Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean

Authors: CHAMARTHI, SIVA - University Of Arkansas; KALER, AVJINDER - University Of Arkansas; Abdel-Haleem, Hussein; FRITSCHI, FELIX - University Of Missouri; Gillman, Jason; Ray, Jeffery - Jeff; Smith, James - Rusty; PURCELL, LARRY - University Of Arkansas

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/8/2022
Publication Date: 11/21/2022
Citation: Chamarthi, S., Kaler, A., Abdel-Haleem, H.A., Fritschi, F., Gillman, J.D., Ray, J.D., Smith, J.R., Purcell, L. 2022. Identification of genomic regions associated with the plasticity of carbon 13 ratio in soybean. The Plant Genome. 16(1). Article e20284. https://doi.org/10.1002/tpg2.20284.
DOI: https://doi.org/10.1002/tpg2.20284

Interpretive Summary: Drought is a major yield-reducing abiotic stressor in soybean. Improving soybean resiliency to drought is increasingly important due to the impacts of climate change and decreasing water supplies for irrigation. Improvements in water use efficiency (WUE) for soybean through selection for carbon discrimination ratio appears possible due to the positive association between C13 ratio and WUE, and high heritability of C13 ratio trait. The objectives of this study were to identify genomic regions associated with the stability of C13 ratio in diverse soybean panels, and identify individual accessions that differed in their C13 ratio response across diverse growing environments. Genome-wide association mapping approach identified 74 significant single nucleotide polymorphisms markers. Out of the 74 markers, 71 candidate genes were identified. Among the 71 candidate genes identified, 32 SNPs were located within genes that have biological annotations associated with drought stress tolerance such as transpiration or water conservation, water transport, root development, root hair elongation, and stomatal complex morphogenesis. Those genomic regions and candidate genes may provide the basis for genomic selection and rapid improvement of drought tolerance in soybean.

Technical Abstract: Improving water use efficiency (WUE) for soybean [Glycine max (L.) Merr.] through selection for high carbon isotope (C13) ratio may increase drought tolerance, but increased WUE may limit growth in productive environments. An ideal genotype would be plastic for C13 ratio; that is, be able to alter C13 ratio in response to the environment. Our objective was to identify genomic regions associated with C13 ratio plasticity, C13 ratio stability, and overall C13 ratio in two panels of diverse Maturity Group IV soybean accessions. A second objective was to identify accessions that differed in their C13 ratio plasticity. Panel 1 (205 accessions) was evaluated in seven irrigated and four drought environments, and Panel 2 (373 accessions) was evaluated in four environments. Plasticity was quantified as the slope from regressing C13 ratio of individual genotypes against an environmental index calculated based on the mean within and across environments. The regression intercept was considered a measure of C13 ratio over all environments, and the root mean square error was considered a measure of stability. Combined over both panels, genome-wide association mapping (GWAM) identified 19 single nucleotide polymorphisms (SNPs) for plasticity, 39 SNPs for C13 ratio, and 16 SNPs for stability. Among these SNPs, 71 candidate genes had annotations associated with transpiration or water conservation and transport, root development, root hair elongation, and stomatal complex morphogenesis. The genomic regions associated with plasticity and stability identified in the current study will be a useful resource for implementing genomic selection for improving drought tolerance in soybean.