Quantitative trait loci underlying flooding tolerance in soybean (Glycine max)

Abstract

AbstractFlooding stress typically causes oxygen deprivation (hypoxia) in plants, which damages roots and substantially affects soybean growth, survival and yield. Identifying quantitative trait loci (QTLs) and understanding the inheritance of flooding tolerance will help in developing soybean cultivars with tolerance to flooding. The objective of this study was to map QTLs responsible for flooding tolerance using an F5‐derived recombinant inbred line (RIL) population derived from a ‘Benning’ × PI 416937 cross. RILs, along with the parents ‘Benning’ and PI 416937, were grown in 2012, 2014 and 2015 at Stuttgart, AR, and phenotyped for flooding tolerance using a visual determination of plant health and the survival rate of plants in the field. The population was genotyped with the SoySNP6K Infinium BeadChips. Analysis of variance revealed significant effects of genotype, environment and genotype × environment interaction (P < .0001) on flooding tolerance. QTL analysis detected nine significant QTL (logarithm of the odds [LOD] > 3.0) for flooding tolerance on chromosomes (Chrs) 1, 4, 5, 16 and 18 for both flooding tolerance scores (FTSs) and survival rates (SRs) using best linear unbiased prediction (BLUP) values over three years. Three QTLs, located on Chrs 1, 5 and 16, were in common for both FTS and SR traits, and individual QTLs explained 7.6% to 11.0% of the phenotypic variation. The results suggested that flooding tolerance is a complex trait, which is controlled by multiple QTLs and significantly affected by QTL × environment interactions. The QTL and marker information could be used to assist soybean breeders to develop flooding tolerant cultivars.