does not contribute to promoting flowering at 30 °C. 30 °C-induced up-regulation of FT2a and FT5a leads to early flowering, independent of E1. Therefore, distinct responsive mechanisms are adopted by soybean when facing different levels of high temperatures for successful flowering and reproduction.
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Affiliation(s)
- Yang Tang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Huan Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lidong Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Tong Su
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Shichen Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Qun Cheng
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and Agroecology, Chinese Academy of SciencesHarbinChina
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life SciencesGuangzhou UniversityGuangzhouChina
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and Agroecology, Chinese Academy of SciencesHarbinChina
- College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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55
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Bandillo NB, Jarquin D, Posadas LG, Lorenz AJ, Graef GL. Genomic selection performs as effectively as phenotypic selection for increasing seed yield in soybean. THE PLANT GENOME 2023; 16:e20285. [PMID: 36447395 DOI: 10.1002/tpg2.20285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/08/2022] [Indexed: 05/10/2023]
Abstract
Increasing the rate of genetic gain for seed yield remains the primary breeding objective in both public and private soybean [Glycine max (L.) Merr.] breeding programs. Genomic selection (GS) has the potential to accelerate the rate of genetic gain for soybean seed yield. Limited studies to date have validated GS accuracy and directly compared GS with phenotypic selection (PS), and none have been reported in soybean. This study conducted the first empirical validation of GS for increasing seed yield using over 1,500 lines and over 7 yr (2010-2016) of replicated experiments in the University of Nebraska-Lincoln soybean breeding program. The study was designed to capture the varying genetic relatedness of the training population to three validation sets: two large biparental populations (TBP-1 and TBP-2) and a large validation set comprised of 457 preselected advanced lines derived from 45 biparental populations (TMP). We found that prediction accuracy (.54) realized in our validation experiments was comparable with what we obtained from a series of cross-validation experiments (.64). Both GS and PS were more effective for increasing the population mean performance compared with random selection (RS). We found a selection advantage of GS over PS, where higher genetic gain and identification of top-performing lines was maximized at 10-20% selected proportion. Genomic selection led to small increases in genetic similarity when compared with PS and RS presumably because of a significant shift on allelic frequencies toward the extremes, suggesting that it could erode genetic diversity more quickly. Overall, we found that GS can perform as effectively as PS but that measures should be considered to protect against loss of genetic variance when using GS.
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Affiliation(s)
- Nonoy B Bandillo
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, 363 Keim Hall, Lincoln, NE, 68583, USA
- Dep. of Plant Sciences, North Dakota State Univ., NDSU Dep. 7670, P.O. Box 6050, Fargo, ND, 58108-6050, USA
| | - Diego Jarquin
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, 363 Keim Hall, Lincoln, NE, 68583, USA
- Agronomy Dep., Univ. of Florida, 2089 McCarthy Hall B, Gainesville, FL, 32611, USA
| | - Luis G Posadas
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, 363 Keim Hall, Lincoln, NE, 68583, USA
| | - Aaron J Lorenz
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, 363 Keim Hall, Lincoln, NE, 68583, USA
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, 55108-6026, USA
| | - George L Graef
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, 363 Keim Hall, Lincoln, NE, 68583, USA
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56
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Liu Z, Liu W, Wang Z, Qi K, Xie Z, Zhang S, Wu J, Wang P. Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus. PHYSIOLOGIA PLANTARUM 2023; 175:e13893. [PMID: 36929905 DOI: 10.1111/ppl.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.
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Affiliation(s)
- Zhe Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, China
| | - Weijuan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhangqing Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
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Identifications of QTLs and Candidate Genes Associated with Pseudomonas syringae Responses in Cultivated Soybean ( Glycine max) and Wild Soybean ( Glycine soja). Int J Mol Sci 2023; 24:ijms24054618. [PMID: 36902050 PMCID: PMC10003559 DOI: 10.3390/ijms24054618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/06/2023] Open
Abstract
Soybeans (Glycine max) are a key food crop, serving as a valuable source of both oil and plant-derived protein. Pseudomonas syringae pv. glycinea (Psg) is among the most aggressive and prevalent pathogens affecting soybean production, causing a form of bacterial spot disease that impacts soybean leaves and thereby reduces crop yields. In this study, 310 natural soybean varieties were screened for Psg resistance and susceptibility. The identified susceptible and resistant varieties were then used for linkage mapping, BSA-seq, and whole genome sequencing (WGS) analyses aimed at identifying key QTLs associated with Psg responses. Candidate Psg-related genes were further confirmed through WGS and qPCR analyses. Candidate gene haplotype analyses were used to explore the associations between haplotypes and soybean Psg resistance. In addition, landrace and wild soybean plants were found to exhibit a higher degree of Psg resistance as compared to cultivated soybean varieties. In total, 10 QTLs were identified using chromosome segment substitution lines derived from Suinong14 (cultivated soybean) and ZYD00006 (wild soybean). Glyma.10g230200 was found to be induced in response to Psg, with the Glyma.10g230200 haplotype corresponding to soybean disease resistance. The QTLs identified herein can be leveraged to guide the marker-assisted breeding of soybean cultivars that exhibit partial resistance to Psg. Moreover, further functional and molecular studies of Glyma.10g230200 have the potential to offer insight into the mechanistic basis for soybean Psg resistance.
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58
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Roy A, Reddy MH, Sarkar M, Sagolsem D, Murmu SK, Das C, Roy D, Ganguly S, Nath R, Bhattacharyya PK, Sarker A, Bhattacharyya S. A mis-splicing early flowering 3 (elf3) allele of lentil is associated with yield enhancement under terminal heat stress. J Appl Genet 2023; 64:265-273. [PMID: 36821070 DOI: 10.1007/s13353-023-00753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 01/28/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
There is a vast scope of area expansion of lentils after harvesting wet rice in South Asia. However, due to the photoperiod effect and terminal heat, the existing short-duration varieties failed to minimize yield loss under late-sown conditions. A mis-splicing causing A/G SNP present in the last nucleotide of exon 3 of early flowering 3 (ELF3) gene (elf3 allele) in a lentil line, L4710, is associated with the photoperiod insensitive flowering and the fast absolute growth rate (AGR). None of the Indian cultivars tested in this study, either early or late, possesses the non-functional elf3 allele. However, the A to G transition in ELF3-exon2 replaces glycine with aspartic acid at the 403rd amino acid in all the Indian varieties tested, compared to the reference sequence of Mediterranean accession, ILL5588. Therefore, targeting A/G SNP of exon 3, a PCR-based codominant marker is developed. The elf3 allele is correlated with the fast AGR and early flowering, but low yield and biomass, in an L4710 × LL56-derived RIL-population, compared to ELF3 carrying alleles when sown on 15th November. However, in a month of delayed sowing (20th December), the same elf3-RILs revealed a higher yield and biomass with slower AGR Moreover, three elf3-carrying lines, grown in delayed condition (20 December) for two consecutive years in three locations, outyielded three popular high-yielding cultivars that carry functional ELF3. Thus, elf3-carrying high-yielding lines could be the breeder's choice to expand and enhance lentil yield in short-season environments and in vast rice fallows of south Asia, where delayed rice harvest occurs frequently.
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Affiliation(s)
- Anirban Roy
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - M Hemakumar Reddy
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Moutushi Sarkar
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Diana Sagolsem
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Sumit K Murmu
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Camellia Das
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Debarati Roy
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Shamba Ganguly
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Rajib Nath
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Prabir K Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Asutosh Sarker
- ICARDA, South Asia-China Regional Office, New Delhi, 110012, India
| | - Somnath Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India.
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59
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Qiu L, Zhou P, Wang H, Zhang C, Du C, Tian S, Wu Q, Wei L, Wang X, Zhou Y, Huang R, Huang X, Ouyang X. Photoperiod Genes Contribute to Daylength-Sensing and Breeding in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:899. [PMID: 36840246 PMCID: PMC9959395 DOI: 10.3390/plants12040899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa L.), one of the most important food crops worldwide, is a facultative short-day (SD) plant in which flowering is modulated by seasonal and temperature cues. The photoperiodic molecular network is the core network for regulating flowering in rice, and is composed of photoreceptors, a circadian clock, a photoperiodic flowering core module, and florigen genes. The Hd1-DTH8-Ghd7-PRR37 module, a photoperiodic flowering core module, improves the latitude adaptation through mediating the multiple daylength-sensing processes in rice. However, how the other photoperiod-related genes regulate daylength-sensing and latitude adaptation remains largely unknown. Here, we determined that mutations in the photoreceptor and circadian clock genes can generate different daylength-sensing processes. Furthermore, we measured the yield-related traits in various mutants, including the main panicle length, grains per panicle, seed-setting rate, hundred-grain weight, and yield per panicle. Our results showed that the prr37, elf3-1 and ehd1 mutants can change the daylength-sensing processes and exhibit longer main panicle lengths and more grains per panicle. Hence, the PRR37, ELF3-1 and Ehd1 locus has excellent potential for latitude adaptation and production improvement in rice breeding. In summary, this study systematically explored how vital elements of the photoperiod network regulate daylength sensing and yield traits, providing critical information for their breeding applications.
