Liu Michelle, Chambers Avery, Chambers Braidy, Aleman Alberto, Stift Marc, Mamonova Katya, Freeland Joanna, Dorken Marcel
Department of Biology Trent University Peterborough Ontario Canada.
Environmental and Life Sciences Graduate Program Trent University Peterborough Ontario Canada.
Ecol Evol. 2025 Apr 23;15(4):e71056. doi: 10.1002/ece3.71056. eCollection 2025 Apr.
has become a useful system for the study of comparative genomics, hybridization, polyploidization, and evolutionary transitions from outcrossing to selfing. Previous studies of its mating system have used microsatellite loci, but low allelic diversity, particularly in self-compatible populations characterized by low levels of outcrossing, reduces the utility of these markers for more detailed studies. Here, we aimed to develop population-level SNP markers for ssp. sampled from a self-compatible population at Rondeau Provincial Park, Ontario, Canada. We performed de novo SNP discovery and identified 6808 putative SNPs from genome-wide sequences of 22 individuals originating from a highly selfing population. Further filtering and marker validation enabled the development of 17 SNP marker loci that can be visualized using standard PCR-RFLP protocols. These markers had average minor-allele frequencies of 0.40 in the target population, and four of seven markers were variable in a small sample from nine other populations. These PCR-RFLP markers have the potential to be useful for the analysis of mating patterns within and beyond the inbred self-compatible populations of studied here and enable the continued development of as a model for studying evolutionary transitions from outcrossing to selfing.
已成为用于比较基因组学、杂交、多倍体化以及从异交到自交的进化转变研究的有用系统。此前对其交配系统的研究使用了微卫星位点，但等位基因多样性较低，尤其是在以低异交水平为特征的自交亲和种群中，这降低了这些标记在更详细研究中的效用。在此，我们旨在为加拿大安大略省朗多省立公园一个自交亲和种群中采集的ssp.开发种群水平的单核苷酸多态性（SNP）标记。我们进行了从头SNP发现，并从来自一个高度自交种群的22个个体的全基因组序列中鉴定出6808个推定的SNP。进一步的筛选和标记验证使得能够开发出17个SNP标记位点，这些位点可使用标准的聚合酶链反应-限制性片段长度多态性（PCR-RFLP）协议进行可视化。这些标记在目标种群中的平均次要等位基因频率为0.40，并且在来自其他九个种群的一个小样本中，七个标记中的四个是可变的。这些PCR-RFLP标记有可能用于分析此处研究的自交亲和近交种群内外的交配模式，并有助于将其持续开发为研究从异交到自交的进化转变的模型。
