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Duk MA, Gursky VV, Samsonova MG, Surkova SY. Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of M. trancatula. Life (Basel) 2023; 14:26. [PMID: 38255642 PMCID: PMC10817331 DOI: 10.3390/life14010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/04/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in Arabidopsis but remains largely unknown in legumes. The orthologs of the FLC gene, a major regulator of vernalization response in Arabidopsis, are absent or non-functional in the vernalization-sensitive legume species. Nevertheless, the legume integrator genes FT and SOC1 are involved in the transition of the vernalization signal to meristem identity genes, including PIM (AP1 ortholog). However, the regulatory contribution of these genes to PIM activation in legumes remains elusive. Here, we presented the theoretical and data-driven analyses of a feed-forward regulatory motif that includes a vernalization-responsive FT gene and several SOC1 genes, which independently activate PIM and thereby mediate floral transition. Our theoretical model showed that the multiple regulatory branches in this regulatory motif facilitated the elimination of no-sense signals and amplified useful signals from the upstream regulator. We further developed and analyzed four data-driven models of PIM activation in Medicago trancatula in vernalized and non-vernalized conditions in wild-type and fta1-1 mutants. The model with FTa1 providing both direct activation and indirect activation via three intermediate activators, SOC1a, SOC1b, and SOC1c, resulted in the most relevant PIM dynamics. In this model, the difference between regulatory inputs of SOC1 genes was nonessential. As a result, in the M. trancatula model, the cumulative action of SOC1a, SOC1b, and SOC1c was favored. Overall, in this study, we first presented the in silico analysis of vernalization-induced flowering in legumes. The considered vernalization network motif can be supplemented with additional regulatory branches as new experimental data become available.
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Affiliation(s)
- Maria A. Duk
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Vitaly V. Gursky
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia
| | - Maria G. Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Yu. Surkova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
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2
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Babaei S, Singh MB, Bhalla PL. Circular RNAs modulate the floral fate acquisition in soybean shoot apical meristem. BMC PLANT BIOLOGY 2023; 23:322. [PMID: 37328881 DOI: 10.1186/s12870-023-04319-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/26/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Soybean (Glycine max), a major oilseed and protein source, requires a short-day photoperiod for floral induction. Though key transcription factors controlling flowering have been identified, the role of the non-coding genome is limited. Circular RNAs (circRNAs) recently emerged as a novel class of RNAs with critical regulatory functions. However, a study on circRNAs during the floral transition of a crop plant is lacking. We investigated the expression and potential function of circRNAs in floral fate acquisition by soybean shoot apical meristem in response to short-day treatment. RESULTS Using deep sequencing and in-silico analysis, we denoted 384 circRNAs, with 129 exhibiting short-day treatment-specific expression patterns. We also identified 38 circRNAs with predicted binding sites for miRNAs that could affect the expression of diverse downstream genes through the circRNA-miRNA-mRNA network. Notably, four different circRNAs with potential binding sites for an important microRNA module regulating developmental phase transition in plants, miR156 and miR172, were identified. We also identified circRNAs arising from hormonal signaling pathway genes, especially abscisic acid, and auxin, suggesting an intricate network leading to floral transition. CONCLUSIONS This study highlights the gene regulatory complexity during the vegetative to reproductive transition and paves the way to unlock floral transition in a crop plant.
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Affiliation(s)
- Saeid Babaei
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Science, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Science, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Science, The University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
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3
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Lee S, Singh MB, Bhalla PL. Functional analysis of soybean miR156 and miR172 in tobacco highlights their role in plant morphology and floral transition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:393-401. [PMID: 36753825 DOI: 10.1016/j.plaphy.2023.01.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Soybean (Glycine max), a significant oilseed and protein source for humans and livestock feed, needs short day photoperiod for floral induction. Further, soybean has a paleopolyploid genome with multiple copies of flowering genes adding to the complexity of genetic regulation of flowering, and seed set, especially in investigating the role of the noncoding genome. microRNAs, a class of noncoding RNA, play a regulatory role in plant development. miR156 and miR172 are major components of the essential regulatory hub controlling juvenile and vegetative developments and initiation of reproductive phase change leading to flowering. These microRNAs have been originally isolated and studied from model plant, Arabidopsis. However, a study on soybean microRNAs is lacking. We investigated the temporal expression patterns of gma-miR156a and gma-miR172a and found inversely related - gma-miR156a expression was higher in the vegetative stage, and gma-miR172a expression was elevated under inductive flowering conditions. The functions of gma-miR156a and gma-miR172a were evaluated via heterologous expressions in transgenic tobacco plants (Nicotiana tabacum L.). The analysis of overexpression transgenic lines highlighted that gma-miR156a plays a role in juvenile development via repression of the SPL transcription factor family. In contrast, gma-miR172a plays a pivotal role in the reproductive development phase by down-regulating its target genes, AP2. In addition, ectopic expression of gma-miR156a and gma-miR172a affected plant morphology and physiology during plant growth. Collectively, our results suggest that gma-miR156a and gma-miR172a regulate multiple morpho-physiological traits that could be used to enhance crop yield under changing climate conditions.