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Affiliation(s)
- Leilei Qiu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Peng Zhou
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
| | - Hao Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang 110101, China
| | - Chengxing Du
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shujun Tian
- Liaoning Rice Research Institute, Shenyang 110101, China
| | - Qinqin Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Litian Wei
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoying Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yiming Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Rongyu Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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60
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Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
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Affiliation(s)
- Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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Genome-wide signatures of the geographic expansion and breeding of soybean. SCIENCE CHINA. LIFE SCIENCES 2023; 66:350-365. [PMID: 35997916 DOI: 10.1007/s11427-022-2158-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/30/2022] [Indexed: 10/15/2022]
Abstract
Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean (Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces (G. max (L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.
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Qiu G, Han Z, Wang Q, Wang T, Sun Z, Yu Y, Han X, Yu H. Toxicity effects of nanoplastics on soybean (Glycine max L.): Mechanisms and transcriptomic analysis. CHEMOSPHERE 2023; 313:137571. [PMID: 36535503 DOI: 10.1016/j.chemosphere.2022.137571] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Microplastic (MP) pollution has become a major concern in recent years. In agricultural production, MPs can not only affect the growth of crops but also affect yield. Compared with micron-sized MPs, nanoplastics (NPs) may be more harmful to plants. However, the effects of NPs on plant growth and development have attracted relatively little attention. As such, research has currently plateaued at the level of morphology and physiology, and the molecular mechanisms are still unclear. In this study, soybeans (Glycine max L.) were treated with polystyrene nanoplastics (PS-NPs) to observe phenotypic changes and measure the effects of PS-NPs on diverse aspects of soybeans. Compared to the control group, the soybean stem and root lengths were inhibited by 11.78% and 12.58%, respectively. The reactive oxygen species content and the antioxidant enzyme activities changed significantly (p < 0.05). The accumulation of manganese (Mn) and magnesium (Mg) in the roots revealed that root transmembrane transport was affected by PS-NPs stress. The content of salicylic acid 2-O-β-glucoside was inhibited whereas the accumulation of l-tryptophan, the precursor of auxin synthesis, was significantly increased (p < 0.05) in leaves. Transcriptomic analysis showed that PS-NPs could affect soybean DNA repair, membrane protein transport, and hormone synthesis and response. This study revealed the toxicity of NPs to soybeans and that NPs affected a variety of biological processes through transcriptome and hormone metabolome analysis, which provides a theoretical basis to further study the molecular mechanism of the effects on plants.
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Affiliation(s)
- Guankai Qiu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhongmin Han
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Quanying Wang
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Tianye Wang
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhenghao Sun
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yong Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xuerong Han
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Hongwen Yu
- Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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Abstract
A new study shows that natural variation in the flowering repressor E1-like-a (Tof4/E1La) promoted wild soybean adaptation to high latitudes. This lost early-flowering allele can be reintroduced into cultivated soybean for developing early-maturing cultivars.
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Affiliation(s)
- Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China; Sanya Institute of China Agricultural University, Hainan, China.
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64
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Dong L, Li S, Wang L, Su T, Zhang C, Bi Y, Lai Y, Kong L, Wang F, Pei X, Li H, Hou Z, Du H, Du H, Li T, Cheng Q, Fang C, Kong F, Liu B. The genetic basis of high-latitude adaptation in wild soybean. Curr Biol 2023; 33:252-262.e4. [PMID: 36538932 DOI: 10.1016/j.cub.2022.11.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022]
Abstract
In many plants, flowering time is influenced by daylength as an adaptive response. In soybean (Glycine max) cultivars, however, photoperiodic flowering reduces crop yield and quality in high-latitude regions. Understanding the genetic basis of wild soybean (Glycine soja) adaptation to high latitudes could aid breeding of improved cultivars. Here, we identify the Tof4 (Time of flowering 4) locus, which encodes by an E1-like protein, E1La, that represses flowering and enhances adaptation to high latitudes in wild soybean. Moreover, we found that Tof4 physically associates with the promoters of two important FLOWERING LOCUS T (FT2a and FT5a) and with Tof5 to inhibit their transcription under long photoperiods. The effect of Tof4 on flowering and maturity is mediated by FT2a and FT5a proteins. Intriguingly, Tof4 and the key flowering repressor E1 independently but additively regulate flowering time, maturity, and grain yield in soybean. We determined that weak alleles of Tof4 have undergone natural selection, facilitating adaptation to high latitudes in wild soybean. Notably, over 71.5% of wild soybean accessions harbor the mutated alleles of Tof4 or a previously reported gain-of-function allele Tof5H2, suggesting that these two loci are the genetic basis of wild soybean adaptation to high latitudes. Almost no cultivated soybean carries the mutated tof4 allele. Introgression of the tof4-1 and Tof5H2 alleles into modern soybean or editing E1 family genes thus represents promising avenues to obtain early-maturity soybean, thereby improving productivity in high latitudes.
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Affiliation(s)
- Lidong Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Shichen Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Tong Su
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chunbao Zhang
- Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yingdong Bi
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Yongcai Lai
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fan Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xinxin Pei
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhihong Hou
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiping Du
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hao Du
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Tai Li
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qun Cheng
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China; The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
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65
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Wang F, Li S, Kong F, Lin X, Lu S. Altered regulation of flowering expands growth ranges and maximizes yields in major crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1094411. [PMID: 36743503 PMCID: PMC9892950 DOI: 10.3389/fpls.2023.1094411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/04/2023] [Indexed: 06/14/2023]
Abstract
Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.
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Affiliation(s)
| | | | | | - Xiaoya Lin
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
| | - Sijia Lu
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
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66
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Wang X, Han J, Li R, Qiu L, Zhang C, Lu M, Huang R, Wang X, Zhang J, Xie H, Li S, Huang X, Ouyang X. Gradual daylength sensing coupled with optimum cropping modes enhances multi-latitude adaptation of rice and maize. PLANT COMMUNICATIONS 2023; 4:100433. [PMID: 36071669 PMCID: PMC9860186 DOI: 10.1016/j.xplc.2022.100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
To expand crop planting areas, reestablishment of crop latitude adaptation based on genetic variation in photoperiodic genes can be performed, but it is quite time consuming. By contrast, a crop variety that already exhibits multi-latitude adaptation has the potential to increase its planting areas to be more widely and quickly available. However, the importance and potential of multi-latitude adaptation of crop varieties have not been systematically described. Here, combining daylength-sensing data with the cropping system of elite rice and maize varieties, we found that varieties with gradual daylength sensing coupled with optimum cropping modes have an enhanced capacity for multi-latitude adaptation in China. Furthermore, this multi-latitude adaptation expanded their planting areas and indirectly improved China's nationwide rice and maize unit yield. Thus, coupling the daylength-sensing process with optimum cropping modes to enhance latitude adaptability of excellent varieties represents an exciting approach for deploying crop varieties with the potential to expand their planting areas and quickly improve nationwide crop unit yield in developing countries.
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Affiliation(s)
- Xiaoying Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiupan Han
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Rui Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Leilei Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang 110101, China
| | - Ming Lu
- Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Rongyu Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100083, China
| | - Jianfu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
| | - Huaan Xie
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China.
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67
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Zhang C, Xu X, Chen F, Yuan S, Wu T, Jiang B, Sapey E, Wu C, Sun S, Guo C, Han T. Establishment of a novel experimental system for studying the photoperiodic response of short-day dicots using soybean 'cotyledon-only plant' as material. FRONTIERS IN PLANT SCIENCE 2023; 13:1101715. [PMID: 36684791 PMCID: PMC9853180 DOI: 10.3389/fpls.2022.1101715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Soybean is an important model crop for photoperiodic response studies in plants and contributes significantly to the study of plant development and physiology in the past century. Because soybean plant is much bigger in size and longer in life cycle than Arabidopsis, it needs much more space for growth and time for investigation, which significantly hamper the efficiency of research. In the current study, we tested the photoperiodic response of a distinctive artificially-made cotyledon-only plant (COP) using a photoperiod-sensitive soybean variety Zigongdongdou (ZGDD) and other varieties with diverse sensitivity to photoperiod. ZGDD COPs flowered 39.4 ± 2.5 d after emergence under short-day conditions but maintained vegetative growth under long-day and night break conditions, which is similar to the case in the intact ZGDD plants. The COPs of early-maturing and medium-maturing soybean varieties also grew and flowered normally under natural day-length conditions. At the molecular level, the key genes in the photoperiodic pathway such as E1, GmFT1a, GmFT2a, and GmFT5a in the COPs also showed the same photoperiod sensitivity as in the intact plants. In addition, a simpler material of COP with only one cotyledon and root was generated and found to be sensitive to photoperiod as well. Notably, the COPs are only one-fifth the height of intact plants and one-third the maximum diameter of the intact plants grown in chambers 30 d after emergence. Based on COPs, we established a novel experimental system characterized by an entire photoperiodic response and longer longevity of cotyledons in addition to small plant size, ensuring the consistency, reliability, and stability of plant materials. COPs have the potential to be a novel model material for studies of the developmental biology of soybean and other dicots.
