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Kangben F, Kumar S, Li Z, Sreedasyam A, Dardick C, Jones D, Saski CA. Phylogenetic and functional analysis of tiller angle control homeologs in allotetraploid cotton. FRONTIERS IN PLANT SCIENCE 2024; 14:1320638. [PMID: 38356867 PMCID: PMC10864623 DOI: 10.3389/fpls.2023.1320638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/20/2023] [Indexed: 02/16/2024]
Abstract
Introduction Plants can adapt their growth to optimize light capture in competitive environments, with branch angle being a crucial factor influencing plant phenotype and physiology. Decreased branch angles in cereal crops have been shown to enhance productivity in high-density plantings. The Tiller Angle Control (TAC1) gene, known for regulating tiller inclination in rice and corn, has been found to control branch angle in eudicots. Manipulating TAC1 in field crops like cotton offers the potential for improving crop productivity. Methods Using a homolog-based methodology, we examined the distribution of TAC1-related genes in cotton compared to other angiosperms. Furthermore, tissue-specific qPCR analysis unveiled distinct expression patterns of TAC1 genes in various cotton tissues. To silence highly expressed specific TAC1 homeologs in the stem, we applied CRISPR-Cas9 gene editing and Agrobacterium-mediated transformation, followed by genotyping and subsequent phenotypic validation of the mutants. Results Gene duplication events of TAC1 specific to the Gossypium lineage were identified, with 3 copies in diploid progenitors and 6 copies in allotetraploid cottons. Sequence analysis of the TAC1 homeologs in Gossypium hirsutum revealed divergence from other angiosperms with 1-2 copies, suggesting possible neo- or sub-functionalization for the duplicated copies. These TAC1 homeologs exhibited distinct gene expression patterns in various tissues over developmental time, with elevated expression of A11G109300 and D11G112200, specifically in flowers and stems, respectively. CRISPR-mediated loss of these TAC1 homeologous genes resulted in a reduction in branch angle and altered petiole angles, and a 5 to 10-fold reduction in TAC1 expression in the mutants, confirming their role in controlling branch and petiole angles. This research provides a promising strategy for genetically engineering branch and petiole angles in commercial cotton varieties, potentially leading to increased productivity.
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Affiliation(s)
- Foster Kangben
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sonika Kumar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Chris Dardick
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Appalachian Fruit Research Station, Kearneysville, WV, United States
| | - Don Jones
- Department of Agricultural Research, Cotton Incorporated, Cary, NC, United States
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
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Sang Y, Liu X, Yuan C, Yao T, Li Y, Wang D, Zhao H, Wang Y. Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China. BMC PLANT BIOLOGY 2023; 23:625. [PMID: 38062401 PMCID: PMC10702129 DOI: 10.1186/s12870-023-04646-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure. RESULTS The results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance. CONCLUSIONS The identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.
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Affiliation(s)
- Yongsheng Sang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, PR China
| | - Xiaodong Liu
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, 130118, Jilin, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
| | - Tong Yao
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, PR China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824, USA
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China.
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China.
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Jacquet S, Li S, Mian R, Kassem MA, Rashad L, Viera S, Reta F, Reta J, Yuan J. Evaluating the Response of Glycine soja Accessions to Fungal Pathogen Macrophomina phaseolina during Seedling Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:3807. [PMID: 38005704 PMCID: PMC10675638 DOI: 10.3390/plants12223807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 10/13/2023] [Indexed: 11/26/2023]
Abstract
Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot.
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Affiliation(s)
- Shirley Jacquet
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), 141 Experiment Station Road, P.O. Box 345, Stoneville, MS 38776, USA;
| | - Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), 3127 Ligon St., Raleigh, NC 27607, USA;
| | - My Abdelmajid Kassem
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Layla Rashad
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Sonia Viera
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Francisco Reta
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Juan Reta
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Jiazheng Yuan
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
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Liu Y, Yi C, Fan C, Liu Q, Liu S, Shen L, Zhang K, Huang Y, Liu C, Wang Y, Tian Z, Han F. Pan-centromere reveals widespread centromere repositioning of soybean genomes. Proc Natl Acad Sci U S A 2023; 120:e2310177120. [PMID: 37816061 PMCID: PMC10589659 DOI: 10.1073/pnas.2310177120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023] Open
Abstract
Centromere repositioning refers to a de novo centromere formation at another chromosomal position without sequence rearrangement. This phenomenon was frequently encountered in both mammalian and plant species and has been implicated in genome evolution and speciation. To understand the dynamic of centromeres on soybean genome, we performed the pan-centromere analysis using CENH3-ChIP-seq data from 27 soybean accessions, including 3 wild soybeans, 9 landraces, and 15 cultivars. Building upon the previous discovery of three centromere satellites in soybean, we have identified two additional centromere satellites that specifically associate with chromosome 1. These satellites reveal significant rearrangements in the centromere structures of chromosome 1 across different accessions, consequently impacting the localization of CENH3. By comparative analysis, we reported a high frequency of centromere repositioning on 14 out of 20 chromosomes. Most newly emerging centromeres formed in close proximity to the native centromeres and some newly emerging centromeres were apparently shared in distantly related accessions, suggesting their emergence is independent. Furthermore, we crossed two accessions with mismatched centromeres to investigate how centromere positions would be influenced in hybrid genetic backgrounds. We found that a significant proportion of centromeres in the S9 generation undergo changes in size and position compared to their parental counterparts. Centromeres preferred to locate at satellites to maintain a stable state, highlighting a significant role of centromere satellites in centromere organization. Taken together, these results revealed extensive centromere repositioning in soybean genome and highlighted how important centromere satellites are in constraining centromere positions and supporting centromere function.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Qian Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
| | - Kaibiao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
- College of Advanced Agricultural Sciences, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Yingxiang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou510642, China
| | - 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, Beijing100101, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing100101, China
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5
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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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Bohra A, Tiwari A, Kaur P, Ganie SA, Raza A, Roorkiwal M, Mir RR, Fernie AR, Smýkal P, Varshney RK. The Key to the Future Lies in the Past: Insights from Grain Legume Domestication and Improvement Should Inform Future Breeding Strategies. PLANT & CELL PHYSIOLOGY 2022; 63:1554-1572. [PMID: 35713290 PMCID: PMC9680861 DOI: 10.1093/pcp/pcac086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 05/11/2023]
Abstract
Crop domestication is a co-evolutionary process that has rendered plants and animals significantly dependent on human interventions for survival and propagation. Grain legumes have played an important role in the development of Neolithic agriculture some 12,000 years ago. Despite being early companions of cereals in the origin and evolution of agriculture, the understanding of grain legume domestication has lagged behind that of cereals. Adapting plants for human use has resulted in distinct morpho-physiological changes between the wild ancestors and domesticates, and this distinction has been the focus of several studies aimed at understanding the domestication process and the genetic diversity bottlenecks created. Growing evidence from research on archeological remains, combined with genetic analysis and the geographical distribution of wild forms, has improved the resolution of the process of domestication, diversification and crop improvement. In this review, we summarize the significance of legume wild relatives as reservoirs of novel genetic variation for crop breeding programs. We describe key legume features, which evolved in response to anthropogenic activities. Here, we highlight how whole genome sequencing and incorporation of omics-level data have expanded our capacity to monitor the genetic changes accompanying these processes. Finally, we present our perspective on alternative routes centered on de novo domestication and re-domestication to impart significant agronomic advances of novel crops over existing commodities. A finely resolved domestication history of grain legumes will uncover future breeding targets to develop modern cultivars enriched with alleles that improve yield, quality and stress tolerance.
