Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
Iowa Department of Natural Resources, Spirit Lake Fish Hatchery, Spirit Lake, IA 51360, USA.
Genes (Basel). 2021 Jun 30;12(7):1021. doi: 10.3390/genes12071021.
Muskellunge () is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa's propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.
白斑狗鱼是北美的最大和最珍贵的游钓鱼类。然而，对于爱荷华州繁殖计划中的白斑狗鱼遗传多样性却知之甚少。我们使用了来自爱荷华州的 12 个亲鱼的全基因组测序和来自加拿大圣劳伦斯河的 625 个个体的公开 RAD-seq 数据，研究了种群间的遗传差异，分析了选择的特征，并评估了两个种群的遗传多样性水平。由于没有参考基因组，因此将读数比对到狗鱼的基因组上。变异调用为爱荷华州群体产生了 7886471 个双等位基因变体，为加拿大群体产生了 16867 个与加拿大样本重叠的高质量 SNP。主成分分析（PCA）和混合分析表明加拿大和爱荷华州种群之间存在很大的遗传差异。基于窗口的 pooled 杂合度在爱荷华州群体中发现了 6 个高度杂合的窗口，种群间的 Fst 发现了 14 个固定统计量（Fst）值大于 0.9 的窗口。加拿大的近交率（Froh = 0.32）似乎更高，因为爱荷华州种群的近交（Froh = 0.03），可能是由于亚种群的隔离。尽管近亲繁殖似乎不是爱荷华州白斑狗鱼的一个迫在眉睫的问题，但加拿大种群似乎存在较高的近交率。最后，这种方法可以用来评估北美白斑狗鱼种群当前管理实践的长期生存能力。
