Mueen Alam Khan1,2, Fei Tong1,2, Wubin Wang1,2,3,4,5, Jianbo He1,2,3,4, Tuanjie Zhao1,2,3,4,5, Junyi Gai6,7,8,9,10. 1. Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. 2. National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China. 3. Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China. 4. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China. 5. Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. 6. Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn. 7. National Center for Soybean Improvement, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn. 8. Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn. 9. National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn. 10. Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.
Abstract
MAIN CONCLUSION: RTM-GWAS identified 111 DT QTLs, 262 alleles with high proportion of QEI and genetic variation accounting for 88.55-95.92% PV in NAM, from which QTL-allele matrices were established and candidate genes annotated. Drought tolerance (DT) is one of the major challenges for world soybean production. A nested association mapping (NAM) population with 403 lines comprising two recombinant inbred line (RIL) populations: M8206 × TongShan and ZhengYang × M8206 was tested for DT using polyethylene-glycol (PEG) treatment under spring and summer environments. The population was sequenced using restriction-site-associated DNA sequencing (RAD-seq) filtered with minor allele frequency (MAF) ≥ 0.01, 55,936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNP linkage disequilibrium blocks (SNPLDBs). The restricted two-stage multi-locus genome-wide association studies (RTM-GWAS) identified 73 and 38 QTLs with 174 and 88 alleles contributed main effect 40.43 and 26.11% to phenotypic variance (PV) and QTL-environment interaction (QEI) effect 24.64 and 10.35% to PV for relative root length (RRL) and relative shoot length (RSL), respectively. The DT traits were characterized with high proportion of QEI variation (37.52-41.65%), plus genetic variation (46.90-58.40%) in a total of 88.55-95.92% PV. The identified QTLs-alleles were organized into main-effect and QEI-effect QTL-allele matrices, showing the genetic and QEI architecture of the three parents/NAM population. From the matrices, the possible best genotype was predicted to have a weighted average value over two indicators (WAV) of 1.873, while the top ten optimal crosses among RILs with 95th percentile WAV 1.098-1.132, transgressive over the parents (0.651-0.773) but much less than 1.873, implying further pyramiding potential. From the matrices, 134 candidate genes were annotated involved in nine biological processes. The present results provide a novel way for molecular breeding in QTL-allele-based genomic selection for optimal cross selection.
MAIN CONCLUSION: RTM-GWAS identified 111 DT QTLs, 262 alleles with high proportion of QEI and genetic variation accounting for 88.55-95.92% PV in NAM, from which QTL-allele matrices were established and candidate genes annotated. Drought tolerance (DT) is one of the major challenges for world soybean production. A nested association mapping (NAM) population with 403 lines comprising two recombinant inbred line (RIL) populations: M8206 × TongShan and ZhengYang × M8206 was tested for DT using polyethylene-glycol (PEG) treatment under spring and summer environments. The population was sequenced using restriction-site-associated DNA sequencing (RAD-seq) filtered with minor allele frequency (MAF) ≥ 0.01, 55,936 single nucleotide polymorphisms (SNPs) were obtained and organized into 6137 SNP linkage disequilibrium blocks (SNPLDBs). The restricted two-stage multi-locus genome-wide association studies (RTM-GWAS) identified 73 and 38 QTLs with 174 and 88 alleles contributed main effect 40.43 and 26.11% to phenotypic variance (PV) and QTL-environment interaction (QEI) effect 24.64 and 10.35% to PV for relative root length (RRL) and relative shoot length (RSL), respectively. The DT traits were characterized with high proportion of QEI variation (37.52-41.65%), plus genetic variation (46.90-58.40%) in a total of 88.55-95.92% PV. The identified QTLs-alleles were organized into main-effect and QEI-effect QTL-allele matrices, showing the genetic and QEI architecture of the three parents/NAM population. From the matrices, the possible best genotype was predicted to have a weighted average value over two indicators (WAV) of 1.873, while the top ten optimal crosses among RILs with 95th percentile WAV 1.098-1.132, transgressive over the parents (0.651-0.773) but much less than 1.873, implying further pyramiding potential. From the matrices, 134 candidate genes were annotated involved in nine biological processes. The present results provide a novel way for molecular breeding in QTL-allele-based genomic selection for optimal cross selection.
Authors: Z K Li; S B Yu; H R Lafitte; N Huang; B Courtois; S Hittalmani; C H M Vijayakumar; G F Liu; G C Wang; H E Shashidhar; J Y Zhuang; K L Zheng; V P Singh; J S Sidhu; S Srivantaneeyakul; G S Khush Journal: Theor Appl Genet Date: 2003-09-05 Impact factor: 5.699
Authors: Felipe Roberto Francisco; Alexandre Hild Aono; Carla Cristina da Silva; Paulo S Gonçalves; Erivaldo J Scaloppi Junior; Vincent Le Guen; Roberto Fritsche-Neto; Livia Moura Souza; Anete Pereira de Souza Journal: Front Plant Sci Date: 2021-12-21 Impact factor: 5.753