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Affiliation(s)
- Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Abha Tiwari
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kalyanpur, Kanpur 208024, India
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, Santiniketan Road, Bolpur 731235, India
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Manish Roorkiwal
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), UAE University, Sheik Khalifa Bin Zayed Street, Al Ain, Abu Dhabi 15551, UAE
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture, SKUAST, Shalimar, Srinagar 190025, India
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacky University, Křížkovského 511/8, Olomouc 78371, Czech Republic
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Zhu W, Yang C, Yong B, Wang Y, Li B, Gu Y, Wei S, An Z, Sun W, Qiu L, He C. An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement. THE NEW PHYTOLOGIST 2022; 236:1375-1392. [PMID: 36068955 DOI: 10.1111/nph.18461] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One-hundred-seed weight is one of the most important domesticated traits determining soybean yield; however, its underlying genetic basis remains elusive. We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild-type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co-located in a well-identified quantitative trait locus (QTL)-rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182nd residue in Gmsss1 conferred an enhancing effect on seed weight. GmSSS1 underwent diversification in wild-type and cultivated soybean, and the alleles encoding the Gmsss1-type substitution of 182nd -Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement. We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yongzhe Gu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Zhenghong An
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Wenkai Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (
Phaseolus coccineus
L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Department of Plant Sciences University of Saskatchewan Saskatoon SK S7N 5A2 Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Environmental Genomics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center University of California, Davis Davis California 95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali Università Politecnica delle Marche Ancona 60131 Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
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9
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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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10
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Montes CM, Fox C, Sanz-Sáez Á, Serbin SP, Kumagai E, Krause MD, Xavier A, Specht JE, Beavis WD, Bernacchi CJ, Diers BW, Ainsworth EA. High-throughput characterization, correlation, and mapping of leaf photosynthetic and functional traits in the soybean (Glycine max) nested association mapping population. Genetics 2022; 221:iyac065. [PMID: 35451475 PMCID: PMC9157091 DOI: 10.1093/genetics/iyac065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 04/03/2022] [Indexed: 11/14/2022] Open
Abstract
Photosynthesis is a key target to improve crop production in many species including soybean [Glycine max (L.) Merr.]. A challenge is that phenotyping photosynthetic traits by traditional approaches is slow and destructive. There is proof-of-concept for leaf hyperspectral reflectance as a rapid method to model photosynthetic traits. However, the crucial step of demonstrating that hyperspectral approaches can be used to advance understanding of the genetic architecture of photosynthetic traits is untested. To address this challenge, we used full-range (500-2,400 nm) leaf reflectance spectroscopy to build partial least squares regression models to estimate leaf traits, including the rate-limiting processes of photosynthesis, maximum Rubisco carboxylation rate, and maximum electron transport. In total, 11 models were produced from a diverse population of soybean sampled over multiple field seasons to estimate photosynthetic parameters, chlorophyll content, leaf carbon and leaf nitrogen percentage, and specific leaf area (with R2 from 0.56 to 0.96 and root mean square error approximately <10% of the range of calibration data). We explore the utility of these models by applying them to the soybean nested association mapping population, which showed variability in photosynthetic and leaf traits. Genetic mapping provided insights into the underlying genetic architecture of photosynthetic traits and potential improvement in soybean. Notably, the maximum Rubisco carboxylation rate mapped to a region of chromosome 19 containing genes encoding multiple small subunits of Rubisco. We also mapped the maximum electron transport rate to a region of chromosome 10 containing a fructose 1,6-bisphosphatase gene, encoding an important enzyme in the regeneration of ribulose 1,5-bisphosphate and the sucrose biosynthetic pathway. The estimated rate-limiting steps of photosynthesis were low or negatively correlated with yield suggesting that these traits are not influenced by the same genetic mechanisms and are not limiting yield in the soybean NAM population. Leaf carbon percentage, leaf nitrogen percentage, and specific leaf area showed strong correlations with yield and may be of interest in breeding programs as a proxy for yield. This work is among the first to use hyperspectral reflectance to model and map the genetic architecture of the rate-limiting steps of photosynthesis.
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Affiliation(s)
| | - Carolyn Fox
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Álvaro Sanz-Sáez
- Department of Crop, Soil, and Environmental Sciences, Auburn, AL 36849, USA
| | - Shawn P Serbin
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Etsushi Kumagai
- Institute of Agro-environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8604, Japan
| | - Matheus D Krause
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA 50011, USA
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
- Department of Biostatistics, Corteva Agrisciences, Johnston, IA 50131, USA
| | - James E Specht
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - William D Beavis
- Department of Agronomy, Iowa State University, Agronomy Hall, Ames, IA 50011, USA
| | - Carl J Bernacchi
- Global Change and Photosynthesis Research Unit, USDA ARS, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Elizabeth A Ainsworth
- Global Change and Photosynthesis Research Unit, USDA ARS, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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11
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Li YF, Li YH, Su SS, Reif JC, Qi ZM, Wang XB, Wang X, Tian Y, Li DL, Sun RJ, Liu ZX, Xu ZJ, Fu GH, Ji YL, Chen QS, Liu JQ, Qiu LJ. SoySNP618K array: A high-resolution single nucleotide polymorphism platform as a valuable genomic resource for soybean genetics and breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:632-648. [PMID: 34914170 DOI: 10.1111/jipb.13202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/05/2021] [Indexed: 05/13/2023]
Abstract
Innovations in genomics have enabled the development of low-cost, high-resolution, single nucleotide polymorphism (SNP) genotyping arrays that accelerate breeding progress and support basic research in crop science. Here, we developed and validated the SoySNP618K array (618,888 SNPs) for the important crop soybean. The SNPs were selected from whole-genome resequencing data containing 2,214 diverse soybean accessions; 29.34% of the SNPs mapped to genic regions representing 86.85% of the 56,044 annotated high-confidence genes. Identity-by-state analyses of 318 soybeans revealed 17 redundant accessions, highlighting the potential of the SoySNP618K array in supporting gene bank management. The patterns of population stratification and genomic regions enriched through domestication were highly consistent with previous findings based on resequencing data, suggesting that the ascertainment bias in the SoySNP618K array was largely compensated for. Genome-wide association mapping in combination with reported quantitative trait loci enabled fine-mapping of genes known to influence flowering time, E2 and GmPRR3b, and of a new candidate gene, GmVIP5. Moreover, genomic prediction of flowering and maturity time in 502 recombinant inbred lines was highly accurate (>0.65). Thus, the SoySNP618K array is a valuable genomic tool that can be used to address many questions in applied breeding, germplasm management, and basic crop research.
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Affiliation(s)
- Yan-Fei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shan-Shan Su
- Beijing Compass Biotechnology Co. Ltd, Beijing, 102206, China
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466, Germany
| | - Zhao-Ming Qi
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Xiao-Bo Wang
- School of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Xing Wang
- Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu, Xuzhou, 221131, China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - De-Lin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Ru-Jian Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
- Hulun Buir Institution of Agricultural Sciences, Zhalantun, Inner Mongolia, 021000, China
| | - Zhang-Xiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ze-Jun Xu
- Xuzhou Institute of Agricultural Sciences of Xu-huai Region of Jiangsu, Xuzhou, 221131, China
| | - Guang-Hui Fu
- Suzhou Academy of Agricultural Sciences, Suzhou, 234000, China
| | - Ya-Liang Ji
- Beijing Compass Biotechnology Co. Ltd, Beijing, 102206, China
| | - Qing-Shan Chen
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Ji-Qiang Liu
- Beijing Compass Biotechnology Co. Ltd, Beijing, 102206, China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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12
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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13
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Assessment of the Breeding Potential of a Set of Genotypes Selected from a Natural Population of Akebia trifoliata (Three–Leaf Akebia). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Akebia trifoliata (three-leaf akebia) has long been used as a medicinal herb and has the potential to be used in diverse ways, especially as a fruit crop. However, efforts to domesticate and cultivate new varieties for commercial use are only in their infancy. Here, we evaluated the genetic diversity of 29 genotypes, which were previously selected from a natural population consisting of 1447 genotypes and exhibiting high resistance to fungal diseases and a smooth peel of A. trifoliata using 85 genome-specific single sequence repeat (SSR) markers. We also characterized variation in 19 phenotypic traits and nutritional components. Large variation in phenotypic traits and nutritional components was observed, especially in vitamin C, seed/pulp, and fruit color. Correlation analyses revealed that many phenotypic traits and nutritional components were significantly correlated. A principal component analysis identified five principal components, which explained 83.2% of the total variation in the data. The results of the SSR analysis revealed that 80 of the 85 SSR markers were polymorphic; the total number of alleles amplified was 532. The expected heterozygosity was 0.672, and Shannon’s information index was 1.328. A Ward dendrogram and unweighted pair group method with arithmetic mean dendrogram revealed high diversity among the 29 genotypes and suggested that the measured morphological and nutritional traits were genetically independent of disease resistance and texture traits, as well as SSR marker loci. Finally, our results suggest that additional rounds of selection from the selected population, despite its small size, could be effective for the development of new A. trifoliata fruit cultivars.
