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Xiang X, Yang H, Yuan X, Dong X, Mai S, Zhang Q, Chen L, Cao D, Chen H, Guo W, Li L. CRISPR/Cas9-mediated editing of GmDWF1 brassinosteroid biosynthetic gene induces dwarfism in soybean. PLANT CELL REPORTS 2024; 43:116. [PMID: 38622229 DOI: 10.1007/s00299-024-03204-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/24/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE The study on the GmDWF1-deficient mutant dwf1 showed that GmDWF1 plays a crucial role in determining soybean plant height and yield by influencing the biosynthesis of brassinosteroids. Soybean has not adopted the Green Revolution, such as reduced height for increased planting density, which have proven beneficial for cereal crops. Our research identified the soybean genes GmDWF1a and GmDWF1b, homologous to Arabidopsis AtDWF1, and found that they are widely expressed, especially in leaves, and linked to the cellular transport system, predominantly within the endoplasmic reticulum and intracellular vesicles. These genes are essential for the synthesis of brassinosteroids (BR). Single mutants of GmDWF1a and GmDWF1b, as well as double mutants of both genes generated through CRISPR/Cas9 genome editing, exhibit a dwarf phenotype. The single-gene mutant exhibits moderate dwarfism, while the double mutant shows more pronounced dwarfism. Despite the reduced stature, all types of mutants preserve their node count. Notably, field tests have shown that the single GmDWF1a mutant produced significantly more pods than wild-type plants. Spraying exogenous brassinolide (BL) can compensate for the loss in plant height induced by the decrease in endogenous BRs. Comparing transcriptome analyses of the GmDWF1a mutant and wild-type plants revealed a significant impact on the expression of many genes that influence soybean growth. Identifying the GmDWF1a and GmDWF1b genes could aid in the development of compact, densely planted soybean varieties, potentially boosting productivity.
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Affiliation(s)
- Xumin Xiang
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-Rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xi Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xue Dong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Sihua Mai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Qianqian Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Li Li
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-Rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
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Istanbuli T, Nassar AE, Abd El-Maksoud MM, Tawkaz S, Alsamman AM, Hamwieh A. Genome-wide association study reveals SNP markers controlling drought tolerance and related agronomic traits in chickpea across multiple environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1260690. [PMID: 38525151 PMCID: PMC10957531 DOI: 10.3389/fpls.2024.1260690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/06/2024] [Indexed: 03/26/2024]
Abstract
Chickpea, renowned for its exceptional nutritional value, stands as a crucial crop, serving as a dietary staple in various parts of the world. However, its productivity faces a significant challenge in the form of drought stress. This challenge highlights the urgent need to find genetic markers linked to drought tolerance for effective breeding programs. The primary objective of this study is to identify genetic markers associated with drought tolerance to facilitate effective breeding programs. To address this, we cultivated 185 chickpea accessions in two distinct locations in Lebanon over a two-year period, subjecting them to both irrigated and rain-fed environments. We assessed 11 drought-linked traits, including morphology, growth, yield, and tolerance score. SNP genotyping revealed 1344 variable SNP markers distributed across the chickpea genome. Genetic diversity across populations originating from diverse geographic locations was unveiled by the PCA, clustering, and structure analysis indicating that these genotypes have descend from five or four distinct ancestors. A genome-wide association study (GWAS) revealed several marker trait associations (MTAs) associated with the traits evaluated. Within the rainfed conditions, 11 significant markers were identified, each associated with distinct chickpea traits. Another set of 11 markers exhibited associations in both rainfed and irrigated environments, reflecting shared genetic determinants across these conditions for the same trait. The analysis of linkage disequilibrium (LD) highlighted two genomic regions with notably strong LD, suggesting significant interconnections among several investigated traits. This was further investigated by the correlation between major markers associated with these traits. Gene annotation of the identified markers has unveiled insights into 28 potential genes that play a role in influencing various chickpea drought-linked traits. These traits encompass crucial aspects such as blooming organ development, plant growth, seed weight, starch metabolism, drought regulation, and height index. Among the identified genes are CPN60-2, hsp70, GDSL(GELP), AHL16, NAT3, FAB1B, bZIP, and GL21. These genes collectively contribute to the multifaceted response of chickpea plants to drought stress. Our identified genetic factors exert their influence in both irrigated and rainfed environments, emphasizing their importance in shaping chickpea characteristics.