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Affiliation(s)
- Sangil Lee
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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4
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Gretsova M, Surkova S, Kanapin A, Samsonova A, Logacheva M, Shcherbakov A, Logachev A, Bankin M, Nuzhdin S, Samsonova M. Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer. Int J Mol Sci 2023; 24:ijms24032692. [PMID: 36769014 PMCID: PMC9916832 DOI: 10.3390/ijms24032692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Chickpea (Cicer arietinum L.) is a major grain legume and a good source of plant-based protein. However, comprehensive knowledge of flowering time control in Cicer is lacking. In this study, we acquire high-throughput transcriptome sequencing data and analyze changes in gene expression during floral transition in the early flowering cultivar ICCV 96029, later flowering C. arietinum accessions, and two wild species, C. reticulatum and C. echinospermum. We identify Cicer orthologs of A. thaliana flowering time genes and analyze differential expression of 278 genes between four species/accessions, three tissue types, and two conditions. Our results show that the differences in gene expression between ICCV 96029 and other cultivated chickpea accessions are vernalization-dependent. In addition, we highlight the role of FTa3, an ortholog of FLOWERING LOCUS T in Arabidopsis, in the vernalization response of cultivated chickpea. A common set of differentially expressed genes was found for all comparisons between wild species and cultivars. The direction of expression change for different copies of the FT-INTERACTING PROTEIN 1 gene was variable in different comparisons, which suggests complex mechanisms of FT protein transport. Our study makes a contribution to the understanding of flowering time control in Cicer, and can provide genetic strategies to further improve this important agronomic trait.
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Affiliation(s)
- Maria Gretsova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Svetlana Surkova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Alexander Kanapin
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Anastasia Samsonova
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Maria Logacheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Andrey Shcherbakov
- Laboratory of Microbial Technology, All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia
| | - Anton Logachev
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Mikhail Bankin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Sergey Nuzhdin
- Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Maria Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- Correspondence:
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5
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Meng Y, Wang C, Li Q, Ji W, Wen J, Mysore KS, Pei Y, Niu L, Lin H. DPB3 and DPB4 proteins regulate Medicago flowering and leaf anthocyanin biosynthesis. J Genet Genomics 2023:S1673-8527(23)00022-X. [PMID: 36693566 DOI: 10.1016/j.jgg.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023]
Affiliation(s)
- Yingying Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chongnan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiqi Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Wenkai Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangqi Wen
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Kirankumar S Mysore
- Department of Biochemistry and Molecular Biology, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK 73401, USA
| | - Yanxi Pei
- College of Life Science, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Lifang Niu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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6
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Yun J, Wang C, Zhang F, Chen L, Sun Z, Cai Y, Luo Y, Liao J, Wang Y, Cha Y, Zhang X, Ren Y, Wu J, Hasegawa PM, Tian C, Su H, Ferguson BJ, Gresshoff PM, Hou W, Han T, Li X. A nitrogen fixing symbiosis-specific pathway required for legume flowering. SCIENCE ADVANCES 2023; 9:eade1150. [PMID: 36638166 PMCID: PMC9839322 DOI: 10.1126/sciadv.ade1150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/09/2022] [Indexed: 05/26/2023]
Abstract
Symbiotic nitrogen fixation boosts legume growth and production in nitrogen-poor soils. It has long been assumed that fixed nitrogen increases reproductive success, but until now, the regulatory mechanism was unknown. Here, we report a symbiotic flowering pathway that couples symbiotic and nutrient signals to the flowering induction pathway in legumes. We show that the symbiotic microRNA-microRNA172c (miR172c) and fixed nitrogen systemically and synergistically convey symbiotic and nutritional cues from roots to leaves to promote soybean (Glycine max) flowering. The combinations of symbiotic miR172c and local miR172c elicited by fixed nitrogen and development in leaves activate florigen-encoding FLOWERING LOCUS T (FT) homologs (GmFT2a/5a) by repressing TARGET OF EAT1-like 4a (GmTOE4a). Thus, FTs trigger reproductive development, which allows legumes to survive and reproduce under low-nitrogen conditions.