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14
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Zuo JF, Ikram M, Liu JY, Han CY, Niu Y, Dunwell JM, Zhang YM. Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement. Comput Struct Biotechnol J 2022; 20:2951-2964. [PMID: 35782726 PMCID: PMC9213226 DOI: 10.1016/j.csbj.2022.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/01/2022] Open
Abstract
Due to reduced diversity, it is essential to map domesticated and improved genes. 13 known and 442 candidate genes were mined for seed size- and oil-related traits. All the genes were used to explain trait changes in domestication and improvement. 56 domesticated and 15 improved genes may be valuable for future soybean breeding. This study provides useful gene resources for future breeding and biology research.
To address domestication and improvement studies of soybean seed size- and oil-related traits, a series of domesticated and improved regions, loci, and candidate genes were identified in 286 soybean accessions using domestication and improvement analyses, genome-wide association studies, quantitative trait locus (QTL) mapping and bulked segregant analyses in this study. As a result, 534 candidate domestication regions (CDRs) and 458 candidate improvement regions (CIRs) were identified in this study and integrated with those in five and three previous studies, respectively, to obtain 952 CDRs and 538 CIRs; 1469 loci for soybean seed size- and oil-related traits were identified in this study and integrated with those in Soybase to obtain 433 QTL clusters. The two results were intersected to obtain 245 domestication and 221 improvement loci for the above traits. Around these trait-related domestication and improvement loci, 7 domestication and 7 improvement genes were found to be truly associated with these traits, and 372 candidate domestication and 87 candidate improvement genes were identified using gene expression, SNP variants in genome, miRNA binding, KEGG pathway, DNA methylation, and haplotype analysis. These genes were used to explain the trait changes in domestication and improvement. As a result, the trait changes can be explained by their frequencies of elite haplotypes, base mutations in coding region, and three factors affecting their expression levels. In addition, 56 domestication and 15 improvement genes may be valuable for future soybean breeding. This study can provide useful gene resources for future soybean breeding and molecular biology research.
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Affiliation(s)
- Jian-Fang Zuo
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Ikram
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin-Yang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chun-Yu Han
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuan Niu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Corresponding author.
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15
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Shaibu AS, Ibrahim H, Miko ZL, Mohammed IB, Mohammed SG, Yusuf HL, Kamara AY, Omoigui LO, Karikari B. Assessment of the Genetic Structure and Diversity of Soybean ( Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers. PLANTS (BASEL, SWITZERLAND) 2021; 11:68. [PMID: 35009071 PMCID: PMC8747349 DOI: 10.3390/plants11010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022]
Abstract
Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon's diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.
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Affiliation(s)
- Abdulwahab S. Shaibu
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Hassan Ibrahim
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Zainab L. Miko
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Ibrahim B. Mohammed
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Sanusi G. Mohammed
- Centre for Dryland Agriculture, Bayero University Kano, Kano 700001, Nigeria;
| | - Hauwa L. Yusuf
- Department of Food Science and Technology, Bayero University Kano, Kano 700001, Nigeria;
| | - Alpha Y. Kamara
- International Institute of Tropical Agriculture, Ibadan 200211, Nigeria; (A.Y.K.); (L.O.O.)
| | - Lucky O. Omoigui
- International Institute of Tropical Agriculture, Ibadan 200211, Nigeria; (A.Y.K.); (L.O.O.)
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P.O. Box TL 1882, Tamale 00233, Ghana;
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16
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Hu X, Zuo J. The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis. BMC Genomics 2021; 22:511. [PMID: 34233625 PMCID: PMC8261996 DOI: 10.1186/s12864-021-07787-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. RESULTS In this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication. CONCLUSIONS This study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China.
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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17
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Page AML, Chapman MA. Identifying genomic regions targeted during eggplant domestication using transcriptome data. J Hered 2021; 112:519-525. [PMID: 34130314 PMCID: PMC8634079 DOI: 10.1093/jhered/esab035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/11/2021] [Indexed: 11/15/2022] Open
Abstract
Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A “bottom-up” population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low π for the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.
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Affiliation(s)
- Anna M L Page
- Biological Sciences, University of Southampton, Southampton, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, UK
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18
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Zhao B, Zhang S, Yang W, Li B, Lan C, Zhang J, Yuan L, Wang Y, Xie Q, Han J, Mur LAJ, Hao X, Roberts JA, Miao Y, Yu K, Zhang X. Multi-omic dissection of the drought resistance traits of soybean landrace LX. PLANT, CELL & ENVIRONMENT 2021; 44:1379-1398. [PMID: 33554357 DOI: 10.1111/pce.14025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
With diverse genetic backgrounds, soybean landraces are valuable resource for breeding programs. Herein, we apply multi-omic approaches to extensively characterize the molecular basis of drought tolerance in the soybean landrace LX. Initial screens established that LX performed better with PEG6000 treatment than control cultivars. LX germinated better than William 82 under drought conditions and accumulated more anthocyanin and flavonoids. Untargeted mass spectrometry in combination with transcriptomic analyses revealed the chemical diversity and genetic basis underlying the overall performance of LX landrace. Under control and drought conditions, significant differences in the expression of a suite of secondary metabolism genes, particularly those involved in the general phenylpropanoid pathway and flavonoid but not lignin biosynthesis, were seen in LX and William 82. The expression of these genes correlated with the corresponding metabolites in LX plants. Further correlation analysis between metabolites and transcripts identified pathway structural genes and transcription factors likely are responsible for the LX agronomic traits. The activities of some key biosynthetic genes or regulators were confirmed through heterologous expression in transgenic Arabidopsis and hairy root transformation in soybean. We propose a regulatory mechanism based on flavonoid secondary metabolism and adaptive traits of this landrace which could be of relevance to cultivated soybean.
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Affiliation(s)
- Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Shulin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Wenqi Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Bingyan Li
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Chen Lan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Yu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Jiwan Han
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Luis A J Mur
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Xingyu Hao
- College of Agronomy, Shanxi Agricultural University, Taigu, China
| | - Jeremy A Roberts
- Faculty of Science and Engineering, School of Biological & Marine Sciences, University of Plymouth, Devon, UK
| | - Yuchen Miao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Ke Yu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Kaifeng, China
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Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process. PLANTS 2021; 10:plants10030585. [PMID: 33808668 PMCID: PMC8003350 DOI: 10.3390/plants10030585] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022]
Abstract
Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.
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20
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Kajiya-Kanegae H, Nagasaki H, Kaga A, Hirano K, Ogiso-Tanaka E, Matsuoka M, Ishimori M, Ishimoto M, Hashiguchi M, Tanaka H, Akashi R, Isobe S, Iwata H. Whole-genome sequence diversity and association analysis of 198 soybean accessions in mini-core collections. DNA Res 2021; 28:dsaa032. [PMID: 33492369 PMCID: PMC7934572 DOI: 10.1093/dnares/dsaa032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.
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Affiliation(s)
- Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hideki Nagasaki
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Eri Ogiso-Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Motoyuki Ishimori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8518, Japan
| | | | - Hidenori Tanaka
- Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Ryo Akashi
- Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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21
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Li L, Zhang C, Huang J, Liu Q, Wei H, Wang H, Liu G, Gu L, Yu S. Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:109-123. [PMID: 32652678 PMCID: PMC7769233 DOI: 10.1111/pbi.13446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 05/05/2023]
Abstract
Although upland cotton (Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole-genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome-wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.