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Affiliation(s)
- Tawffiq Istanbuli
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Ahmed E. Nassar
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | | | - Sawsan Tawkaz
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Alsamman M. Alsamman
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Aladdin Hamwieh
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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Qin C, Li YH, Li D, Zhang X, Kong L, Zhou Y, Lyu X, Ji R, Wei X, Cheng Q, Jia Z, Li X, Wang Q, Wang Y, Huang W, Yang C, Liu L, Wang X, Xing G, Hu G, Shan Z, Wang R, Li H, Li H, Zhao T, Liu J, Lu Y, Hu X, Kong F, Qiu LJ, Liu B. PH13 improves soybean shade traits and enhances yield for high-density planting at high latitudes. Nat Commun 2023; 14:6813. [PMID: 37884530 PMCID: PMC10603158 DOI: 10.1038/s41467-023-42608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Shading in combination with extended photoperiods can cause exaggerated stem elongation (ESE) in soybean, leading to lodging and reduced yields when planted at high-density in high-latitude regions. However, the genetic basis of plant height in adaptation to these regions remains unclear. Here, through a genome-wide association study, we identify a plant height regulating gene on chromosome 13 (PH13) encoding a WD40 protein with three main haplotypes in natural populations. We find that an insertion of a Ty1/Copia-like retrotransposon in the haplotype 3 leads to a truncated PH13H3 with reduced interaction with GmCOP1s, resulting in accumulation of STF1/2, and reduced plant height. In addition, PH13H3 allele has been strongly selected for genetic improvement at high latitudes. Deletion of both PH13 and its paralogue PHP can prevent shade-induced ESE and allow high-density planting. This study provides insights into the mechanism of shade-resistance and offers potential solutions for breeding high-yielding soybean cultivar for high-latitude regions.
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Affiliation(s)
- Chao Qin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ying-Hui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Delin Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueru Zhang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China
| | - Yonggang Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
| | - Xiangguang Lyu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ronghuan Ji
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuzhi Wei
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qican Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiwei Jia
- Longping Biotechnology (Hainan) Co., Ltd, Yazhou-Bay Science and Technology City, Sanya, Hainan, 572025, China
| | - Xiaojiao Li
- Longping Biotechnology (Hainan) Co., Ltd, Yazhou-Bay Science and Technology City, Sanya, Hainan, 572025, China
| | - Qiang Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, 150086, China
| | - Yueqiang Wang
- Jilin Academy of Agricultural Sciences, Changchun, Jilin, 130033, China
| | - Wen Huang
- Tonghua Academy of Agricultural Sciences, Tonghua, Jilin, 135007, China
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, 050035, China
| | - Like Liu
- Liaocheng University, Liaocheng, Shandong, 252000, China
| | - Xing Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, Jiangsu, 221131, China
| | - Guangnan Xing
- Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Guoyu Hu
- Anhui Academy of Agricultural Sciences, Hefei, Anhui, 230041, China
| | - Zhihui Shan
- Oil Crops Research Institute, Chinese Academy of Agriculture Sciences, Wuhan, Hubei, 430062, China
| | - Ruizhen Wang
- Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, 330200, China
| | - Haiyan Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
| | - Hongyu Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuping Lu
- Longping Biotechnology (Hainan) Co., Ltd, Yazhou-Bay Science and Technology City, Sanya, Hainan, 572025, China
| | - Xiping Hu
- Beidahuang KenFeng Seed Co., Ltd, Binxi Economic Development Zone, Harbin, Heilongjiang, 150090, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong, 510006, China.
| | - Li-Juan Qiu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Zatybekov A, Yermagambetova M, Genievskaya Y, Didorenko S, Abugalieva S. Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:3445. [PMID: 37836185 PMCID: PMC10575313 DOI: 10.3390/plants12193445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is a nutrient-rich crop that offers a sustainable source of dietary protein and edible oil. Determining the level of genetic diversity and relationships between various genetic resources involved in breeding programs is very important in crop improvement strategies. This study evaluated 100 soybean accessions with diverse origins for 10 important agronomic traits, including plant height (PH), an important plant adaptation-related trait impacting yield, in conditions in southeastern Kazakhstan for 2 years. The comparison of different groups of PH (tall, middle, and short) using a t-test suggested that the group of plants with the tallest PH provided a higher yield (p < 0.001) in relatively dry field conditions. The genetic diversity of the accessions was estimated using 25 simple sequence repeat (SSR) markers previously known to be associated with plant height. The results showed a significant variation among different groups of origin for all measured agronomic traits, as well as high genetic diversity, with the PIC (polymorphism information content) varying from 0.140 to 0.732, with an average of 0.524. Nei's diversity index ranged between 0.152 and 0.747, with an average of 0.526. The principal coordinate analysis (PCoA) of the studied soybean collection showed that Kazakhstan accessions were genetically distant from European, East Asian, and North American cultivars. Twelve out of twenty-five SSR markers demonstrated significant associations with ten studied agronomic traits, including PH (p < 0.05). Six SSRs with pleiotropic effects for studied traits were selected, and their haplotypes with phenotypic effects were generated for each soybean accession. The obtained results can be used in soybean improvement programs, including molecular-assisted breeding projects.
