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


Siwar Haidar, Simon Lackey, Elroy Cober, Malcolm Morrison, Ashkan Golshani, Bahram Samanfar: Genome-wide analysis of cold imbibition stress in soybean, Glycine max. Carleton Life Science day 6, 2023 Canada.


In Canada, planting crops early in the frost free season is important to ensure they have enough time to mature before harvesting. However, early planting can be risky as cold soil may cause seed germination to fail. This study hypothesized that some Glycine max breeding lines may have genetic differences in their tolerance to cold imbibition stress. This study involved imbibing soybean lines in both cold and warm environments and collecting data on radicle emergence from day two to seven. The data was analyzed using a three parameter exponential equation to estimate maximum germination, time to one-half maximum, and the uniformity of germination. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and genome-wide association studies (GWAS) were conducted using the rMVP R package, with GLM, MLM, and FarmCPU as methods. A threshold for significance was established using the qvalue package in R, and five significant SNPs were identified then filtered based on percent variance explained and allele substitution effect. Haplotype block analysis and assumed linkage blocks of ±100kbp were used to identify candidate genes from SoyBase. Gene ontology analysis was used to select 14 candidate genes with predicted functions related to germination pathways. Follow-up experiments are being conducted to further narrow down the candidate list.

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