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Affiliation(s)
- Libei Li
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Chi Zhang
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Jianqin Huang
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
| | - Qibao Liu
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Hengling Wei
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Hantao Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Guoyuan Liu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Lijiao Gu
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
| | - Shuxun Yu
- State Key Laboratory of Subtropical SilvicultureZhejiang A & F UniversityLin'an, Hangzhou
- State Key Laboratory of Cotton BiologyInstitute of Cotton Research of CAASAnyangHenanChina
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22
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Hawliczek A, Bolibok L, Tofil K, Borzęcka E, Jankowicz-Cieślak J, Gawroński P, Kral A, Till BJ, Bolibok-Brągoszewska H. Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions. BMC Genomics 2020; 21:845. [PMID: 33256606 PMCID: PMC7706248 DOI: 10.1186/s12864-020-07240-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/18/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Discovery of DNA variations is an important step in the efficient use of these resources. While technologies have improved and costs dropped, it remains impractical to consider resequencing millions of accessions. Candidate genes are known for most agronomic traits, providing a list of high priority targets. Heterogeneity in seed stocks means that multiple samples from an accession need to be evaluated to recover available alleles. To address this we developed a pooled amplicon sequencing approach and applied it to the out-crossing cereal rye (Secale cereale L.). RESULTS Using the amplicon sequencing approach 95 rye accessions of different improvement status and worldwide origin, each represented by a pooled sample comprising DNA of 96 individual plants, were evaluated for sequence variation in six candidate genes with significant functions on biotic and abiotic stress resistance, and seed quality. Seventy-four predicted deleterious variants were identified using multiple algorithms. Rare variants were recovered including those found only in a low percentage of seed. CONCLUSIONS We conclude that this approach provides a rapid and flexible method for evaluating stock heterogeneity, probing allele diversity, and recovering previously hidden variation. A large extent of within-population heterogeneity revealed in the study provides an important point for consideration during rye germplasm conservation and utilization efforts.
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Affiliation(s)
- Anna Hawliczek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Institute of Forest Sciences, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Joanna Jankowicz-Cieślak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Adam Kral
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria.
- Veterinary Genetics Laboratory, University of California, Davis, Davis, California, USA.
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences - SGGW, Warsaw, Poland.
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Song Q, Yan L, Quigley C, Fickus E, Wei H, Chen L, Dong F, Araya S, Liu J, Hyten D, Pantalone V, Nelson RL. Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:800-811. [PMID: 32772442 PMCID: PMC7702105 DOI: 10.1111/tpj.14960] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/30/2020] [Indexed: 05/10/2023]
Abstract
The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000-2000 genome-wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.
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Affiliation(s)
- Qijian Song
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Long Yan
- Shijiazhuang Branch Center of National Center for Soybean Improvement/the Key Laboratory of Crop Genetics and BreedingInstitute of Cereal and Oil CropsHebei Academy of Agricultural and Forestry SciencesShijiazhuangChina
| | - Charles Quigley
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Edward Fickus
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - He Wei
- Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouHenan ProvinceChina
| | - Linfeng Chen
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Faming Dong
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Susan Araya
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Jinlong Liu
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - David Hyten
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | | | - Randall L. Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
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24
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Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z. Pan-Genome of Wild and Cultivated Soybeans. Cell 2020; 182:162-176.e13. [PMID: 32553274 DOI: 10.1016/j.cell.2020.05.023] [Citation(s) in RCA: 391] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022]
Abstract
Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.
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Affiliation(s)
- Yucheng Liu
- 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; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Li
- Berry Genomics Corporation, Beijing 100015, China
| | - Yanting Shen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hua Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Liu
- 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
| | - Guo-An Zhou
- 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
| | | | - Zhi Liu
- 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; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing 100015, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yan Li
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Min Zhang
- 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
| | - Zheng Wang
- 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
| | - Baoge Zhu
- 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
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - 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; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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25
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Elessawy FM, Bazghaleh N, Vandenberg A, Purves RW. Polyphenol profile comparisons of seed coats of five pulse crops using a semi-quantitative liquid chromatography-mass spectrometric method. PHYTOCHEMICAL ANALYSIS : PCA 2020; 31:458-471. [PMID: 31869515 DOI: 10.1002/pca.2909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Pulse crops are nutritious and therefore widely grown. Pulse seed coats are typically discarded, despite their high content of polyphenols that are known for their antioxidant properties and health benefits. A better understanding of polyphenol diversity and biochemical pathways will ultimately provide insight into how polyphenols are linked to health benefits, which will help to better utilise these seed coats. OBJECTIVES To explore polyphenol profiles among seed coats of diverse genotypes of five pulse crops using a targeted liquid chromatography mass spectrometry (LC-MS) method. METHODS Four genotypes of each of common bean, chickpea, pea, lentil and faba bean seed coats were selected for analysis. Following extraction, polyphenols were quantified using LC-MS. RESULTS An LC-MS method was developed to quantify 98 polyphenols from 13 different classes in 30 min. The low-tannin seed coats had the lowest concentrations of all polyphenols. Chickpea and pea seed coats had the most similar polyphenolic profiles. The black common bean showed the most diverse seed coat polyphenol profile, including several anthocyanins not detected in any of the other seed coats. CONCLUSION The LC-MS method reported herein was used to show polyphenol diversity within several polyphenol classes among the pulse crop seed coats. Detected in all seed coats, flavonols and hydroxybenzoic acids appear well-conserved in the edible Fabaceae. The presence of anthocyanins, flavan-3-ols and proanthocyanins in the coloured seed coats suggests that unique divergent branches were introduced in the flavonoid biosynthetic pathway, possibly in response to environmental stressors.
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Affiliation(s)
- Fatma M Elessawy
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Navid Bazghaleh
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Randy W Purves
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Centre for Veterinary Drug Residues, Canadian Food Inspection Agency, Saskatoon, Saskatchewan, Canada
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26
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Liu S, Zhang M, Feng F, Tian Z. Toward a "Green Revolution" for Soybean. MOLECULAR PLANT 2020; 13:688-697. [PMID: 32171732 DOI: 10.1016/j.molp.2020.03.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/03/2020] [Accepted: 03/06/2020] [Indexed: 05/25/2023]
Abstract
Soybean (Glycine max), as an economically important food and oilseedcrop, is a major source of plant proteins and oils. Although considerable progress has been made in increasing the yields of rice, wheat, and maize through the "Green Revolution", little improvements have been made for soybean. With the increasing demand of soybean production and the rapid development of crop breeding technologies, time has come for this important crop to undergo a Green Revolution. Here, we briefly summarize the history of crop breeding and Green Revolution in other crops. We then discuss the possible directions and potential approaches toward achieving a Green Revolution for soybean. We provide our views and perspectives on how to breed new soybean varieties with improved yield.
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Affiliation(s)
- Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Feng
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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27
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Li C, Li YH, Li Y, Lu H, Hong H, Tian Y, Li H, Zhao T, Zhou X, Liu J, Zhou X, Jackson SA, Liu B, Qiu LJ. A Domestication-Associated Gene GmPRR3b Regulates the Circadian Clock and Flowering Time in Soybean. MOLECULAR PLANT 2020; 13:745-759. [PMID: 32017998 DOI: 10.1016/j.molp.2020.01.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/28/2019] [Accepted: 01/29/2020] [Indexed: 05/24/2023]
Abstract
Improved soybean cultivars have been adapted to grow at a wide range of latitudes, enabling expansion of cultivation worldwide. However, the genetic basis of this broad adaptation is still not clear. Here, we report the identification of GmPRR3b as a major flowering time regulatory gene that has been selected during domestication and genetic improvement for geographic expansion. Through a genome-wide association study of a diverse soybean landrace panel consisting of 279 accessions, we identified 16 candidate quantitative loci associated with flowering time and maturity time. The strongest signal resides in the known flowering gene E2, verifying the effectiveness of our approach. We detected strong signals associated with both flowering and maturity time in a genomic region containing GmPRR3b. Haplotype analysis revealed that GmPRR3bH6 is the major form of GmPRR3b that has been utilized during recent breeding of modern cultivars. mRNA profiling analysis showed that GmPRR3bH6 displays rhythmic and photoperiod-dependent expression and is preferentially induced under long-day conditions. Overexpression of GmPRR3bH6 increased main stem node number and yield, while knockout of GmPRR3bH6 using CRISPR/Cas9 technology delayed growth and the floral transition. GmPRR3bH6 appears to act as a transcriptional repressor of multiple predicted circadian clock genes, including GmCCA1a, which directly upregulates J/GmELF3a to modulate flowering time. The causal SNP (Chr12:5520945) likely endows GmPRR3bH6 a moderate but appropriate level of activity, leading to early flowering and vigorous growth traits preferentially selected during broad adaptation of landraces and improvement of cultivars.