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Affiliation(s)
- Jinxia Yun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Can Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fengrong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Chen
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengxi Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yupeng Cai
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanqing Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junwen Liao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongliang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanyan Cha
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuehai Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ya Ren
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Wu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Paul M. Hasegawa
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Changfu Tian
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Soil Microbiology, and Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Huanan Su
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Brett J. Ferguson
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Peter M. Gresshoff
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Wensheng Hou
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong, China
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7
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Surkova SY, Samsonova MG. Mechanisms of Vernalization-Induced Flowering in Legumes. Int J Mol Sci 2022; 23:ijms23179889. [PMID: 36077286 PMCID: PMC9456104 DOI: 10.3390/ijms23179889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repressor. FLC silencing releases the expression of the main flowering inductor FLOWERING LOCUS T (FT), resulting in a floral transition. Remarkably, no FLC homologues have been identified in the vernalization-responsive legumes, and the mechanisms of cold-mediated transition to flowering in these species remain elusive. Nevertheless, legume FT genes have been shown to retain the function of the main vernalization signal integrators. Unlike Arabidopsis, legumes have three subclades of FT genes, which demonstrate distinct patterns of regulation with respect to environmental cues and tissue specificity. This implies complex mechanisms of vernalization signal propagation in the flowering network, that remain largely elusive. Here, for the first time, we summarize the available information on the genetic basis of cold-induced flowering in legumes with a special focus on the role of FT genes.
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8
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Ergon Å, Milvang ØW, Skøt L, Ruttink T. Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes. Mol Genet Genomics 2022; 297:1587-1600. [PMID: 36001174 DOI: 10.1007/s00438-022-01942-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
Abstract
MAIN CONCLUSION Through selective genotyping of pooled phenotypic extremes, we identified a number of loci and candidate genes putatively controlling timing of stem elongation in red clover. We have identified candidate genes controlling the timing of stem elongation prior to flowering in red clover (Trifolium pratense L.). This trait is of ecological and agronomic significance, as it affects fitness, competitivity, climate adaptation, forage and seed yield, and forage quality. We genotyped replicate pools of phenotypically extreme individuals (early and late-elongating) within cultivar Lea using genotyping-by-sequencing in pools (pool-GBS). After calling and filtering SNPs and GBS locus haplotype polymorphisms, we estimated allele frequencies and searched for markers with significantly different allele frequencies in the two phenotypic groups using BayeScan, an FST-based test utilizing replicate pools, and a test based on error variance of replicate pools. Of the three methods, BayeScan was the least stringent, and the error variance-based test the most stringent. Fifteen significant markers were identified in common by all three tests. The candidate genes flanking the markers include genes with potential roles in the vernalization, autonomous, and photoperiod regulation of floral transition, hormonal regulation of stem elongation, and cell growth. These results provide a first insight into the potential genes and mechanisms controlling transition to stem elongation in a perennial legume, which lays a foundation for further functional studies of the genetic determinants regulating this important trait.
