Detecting the QTL-allele system controlling seed-flooding tolerance in a nested association mapping population of soybean

Soil flooding stress, including seed-flooding, is a key issue in soybean production in highrainfall 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 multiallele 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 χ~2 test. The results may provide a way to match the breeding by design strategy.