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Affiliation(s)
- Cong Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yanfei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Hongyu Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Tao Zhao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Xiaowei Zhou
- Novogene Bioinformatics Institute, Beijing, P.R. China
| | - Jun Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Xinan Zhou
- Key Laboratory of Oil Crop Biology (MOA), Oil Crops Research Institute of Chinese Academy of Agriculture Sciences, Wuhan, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P.R. China.
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Karikari B, Bhat JA, Denwar NN, Zhao T. Exploring the genetic base of the soybean germplasm from Africa, America and Asia as well as mining of beneficial allele for flowering and seed weight. 3 Biotech 2020; 10:195. [PMID: 32296618 DOI: 10.1007/s13205-020-02186-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 11/26/2022] Open
Abstract
Genetic diversity is the foundation for any breeding program. The present study analyzed the genetic base of 163 soybean genotypes from three continents viz. Africa, America and Asia using 68 trait-linked simple sequence repeats (SSR) markers. The average number of alleles among the germplasm from the three continents followed the trend as Asia (9) > America (8) > Africa (7). Similar trends were observed for gene diversity (0.76 > 0.74 > 0.71) and polymorphism information content (PIC) (0.73 > 0.71 > 0.68). These findings revealed that soybean germplasm from Asia has wider genetic base followed by America, and least in Africa. The 163 genotypes were grouped into 4 clusters by phylogenetic analysis, whereas model-based population structure analysis also divided them into 4 subpopulations comprising 80.61% pure lines and 19.39% admixtures. The genotypes from Africa were easily distinguished from those of other two continents using phylogenetic analysis, indicating important role of geographyical differentiation for this genetic variability. Our results indicated that soybean germplasm has moved from Asia to America, and from America to Africa. Analysis of molecular variance (AMOVA) showed 8.41% variation among the four subpopulations, whereas 63.12% and 28.47% variation existed among and within individuals in the four subpopulations, respectively. Based on the association mapping, a total of 21 SSR markers showed significant association with days to flowering (DoF) and 100-seed weight (HSW). Two markers Satt365 and Satt581 on chromosome 6 and 10, respectively, showed pleiotropic effect or linkage on both traits. Genotype A50 (Gakuran Daizu/PI 506679) from Japan has 8 out of the 13 beneficial alleles for increased HSW. The diverse genotypes, polymorphic SSR markers and desirable alleles identified for DoF and HSW will be used in future breeding programs to improve reproductive, yield and quality traits.
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Affiliation(s)
- Benjamin Karikari
- 1MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Javaid A Bhat
- 1MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Nicholas N Denwar
- Council of Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Tuanjie Zhao
- 1MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
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Li MW, Wang Z, Jiang B, Kaga A, Wong FL, Zhang G, Han T, Chung G, Nguyen H, Lam HM. Impacts of genomic research on soybean improvement in East Asia. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1655-1678. [PMID: 31646364 PMCID: PMC7214498 DOI: 10.1007/s00122-019-03462-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/15/2019] [Indexed: 05/10/2023]
Abstract
It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea.
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Affiliation(s)
- 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 Special Administrative Region China
| | - 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 Special Administrative Region China
| | - Bingjun Jiang
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - 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 Special Administrative Region China
| | - Guohong Zhang
- Institute of Dryland Agriculture, Gansu Academy of Agricultural Sciences, Key Laboratory of Northwest Drought Crop Cultivation of Chinese Ministry of Agriculture, Lanzhou, 730070 China
| | - Tianfu Han
- Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam 59626 Korea
| | - Henry Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO USA
| | - 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 Special Administrative Region China
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Kofsky J, Zhang H, Song BH. Genetic Architecture of Early Vigor Traits in Wild Soybean. Int J Mol Sci 2020; 21:E3105. [PMID: 32354037 PMCID: PMC7247153 DOI: 10.3390/ijms21093105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
A worldwide food shortage has been projected as a result of the current increase in global population and climate change. In order to provide sufficient food to feed more people, we must develop crops that can produce higher yields. Plant early vigor traits, early growth rate (EGR), early plant height (EPH), inter-node length, and node count are important traits that are related to crop yield. Glycine soja, the wild counterpart to cultivated soybean, Glycine max, harbors much higher genetic diversity and can grow in diverse environments. It can also cross easily with cultivated soybean. Thus, it holds a great potential in developing soybean cultivars with beneficial agronomic traits. In this study, we used 225 wild soybean accessions originally from diverse environments across its geographic distribution in East Asia. We quantified the natural variation of several early vigor traits, investigated the relationships among them, and dissected the genetic basis of these traits by applying a Genome-Wide Association Study (GWAS) with genome-wide single nucleotide polymorphism (SNP) data. Our results showed positive correlation between all early vigor traits studied. A total of 12 SNPs significantly associated with EPH were identified with 4 shared with EGR. We also identified two candidate genes, Glyma.07G055800.1 and Glyma.07G055900.1, playing important roles in influencing trait variation in both EGR and EPH in G. soja.
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Affiliation(s)
| | | | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (J.K.); (H.Z.)
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Li Y, Li D, Jiao Y, Schnable JC, Li Y, Li H, Chen H, Hong H, Zhang T, Liu B, Liu Z, You Q, Tian Y, Guo Y, Guan R, Zhang L, Chang R, Zhang Z, Reif J, Zhou X, Schnable PS, Qiu L. Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:389-401. [PMID: 31278885 PMCID: PMC6953199 DOI: 10.1111/pbi.13206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 05/22/2023]
Abstract
Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS® . Based on 99 085 high-quality SNPs, landraces were classified into three sub-populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour-joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait-associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub-populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.
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Affiliation(s)
- Ying‐hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Delin Li
- Data Biotech (Beijing) Co., Ltd.BeijingChina
- Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Yong‐qing Jiao
- Key Laboratory of Oil Crop Biology (MOA)Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina
| | - James C. Schnable
- Data Biotech (Beijing) Co., Ltd.BeijingChina
- Departmentof Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Data2Bio LLCAmesIAUSA
| | - Yan‐fei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui‐hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Huai‐zhu Chen
- Guangxi Academy of Agricultural SciencesNanningChina
| | - Hui‐long Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ting Zhang
- Data Biotech (Beijing) Co., Ltd.BeijingChina
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhang‐xiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Qing‐bo You
- Key Laboratory of Oil Crop Biology (MOA)Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Rong‐xia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Li‐juan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ru‐zhen Chang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhiwu Zhang
- Department of Crop and Soil SciencesWashington State UniversityPullmanWAUSA
| | - Jochen Reif
- Department of Breeding ResearchLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Xin‐an Zhou
- Key Laboratory of Oil Crop Biology (MOA)Oil Crops Research Institute of Chinese Academy of Agriculture SciencesWuhanChina
| | - Patrick S. Schnable
- Data Biotech (Beijing) Co., Ltd.BeijingChina
- Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Data2Bio LLCAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Li‐juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Jeong N, Moon JK, Kim N. Dissection of soybean populations according to selection signatures based on whole-genome sequences. Gigascience 2019; 8:giz151. [PMID: 31869408 PMCID: PMC6927394 DOI: 10.1093/gigascience/giz151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. RESULTS This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. CONCLUSIONS Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.
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Affiliation(s)
- Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
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Tian Y, Liu B, Shi X, Reif JC, Guan R, Li YH, Qiu LJ. Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Hegstad JM, Nelson RL, Renny-Byfield S, Feng L, Chaky JM. Introgression of novel genetic diversity to improve soybean yield. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2541-2552. [PMID: 31209537 DOI: 10.1007/s00122-019-03369-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Exotic soybean germplasm can be used to increase novel genetic diversity and yield potential of cultivars. Modern North American soybean (Glycine max [L.] Merr.) cultivars have been derived from only a few ancestors. The objectives of this research were to develop breeding lines with novel genetic diversity that were equivalent to the yield of a commercial cultivar parent and within those lines identify regions of novel genetic diversity that were not present in the Corteva Agriscience elite soybean germplasm pool. Nine lines created from diverse germplasm (USDA-ARS breeding program at the University of Illinois) were crossed to a RM34Elite parent to develop populations and sublines for yield testing. Across yield tests at 30 locations conducted between 2014 and 2016, eleven breeding lines were identified that were equivalent to or significantly higher in yield when compared to the RM34Elite parent. Among the eleven final lines, the introgressed novel haplotypes that were not present in current Corteva Agriscience soybean germplasm occupied an estimated 0.8-10.0% of the genome. JH-2665, the highest yielding line across 3 years of testing, yielded 280 kg/ha more than the RM34Elite parent and had an estimated 8.6% of the genome containing novel diversity haplotypes. JH-2665 had 96 regions of novel diversity introgression ranging from 1 to 12 cM in size, with six regions over 6 cM in length. The methods reported demonstrate how high-yielding lines with novel genetic diversity can be developed. This material will be useful for expanding the genetic diversity needed to improve genetic gain in future soybean cultivar development.
