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

作者：Siwar Haidar, Simon Lackey, Martin Charette, Mohsen Yoosefzadeh-Najafabadi, Alison Claire Gahagan, Thomas Hotte, François Belzile, Istvan Rajcan, Ashkan Golshani, Malcolm J. Morrison, Elroy R. Cober, Bahram Samanfar · 发表于：Frontiers in Plant Science · 年份：2023 · DOI：10.3389/fpls.2023.1221644 · 被引用次数：16 · 研究领域：Soybean genetics and cultivation、Legume Nitrogen Fixing Symbiosis、Plant pathogens and resistance mechanisms

In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of 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 to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic va...