Unraveling the genetic architecture for carbon and nitrogen related traits and leaf hydraulic conductance in soybean using genome-wide association analyses

Background Drought stress is a major limiting factor of soybean [Glycine max (L.) Merr.] production around the world. Soybean plants can ameliorate this stress with improved water-saving, sustained N-2 fixation during water deficits, and/or limited leaf hydraulic conductance. In this study, carbon isotope composition (delta C-13), which can relate to variation in water-saving capability, was measured. Additionally, nitrogen isotope composition (delta N-15) and nitrogen concentration that relate to nitrogen fixation were evaluated. Decrease in transpiration rate (DTR) of de-rooted soybean shoots in a silver nitrate (AgNO3) solution compared to deionized water under high vapor pressure deficit (VPD) conditions was used as a surrogate measurement for limited leaf hydraulic conductance. A panel of over 200 genetically diverse soybean accessions genotyped with the SoySNP50K iSelect BeadChips was evaluated for the carbon and nitrogen related traits in two field environments (Athens, GA in 2015 and 2016) and for transpiration response to AgNO3 in a growth chamber. A multiple loci linear mixed model was implemented in FarmCPU to perform genome-wide association analyses for these traits. Results Thirty two, 23, 26, and nine loci for delta C-13, delta N-15, nitrogen concentration, and transpiration response to AgNO3, respectively, were significantly associated with these traits. Candidate genes that relate to drought stress tolerance enhancement or response were identified near certain loci that could be targets for improving and understanding these traits. Soybean accessions with favorable breeding values were also identified. Low correlations were observed between many of the traits and the genetic loci associated with each trait were largely unique, indicating that these drought tolerance related traits are governed by different genetic loci. Conclusions The genomic regions and germplasm identified in this study can be used by breeders to understand the genetic architecture for these traits and to improve soybean drought tolerance. Phenotyping resources needed, trait heritability, and relationship to the target environment should be considered before deciding which of these traits to ultimately employ in a specific breeding program. Potential marker-assisted selection efforts could focus on loci which explain the greatest amount of phenotypic variation for each trait, but may be challenging due to the quantitative nature of these traits.