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Affiliation(s)
- J M Hegstad
- Corteva Agriscience, 8305 NW 62nd Ave., Johnston, IA, 50131, USA.
| | | | - S Renny-Byfield
- Corteva Agriscience, 8305 NW 62nd Ave., Johnston, IA, 50131, USA
| | - L Feng
- Corteva Agriscience, 8305 NW 62nd Ave., Johnston, IA, 50131, USA
| | - J M Chaky
- Corteva Agriscience, 8305 NW 62nd Ave., Johnston, IA, 50131, USA
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Liu J, Rasheed A, He Z, Imtiaz M, Arif A, Mahmood T, Ghafoor A, Siddiqui SU, Ilyas MK, Wen W, Gao F, Xie C, Xia X. Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2509-2523. [PMID: 31139853 DOI: 10.1007/s00122-019-03367-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.
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Affiliation(s)
- Jindong Liu
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
- Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan Office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Anjuman Arif
- National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | | | - Abdul Ghafoor
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Sadar Uddin Siddiqui
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Weie Wen
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Chaojie Xie
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Manrique S, Friel J, Gramazio P, Hasing T, Ezquer I, Bombarely A. Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3007-3019. [PMID: 31152173 DOI: 10.1093/jxb/erz231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 05/02/2019] [Indexed: 05/26/2023]
Abstract
Plant domestication is the process of adapting plants to human use by selecting specific traits. The selection process often involves the modification of some components of the plant reproductive mechanisms. Allelic variants of genes associated with flowering time, vernalization, and the circadian clock are responsible for the adaptation of crops, such as rice, maize, barley, wheat, and tomato, to non-native latitudes. Modifications in the plant architecture and branching have been selected for higher yields and easier harvests. These phenotypes are often produced by alterations in the regulation of the transition of shoot apical meristems to inflorescences, and then to floral meristems. Floral homeotic mutants are responsible for popular double-flower phenotypes in Japanese cherries, roses, camellias, and lilies. The rise of peloric flowers in ornamentals such as snapdragon and florists' gloxinia is associated with non-functional alleles that control the relative expansion of lateral and ventral petals. Mechanisms to force outcrossing such as self-incompatibility have been removed in some tree crops cultivars such as almonds and peaches. In this review, we revisit some of these important concepts from the plant domestication perspective, focusing on four topics related to the pre-fertilization mechanisms: flowering time, inflorescence architecture, flower development, and pre-fertilization self-incompatibility mechanisms.
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Affiliation(s)
- Silvia Manrique
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - James Friel
- Genetics and Biotechnology Laboratory, Plant and AgriBioscience Research Center (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, USA
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tomas Hasing
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, USA
| | - Ignacio Ezquer
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Aureliano Bombarely
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
- School of Plant and Environmental Sciences (SPES), Virginia Tech, Blacksburg, VA, USA
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Malaviya DR, Roy AK, Kaushal P, Yadav A, Pandey DK. Complementary gene interaction and xenia effect controls the seed coat colour in interspecific cross between Trifolium alexandrinum and T. apertum. Genetica 2019; 147:197-203. [PMID: 30937602 DOI: 10.1007/s10709-019-00063-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
Trifolium alexandrinum (Egyptian clover) is a widely cultivated winter annual fodder. Present work deals with inheritance of the seed coat colour in segregating progenies of the interspecific cross between T. alexandrinum and T. apertum. Although, both the parent species possessed yellow seed coat, the F1 seeds were black coloured in the reciprocal cross (T. apertum × T. alexandrinum). Seeds borne on individual F2 plants and the advancing generations segregated in yellow and black seed coat colour, which confirmed xenia effect. F2 seeds collected from individual F1 plants exhibited nine black and seven yellow segregation ratio. The segregation of the seed coat colour recorded from F3 to F5 generations revealed that yellow seed coat was true breeding (i.e. non-segregating) in this interspecific cross (including the reciprocal crosses). However, the black seeded progenies were either true breeding or segregated in nine black: seven yellow ratio or three black: one yellow ratio suggesting a complementary gene interaction or duplicate recessive epistasis. It indicated that the seed coat colour is controlled by complementary gene interaction along with xenia effect in interspecific crosses between T. alexandrinum and T. apertum. Occurrence of the complementary genes across the species could suggest T. apertum to be the progenitor of T. alexandrinum. Inheritance of seed coat colour in reference to its importance in Egyptian clover breeding is also discussed.
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Affiliation(s)
- D R Malaviya
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India. .,ICAR-Indian Institute of Sugarcane Research, Lucknow, 226002, India.
| | - A K Roy
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - P Kaushal
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India.,ICAR-National Institute of Biotic Stress Management, Raipur, 493225, India
| | - A Yadav
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - D K Pandey
- ICAR-Indian Institute of Sugarcane Research, Lucknow, 226002, India
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Du H, Li X, Ning L, Qin R, Du Q, Wang Q, Song H, Huang F, Wang H, Yu D. RNA-Seq analysis reveals transcript diversity and active genes after common cutworm (Spodoptera litura Fabricius) attack in resistant and susceptible wild soybean lines. BMC Genomics 2019; 20:237. [PMID: 30902045 PMCID: PMC6431011 DOI: 10.1186/s12864-019-5599-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/12/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes. RESULTS The transcriptomes of two wild accessions (W11 and W99) with different resistance to CCW were analyzed at early- and late-induction time points. After induction, the susceptible accession W11 differentially expressed 1268 and 508 genes at the early and late time points, respectively. Compared with W11, the resistant accession W99 differentially expressed 1270 genes at the early time point and many more genes (2308) at the late time point. In total, 3836 non-redundant genes were identified in both lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the differentially expressed genes (DEGs) in W99 at the late time point were mostly associated with specific processes and pathways. Among the non-redundant genes, 146 genes were commonly up-regulated in the treatment condition compared with the control condition at the early- and late-induction time points in both accessions used in this experiment. Approximately 40% of the common DEGs were related to secondary metabolism, disease resistance, and signal transduction based on their putative function. Excluding the common DEGs, W99 expressed more unique DEGs than W11. Further analysis of the 3836 DEGs revealed that the induction of CCW not only up-regulated defense-related genes, including 37 jasmonic acid (JA)-related genes, 171 plant-pathogen-related genes, and 17 genes encoding protease inhibitors, but also down-regulated growth-related genes, including 35 photosynthesis-related genes, 48 nutrition metabolism genes, and 28 auxin metabolism genes. Therefore, representative defense-related and growth-related genes were chosen for binding site prediction via co-expression of transcription factors (TFs) and spatial expression pattern analyses. In total, 53 binding sites of 28 TFs were identified based on 3 defense-related genes and 3 growth-related genes. Phosphate transporter PT1, which is a representative growth-related gene, was transformed into soybean, and the transgenic soybean plants were susceptible to CCW. CONCLUSIONS In summary, we described transcriptome reprograming after herbivore induction in wild soybean, identified the susceptibility of growth-related genes, and provided new resources for the breeding of herbivore-resistant cultivated soybeans.
