Pitt Daniel, Bruford Michael W, Barbato Mario, Orozco-terWengel Pablo, Martínez Rodrigo, Sevane Natalia
School of Biosciences Cardiff University Cardiff UK.
Sustainable Places Research Institute Cardiff University Cardiff UK.
Evol Appl. 2018 May 18;12(1):105-122. doi: 10.1111/eva.12641. eCollection 2019 Jan.
The introduction of Iberian cattle in the Americas after Columbus' arrival imposed high selection pressures on a limited number of animals over a brief period of time. Knowledge of the genomic regions selected during this process may help in enhancing climatic resilience and sustainable animal production. We first determined taurine and indicine contributions to the genomic structure of modern Creole cattle. Second, we inferred their demographic history using approximate Bayesian computation (ABC), linkage disequilibrium (LD) and Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) and population differentiation ( ) to disentangle the genetic mechanisms involved in adaptation and phenotypic change by a rapid and major environmental transition. To tackle these questions, we combined SNP array data (~54,000 SNPs) in Creole breeds with their modern putative Iberian ancestors. Reconstruction of the population history of Creoles from the end of the 15th century indicated a major demographic expansion until the introduction of zebu and commercial breeds into the Americas ~180 years ago, coinciding with a drastic contraction. NeS analysis provided insights into short-term complexity in population change and depicted a decrease/expansion episode at the end of the ABC-inferred expansion, as well as several additional fluctuations in with the attainment of the current small only towards the end of the 20th century. Selection signatures for tropical adaptation pinpointed the thermoregulatory slick hair coat region, identifying a new candidate gene (), as well as novel candidate regions involved in immune function, behavioural processes, iron metabolism and adaptation to new feeding conditions. The outcomes from this study will help in future-proofing farm animal genetic resources (FAnGR) by providing molecular tools that allow selection for improved cattle performance, resilience and welfare under climate change.
哥伦布抵达美洲后，伊比利亚牛的引入在短时间内对数量有限的动物施加了高强度的选择压力。了解这一过程中所选的基因组区域可能有助于增强气候适应能力和实现可持续的动物生产。我们首先确定了瘤牛和印度牛对现代克里奥尔牛基因组结构的贡献。其次，我们使用近似贝叶斯计算（ABC）、连锁不平衡（LD）和斜率（NeS）分析推断了它们的种群历史。第三，我们基于跨群体扩展单倍型纯合性（XP-EHH）和种群分化（ ）进行全基因组扫描以寻找选择信号，从而通过快速且重大的环境转变来厘清参与适应和表型变化的遗传机制。为了解决这些问题，我们将克里奥尔牛品种及其现代假定的伊比利亚祖先的单核苷酸多态性（SNP）阵列数据（约54,000个SNP）相结合。对15世纪末以来克里奥尔牛种群历史的重建表明，在大约180年前瘤牛和商业品种引入美洲之前，种群经历了一次主要的人口扩张，之后紧接着是急剧收缩。NeS分析为种群变化的短期复杂性提供了见解，并描绘了ABC推断扩张结束时的减少/扩张事件，以及随着20世纪末才达到当前小种群规模而出现的几次额外波动。热带适应的选择信号确定了体温调节光滑被毛区域，鉴定出一个新的候选基因（ ），以及涉及免疫功能、行为过程、铁代谢和适应新饲养条件的新候选区域。这项研究的结果将通过提供分子工具来帮助保障农场动物遗传资源（FAnGR）的未来发展，这些工具可用于在气候变化条件下选择提高牛的性能、适应能力和福利。