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Affiliation(s)
- Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
| | - Moldir Yermagambetova
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
| | - Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
| | - Svetlana Didorenko
- Department of Oilseed Crop., Kazakh Research Institute of Agriculture and Plant Growing, Almalybak 040909, Kazakhstan;
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
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5
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Licata M, Farruggia D, Iacuzzi N, Matteo R, Tuttolomondo T, Di Miceli G. Effects of Genotype and Climate on Productive Performance of High Oleic Carthamus tinctorius L. under Rainfed Conditions in a Semi-Arid Environment of Sicily (Italy). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091733. [PMID: 37176792 PMCID: PMC10181448 DOI: 10.3390/plants12091733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
Safflower (Carthamus tinctorius L.) is a promising oilseed crop for cultivation in central Southern Italy due to its high tolerance to drought and salinity stress and appreciable seed and oil yields. The genetic diversity of cultivars and climate factors can affect fatty acid composition and yield traits. This study aimed to assess the effects of genotype and climate conditions on the productive performance of eight high oleic safflower genotypes under rainfed conditions in Sicily (Italy). These genotypes were compared to the Montola 2000 cultivar, which was used as a reference. Tests were carried out during the growing seasons of 2014-2015 and 2015-2016. The experimental design was a randomized complete block design with three replications. Morphological and yield components were significantly affected by genotype while the year had a significant effect on plant height only. In general, CTI 17 produced the highest seed yield (1.40 t ha-1) and oil yield (0.58 t ha-1). The seed oil content was found on 40.2% of dry matter, on average. The "genotype" factor significantly affected oil content and fatty acid composition. Oleic acid content was on average 66.1% and did not vary greatly over the two growing seasons. The above- and belowground plant parts showed the highest carbon content and the lowest nitrogen content as a percentage of dry matter. The results indicate that, under rainfed conditions, yield parameters of high oleic safflower genotypes can be profitable in southern Italy though significantly dependent upon genotype.
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Affiliation(s)
- Mario Licata
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze 13, 90128 Palermo, Italy
| | - Davide Farruggia
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze 13, 90128 Palermo, Italy
| | - Nicolò Iacuzzi
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze 13, 90128 Palermo, Italy
| | - Roberto Matteo
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Via di Corticella 133, 40128 Bologna, Italy
| | - Teresa Tuttolomondo
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze 13, 90128 Palermo, Italy
| | - Giuseppe Di Miceli
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze 13, 90128 Palermo, Italy
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Yang Q, Zhang J, Shi X, Chen L, Qin J, Zhang M, Yang C, Song Q, Yan L. Development of SNP marker panels for genotyping by target sequencing (GBTS) and its application in soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:26. [PMID: 37313526 PMCID: PMC10248699 DOI: 10.1007/s11032-023-01372-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/16/2023] [Indexed: 06/15/2023]
Abstract
A high-throughput genotyping platform with customized flexibility, high genotyping accuracy, and low cost is critical for marker-assisted selection and genetic mapping in soybean. Three assay panels were selected from the SoySNP50K, 40K, 20K, and 10K arrays, containing 41,541, 20,748, and 9670 SNP markers, respectively, for genotyping by target sequencing (GBTS). Fifteen representative accessions were used to assess the accuracy and consistency of the SNP alleles identified by the SNP panels and sequencing platform. The SNP alleles were 99.87% identical between technical replicates and 98.86% identical between the 40K SNP GBTS panel and 10× resequencing analysis. The GBTS method was also accurate in the sense that the genotypic dataset of the 15 representative accessions correctly revealed the pedigree of the accessions, and the biparental progeny datasets correctly constructed the linkage maps of the SNPs. The 10K panel was also used to genotype two parent-derived populations and analyze QTLs controlling 100-seed weight, resulting in the identification of the stable associated genetic locus Locus_OSW_06 on chromosome 06. The markers flanking the QTL explained 7.05% and 9.83% of the phenotypic variation, respectively. Compared with GBS and DNA chips, the 40K, 20K, and 10K panels reduced costs by 5.07% and 58.28%, 21.44% and 65.48%, and 35.74% and 71.76%, respectively. Low-cost genotyping panels could facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and genomic selection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01372-6.