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Affiliation(s)
- Åshild Ergon
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
| | - Øystein W Milvang
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Leif Skøt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, B-9090 Melle, Belgium
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9
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Li C, Jiang H, Li Y, Liu C, Qi Z, Wu X, Zhang Z, Hu Z, Zhu R, Guo T, Wang Z, Zheng W, Zhang Z, Zhao H, Wang N, Shan D, Xin D, Luan F, Chen Q. Identification of Finely Mapped Quantitative Trait Locus and Candidate Gene Mining for the Three-Seeded Pod Trait in Soybean. FRONTIERS IN PLANT SCIENCE 2021; 12:715488. [PMID: 34899770 PMCID: PMC8663486 DOI: 10.3389/fpls.2021.715488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/19/2021] [Indexed: 06/14/2023]
Abstract
The three-seeded pod number is an important trait that positively influences soybean yield. Soybean variety with increased three-seeded pod number contributes to the seed number/plant and higher yield. The candidate genes of the three-seeded pod may be the key for improving soybean yield. In this study, identification and validation of candidate genes for three-seeded pod has been carried out. First, a total of 36 quantitative trait locus (QTL) were detected from the investigation of recombinant inbred lines including 147 individuals derived from a cross between Charleston and Dongning 594 cultivars. Five consensus QTLs were integrated. Second, an introgressed line CSSL-182 carrying the target segment for the trait from the donor parent was selected to verify the consensus QTL based on its phenotype. Third, a secondary group was constructed by backcrossing with CSSL-182, and two QTLs were confirmed. There were a total of 162 genes in the two QTLs. The mining of candidate genes resulted in the annotation of eight genes with functions related to pod and seed sets. Finally, haplotype analysis and quantitative reverse transcriptase real-time PCR were carried to verify the candidate genes. Four of these genes had different haplotypes in the resource group, and the differences in the phenotype were highly significant. Moreover, the differences in the expression of the four genes during pod and seed development were also significant. These four genes were probably related to the development process underlying the three-seeded pod in soybean. Herein, we discuss the past and present studies related to the three-seeded pod trait in soybean.
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Affiliation(s)
- Candong Li
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
- College of Life Science, Northeast Agricultural University, Harbin, China
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hongwei Jiang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yingying Li
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Chunyan Liu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhaoming Qi
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xiaoxia Wu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhanguo Zhang
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhenbang Hu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Rongsheng Zhu
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Tai Guo
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhixin Wang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Zheng
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhenyu Zhang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Haihong Zhao
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Nannan Wang
- Jiamusi Branch Institute, Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dapeng Shan
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Dawei Xin
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Feishi Luan
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Qingshan Chen
- Country College of Agriculture, Northeast Agricultural University, Harbin, China
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10
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Arya H, Singh MB, Bhalla PL. Overexpression of
PIF4
affects plant morphology and accelerates reproductive phase transitions in soybean. Food Energy Secur 2021. [DOI: 10.1002/fes3.291] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Hina Arya
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory School of Agriculture and Food Faculty of Veterinary and Agricultural Sciences The University of Melbourne Victoria Australia
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11
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Bu T, Lu S, Wang K, Dong L, Li S, Xie Q, Xu X, Cheng Q, Chen L, Fang C, Li H, Liu B, Weller JL, Kong F. A critical role of the soybean evening complex in the control of photoperiod sensitivity and adaptation. Proc Natl Acad Sci U S A 2021; 118:e2010241118. [PMID: 33558416 PMCID: PMC7923351 DOI: 10.1073/pnas.2010241118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Photoperiod sensitivity is a key factor in plant adaptation and crop production. In the short-day plant soybean, adaptation to low latitude environments is provided by mutations at the J locus, which confer extended flowering phase and thereby improve yield. The identity of J as an ortholog of Arabidopsis ELF3, a component of the circadian evening complex (EC), implies that orthologs of other EC components may have similar roles. Here we show that the two soybean homeologs of LUX ARRYTHMO interact with J to form a soybean EC. Characterization of mutants reveals that these genes are highly redundant in function but together are critical for flowering under short day, where the lux1 lux2 double mutant shows extremely late flowering and a massively extended flowering phase. This phenotype exceeds that of any soybean flowering mutant reported to date, and is strongly reminiscent of the "Maryland Mammoth" tobacco mutant that featured in the seminal 1920 study of plant photoperiodism by Garner and Allard [W. W. Garner, H. A. Allard, J. Agric. Res. 18, 553-606 (1920)]. We further demonstrate that the J-LUX complex suppresses transcription of the key flowering repressor E1 and its two homologs via LUX binding sites in their promoters. These results indicate that the EC-E1 interaction has a central role in soybean photoperiod sensitivity, a phenomenon also first described by Garner and Allard. EC and E1 family genes may therefore constitute key targets for customized breeding of soybean varieties with precise flowering time adaptation, either by introgression of natural variation or generation of new mutants by gene editing.
