PDF(Pubmed)
Abstract：
Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated with selection is an important goal for understanding adaptation and can also facilitate better predictions about the likely fitness of selected strains if they escape aquaculture farms. Here, we hypothesize domestication as a genetic change induced by inadvertent selection in culture. Our premise is that standardized culture protocols generate parallel domestication effects across independent strains. Using eastern oyster as a model and a newly developed 600K SNP array, this study tested for parallel domestication effects in multiple independent selection lines compared with their progenitor wild populations. A single contrast was made between pooled selected strains (1-17 generations in culture) and all wild progenitor samples combined. Population structure analysis indicated rank order levels of differentiation as [wild - wild] < [wild - cultured] < [cultured - cultured]. A genome scan for parallel adaptation to the captive environment applied two methodologically distinct outlier tests to the wild versus selected strain contrast and identified a total of 1174 candidate SNPs. Contrasting wild versus selected strains revealed the early evolutionary consequences of domestication in terms of genomic differentiation, standing genetic diversity, effective population size, relatedness, runs of homozygosity profiles, and genome-wide linkage disequilibrium patterns. Random Forest was used to identify 37 outlier SNPs that had the greatest discriminatory power between bulked wild and selected oysters. The outlier SNPs were in genes enriched for cytoskeletal functions, hinting at possible traits under inadvertent selection during larval culture or pediveliger setting at high density. This study documents rapid genomic changes stemming from hatchery-based cultivation of eastern oysters, identifies candidate loci responding to domestication in parallel among independent aquaculture strains, and provides potentially useful genomic resources for monitoring interbreeding between farm and wild oysters.
摘要：
高繁殖力水产养殖物种的生产性状选择性育种取得了相对较快的成功。发现与选择相关的遗传变化是理解适应性的重要目标，也可以促进更好地预测所选菌株逃离水产养殖场的可能性。这里,我们假设驯化是由培养中的无意选择引起的遗传变化。我们的前提是标准化培养方案在独立菌株之间产生平行驯化效应。使用东部牡蛎作为模型和新开发的600KSNP阵列，这项研究测试了多个独立选择系与其祖先野生种群相比的平行驯化效果。在合并的选定菌株(培养物中1-17代)和组合的所有野生祖先样品之间进行单一对比。种群结构分析表明，分化的等级顺序为[野生-野生]<[野生-培养]<[培养-培养]。用于平行适应圈养环境的基因组扫描将两种方法上不同的异常值测试应用于野生与选定菌株的对比，并鉴定了总共1174个候选SNP。对比野生菌株和选定菌株揭示了驯化在基因组分化方面的早期进化后果，常设遗传多样性，有效人口规模，亲缘关系，纯合性谱的运行，和全基因组连锁不平衡模式。随机森林用于鉴定37个异常SNP，这些SNP在大型野生牡蛎和选定牡蛎之间具有最大的区分能力。异常SNPs位于富含细胞骨架功能的基因中，暗示在幼体培养或高密度设置中无意选择下可能的性状。这项研究记录了基于孵化场的东部牡蛎种植引起的快速基因组变化，在独立的水产养殖菌株中平行识别响应驯化的候选基因座，并为监测农场和野生牡蛎之间的杂交提供了潜在有用的基因组资源。