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Affiliation(s)
- Qing Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Jianan Zhang
- Mol Breeding Biotechnology Co., Ltd., 136 Huanghe Parkway, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Lei Chen
- School of Life Sciences, Yantai University, 30# Qingquan Road, Lai Shan District, Yantai, 264005 Shandong People’s Republic of China
| | - Jun Qin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD USA
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, High-Tech Industrial Development Zone, 162 Hengshan St, Shijiazhuang, 050035 Hebei People’s Republic of China
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7
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T. V. N, S. RP, R. L. R. Population structure and genetic diversity characterization of soybean for seed longevity. PLoS One 2022; 17:e0278631. [PMID: 36472991 PMCID: PMC9725150 DOI: 10.1371/journal.pone.0278631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/19/2022] [Indexed: 12/12/2022] Open
Abstract
Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.
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Affiliation(s)
- Naflath T. V.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Rajendra Prasad S.
- Department of Seed Science and Technology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
| | - Ravikumar R. L.
- Department of Plant Biotechnology, College of Agriculture, UAS, GKVK, Bangalore, Karnataka, India
- * E-mail:
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8
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Manggabarani AM, Hashiguchi T, Hashiguchi M, Hayashi A, Kikuchi M, Mustamin Y, Bamba M, Kodama K, Tanabata T, Isobe S, Tanaka H, Akashi R, Nakaya A, Sato S. Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations. DNA Res 2022; 29:6653298. [PMID: 35916715 PMCID: PMC9358015 DOI: 10.1093/dnares/dsac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Indexed: 11/14/2022] Open
Abstract
Abstract
As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (G×E). To achieve this goal, we conducted the field experiments for soybean core collections using multiple sowing times in multi-latitudinal fields. Sowing time shifts altered the flowering time (FT) and growth phenotypes, and resulted in increasing the combinations of genotypes and environments. Genome-wide association studies for the obtained phenotypes revealed the effects of field and sowing time to the significance of detected alleles, indicating the presence of G×E. By using accumulated phenotypic and environmental data in 2018 and 2019, we constructed multiple regression models for FT and growth pattern. Applicability of the constructed models was evaluated by the field experiments in 2020 including a novel field, and high correlation between the predicted and measured values was observed, suggesting the robustness of the models. The models presented here would allow us to predict the phenotype of the core collections in a given environment.
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Affiliation(s)
| | - Takuyu Hashiguchi
- Faculty of Agriculture, University of Miyazaki , Miyazaki 889-2192, Japan
| | | | - Atsushi Hayashi
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | - Masataka Kikuchi
- Graduate School of Medicine, Osaka University , Suita, Osaka 565-0871, Japan
| | - Yusdar Mustamin
- Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Masaru Bamba
- Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
| | - Kunihiro Kodama
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, Japan
| | | | - Sachiko Isobe
- Kazusa DNA Research Institute , Kisarazu, Chiba 292-0818, 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
| | - Akihiro Nakaya
- Graduate School of Medicine, Osaka University , Suita, Osaka 565-0871, Japan
- Graduate School of Frontier Sciences, The University of Tokyo , Kashiwa, Chiba 277-0882, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University , Sendai, Miyagi 980-8577, Japan
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Zhou X, Wang D, Mao Y, Zhou Y, Zhao L, Zhang C, Liu Y, Chen J. The Organ Size and Morphological Change During the Domestication Process of Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:913238. [PMID: 35755657 PMCID: PMC9221068 DOI: 10.3389/fpls.2022.913238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most important legume crops that can provide the rich source of protein and oil for human beings and livestock. In the twenty-one century, the total production of soybean is seriously behind the needs of a growing world population. Cultivated soybean [Glycine max (L.) Merr.] was domesticated from wild soybean (G. soja Sieb. and Zucc.) with the significant morphology and organ size changes in China around 5,000 years ago, including twisted stems to erect stems, small seeds to large seeds. Then it was spread worldwide to become one of the most popular and important crops. The release of the reference soybean genome and omics data provides powerful tools for researchers and breeders to dissect the functional genes and apply the germplasm in their work. Here, we summarized the function genes related to yield traits and organ size in soybean, including stem growth habit, leaf size and shape, seed size and weight. In addition, we also summarized the selection of organ traits during soybean domestication. In the end, we also discussed the application of new technology including the gene editing on the basic research and breeding of soybean, and the challenges and research hotspots in the future.
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Affiliation(s)
- Xuan Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongfa Wang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yawen Mao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yueqiong Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Limei Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Chunbao Zhang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yu Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
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