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

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. This early planting has inherent risks; imbibition may begin with cold soil and seeds may fail to germinate. We hypothesize that genetic differences exist in elite Glycine max breeding lines for tolerance to cold imbibition stress. Lines were germinated in cold and warm environments and emerged radicle observations were taken from day two to seven. A three parameter exponential rise to a maximum equation was fit to estimate maximum germination, time to one-half maximum, and the uniformity of germination. Genome-wide associate studies, GWAS, is a set of tools used to investigate the links between genotype and phenotype for important traits. In the current study 137 soybean lines were genotyped using a genotype-by-sequencing approach to identify single nucleotide polymorphisms, SNPs. GWAS was carried out in R using rMVP package and GLM, MLM, and FarmCPU methods. A significance threshold for SNPs was calculated using the qvalue package in R. Five significant SNPs were identified and were filtered based on percent variance explained and allele effect was calculated. Haplotype block analysis and assumed linkage blocks of ±100kbp were used to retrieve candidate genes from SoyBase. Detailed gene ontology analysis was performed to select 14 candidate genes whose function is predicted to include germination related pathways. Follow-up experiments are underway to reduce this candidate list even further.