Genome-wide analysis of cold imbibition stress in soybean, Glycine max

• DOI: 10.3389/fpls.2023.1221644
• Publication Date: 2023-08-21T19:24:53Z
• Authors: Siwar Haidar; Simon Lackey; Martin Charette; Mohsen Yoosefzade...; A. Claire Gahagan; Thomas Hotte; Francois Belzile; Istvan Rajcan; Ashkan Golshani; Malcolm J. Morrison; Elroy R. Cober; Bahram Samanfar
• Keywords: Imbibition; Radicle; Kharif crop; Frost (temperature)

In Canada, the length of frost-free season necessitates planting crops as early possible to ensure that plants have enough time reach full maturity before they are harvested. Early carries inherent risks cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged investigate effect on Seed from 137 elite cultivars, grown in field at Ottawa, ON, over three years, were placed filter paper petri dishes and allowed imbibe 16 hours either 4°C or 20°C prior being transferred constant 20°C. Observations germination, defined presence 1 cm radicle, done day two seven. three-parameter exponential rise maximum equation (3PERM) fitted estimate one-half germination uniformity each cultivar. Genotype-by-sequencing used identify SNPs lines, using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, FarmCPU methods), haplotype block analysis, assumed linkage blocks ±100 kbp, threshold significance established qvalue package R, five significant chromosomes 1, 3, 4, 6, 13 after imbibition. Percent phenotypic variance explained (PVE) allele substitution (ASE) eliminated candidate SNPs, leaving QTL regions (Chr3-3419152, Chr6-5098454, Chr13-29649544). Based gene ontology (GO) enrichment 14 genes whose function is predicted include tolerance related pathways genes. The QTLs can be select future cultivars tolerant mitigate associated planting.