Detecting the QTL-allele system controlling seed-flooding tolerance in a nested association mapping population of soybean
Muhammad Jaffer Ali,
Guangnan Xing,
Jianbo He,
Tuanjie Zhao,
Junyi Gai
Affiliations
Muhammad Jaffer Ali
Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
Guangnan Xing
Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
Jianbo He
Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
Tuanjie Zhao
Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
Junyi Gai
Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; MARA Key Laboratory of Biology and Genetic Improvement of Soybean (General), Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China; Corresponding author at: Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
Soil flooding stress, including seed-flooding, is a key issue in soybean production in high-rainfall and poorly drained areas. A nested association mapping (NAM) population comprising 230 lines of two recombinant inbred line (RIL) populations with a common parent was established and tested for seed-flooding tolerance using relative seedling length as indicator in two environments. The population was genotyped using RAD-seq (restriction site-associated DNA sequencing) to generate 6137 SNPLDB (SNP linkage disequilibrium block) markers. Using RTM-GWAS (restricted two-stage multi-locus multi-allele genome-wide association study), 26 main-effect QTL with 63 alleles and 12 QEI (QTL × environment) QTL with 27 alleles in a total of 33 QTL with 78 alleles (12 dual-effect alleles) were identified, explaining respectively 50.95% and 14.79% of phenotypic variation. The QTL-alleles were organized into main-effect and QEI matrices to show the genetic architecture of seed-flooding tolerance of the three parents and the NAM population. From the main-effect matrix, the best genotype was predicted to have genotypic value 1.924, compared to the parental value range 0.652–1.069, and 33 candidate genes involved in six biological processes were identified and confirmed by χ2 test. The results may provide a way to match the breeding by design strategy.