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Affiliation(s)
- Chunlei Zhang
- College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Xu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fulu Chen
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Enoch Sapey
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
- Council for Scientific and Industrial Research (CSIR)-Oil Palm Research Institute, Kade, Ghana
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changhong Guo
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tianfu Han
- College of Life Science and Technology, Harbin Normal University, Harbin, China
- Ministry of Agriculture and Rural Affairs (MARA) Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, China
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68
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Zhao Y, Zhao B, Xie Y, Jia H, Li Y, Xu M, Wu G, Ma X, Li Q, Hou M, Li C, Xia Z, He G, Xu H, Bai Z, Kong D, Zheng Z, Liu Q, Liu Y, Zhong J, Tian F, Wang B, Wang H. The evening complex promotes maize flowering and adaptation to temperate regions. THE PLANT CELL 2023; 35:369-389. [PMID: 36173348 PMCID: PMC9806612 DOI: 10.1093/plcell/koac296] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/16/2022] [Indexed: 05/30/2023]
Abstract
Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.
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Affiliation(s)
- Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Hong Jia
- Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Guangxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Quanquan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gang He
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hua Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhijing Bai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dexin Kong
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhigang Zheng
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Liu
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yuting Liu
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jinshun Zhong
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Feng Tian
- Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Haiyang Wang
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
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Kong L, Wang Y, Chen L, Fang R, Li Y, Fang C, Dong L, Yuan X, Kong F, Liu B, Cheng Q, Lu S. Candidate loci for breeding compact plant-type soybean varieties. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:6. [PMID: 37312867 PMCID: PMC10248646 DOI: 10.1007/s11032-022-01352-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/24/2022] [Indexed: 06/15/2023]
Abstract
Plant height and node number are important agronomic traits that influence yield in soybean (Glycine max L.). Here, to better understand the genetic basis of the traits, we used two recombinant inbred line (RIL) populations to detect quantitative trait loci (QTLs) associated with plant height and node number in different environments. This analysis detected 9 and 21 QTLs that control plant height and node number, respectively. Among them, we identified two genomic regions that overlap with Determinate stem 1 (Dt1) and Dt2, which are known to influence both plant height and node number. Furthermore, different combinations of Dt1 and Dt2 alleles were enriched in distinct latitudes. In addition, we determined that the QTLs qPH-13-SE and qPH-13-DW in the two RIL populations overlap with genomic intervals associated with plant height and the QTL qNN-04-DW overlaps with an interval associated with node number. Combining the dwarf allele of qPH-13-SE/qPH-13-DW and the multiple-node allele of qNN-04-DW produced plants with ideal plant architecture, i.e., shorter main stems with more nodes. This plant type may help increase yield at high planting density. This study thus provides candidate loci for breeding elite soybean cultivars for plant height and node number. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01352-2.
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Affiliation(s)
- Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yanping Wang
- Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Liyu Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Ran Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lidong Dong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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70
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Wang L, Li H, He M, Dong L, Huang Z, Chen L, Nan H, Kong F, Liu B, Zhao X. GIGANTEA orthologs, E2 members, redundantly determine photoperiodic flowering and yield in soybean. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:188-202. [PMID: 36287141 DOI: 10.1111/jipb.13398] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Soybean (Glycine max L.) is a typical photoperiod-sensitive crop, such that photoperiod determines its flowering time, maturity, grain yield, and phenological adaptability. During evolution, the soybean genome has undergone two duplication events, resulting in about 75% of all genes being represented by multiple copies, which is associated with rampant gene redundancy. Among duplicated genes, the important soybean maturity gene E2 has two homologs, E2-Like a (E2La) and E2-Like b (E2Lb), which encode orthologs of Arabidopsis GIGANTEA (GI). Although E2 was cloned a decade ago, we still know very little about its contribution to flowering time and even less about the function of its homologs. Here, we generated single and double mutants in E2, E2La, and E2Lb by genome editing and determined that E2 plays major roles in the regulation of flowering time and yield, with the two E2 homologs depending on E2 function. At high latitude regions, e2 single mutants showed earlier flowering and high grain yield. Remarkably, in terms of genetic relationship, genes from the legume-specific transcription factor family E1 were epistatic to E2. We established that E2 and E2-like proteins form homodimers or heterodimers to regulate the transcription of E1 family genes, with the homodimer exerting a greater function than the heterodimers. In addition, we established that the H3 haplotype of E2 is the ancestral allele and is mainly restricted to low latitude regions, from which the loss-of-function alleles of the H1 and H2 haplotypes were derived. Furthermore, we demonstrated that the function of the H3 allele is stronger than that of the H1 haplotype in the regulation of flowering time, which has not been shown before. Our findings provide excellent allelic combinations for classical breeding and targeted gene disruption or editing.
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Affiliation(s)
- Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Milan He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | | | - Zerong Huang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Liyu Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Haiyang Nan
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiaohui Zhao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
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71
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Yue L, Pei X, Kong F, Zhao L, Lin X. Divergence of functions and expression patterns of soybean bZIP transcription factors. FRONTIERS IN PLANT SCIENCE 2023; 14:1150363. [PMID: 37123868 PMCID: PMC10146240 DOI: 10.3389/fpls.2023.1150363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Soybean (Glycine max) is a major protein and oil crop. Soybean basic region/leucine zipper (bZIP) transcription factors are involved in many regulatory pathways, including yield, stress responses, environmental signaling, and carbon-nitrogen balance. Here, we discuss the members of the soybean bZIP family and their classification: 161 members have been identified and clustered into 13 groups. Our review of the transcriptional regulation and functions of soybean bZIP members provides important information for future study of bZIP transcription factors and genetic resources for soybean breeding.
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Affiliation(s)
- Lin Yue
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xinxin Pei
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin, China
- *Correspondence: Xiaoya Lin, ; Lin Zhao,
| | - Xiaoya Lin
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- *Correspondence: Xiaoya Lin, ; Lin Zhao,
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72
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Zhang L, Zhang Y, Liu J, Li H, Liu B, Zhao T. N6-methyladenosine mRNA methylation is important for the light response in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1153840. [PMID: 37082338 PMCID: PMC10110966 DOI: 10.3389/fpls.2023.1153840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is the most prevalent and abundant modification in eukaryotic mRNA and posttranscriptionally modulates the transcriptome at almost all stages of mRNA metabolism. In plants, m6A is crucial for embryonic-phase growth, flowering time control, microspore generation and fruit maturation. However, the role of m6A in plant responses to light, the most important environmental stimulus, remains unexplored. Here, we profile the m6A transcriptome of Williams 82, a soybean cultivar, and reveal that m6A is highly conserved and plays an important role in the response to light stimuli in soybean. Similar to the case in Arabidopsis, m6A in soybean is enriched not only around the stop codon and within the 3'UTR but also around the start codon. Moreover, genes with methylation occurring in the 3'UTR have higher expression levels and are more prone to alternative splicing. The core genes in the light signaling pathway, GmSPA1a, GmPRR5e and GmBIC2b, undergo changes in methylation modification and transcription levels in response to light. KEGG pathway analysis revealed that differentially expressed genes with differential m6A peaks were involved in the "photosynthesis" and "circadian rhythm" pathways. Our results highlight the important role played by epitranscriptomic mRNA methylation in the light response in soybean and provide a solid basis for determining the functional role of light on RNA m6A modification in this plant.
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73
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Wan Z, Liu Y, Guo D, Fan R, Liu Y, Xu K, Zhu J, Quan L, Lu W, Bai X, Zhai H. CRISPR/Cas9-mediated targeted mutation of the E1 decreases photoperiod sensitivity, alters stem growth habits, and decreases branch number in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:1066820. [PMID: 36589055 PMCID: PMC9794841 DOI: 10.3389/fpls.2022.1066820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The distribution of elite soybean (Glycine max) cultivars is limited due to their highly sensitive to photoperiod, which affects the flowering time and plant architecture. The recent emergence of CRISPR/Cas9 technology has uncovered new opportunities for genetic manipulation of soybean. The major maturity gene E1 of soybean plays a critical role in soybean photoperiod response. Here, we performed CRISPR/Cas9-mediated targeted mutation of E1 gene in soybean cultivar Tianlong1 carrying the dominant E1 to investigate its precise function in photoperiod regulation, especially in plant architecture regulation. Four types of mutations in the E1 coding region were generated. No off-target effects were observed, and homozygous trans-clean mutants without T-DNA were obtained. The photoperiod sensitivity of e1 mutants decreased relative to the wild type plants; however, e1 mutants still responded to photoperiod. Further analysis revealed that the homologs of E1, E1-La, and E1-Lb, were up-regulated in the e1 mutants, indicating a genetic compensation response of E1 and its homologs. The e1 mutants exhibited significant changes in the architecture, including initiation of terminal flowering, formation of determinate stems, and decreased branch numbers. To identify E1-regulated genes related to plant architecture, transcriptome deep sequencing (RNA-seq) was used to compare the gene expression profiles in the stem tip of the wild-type soybean cultivar and the e1 mutants. The expression of shoot identity gene Dt1 was significantly decreased, while Dt2 was significantly upregulated. Also, a set of MADS-box genes was up-regulated in the stem tip of e1 mutants which might contribute to the determinate stem growth habit.