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Affiliation(s)
- Tiantian Bu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Kai Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Shilin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qun Cheng
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Haiyang Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 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, 150081 Harbin, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, 7001 TAS, Australia
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 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, 150081 Harbin, China
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12
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Zhang S, Singh MB, Bhalla PL. Molecular characterization of a soybean FT homologue, GmFT7. Sci Rep 2021; 11:3651. [PMID: 33574496 PMCID: PMC7878754 DOI: 10.1038/s41598-021-83305-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/29/2021] [Indexed: 11/16/2022] Open
Abstract
Soybean (Glycine max) is a vital oilseed legume crop that provides protein and oil for humans and feedstock for animals. Flowering is a prerequisite for seed production. Floral transition, from vegetative to reproductive stage, in a plant, is regulated by environmental (light, temperature) and endogenous factors. In Arabidopsis, Flowering Locus T (FT) protein is shown to be a mobile signal that moves from leaf to shoot apical meristem to induce flowering. However, FTs role in soybean is not fully resolved due to the presence of multiple (ten) homologs in the genome. Two of the ten FT homologs (GmFT2a and GmFT5a) have a role in the floral transition while GmFT1a and GmFT4 suppress soybean flowering. Recent deep sequencing data revealed that six FT homologs are expressed in shoot apical meristem and leaves during floral transition. One FT homolog, GmFT7 showed strong expression during soybean floral transition. Though bioinformatic analyses revealed that GmFT7 had high similarity with GmFT2a, ectopic GmFT7 expression in Arabidopsis could not promote flowering or rescue the late-flowering phenotype of Arabidopsis ft-10 mutant.
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Affiliation(s)
- Senhao Zhang
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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13
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Garduza-Acosta B, Lagunes-Espinoza LC, Bautista-Muñoz CC, García-de-Los-Santos G, Zaldívar-Cruz JM, Hernández-Flores A. Germination of Crotalaria and Lupinus (Fabaceae) seeds submitted to different pre-germination treatments and their effect on enzymatic activity during early germination. BRAZ J BIOL 2019; 80:23-29. [PMID: 31017230 DOI: 10.1590/1519-6984.185813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/16/2018] [Indexed: 11/21/2022] Open
Abstract
Most of the wild and native legume seeds has a hard and impermeable testa, which causes physical dormancy and prevents them from germinating even when environmental conditions are favorable. The study evaluated the effect of scarification treatments on germination and enzymatic activity of Crotalaria longirostrata (Cl) and Lupinus exaltatus (Le) seeds. After scarification treatments, germination percentage (GP) and rate (GR) were assessed during 30 days after seeding (DAS); and water absorption (WA) and specific enzymatic activity (SEA) during early germination (0, 6, 18, 36, 72, 120 h) in a growing chamber at 25 °C and photoperiod of 12 h. Scarification with 98% H2SO4 15 min increased GP and GR in both species. At 30 DAS, GP and GR of Le seeds were 34% and 0.97 seeds day-1, respectively. In Cl seeds, GP was 64% and GR 0.90 seeds day-1. Scarification with H2O at 80 °C 1 min also promoted germination in Cl (52%). At 120 h after seeding, Le and Cl seeds showed already a high GP with acid scarification (31% and 48%, respectively). In seeds of both species, scarification treatments affected WA and SEA during early germination. During this period, scarification treatments that increased GP also showed a higher α-D-galactosidase activity. The maximum enzyme activity was observed 72 h after hot water scarification in Cl (82.6 U/mg total protein), followed by acid scarification (54.5 U/mg total protein). In Le, the activity peak was 36 h after acid scarification (9.5 U/mg total protein). No relationship was observed between β-glucosidase activity and GP in both species. In conclusion, during early germination of both species, the increase in GP is accompanied by a rise in α-D-galactosidase activity between 36 and 72 h after seeding; and in Cl seeds, an alternative scarification treatment to increase GP may be the use of hot water.
