Haidar Siwar, Lackey Simon, Charette Martin, Yoosefzadeh-Najafabadi Mohsen, Gahagan A Claire, Hotte Thomas, Belzile Francois, Rajcan Istvan, Golshani Ashkan, Morrison Malcolm J, Cober Elroy R, Samanfar Bahram
Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada.
Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada.
Front Plant Sci. 2023 Aug 21;14:1221644. doi: 10.3389/fpls.2023.1221644. eCollection 2023.
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.
在加拿大，无霜期的时长使得必须尽早种植作物，以确保植株在收获前有足够时间达到完全成熟。过早种植存在冷水浸种（具体指水温低于4°C）影响种子萌发的固有风险。利用为先前确定的加拿大大豆全基因组关联研究（GWAS）面板开发的标记数据集，来研究冷水浸种对萌发的影响。从在安大略省渥太华田间种植了三年的137个大豆优良品种的种子库中选取种子，将其放置在培养皿中的滤纸上，在转移至20°C恒温环境之前，先在4°C或20°C条件下浸种16小时。从第二天到第七天对种子萌发情况进行观察，种子萌发定义为胚根长度达到1厘米。采用三参数指数上升至最大值方程（3PERM）来估算每个品种的萌发率、达到最大萌发率一半所需的时间以及萌发均匀度。通过基因型测序来鉴定137个大豆品系中的单核苷酸多态性（SNP），并使用全基因组关联研究（GWAS - rMVP R包，采用广义线性模型（GLM）、混合线性模型（MLM）和FarmCPU作为分析方法）、单倍型块分析以及假定的±100千碱基对连锁块，利用R语言中的qvalue包确定显著性阈值，并在染色体1、3、4、6和13上鉴定出五个与冷水浸种后最大萌发率相关的显著SNP。表型变异解释率（PVE）和等位基因替代效应（ASE）剔除了五个候选SNP中的两个，在染色体3、6和13上留下三个数量性状基因座（QTL）区域（Chr3 - 3419152、Chr6 - 5098454和Chr13 - 29649544）。基于基因本体（GO）富集分析，确定了14个候选基因，其功能预计包括与萌发和耐寒相关的途径。所鉴定出的QTL可用于选择未来耐冷水浸种的大豆品种，并降低与大豆过早种植相关的风险。