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Affiliation(s)
- Zhao Wan
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingxiang Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Dandan Guo
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Rong Fan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Yang Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Kun Xu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jinlong Zhu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Le Quan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Wentian Lu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Xi Bai
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Hong Zhai
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P. Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genet 2022; 18:e1010513. [PMID: 36477175 PMCID: PMC9728896 DOI: 10.1371/journal.pgen.1010513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
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Affiliation(s)
- Xiang Luo
- College of Agriculture, Henan University, Kaifeng, Henan, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Xi’an Botanical Garden of Shaanxi Province, Xi’an, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Chen
- Shandong Institute of Pomology, National Germplasm Repository of Walnut and Chestnut, Tai’an, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, United States of America
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - Maria Malvolti
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Terni, Italy
| | - Kai Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chaobin Liu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Chengkui Qiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- * E-mail: (JX); (SC); (PZ)
| | - Shangying Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (JX); (SC); (PZ)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- * E-mail: (JX); (SC); (PZ)
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75
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Xia Z, Zhai H, Zhang Y, Wang Y, Wang L, Xu K, Wu H, Zhu J, Jiao S, Wan Z, Zhu X, Gao Y, Liu Y, Fan R, Wu S, Chen X, Liu J, Yang J, Song Q, Tian Z. QNE1 is a key flowering regulator determining the length of the vegetative period in soybean cultivars. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2472-2490. [PMID: 35802303 DOI: 10.1007/s11427-022-2117-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
The soybean E1 gene is a major regulator that plays an important role in flowering time and maturity. However, it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of northern China. We mapped the novel quantitative trait locus QNE1 (QTL near E1) for flowering time to the region proximal to E1 on chromosome 6 in two mapping populations. Positional cloning revealed Glyma.06G204300, encoding a TCP-type transcription factor, as a strong candidate gene for QNE1. Association analysis further confirmed that functional single nucleotide polymorphisms (SNPs) at nucleotides 686 and 1,063 in the coding region of Glyma.06G204300 were significantly associated with flowering time. The protein encoded by the candidate gene is localized primarily to the nucleus. Furthermore, soybean and Brassica napus plants overexpressing Glyma.06G204300 exhibited early flowering. We conclude that despite their similar effects on flowering time, QNE1 and E4 may control flowering time through different regulatory mechanisms, based on expression studies and weighted gene co-expression network analysis of flowering time-related genes. Deciphering the molecular basis of QNE1 control of flowering time enriches our knowledge of flowering gene networks in soybean and will facilitate breeding soybean cultivars with broader latitudinal adaptation.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, China
| | - Yaying Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Lu Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jinglong Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Shuang Jiao
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Zhao Wan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiaobin Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Yingxiang Liu
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Rong Fan
- College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Shihao Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jinyu Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jiayin Yang
- Huaiyin Institute of Agricultural Science of Xuhuai Region, Jiangsu Academy of Agricultural Sciences, Huai'an, 223001, China
| | - Qijian Song
- USDA ARS, Soybean Genome & Improvement Lab, Beltsville, 20705, USA
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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76
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Wang Z, Huang C, Niu Y, Yung WS, Xiao Z, Wong FL, Huang M, Wang X, Man CK, Sze CC, Liu A, Wang Q, Chen Y, Liu S, Wu C, Liu L, Hou W, Han T, Li MW, Lam HM. QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4507-4522. [PMID: 36422673 DOI: 10.1007/s00122-022-04235-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.
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Affiliation(s)
- Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Cheng Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yongchao Niu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai-Shing Yung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mingkun Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Xin Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chun-Kuen Man
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qianwen Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, & School of Agriculture and Environment, The University of Western Australia, Perth, WA6001, Australia
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Liu
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lifeng Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Tianfu Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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77
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Lv T, Wang L, Zhang C, Liu S, Wang J, Lu S, Fang C, Kong L, Li Y, Li Y, Hou X, Liu B, Kong F, Li X. Identification of two quantitative genes controlling soybean flowering using bulked-segregant analysis and genetic mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:987073. [PMID: 36531378 PMCID: PMC9749486 DOI: 10.3389/fpls.2022.987073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Photoperiod responsiveness is important to soybean production potential and adaptation to local environments. Varieties from temperate regions generally mature early and exhibit extremely low yield when grown under inductive short-day (SD) conditions. The long-juvenile (LJ) trait is essentially a reduction and has been introduced into soybean cultivars to improve yield in tropical environments. In this study, we used next-generation sequencing (NGS)-based bulked segregant analysis (BSA) to simultaneously map qualitative genes controlling the LJ trait in soybean. We identified two genomic regions on scaffold_32 and chromosome 18 harboring loci LJ32 and LJ18, respectively. Further, we identified LJ32 on the 228.7-kb scaffold_32 as the soybean pseudo-response-regulator gene Tof11 and LJ18 on a 301-kb region of chromosome 18 as a novel PROTEIN FLOWERING LOCUS T-RELATED gene, Glyma.18G298800. Natural variants of both genes contribute to LJ trait regulation in tropical regions. The molecular identification and functional characterization of Tof11 and LJ18 will enhance understanding of the molecular mechanisms underlying the LJ trait and provide useful genetic resources for soybean molecular breeding in tropical regions.
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Affiliation(s)
- Tianxiao Lv
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Chunyu Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinxing Wang
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Yunlong Li
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Xiaoming Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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78
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Alcantara M, Acosta P, Azatian A, Calderon C, Candray K, Castillo N, Coria-Gomez L, Duran J, Fam J, Hernandez-Segura D, Hidalgo L, Huerta C, Jordan S, Kagan K, Loya K, Martinez E, Musaev K, Navarro R, Nazarians N, Paglia R, Robles G, Simmons T, Smith S, Soudani F, Valenzuela E, Villalobos J, Iftikhar H, Hanzawa Y. Experimental Verification of Inferred Regulatory Interactions of EARLY FLOWERING 3 ( GmELF3-1 ) in Glycine max. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000687. [PMID: 36506349 PMCID: PMC9729981 DOI: 10.17912/micropub.biology.000687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/28/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
Understanding the roles of evening complex (EC) genes in the circadian clock of plants can inform how diurnal transcriptional loops in the clock gene network function to regulate key physiological and developmental events, including flowering transition. Gene regulatory interactions among soybean's circadian clock and flowering genes were inferred using time-series RNA-seq data and the network inference algorithmic package CausNet. In this study, we seek to clarify the inferred regulatory interactions of the EC gene GmELF3-1. A gene expression analysis using soybean protoplasts as a transient model indicated regulatory roles of GmELF3-1 in expression of selected flowering genes.
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Affiliation(s)
| | - Patrick Acosta
- Department of Biology, California State University Northridge
| | - Ara Azatian
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Carlos Calderon
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kevin Candray
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Natalie Castillo
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Luis Coria-Gomez
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Jose Duran
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Justina Fam
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Diego Hernandez-Segura
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Lennix Hidalgo
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Carlos Huerta
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Shane Jordan
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kimberly Kagan
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Karla Loya
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Eduardo Martinez
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kirill Musaev
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Roxana Navarro
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Narek Nazarians
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Robert Paglia
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Gabriela Robles
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Taylor Simmons
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Shawn Smith
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Faisel Soudani
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Emily Valenzuela
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Jessica Villalobos
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Hira Iftikhar
- Department of Biology, California State University Northridge
| | - Yoshie Hanzawa
- Department of Biology, California State University Northridge
,
Correspondence to: Yoshie Hanzawa (
)
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79
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Zhang Y, Cheng Q, Liao C, Li L, Gou C, Chen Z, Wang Y, Liu B, Kong F, Chen L. GmTOC1b inhibits nodulation by repressing GmNIN2a and GmENOD40-1 in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:1052017. [PMID: 36438085 PMCID: PMC9691777 DOI: 10.3389/fpls.2022.1052017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important factor affecting the yield and quality of leguminous crops. Nodulation is regulated by a complex network comprising several transcription factors. Here, we functionally characterized the role of a TOC1 family member, GmTOC1b, in soybean (Glycine max) nodulation. RT-qPCR assays showed that GmTOC1b is constitutively expressed in soybean. However, GmTOC1b was also highly expressed in nodules, and GmTOC1 localized to the cell nucleus, based on transient transformation in Nicotiana benthamiana leaves. Homozygous Gmtoc1b mutant plants exhibited increased root hair curling and produced more infection threads, resulting in more nodules and greater nodule fresh weight. By contrast, GmTOC1b overexpression inhibited nodulation. Furthermore, we also showed that GmTOC1b represses the expression of nodulation-related genes including GmNIN2a and GmENOD40-1 by binding to their promoters. We conclude that GmTOC1b functions as a transcriptional repressor to inhibit nodulation by repressing the expression of key nodulation-related genes including GmNIN2a, GmNIN2b, and GmENOD40-1 in soybean.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Liyu Chen
- *Correspondence: Liyu Chen, ; Fanjiang Kong,
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80
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Wang J, Hu Z, Liao X, Wang Z, Li W, Zhang P, Cheng H, Wang Q, Bhat JA, Wang H, Liu B, Zhang H, Huang F, Yu D. Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean. Evol Appl 2022; 15:1820-1833. [PMID: 36426120 PMCID: PMC9679240 DOI: 10.1111/eva.13480] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 08/28/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Global climate change has threatened world crop production and food security. Decoding the adaptive genetic basis of wild relatives provides an invaluable genomic resource for climate-smart crop breedinG. Here, we performed whole-genome sequencing of 185 diverse wild soybean (Glycine soja) accessions collected from three major agro-ecological zones in China to parse the genomic basis of local adaptation in wild soybean. The population genomic diversity pattern exhibited clear agro-ecological zone-based population structure, and multiple environmental factors were observed to contribute to the genetic divergence. Demographic analysis shows that wild soybeans from the three ecological zones diverged about 1 × 105 years ago, and then the effective population sizes have undergone different degrees of expansions. Genome-environment association identified multiple genes involved in the local adaptation, such as flowering time and temperature-related genes. A locus containing two adjacent MADS-box transcription factors on chromosome 19 was identified for multiple environmental factors, and it experienced positive selection that enables the adaptation to high-latitude environment. This study provides insights into the genetic mechanism of ecological adaptation in wild soybean that may facilitate climate-resilient soybean breeding.