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Affiliation(s)
- B Garduza-Acosta
- Laboratório de Fisiologia Vegetal, Pós-graduação em Produção Agroalimentar nos Trópicos, Área Agrícola, Colegio de Postgraduados - CP, Campus Tabasco, Periférico Carlos A. Molina, s/n, 86500, H. Cárdenas, Tabasco, México
| | - L C Lagunes-Espinoza
- Laboratório de Fisiologia Vegetal, Pós-graduação em Produção Agroalimentar nos Trópicos, Área Agrícola, Colegio de Postgraduados - CP, Campus Tabasco, Periférico Carlos A. Molina, s/n, 86500, H. Cárdenas, Tabasco, México
| | - C C Bautista-Muñoz
- Laboratório de Fisiologia Vegetal, Pós-graduação em Produção Agroalimentar nos Trópicos, Área Agrícola, Colegio de Postgraduados - CP, Campus Tabasco, Periférico Carlos A. Molina, s/n, 86500, H. Cárdenas, Tabasco, México
| | - G García-de-Los-Santos
- Pós-graduação em Produção de Sementes, Área de Produção e Tecnologia de Sementes, Colegio de Postgraduados - CP, Campus Montecillo, Km 36.5, Carretera México-Texcoco, 56230, Montecillo, Texcoco, Edo de México, México
| | - J M Zaldívar-Cruz
- Laboratório de Fisiologia Vegetal, Pós-graduação em Produção Agroalimentar nos Trópicos, Área Agrícola, Colegio de Postgraduados - CP, Campus Tabasco, Periférico Carlos A. Molina, s/n, 86500, H. Cárdenas, Tabasco, México
| | - A Hernández-Flores
- Laboratório de Fisiologia Vegetal, Pós-graduação em Produção Agroalimentar nos Trópicos, Área Agrícola, Colegio de Postgraduados - CP, Campus Tabasco, Periférico Carlos A. Molina, s/n, 86500, H. Cárdenas, Tabasco, México
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14
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Liew LC, Singh MB, Bhalla PL. A novel role of the soybean clock gene LUX ARRHYTHMO in male reproductive development. Sci Rep 2017; 7:10605. [PMID: 28878247 PMCID: PMC5587693 DOI: 10.1038/s41598-017-10823-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/15/2017] [Indexed: 11/23/2022] Open
Abstract
The evening complex of ELF4-ELF3-LUX proteins is an integral component of a plant circadian clock. LUX ARRHYTHMO (LUX) is one of the key components of the evening complex, and that play a key role in circadian rhythms and flowering. Here, we report that diverged soybean LUX has the additional role in male reproductive development. We studied diurnal and circadian rhythms of soybean LUX (GmLUXa, GmLUXb, and GmLUXc) using qRT-PCR, and show its nuclear localisation by particle bombardment. Yeast-two hybrid (Y2H) studies indicate that both GmLUXb and GmLUXc form an evening complex with GmELF4b and GmELF3a, respectively. Ectopic expression of GmLUXb in Arabidopsis lux mutants can complement functions of AtLUX, whereas GmLUXc generates novel phenotypes of serrated leaves, stunted plants, shortened anther filament, and low seed set. Overall, our results suggest that the LUX gene has diverged in soybean where GmLUXb and GmLUXc share the role to control flowering time, but GmLUXc has evolved to regulate anther filament growth and seed set by regulating the Gibberellin hormone biosynthesis pathway.
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Affiliation(s)
- Lim Chee Liew
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
- Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, VIC 3086, Australia
| | - Mohan B Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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15
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Zhang X, Zhai H, Wang Y, Tian X, Zhang Y, Wu H, Lü S, Yang G, Li Y, Wang L, Hu B, Bu Q, Xia Z. Functional conservation and diversification of the soybean maturity gene E1 and its homologs in legumes. Sci Rep 2016; 6:29548. [PMID: 27405888 PMCID: PMC4942777 DOI: 10.1038/srep29548] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/03/2016] [Indexed: 12/14/2022] Open
Abstract
Gene regulatory networks involved in flowering time and photoperiodic responses in legumes remain unknown. Although the major maturity gene E1 has been successfully deciphered in soybean, knowledge on the functional conservation of this gene is limited to a certain extent to E1 homologs in legumes. The ectopic expression of Phvul.009G204600 (PvE1L), an E1 homolog from common bean, delayed the onset of flowering in soybean. By contrast, the ectopic expression of Medtr2g058520 (MtE1L) from Medicago truncatula did not affect the flowering of soybean. Characterization of the late-flowering mte1l mutant indicated that MtE1L promoted flowering in Medicago truncatula. Moreover, all transgenic E1, PvE1L and MtE1L soybean lines exhibited phenotypic changes in terms of plant height. Transgenic E1 or PvE1L plants were taller than the wild-type, whereas transgenic MtE1L plants produced dwarf phenotype with few nodes and short internode. Thus, functional conservation and diversification of E1 family genes from legumes in the regulation of flowering and plant growth may be associated with lineage specification and genomic duplication.
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Affiliation(s)
- Xingzheng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yaying Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yupeng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Shixiang Lü
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Information Center of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Guang Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Yuqiu Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lu Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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