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Affiliation(s)
- Haiping Du
- 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
| | - 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
| | - Lihua Ning
- Jiangsu Academy of Agricultural Sciences, Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Nanjing, 210014 China
| | - Rui Qin
- 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
| | - Qing Du
- 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
| | - Qing 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
| | - Haina Song
- College of Chemistry and Chemical Engineering, Key Laboratory of Ecological Restoration in Hilly Area, PingDingshan University, Pingdingshan, 467000 China
| | - 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
| | - 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
| | - 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
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Jha UC, Bohra A, Jha R, Parida SK. Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PLANT CELL REPORTS 2019; 38:255-277. [PMID: 30637478 DOI: 10.1007/s00299-019-02374-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/04/2019] [Indexed: 05/21/2023]
Abstract
Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
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Choi HK. Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. Genes Genomics 2019; 41:133-146. [PMID: 30353370 PMCID: PMC6394800 DOI: 10.1007/s13258-018-0751-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/01/2018] [Indexed: 01/25/2023]
Abstract
Recent next generation sequencing-driven mass production of genomic data and multi-omics-integrated approaches have significantly contributed to broadening and deepening our knowledge on the molecular system of living organisms. Accordingly, translational genomics (TG) approach can play a pivotal role in creating an informational bridge between model systems and relatively less studied plants. This review focuses mainly on addressing recent advancement in omics-related technologies, a diverse array of bioinformatic resources and potential applications of TG for the crop breeding. To accomplish above objectives, information on omics data production, various DBs and high throughput technologies was collected, integrated, and used to analyze current status and future perspectives towards omics-assisted crop breeding. Various omics data and resources have been organized and integrated into the databases and/or bioinformatic infrastructures, and thereby serve as the ome's information center for cross-genome translation of biological data. Although the size of accumulated omics data and availability of reference genomes are different among plant families, translational approaches have been actively progressing to access particular biological characteristics. When multi-layered omics data are integrated in a synthetic manner, it will allow providing a stereoscopic view of dynamic molecular behavior and interacting networks of genes occurring in plants. Consequently, TG approach will lead us to broader and deeper insights into target traits for the plant breeding. Furthermore, such systems approach will renovate conventional breeding programs and accelerate precision crop breeding in the future.
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Affiliation(s)
- Hong-Kyu Choi
- Department of Molecular Genetics, College of Natural Resources and Life Science, Dong-A University, Nakdong-Daero 550-Beongil 37, Saha-Gu, Busan, 49315, Republic of Korea.
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Zhao J, Wang Z, Liu H, Zhao J, Li T, Hou J, Zhang X, Hao C. Global status of 47 major wheat loci controlling yield, quality, adaptation and stress resistance selected over the last century. BMC PLANT BIOLOGY 2019; 19:5. [PMID: 30606117 PMCID: PMC6318892 DOI: 10.1186/s12870-018-1612-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/20/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Wheat breeding over the last 100 years has increased productivity by adapting genotypes to local conditions, but the genomic changes and selection signals that caused phenotypic change during breeding are essentially unknown. Studying and understanding human selection of multiple important genes controlling key phenotypic traits will promote wheat molecular breeding. RESULTS A total of 1152 diverse global wheat materials were genotyped based on KASP markers from 47 genes controlling grain yield, grain quality, adaptation, and stress resistance. Significant phenotypic variations between landraces and modern cultivars were found in 11 adaptive and yield-related traits. Thirty-six improvement-selective favorable alleles, including 22 positive prolonged and 14 negative selection alleles, were identified through comparing frequency spectra. Sus1-7A-Hap-H, Sus1-7B-Hap-T, Sus2-2A-Hap-A, TGW6-A1a, Cwi-4A-Hap-C, vrn-A1, PHS1-PHS+ and Lr34+ were subjected to strong selection, and overwhelmingly strong selection had occurred before improvement selection at Psy-A1b, Psy-B1a or b, Psy-D1a and Cwi-5D-Hap-C. However, Rht-B1b, Rht-D1b and 1BL.1RS were rare or absent in Chinese landraces but present in modern Chinese cultivars and introduced accessions. Importantly, Lr68+, Fhb1+, Wx-B1b and Yr15+, currently existing at a low frequency, should be regarded as further major improvement targets in global wheat breeding. Gene flow analysis showed that introduced cultivars especially from the former USSR and Italy contributed to enriched genetic variation in modern Chinese cultivars. CONCLUSIONS This work objectively reports human selection on favorable alleles of multiple crucial genes in Asia, Europe, North America and CIMMYT, and traces the distribution of important genes in global wheat for molecular breeding.
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Affiliation(s)
- Junjie Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Zhiwei Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Mousavi‐Derazmahalleh M, Bayer PE, Hane JK, Valliyodan B, Nguyen HT, Nelson MN, Erskine W, Varshney RK, Papa R, Edwards D. Adapting legume crops to climate change using genomic approaches. PLANT, CELL & ENVIRONMENT 2019; 42:6-19. [PMID: 29603775 PMCID: PMC6334278 DOI: 10.1111/pce.13203] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/10/2018] [Indexed: 05/05/2023]
Abstract
Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.
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Affiliation(s)
- Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
| | - James K. Hane
- CCDM BioinformaticsCentre for Crop Disease Management, Curtin UniversityBentleyWestern Australia6102Australia
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean BiotechnologyUniversity of MissouriColumbiaMO65211USA
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens Kew, Wakehurst PlaceArdinglyWest SussexRH17 6TNUK
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - William Erskine
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- Centre for Plant Genetics and BreedingThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
| | - Rajeev K. Varshney
- UWA School of Agriculture and EnvironmentThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)Patancheru502 324India
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - David Edwards
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawleyWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western Australia35 Stirling HighwayPerthWestern Australia6009Australia
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Torkamaneh D, Laroche J, Rajcan I, Belzile F. Identification of candidate domestication-related genes with a systematic survey of loss-of-function mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1218-1227. [PMID: 30246271 DOI: 10.1111/tpj.14104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Domestication is an important key co-evolutionary process through which humans have extensively altered the genomic make-up and appearance of both plants and animals. The identification of domestication-related genes remains very arduous. In this study, we present a systematic analytical approach that harnesses two recent advances in genomics, whole-genome sequencing (WGS) and prediction of loss-of-function (LOF) mutations, to greatly facilitate the assembly of an enriched catalogue of domestication-related candidate genes. Using WGS data for 296 cultivated (Glycine max) and 64 wild soybean accessions, we identified 8699 LOF variants, and 116 genes that are uniquely fixed for one or more LOF allele(s) in domesticated soybeans. Existing soybean transcriptomic data led us to overcome analytical challenges associated with whole-genome duplications and to identify neo- or subfunctionalized genes. This systematic approach allowed us to identify 110 candidate domestication-related genes in an efficient and rapid way. This catalogue contains previously well characterized domestication genes in soybean, as well as some orthologs from other domesticated crop species. In addition, it comprises many promising candidate domestication genes. Overall, this collection of candidate domestication-related genes in soybean is almost twice as large as the sum of all previously reported candidate genes in all other crops. We believe this systematic approach could readily be used in wide range of species.
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Affiliation(s)
- Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
- Department of Plant Agriculture, Crop Science Bldg., University of Guelph, Guelph, ON, Canada
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, Crop Science Bldg., University of Guelph, Guelph, ON, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
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Wallace JG, Rodgers-Melnick E, Buckler ES. On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics. Annu Rev Genet 2018; 52:421-444. [DOI: 10.1146/annurev-genet-120116-024846] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.
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Affiliation(s)
- Jason G. Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602, USA
| | | | - Edward S. Buckler
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
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Guan S, Xu Q, Ma D, Zhang W, Xu Z, Zhao M, Guo Z. Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice. Gene 2018; 685:96-105. [PMID: 30389557 DOI: 10.1016/j.gene.2018.10.066] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/24/2018] [Accepted: 10/24/2018] [Indexed: 11/17/2022]
Abstract
Weedy rice is an important germplasm resource for rice improvement because it has useful genes for many abiotic stresses including cold tolerance. We identified the cold tolerance and cold sensitivity of two weedy rice lines (WR 03-35 and WR 03-26) and two cultivated rice lines (Kongyu 131 and 9311). During the seedling stage of these lines, we used RNA-seq to measure changes in weedy rice and cultivated rice whole-genome transcriptome before and after cold treatment. We identified 14,213 and 14,730 differentially expressed genes (DEGs) in cold-tolerant genotypes (WR 03-35, Kongyu 131), and 9219 and 720 DEGs were observed in two cold-sensitive genotypes (WR 03-26, 9311). Many common and special DEGs were analyzed in cold-tolerant and cold-sensitive genotypes, respectively. Some typical genes related to cold stress such as the basic helix-loop-helix (bHLH) gene and leucine-rich repeat (LRR) domain gene etc. The number of these DEGs in cold-tolerant genotypes is more than those found in cold-sensitive genotypes. The gene ontology (GO) enrichment analyses showed significantly enriched terms for biological processes, cellular components and molecular functions. In addition, some genes related to several plant hormones such as abscisic acid (ABA), gibberellic acid (GA), auxin and ethylene were identified. To confirm the RNA-seq data, semi-quantitative RT-PCR and qRT-PCR were performed on 12 randomly selected DEGs. The expression patterns of RNA-seq on these genes corresponded with the semi-quantitative RT-PCR and qRT-PCR method. This study suggests the gene resources related to cold stress from weedy rice could be valuable for understanding the mechanisms involved in cold stress and rice breeding for improving cold tolerance.