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Affiliation(s)
- Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Zhenbin Hu
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
| | - Xiliang Liao
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Zhiyu Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural ScienceHarbinChina
| | - Peipei Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Qing Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Javaid Akhter Bhat
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Hui Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Biao Liu
- Nanjing Institute of Environmental SciencesMinistry of Ecology and EnvironmentNanjingChina
| | - Hengyou Zhang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and Agroecology, Chinese Academy of SciencesHarbinChina
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing Agricultural UniversityNanjingChina
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81
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Liang Q, Chen L, Yang X, Yang H, Liu S, Kou K, Fan L, Zhang Z, Duan Z, Yuan Y, Liang S, Liu Y, Lu X, Zhou G, Zhang M, Kong F, Tian Z. Natural variation of Dt2 determines branching in soybean. Nat Commun 2022; 13:6429. [PMID: 36307423 PMCID: PMC9616897 DOI: 10.1038/s41467-022-34153-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/16/2022] [Indexed: 12/25/2022] Open
Abstract
Shoot branching is fundamentally important in determining soybean yield. Here, through genome-wide association study, we identify one predominant association locus on chromosome 18 that confers soybean branch number in the natural population. Further analyses determine that Dt2 is the corresponding gene and the natural variations in Dt2 result in significant differential transcriptional levels between the two major haplotypes. Functional characterization reveals that Dt2 interacts with GmAgl22 and GmSoc1a to physically bind to the promoters of GmAp1a and GmAp1d and to activate their transcription. Population genetic investigation show that the genetic differentiation of Dt2 display significant geographic structure. Our study provides a predominant gene for soybean branch number and may facilitate the breeding of high-yield soybean varieties.
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Affiliation(s)
- Qianjin Liang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Liyu Chen
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xia Yang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Hui Yang
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shulin Liu
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kun Kou
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lei Fan
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhifang Zhang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zongbiao Duan
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yaqin Yuan
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Shan Liang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Yucheng Liu
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xingtong Lu
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Guoan Zhou
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Min Zhang
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fanjiang Kong
- grid.411863.90000 0001 0067 3588Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhixi Tian
- grid.418558.50000 0004 0596 2989State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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82
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Lin X, Dong L, Tang Y, Li H, Cheng Q, Li H, Zhang T, Ma L, Xiang H, Chen L, Nan H, Fang C, Lu S, Li J, Liu B, Kong F. Novel and multifaceted regulations of photoperiodic flowering by phytochrome A in soybean. Proc Natl Acad Sci U S A 2022; 119:e2208708119. [PMID: 36191205 PMCID: PMC9565047 DOI: 10.1073/pnas.2208708119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Photoperiod is an important environmental cue. Plants can distinguish the seasons and flower at the right time through sensing the photoperiod. Soybean is a sensitive short-day crop, and the timing of flowering varies greatly at different latitudes, thus affecting yields. Soybean cultivars in high latitudes adapt to the long day by the impairment of two phytochrome genes, PHYA3 and PHYA2, and the legume-specific flowering suppressor, E1. However, the regulating mechanism underlying phyA and E1 in soybean remains largely unknown. Here, we classified the regulation of the E1 family by phyA2 and phyA3 at the transcriptional and posttranscriptional levels, revealing that phyA2 and phyA3 regulate E1 by directly binding to LUX proteins, the critical component of the evening complex, to regulate the stability of LUX proteins. In addition, phyA2 and phyA3 can also directly associate with E1 and its homologs to stabilize the E1 proteins. Therefore, phyA homologs control the core flowering suppressor E1 at both the transcriptional and posttranscriptional levels, to double ensure the E1 activity. Thus, our results disclose a photoperiod flowering mechanism in plants by which the phytochrome A regulates LUX and E1 activity.
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Affiliation(s)
- Xiaoya Lin
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lidong Dong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Yang Tang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Ting Zhang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lixin Ma
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hongli Xiang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Linnan Chen
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Haiyang Nan
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193 Beijing, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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Dong L, Hou Z, Li H, Li Z, Fang C, Kong L, Li Y, Du H, Li T, Wang L, He M, Zhao X, Cheng Q, Kong F, Liu B. Agronomical selection on loss-of-function of GIGANTEA simultaneously facilitates soybean salt tolerance and early maturity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1866-1882. [PMID: 35904035 DOI: 10.1111/jipb.13332] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Salt stress and flowering time are major factors limiting geographic adaptation and yield productivity in soybean (Glycine max). Although improving crop salt tolerance and latitude adaptation are essential for efficient agricultural production, whether and how these two traits are integrated remains largely unknown. Here, we used a genome-wide association study to identify a major salt-tolerance locus controlled by E2, an ortholog of Arabidopsis thaliana GIGANTEA (GI). Loss of E2 function not only shortened flowering time and maturity, but also enhanced salt-tolerance in soybean. E2 delayed soybean flowering by enhancing the transcription of the core flowering suppressor gene E1, thereby repressing Flowering Locus T (FT) expression. An E2 knockout mutant e2CR displayed reduced accumulation of reactive oxygen species (ROS) during the response to salt stress by releasing peroxidase, which functions in ROS scavenging to avoid cytotoxicity. Evolutionary and population genetic analyses also suggested that loss-of-function e2 alleles have been artificially selected during breeding for soybean adaptation to high-latitude regions with greater salt stress. Our findings provide insights into the coupled selection for adaptation to both latitude and salt stress in soybean; and offer an ideal target for molecular breeding of early-maturing and salt-tolerant cultivars.
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Affiliation(s)
- Lidong Dong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Zhihong Hou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 510062, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaobo Li
- College of Agriculture, Jilin Agricultural Science and Technology University, Jilin, 132101, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Yongli Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Hao Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Tai Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Milan He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Xiaohui Zhao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Qun Cheng
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
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84
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Patnaik A, Alavilli H, Rath J, Panigrahi KCS, Panigrahy M. Variations in Circadian Clock Organization & Function: A Journey from Ancient to Recent. PLANTA 2022; 256:91. [PMID: 36173529 DOI: 10.1007/s00425-022-04002-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Circadian clock components exhibit structural variations in different plant systems, and functional variations during various abiotic stresses. These variations bear relevance for plant fitness and could be important evolutionarily. All organisms on earth have the innate ability to measure time as diurnal rhythms that occur due to the earth's rotations in a 24-h cycle. Circadian oscillations arising from the circadian clock abide by its fundamental properties of periodicity, entrainment, temperature compensation, and oscillator mechanism, which is central to its function. Despite the fact that a myriad of research in Arabidopsis thaliana illuminated many detailed aspects of the circadian clock, many more variations in clock components' organizations and functions remain to get deciphered. These variations are crucial for sustainability and adaptation in different plant systems in the varied environmental conditions in which they grow. Together with these variations, circadian clock functions differ drastically even during various abiotic and biotic stress conditions. The present review discusses variations in the organization of clock components and their role in different plant systems and abiotic stresses. We briefly introduce the clock components, entrainment, and rhythmicity, followed by the variants of the circadian clock in different plant types, starting from lower non-flowering plants, marine plants, dicots to the monocot crop plants. Furthermore, we discuss the interaction of the circadian clock with components of various abiotic stress pathways, such as temperature, light, water stress, salinity, and nutrient deficiency with implications for the reprogramming during these stresses. We also update on recent advances in clock regulations due to post-transcriptional, post-translation, non-coding, and micro-RNAs. Finally, we end this review by summarizing the points of applicability, a remark on the future perspectives, and the experiments that could clear major enigmas in this area of research.
