RESUMEN
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 variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting.
RESUMEN
Soybean (Glycine max (L.) Merr.) is one of the important crops in Canada and has the potential to expand its production further north into the Canadian Prairies. Such expansion, however, requires the search for adapted soybean germplasm useful for the development of productive cultivars with earlier maturity and increased protein concentration. We initiated several research activities to characterize 848 accessions of the soybean collection conserved at Plant Gene Resources of Canada (PGRC) for maturity, oil and protein concentration, and genetic distinctness. The characterization revealed a wide range of variations present in each assessed trait among the PGRC soybean accessions. The trait variabilities allowed for the identification of four core subsets of 35 PGRC soybean accessions, each specifically targeted for early maturity for growing in Saskatoon and Ottawa, and for high oil and protein concentration. The two early maturity core subsets for Saskatoon and Ottawa displayed days to maturity ranging from 103 to 126 days and 94 to 102 days, respectively. The two core subsets for high oil and protein concentration showed the highest oil and protein concentration from 25.0 to 22.7% and from 52.8 to 46.7%, respectively. However, these core subsets did not differ significantly in genetic distinctness (as measured with 19,898 SNP markers across 20 soybean chromosomes) from the whole PGRC soybean collection. These findings are useful, particularly for the management and utilization of the conserved soybean germplasm.