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Affiliation(s)
- Shixin Guan
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Quan Xu
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Dianrong Ma
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Wenzhong Zhang
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhengjin Xu
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China
| | - Minghui Zhao
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China.
| | - Zhifu Guo
- Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China.
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Yuan Y, Wang X, Wang L, Xing H, Wang Q, Saeed M, Tao J, Feng W, Zhang G, Song XL, Sun XZ. Genome-Wide Association Study Identifies Candidate Genes Related to Seed Oil Composition and Protein Content in Gossypium hirsutum L. FRONTIERS IN PLANT SCIENCE 2018; 9:1359. [PMID: 30405645 PMCID: PMC6204537 DOI: 10.3389/fpls.2018.01359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/28/2018] [Indexed: 05/05/2023]
Abstract
Cotton (Gossypium spp.) is a leading natural fiber crop and an important source of vegetable protein and oil for humans and livestock. To investigate the genetic architecture of seed nutrients in upland cotton, a genome-wide association study (GWAS) was conducted in a panel of 196 germplasm resources under three environments using a CottonSNP80K chip of 77,774 loci. Relatively high genetic diversity (average gene diversity being 0.331) and phenotypic variation (coefficient of variation, CV, exceeding 3.9%) were detected in this panel. Correlation analysis revealed that the well-documented negative association between seed protein (PR) and oil may be to some extent attributable to the negative correlation between oleic acid (OA) and PR. Linkage disequilibrium (LD) was unevenly distributed among chromosomes and subgenomes. It ranged from 0.10-0.20 Mb (Chr19) to 5.65-5.75 Mb (Chr25) among the chromosomes and the range of Dt-subgenomes LD decay distances was smaller than At-subgenomes. This panel was divided into two subpopulations based on the information of 41,815 polymorphic single-nucleotide polymorphism (SNP) markers. The mixed linear model considering both Q-matrix and K-matrix [MLM(Q+K)] was employed to estimate the association between the SNP markers and the seed nutrients, considering the false positives caused by population structure and the kinship. A total of 47 SNP markers and 28 candidate quantitative trait loci (QTLs) regions were found to be significantly associated with seven cottonseed nutrients, including protein, total fatty acid, and five main fatty acid compositions. In addition, the candidate genes in these regions were analyzed, which included three genes, Gh_D12G1161, Gh_D12G1162, and Gh_D12G1165 that were most likely involved in the control of cottonseed protein concentration. These results improved our understanding of the genetic control of cottonseed nutrients and provided potential molecular tools to develop cultivars with high protein and improved fatty acid compositions in cotton breeding programs through marker-assisted selection.
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Affiliation(s)
- Yanchao Yuan
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Xianlin Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Liyuan Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Huixian Xing
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Qingkang Wang
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Muhammad Saeed
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Jincai Tao
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Wei Feng
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Guihua Zhang
- Heze Academy of Agricultural Sciences, Heze, China
| | - Xian-Liang Song
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
| | - Xue-Zhen Sun
- State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural University, Taian, China
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Shen Y, Zhang J, Liu Y, Liu S, Liu Z, Duan Z, Wang Z, Zhu B, Guo YL, Tian Z. DNA methylation footprints during soybean domestication and improvement. Genome Biol 2018; 19:128. [PMID: 30201012 PMCID: PMC6130073 DOI: 10.1186/s13059-018-1516-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored. RESULTS To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybean domestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways. CONCLUSIONS This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.
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Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100039 China
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Chang F, Guo C, Sun F, Zhang J, Wang Z, Kong J, He Q, Sharmin RA, Zhao T. Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans. FRONTIERS IN PLANT SCIENCE 2018; 9:1184. [PMID: 30177936 PMCID: PMC6110304 DOI: 10.3389/fpls.2018.01184] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/24/2018] [Indexed: 05/02/2023]
Abstract
Plant height (PH) and the number of nodes on the main stem (NN) serve as major plant architecture traits affecting soybean seed yield. Although many quantitative trait loci for the two traits have been reported, their genetic controls at different developmental stages in soybeans remain unclear. Here, 368 soybean breeding lines were genotyped using 62,423 single nucleotide polymorphism (SNP) markers and phenotyped for the two traits at three different developmental stages over two locations in order to identify their quantitative trait nucleotides (QTNs) using compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) approaches. As a result, 11 and 13 QTNs were found by CMLM to be associated with PH and NN, respectively. Among these QTNs, 8, 3, and 4 for PH and 6, 6, and 8 for NN were found at the three stages, and 3 and 6 were repeatedly detected for PH and NN. In addition, 34 and 30 QTNs were found by mrMLM to be associated with PH and NN, respectively. Among these QTNs, 11, 13, and 16 for PH and 11, 15, and 8 for NN were found at the three stages. A majority of these QTNs overlapped with the previously reported loci. Moreover, one QTN within the known E2 locus for flowering time was detected for the two traits at all three stages, and another that overlapped with the Dt1 locus for stem growth habit was also identified for the two traits at the mature stage. This may explain the highly significant correlation between the two traits. Our findings provide evidence for mixed major plus polygenes inheritance for dynamic traits and an extended understanding of their genetic architecture for molecular dissection and breeding utilization in soybeans.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Tuanjie Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Shen Y, Liu J, Geng H, Zhang J, Liu Y, Zhang H, Xing S, Du J, Ma S, Tian Z. De novo assembly of a Chinese soybean genome. SCIENCE CHINA. LIFE SCIENCES 2018; 61:871-884. [PMID: 30062469 DOI: 10.1007/s11427-018-9360-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding. Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome (cv. Williams 82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.
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Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jing Liu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Haiying Geng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | | | - Shilai Xing
- Berry Genomics Corporation, Beijing, 100015, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100039, China.
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50
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Guo Y, Su B, Tang J, Zhou F, Qiu LJ. Gene-based SNP identification and validation in soybean using next-generation transcriptome sequencing. Mol Genet Genomics 2018; 293:623-633. [PMID: 29280001 DOI: 10.1007/s00438-017-1410-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022]
Abstract
Gene-based molecular markers are increasingly used in crop breeding programs for marker-assisted selection. However, identification of genetic variants associated with important agronomic traits has remained a difficult task in soybean. RNA-Seq provides an efficient way, other than assessing global expression variations of coding genes, to discover gene-based SNPs at the whole genome level. In this study, RNA isolated from four soybean accessions each with three replications was subjected to high-throughput sequencing and a range of 44.2-65.9 million paired-end reads were generated for each library. A total of 75,209 SNPs were identified among different genotypes after combination of replications, 89.1% of which were located in expressed regions and 27.0% resulted in amino acid changes. GO enrichment analysis revealed that most significant enriched genes with nonsynonymous SNPs were involved in ribonucleotide binding or catalytic activity. Of 22 SNPs subjected to PCR amplification and Sanger sequencing, all of them were validated. To test the utility of identified SNPs, these validated SNPs were also assessed by genotyping a relative large population with 393 wild and cultivated soybean accessions. These SNPs identified by RNA-Seq provide a useful resource for genetic and genomic studies of soybean. Moreover, the collection of nonsynonymous SNPs annotated with their predicted functional effects also provides a valuable asset for further discovery of genes, identification of gene variants, and development of functional markers.
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Affiliation(s)
- Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Labs of Crop Germplasm and Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Bohong Su
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Labs of Crop Germplasm and Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Junyong Tang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Labs of Crop Germplasm and Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Fulai Zhou
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Labs of Crop Germplasm and Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Labs of Crop Germplasm and Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, People's Republic of China.
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