Zhao Honggang, Guo Ximing, Wang Wenlu, Wang Zhenwei, Rawson Paul, Wilbur Ami, Hare Matthew
Department of Natural Resources & the Environment Cornell University Ithaca New York USA.
Present address: Center for Aquaculture Technology San Diego California USA.
Evol Appl. 2024 May 29;17(6):e13710. doi: 10.1111/eva.13710. eCollection 2024 Jun.
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.
对生产性状进行选择性育种已在高繁殖力水产养殖物种中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一个重要目标，并且如果选定的品系逃出养殖场，还可以更好地预测它们可能的适应性。在这里，我们假设驯化是养殖中无意选择引起的遗传变化。我们的前提是标准化养殖方案会在独立品系中产生平行的驯化效应。本研究以东部牡蛎为模型，使用新开发的60万个单核苷酸多态性（SNP）阵列，测试了多个独立选择品系与其野生祖先种群相比的平行驯化效应。在合并的选定品系（养殖1至17代）与所有野生祖先样本之间进行了单一对比。种群结构分析表明，分化程度的排序为[野生 - 野生]<[野生 - 养殖]<[养殖 - 养殖]。对适应圈养环境的平行适应性进行全基因组扫描时，对野生与选定品系的对比应用了两种方法上不同的异常值检验，共鉴定出1174个候选SNP。野生与选定品系的对比揭示了驯化在基因组分化、现存遗传多样性、有效种群大小、亲缘关系、纯合性连续区域图谱以及全基因组连锁不平衡模式方面的早期进化后果。随机森林被用于识别37个异常SNP，这些SNP在野生和选定牡蛎群体之间具有最大的区分能力。这些异常SNP存在于富含细胞骨架功能的基因中，这暗示了在幼虫养殖或高密度面盘幼虫附着期间无意选择下可能的性状。本研究记录了基于孵化场养殖的东部牡蛎产生的快速基因组变化，识别出独立水产养殖品系中平行响应驯化的候选基因座，并为监测养殖牡蛎与野生牡蛎之间的杂交提供了潜在有用的基因组资源。
