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

Authors: ZHANG, JUN - University Of Georgia; MCDONALD, SAMUEL - University Of Georgia; WU, CHENGJUN - University Of Arkansas; INGWERS, MILES - University Of Georgia; Abdel-Haleem, Hussein; CHEN, PENGYIN - University Of Missouri; LI, ZENGLU - University Of Georgia

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2022
Publication Date: 2/22/2022
Publication URL: https://handle.nal.usda.gov/10113/7709491
Citation: Zhang, J., McDonald, S.C., Wu, C., Ingwers, M.W., Abdel-Haleem, H.A., Chen, P., Li, Z. 2022. Quantitative trait loci underlying flooding tolerance in soybean (Glycine max). Plant Breeding. 141(2):236-245. https://doi.org/10.1111/pbr.13008.
DOI: https://doi.org/10.1111/pbr.13008

Interpretive Summary: Soybean is a globally important crop used for human food, animal feed, biofuel, and many other products. Flooding is a major abiotic stress in the regions with periodical high rainfall. Soybean is sensitive to flooding, and flooding stress typically results in a considerable reduction of grain yield. Soybeans are especially vulnerable to flooding during the early stages of development when there is also a great risk of economic loss. It was reported that flooding that persists for at least two days can reduce yield by 18% during vegetative stages and by 26% during early reproductive stages of soybean. In this study, we evaluated the foliar damage and survival rate of 146 soybean genotypes under flooding conditions for three years, to identify genomic regions that condition flooding tolerance in soybean and to assist breeders in developing soybean varieties with flooding tolerance by marker-assisted selection. We identified 8 significant genomic regions for flooding tolerance on chromosomes 4, 5, 6, 12, and 13 for both flooding tolerance score and survival rate across three years. The results suggest that soybean flooding tolerance is a complex trait, which is controlled by multiple genes and affected by gene × environment interactions.

Technical Abstract: Flooding tress 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 x 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 x environment interactions. The QTL and marker information could be used to assist soybean breeders to develop flooding tolerant cultivars.