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Affiliation(s)
- Alena Patnaik
- School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha, 752050, India
| | - Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul, 05006, South Korea
| | - Jnanendra Rath
- Institute of Science, Visva-Bharati Central University, Santiniketan, West Bengal, 731235, India
| | - Kishore C S Panigrahi
- School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha, 752050, India
| | - Madhusmita Panigrahy
- School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha, 752050, India.
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85
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Guan J, Zhang J, Gong D, Zhang Z, Yu Y, Luo G, Somta P, Hu Z, Wang S, Yuan X, Zhang Y, Wang Y, Chen Y, Laosatit K, Chen X, Chen H, Sha A, Cheng X, Xie H, Wang L. Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding. Nat Commun 2022; 13:5707. [PMID: 36175442 PMCID: PMC9523027 DOI: 10.1038/s41467-022-33515-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/21/2022] [Indexed: 11/29/2022] Open
Abstract
Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean. Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
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Affiliation(s)
- Jiantao Guan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jintao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Dan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agriculture, Yangtze University, Jingzhou, China
| | - Zhengquan Zhang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yang Yu
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Gaoling Luo
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Zheng Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Suhua Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yaowen Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Yanlan Wang
- Crop Research Institute of Hunan Province, Changsha, China
| | - Yanhua Chen
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aihua Sha
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Xie
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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86
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Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
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Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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87
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Abstract
Chao Fang and Fanjiang Kong introduce the polyploid staple crop, soybean - a major source of dietary protein and oil and model species for root nodulation and plant-developmental studies.
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Affiliation(s)
- Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou 510006, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou 510006, China.
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88
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Wang P, Wang L, Zhang L, Wu T, Sun B, Zhang J, Sapey E, Yuan S, Jiang B, Chen F, Wu C, Hou W, Sun S, Bai J, Han T. Genomic Dissection and Diurnal Expression Analysis Reveal the Essential Roles of the PRR Gene Family in Geographical Adaptation of Soybean. Int J Mol Sci 2022; 23:ijms23179970. [PMID: 36077363 PMCID: PMC9456279 DOI: 10.3390/ijms23179970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Pseudo-response regulator (PRR) family members serve as key components of the core clock of the circadian clock, and play important roles in photoperiodic flowering, stress tolerance, growth, and the development of plants. In this study, 14 soybean PRR genes were identified, and classified into three groups according to phylogenetic analysis and structural characteristics. Real-time quantitative PCR analysis revealed that 13 GmPRRs exhibited obvious rhythmic expression under long-day (LD) and short-day (SD) conditions, and the expression of 12 GmPRRs was higher under LD in leaves. To evaluate the effects of natural variations in GmPRR alleles on soybean adaptation, we examined the sequences of GmPRRs among 207 varieties collected across China and the US, investigated the flowering phenotypes in six environments, and analyzed the geographical distributions of the major haplotypes. The results showed that a majority of non-synonymous mutations in the coding region were associated with flowering time, and we found that the nonsense mutations resulting in deletion of the CCT domain were related to early flowering. Haplotype analysis demonstrated that the haplotypes associated with early flowering were mostly distributed in Northeast China, while the haplotypes associated with late flowering were mostly cultivated in the lower latitudes of China. Our study of PRR family genes in soybean provides not only an important guide for characterizing the circadian clock-controlled flowering pathway but also a theoretical basis and opportunities to breed varieties with adaptation to specific regions and farming systems.
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Affiliation(s)
- Peiguo Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Liwei Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Baiquan Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Junquan Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Enoch Sapey
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
- Council for Scientific and Industrial Research (CSIR)-Oil Palm Research Institute, Kade P.O. Box 74, Ghana
| | - Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Cunxiang Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
| | - Jiangping Bai
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (J.B.); (T.H.)
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China
- Correspondence: (J.B.); (T.H.)
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89
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Li X, Hu D, Cai L, Wang H, Liu X, Du H, Yang Z, Zhang H, Hu Z, Huang F, Kan G, Kong F, Liu B, Yu D, Wang H. CALCIUM-DEPENDENT PROTEIN KINASE38 regulates flowering time and common cutworm resistance in soybean. PLANT PHYSIOLOGY 2022; 190:480-499. [PMID: 35640995 PMCID: PMC9434205 DOI: 10.1093/plphys/kiac260] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/03/2022] [Indexed: 06/02/2023]
Abstract
Photoperiod-sensitive plants such as soybean (Glycine max) often face threats from herbivorous insects throughout their whole growth period and especially during flowering; however, little is known about the relationship between plant flowering and insect resistance. Here, we used gene editing, multiple omics, genetic diversity and evolutionary analyses to confirm that the calcium-dependent protein kinase GmCDPK38 plays a dual role in coordinating flowering time regulation and insect resistance of soybean. Haplotype 2 (Hap2)-containing soybeans flowered later and were more resistant to the common cutworm (Spodoptera litura Fabricius) than those of Hap3. gmcdpk38 mutants with Hap3 knocked out exhibited similar flowering and resistance phenotypes as Hap2. Knocking out GmCDPK38 altered numerous flowering- and resistance-related phosphorylated proteins, genes, and metabolites. For example, the S-adenosylmethionine synthase GmSAMS1 was post-translationally upregulated in the gmcdpk38 mutants. GmCDPK38 has abundant genetic diversity in wild soybeans and was likely selected during soybean domestication. We found that Hap2 was mostly distributed at low latitudes and had a higher frequency in cultivars than in wild soybeans, while Hap3 was widely selected at high latitudes. Overall, our results elucidated that the two distinct traits (flowering time and insect resistance) are mediated by GmCDPK38.
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Affiliation(s)
- Xiao Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Dezhou Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Linyan Cai
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Huiqi Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Liu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiping Du
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhongyi Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Huairen Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, Missouri 63103, USA
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Fanjiang Kong
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Baohui Liu
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Yuan S, Wang Y, Wang J, Zhang C, Zhang L, Jiang B, Wu T, Chen L, Xu X, Cai Y, Sun S, Chen F, Song W, Wu C, Hou W, Yu L, Han T. GmFT3a fine-tunes flowering time and improves adaptation of soybean to higher latitudes. FRONTIERS IN PLANT SCIENCE 2022; 13:929747. [PMID: 35958200 PMCID: PMC9358591 DOI: 10.3389/fpls.2022.929747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/04/2022] [Indexed: 05/30/2023]
Abstract
Onset of flowering of plants is precisely controlled by extensive environmental factors and internal molecular networks, in which FLOWERING LOCUS T (FT) is a key flowering integrator. In soybean, a typical short-day plant, 11 FT homologues are found in its genome, of which several homologues are functionally diversified in flowering pathways and the others including GmFT3a are yet unknown. In the current study, we characterized GmFT3a, which is located on the same chromosome as the flowering promoters GmFT2a and GmFT5a. Overexpression of GmFT3a significantly promoted flowering of Arabidopsis under the inductive long-day (LD) photoperiod. GmFT3a over-expressed soybean also flowered earlier than the control under LD, but they were not significantly different under inductive short-day (SD) conditions, indicating that GmFT3a acts as a flowering promoter in the non-inductive photoperiod in soybean. Compared with other GmFT homologues, GmFT3a exhibited a slighter effect in flowering promotion than GmFT2a, GmFT5a and GmFT2b under LD conditions. GmFT3a promoted flowering by regulating the expression of downstream flowering-related genes and also affected the expression of other GmFTs. According to the re-sequencing data, the regional distributions of two major haplotypes in 176 soybean varieties were analyzed. The varieties with GmFT3a-Hap2 haplotype matured relatively early, and relative higher expression of GmFT3a was detected in early maturing varieties, implying that Hap2 variation may contribute to the adaptation of soybean to higher latitude regions by increasing expression level of genes in metabolism and signaling pathways. The early flowering germplasm generated by overexpression of GmFT3a has potential to be planted at higher latitudes where non-inductive long day is dominant in the growing season, and GmFT3a can be used to fine-tune soybean flowering and maturity time and improve the geographical adaptation.
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Affiliation(s)
- Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yining Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Junya Wang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Chunlei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Lixin Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Li Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Xu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yupeng Cai
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenwen Song
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cunxiang Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijie Yu
- College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Science and Technology, Harbin Normal University, Harbin, China
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91
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Fei J, Jiang Q, Guo M, Lu J, Wang P, Liu S, Qu J, Ma Y, Guan S. Fine Mapping and Functional Research of Key Genes for Photoperiod Sensitivity in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:890780. [PMID: 35903233 PMCID: PMC9315444 DOI: 10.3389/fpls.2022.890780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Maize is native to the tropics and is very sensitive to photoperiod. Planting in temperate regions with increased hours of daylight always leads to late flowering, sterility, leggy plants, and increased numbers of maize leaves. This phenomenon severely affects the utilization of tropical maize germplasm resources. The sensitivity to photoperiod is mainly reflected in differences in plant height (PH), ear height (EH), total leaf number (LN), leaf number under ear (LE), silking stage (SS), and anthesis stage (AT) in the same variety under different photoperiod conditions. These differences are more pronounced for varieties that are more sensitive to photoperiod. In the current study, a high-density genetic map was constructed from a recombinant inbred line (RIL) population containing 209 lines to map the quantitative trait loci (QTL) for photoperiod sensitivity of PH, EH, LN, LE, SS, and AT. A total of 39 QTL were identified, including three consistent major QTL. We identified candidate genes in the consensus major QTL region by combined analysis of transcriptome data, and after enrichment by GO and KEGG, we identified a total of four genes (Zm00001d006212, Zm00001d017241, Zm00001d047761, and Zm00001d047632) enriched in the plant circadian rhythm pathway (KEGG:04712). We analyzed the expression levels of these four genes, and the analysis results showed that there were significant differences in response under different photoperiod conditions for three of them (Zm00001d047761, Zm00001d006212 and Zm00001d017241). The results of functional verification showed that the expression patterns of genes rhythmically oscillated, which can affect the length of the hypocotyl and the development of the shoot apical meristem. We also found that the phenotypes of the positive plants were significantly different from the control plants when they overexpressed the objective gene or when it was knocked out, and the expression period, phase, and amplitude of the target gene also shifted. The objective gene changed its own rhythmic oscillation period, phase, and amplitude with the change in the photoperiod, thereby regulating the photoperiod sensitivity of maize. These results deepen our understanding of the genetic structure of photoperiod sensitivity and lay a foundation for further exploration of the regulatory mechanism of photoperiod sensitivity.
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Affiliation(s)
- Jianbo Fei
- College of Bioscience, Jilin Agricultural University, Changchun, China
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Qingping Jiang
- College of Bioscience, Jilin Agricultural University, Changchun, China
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Mingyang Guo
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Jianyu Lu
- College of Bioscience, Jilin Agricultural University, Changchun, China
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Piwu Wang
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Siyan Liu
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Jing Qu
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Yiyong Ma
- College of Bioscience, Jilin Agricultural University, Changchun, China
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Shuyan Guan
- College of Bioscience, Jilin Agricultural University, Changchun, China
- Joint Laboratory of International Cooperation in Modern Agricultural Technology of Ministry of Education, Jilin Agricultural University, Changchun, China
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92
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Dong W, Li D, Zhang L, Yin B, Zhang Y. Transcriptome Analysis of Short-Day Photoperiod Inducement in Adzuki Bean ( Vigna angularis L.) Based on RNA-Seq. FRONTIERS IN PLANT SCIENCE 2022; 13:893245. [PMID: 35845693 PMCID: PMC9280645 DOI: 10.3389/fpls.2022.893245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
The flowering characteristics of adzuki bean are influenced by several environmental factors. Light is an important ecological factor that induces flowering in adzuki bean, but to date, there have been few reports on the transcriptomic features of photoperiodic regulation of adzuki bean flowering. This study is based on RNA sequencing (RNA-seq) techniques to elucidate the expression of light-related regulatory genes under short-day photoperiod inducement of adzuki bean flowering, providing an important theoretical basis for its accelerated breeding. Short-day photoperiod inducement of 10 h was conducted for 5 day, 10 day, and 15 day periods on "Tang shan hong xiao dou" varieties, which are more sensitive to short-day photoperiod conditions than the other varieties. Plants grown under natural light (14.5 h) for 5 days, 10 days, and 15 days were used as controls to compare the progress of flower bud differentiation and flowering characteristics. The topmost unfolded functional leaves were selected for transcriptome sequencing and bioinformatics analysis. The short-day photoperiod inducement promoted flower bud differentiation and advanced flowering time in adzuki bean. Transcriptomic analysis revealed 5,608 differentially expressed genes (DEGs) for the combination of CK-5d vs. SD-5d, CK-10d vs. SD-10d, and CK-15d vs. SD-15d. The three groups of the DEGs were analyzed using the Gene Ontology (GO) and the Kyoto Encyclopedia of Genomes and Genomes (KEGG) databases; the DEGs were associated with flowering, photosystem, and the circadian rhythm and were mainly concentrated in the hormone signaling and metabolism, circadian rhythm, and antenna protein pathways; So, 13 light-related genes across the three pathways were screened for differential and expression characteristics. Through the functional annotations of orthologs, these genes were related to flowering, which were supposed to be good candidate genes in adzuki bean. The findings provide a deep understanding of the molecular mechanisms of adzuki bean flowering in response to short-day photoperiod inducement, which laid a foundation for the functional verification of genes in the next step, and provide an important reference for the molecular breeding of adzuki bean.
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Affiliation(s)
- Weixin Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
- Hebei Open University, Shijiazhuang, China
| | - Dongxiao Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Lei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Baozhong Yin
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yuechen Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
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93
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Maldonado Dos Santos JV, Sant'Ana GC, Wysmierski PT, Todeschini MH, Garcia A, Meda AR. Genetic relationships and genome selection signatures between soybean cultivars from Brazil and United States after decades of breeding. Sci Rep 2022; 12:10663. [PMID: 35739190 PMCID: PMC9226155 DOI: 10.1038/s41598-022-15022-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Soybean is one of the most important crops worldwide. Brazil and the United States (US) are the world's two biggest producers of this legume. The increase of publicly available DNA sequencing data as well as high-density genotyping data of multiple soybean germplasms has made it possible to understand the genetic relationships and identify genomics regions that underwent selection pressure during soy domestication and breeding. In this study, we analyzed the genetic relationships between Brazilian (N = 235) and US soybean cultivars (N = 675) released in different decades and screened for genomic signatures between Brazilian and US cultivars. The population structure analysis demonstrated that the Brazilian germplasm has a narrower genetic base than the US germplasm. The US cultivars were grouped according to maturity groups, while Brazilian cultivars were separated according to decade of release. We found 73 SNPs that differentiate Brazilian and US soybean germplasm. Maturity-associated SNPs showed high allelic frequency differences between Brazilian and US accessions. Other important loci were identified separating cultivars released before and after 1996 in Brazil. Our data showed important genomic regions under selection during decades of soybean breeding in Brazil and the US that should be targeted to adapt lines from different origins in these countries.
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Affiliation(s)
| | | | | | | | - Alexandre Garcia
- Tropical Melhoramento & Genética (TMG), 87 Celso Garcia Road, Cambe, PR, Brazil
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94
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Zhai H, Wan Z, Jiao S, Zhou J, Xu K, Nan H, Liu Y, Xiong S, Fan R, Zhu J, Jiang W, Pang T, Luo X, Wu H, Yang G, Bai X, Kong F, Xia Z. GmMDE genes bridge the maturity gene E1 and florigens in photoperiodic regulation of flowering in soybean. PLANT PHYSIOLOGY 2022; 189:1021-1036. [PMID: 35234946 PMCID: PMC9157081 DOI: 10.1093/plphys/kiac092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/19/2022] [Indexed: 05/30/2023]
Abstract
Soybean (Glycine max) is highly sensitive to photoperiod, which affects flowering time and plant architecture and thus limits the distribution range of elite soybean cultivars. The major maturity gene E1 confers the most prominent effect on photoperiod sensitivity, but its downstream signaling pathway remains largely unknown. Here, we confirm that the encoded E1 protein is a transcriptional repressor. The expression of seven GmMDE genes (Glycine max MADS-box genes downregulated by E1) was suppressed when E1 was overexpressed and promoted when E1 was knocked out through clustered regularly-interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-mediated mutagenesis. These GmMDEs exhibited similar tissue specificity and expression patterns, including in response to photoperiod, E1 expression, and E1 genotype. E1 repressed GmMDE promoter activity. Results for two GmMDEs showed that E1 epigenetically silences their expression by directly binding to their promoters to increase H3K27me3 levels. The overexpression of GmMDE06 promoted flowering and post-flowering termination of stem growth. The late flowering phenotype of E1-overexpressing soybean lines was reversed by the overexpression of GmMDE06, placing GmMDE06 downstream of E1. The overexpression of GmMDE06 increased the expression of the soybean FLOWERING LOCUS T orthologs GmFT2a and GmFT5a, leading to feedback upregulation of GmMDE, indicating that GmMDE and GmFT2a/GmFT5a form a positive regulatory feedback loop promoting flowering. GmMDE06 also promoted post-flowering termination of stem growth by repressing the expression of the shoot identity gene Dt1. The E1-GmMDEs-GmFT2a/5a-Dt1 signaling pathway illustrates how soybean responds to photoperiod by modulating flowering time and post-flowering stem termination.
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Affiliation(s)
- Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhao Wan
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuang Jiao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jingwen Zhou
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Haiyang Nan
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Yingxiang Liu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Shangshang Xiong
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Fan
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Jinlong Zhu
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Wenting Jiang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Tian Pang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiao Luo
- Institute of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Guang Yang
- Cultivation and Crop Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xi Bai
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding (2013DP173244), Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
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95
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Lu S, Fang C, Abe J, Kong F, Liu B. Current overview on the genetic basis of key genes involved in soybean domestication. ABIOTECH 2022; 3:126-139. [PMID: 36312442 PMCID: PMC9590488 DOI: 10.1007/s42994-022-00074-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/11/2022] [Indexed: 11/28/2022]
Abstract
Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (Glycine max). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.
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Affiliation(s)
- Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-0808 Japan
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
- Guangzhou Key Laboratory of Crop Gene Editing, Guangzhou University, Guangzhou, 510006 China
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96
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Zhuang Y, Li X, Hu J, Xu R, Zhang D. Expanding the gene pool for soybean improvement with its wild relatives. ABIOTECH 2022; 3:115-125. [PMID: 36304518 PMCID: PMC9590452 DOI: 10.1007/s42994-022-00072-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022]
Abstract
Genetic diversity is a cornerstone of crop improvement, However, cultivated soybean (Glycine max) has undergone several genetic bottlenecks, including domestication in China, the introduction of landraces to other areas of the world and, latterly, selective breeding, leading to low genetic diversity the poses a major obstacle to soybean improvement. By contrast, there remains a relatively high level of genetic diversity in soybean's wild relatives, especially the perennial soybeans (Glycine subgenus Glycine), which could serve as potential gene pools for improving soybean cultivars. Wild soybeans are phylogenetically diversified and adapted to various habitats, harboring resistance to various biotic and abiotic stresses. Advances in genome and transcriptome sequencing enable alleles associated with desirable traits that were lost during domestication of soybean to be discovered in wild soybean. The collection and conservation of soybean wild relatives and the dissection of their genomic features will accelerate soybean breeding and facilitate sustainable agriculture and food production.
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Affiliation(s)
- Yongbin Zhuang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Xiaoming Li
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Junmei Hu
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
| | - Ran Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131 Shandong China
| | - Dajian Zhang
- College of Agriculture, and State Key Laboratory of Crop Biology, Shangdong Agricultural University, Tai'an, 271018 Shandong China
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97
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Li J, Zhang Y, Ma R, Huang W, Hou J, Fang C, Wang L, Yuan Z, Sun Q, Dong X, Hou Y, Wang Y, Kong F, Sun L. Identification of ST1 reveals a selection involving hitchhiking of seed morphology and oil content during soybean domestication. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1110-1121. [PMID: 35178867 PMCID: PMC9129076 DOI: 10.1111/pbi.13791] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/29/2021] [Accepted: 01/26/2022] [Indexed: 05/26/2023]
Abstract
Seed morphology and quality of cultivated soybean (Glycine max) have changed dramatically during domestication from their wild relatives, but their relationship to selection is poorly understood. Here, we describe a semi-dominant locus, ST1 (Seed Thickness 1), affecting seed thickness and encoding a UDP-D-glucuronate 4-epimerase, which catalyses UDP-galacturonic acid production and promotes pectin biosynthesis. Interestingly, this morphological change concurrently boosted seed oil content, which, along with up-regulation of glycolysis biosynthesis modulated by ST1, enabled soybean to become a staple oil crop. Strikingly, ST1 and an inversion controlling seed coat colour formed part of a single selective sweep. Structural variation analysis of the region surrounding ST1 shows that the critical mutation in ST1 existed in earlier wild relatives of soybean and the region containing ST1 subsequently underwent an inversion, which was followed by successive selection for both traits through hitchhiking during selection for seed coat colour. Together, these results provide direct evidence that simultaneously variation for seed morphology and quality occurred earlier than variation for seed coat colour during soybean domestication. The identification of ST1 thus sheds light on a crucial phase of human empirical selection in soybeans and provides evidence that our ancestors improved soybean based on taste.
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Affiliation(s)
- Jun Li
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yuhang Zhang
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Ruirui Ma
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wenxuan Huang
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jingjing Hou
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Chao Fang
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lingshuang Wang
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Zhihui Yuan
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Qun Sun
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xuehui Dong
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yufeng Hou
- College of Humanities and Development StudiesChina Agricultural UniversityBeijingChina
| | - Ying Wang
- College of Plant ScienceJilin UniversityChangchunChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Lianjun Sun
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijingChina
- Beijing Key Laboratory for Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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98
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Wang J, Ma C, Ma S, Zheng H, Feng H, Wang Y, Wang J, Liu C, Xin D, Chen Q, Yang M. GmARP is Related to the Type III Effector NopAA to Promote Nodulation in Soybean (Glycine max). Front Genet 2022; 13:889795. [PMID: 35692823 PMCID: PMC9184740 DOI: 10.3389/fgene.2022.889795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022] Open
Abstract
Type III effectors secreted by rhizobia regulate nodulation in the host plant and are important modulators of symbiosis between rhizobia and soybean (Glycine max), although the underlying mechanisms are poorly understood. Here, we studied the type III effector NopAA in Sinorhizobium fredii HH103, confirming its secretion into the extracellular environment under the action of genistein. The enzyme activity of NopAA was investigated in vitro, using xyloglucan and β-glucan as substrates. NopAA functions were investigated by the generation of a NopAA mutant and the effects of NopAA deficiency on symbiosis were analyzed. Soybean genes associated with NopAA were identified in a recombinant inbred line (RIL) population and their functions were verified. NopAA was confirmed to be a type III effector with glycosyl hydrolase activity, and its mutant did not promote nodulation. Quantitative trait locus (QTL) analysis identified 10 QTLs with one, Glyma.19g074200 (GmARP), found to be associated with NopAA and to positively regulate the establishment of symbiosis. All these results support the hypothesis that type III effectors interact with host proteins to regulate the establishment of symbiosis and suggest the possibility of manipulating the symbiotic soybean–rhizobia interaction to promote efficient nitrogen fixation.
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Affiliation(s)
- Jinhui Wang
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Chao Ma
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Shengnan Ma
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haiyang Zheng
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Haojie Feng
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yue Wang
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Jiangxu Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chunyan Liu
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Dawei Xin
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- *Correspondence: Dawei Xin, ; Qingshan Chen, ; Mingliang Yang,
| | - Qingshan Chen
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- *Correspondence: Dawei Xin, ; Qingshan Chen, ; Mingliang Yang,
| | - Mingliang Yang
- College of Agriculture, Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, Harbin, China
- *Correspondence: Dawei Xin, ; Qingshan Chen, ; Mingliang Yang,
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99
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Cao P, Zhao Y, Wu F, Xin D, Liu C, Wu X, Lv J, Chen Q, Qi Z. Multi-Omics Techniques for Soybean Molecular Breeding. Int J Mol Sci 2022; 23:4994. [PMID: 35563386 PMCID: PMC9099442 DOI: 10.3390/ijms23094994] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Soybean is a major crop that provides essential protein and oil for food and feed. Since its origin in China over 5000 years ago, soybean has spread throughout the world, becoming the second most important vegetable oil crop and the primary source of plant protein for global consumption. From early domestication and artificial selection through hybridization and ultimately molecular breeding, the history of soybean breeding parallels major advances in plant science throughout the centuries. Now, rapid progress in plant omics is ushering in a new era of precision design breeding, exemplified by the engineering of elite soybean varieties with specific oil compositions to meet various end-use targets. The assembly of soybean reference genomes, made possible by the development of genome sequencing technology and bioinformatics over the past 20 years, was a great step forward in soybean research. It facilitated advances in soybean transcriptomics, proteomics, metabolomics, and phenomics, all of which paved the way for an integrated approach to molecular breeding in soybean. In this review, we summarize the latest progress in omics research, highlight novel findings made possible by omics techniques, note current drawbacks and areas for further research, and suggest that an efficient multi-omics approach may accelerate soybean breeding in the future. This review will be of interest not only to soybean breeders but also to researchers interested in the use of cutting-edge omics technologies for crop research and improvement.
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Affiliation(s)
- Pan Cao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Ying Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Fengjiao Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Jian Lv
- Department of Innovation, Syngenta Biotechnology China, Beijing 102206, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (P.C.); (Y.Z.); (F.W.); (D.X.); (C.L.)
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100
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Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. FRONTIERS IN PLANT SCIENCE 2022; 13:889066. [PMID: 35574141 PMCID: PMC9100572 DOI: 10.3389/fpls.2022.889066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 05/30/2023]
Abstract
Adaptation of soybean cultivars to the photoperiod in which they are grown is critical for optimizing plant yield. However, despite its importance, only the major loci conferring variation in flowering time and maturity of US soybean have been isolated. By contrast, over 200 genes contributing to floral induction in the model organism Arabidopsis thaliana have been described. In this work, putative alleles of a library of soybean orthologs of these Arabidopsis flowering genes were tested for their latitudinal distribution among elite US soybean lines developed in the United States. Furthermore, variants comprising the alleles of genes with significant differences in latitudinal distribution were assessed for amino acid conservation across disparate genera to infer their impact on gene function. From these efforts, several candidate genes from various biological pathways were identified that are likely being exploited toward adaptation of US soybean to various maturity groups.
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Affiliation(s)
- Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Yen On Chan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Andrew Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - George Graef
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - David Hyten
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Mary Happ
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Brian Diers
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Aaron Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Trupti Joshi
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- MU Data Science and Informatics Institute, University of Missouri, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, United States
- Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO, United States
| | - Kristin Bilyeu
- USDA/ARS Plant Genetics Research Unit, Columbia, MO, United States
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