Adaptive admixture in Creole cattle. Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Admixture is an evolutionary process that enables short-term adaptation. The Creole cattle from Guadeloupe is a tropically adapted breed. Its three-way admixture and long-term isolation offer a unique opportunity for understanding the genetic determinants of adaptive admixture in livestock. Here, we sequenced 23 Creole cattle from Guadeloupe (GUA) and combined our data with sequenced genomes of 99 cattle from 25 breeds representative of European, African and indicine groups to provide the most detailed exploration, to date, of patterns of genetic variation and to detect selection signatures in this population. We detect 17 228 983 single nucleotide polymorphisms (SNPs) and we confirmed the higher level of African and indicine ancestries, compared to the European ancestry, in the GUA genome. We show that, unlike Criollo cattle, GUA population originates directly from West Africa with indicine ancestry inherited via West African ancestors. We relied on consistency of signals across various methods based on excess of haplotype homozygosity, differences in allele frequencies and excess ⁄ deficiency of local ancestry to identify five strong candidate regions showing an excess of indicine ancestry. These encompass immune-, heat-tolerance- and physical exercise-related genes. Moreover, we found that a previously identified horn-related gene, RXFP2 is under strong selective pressure in GUA genome likely owing to human-driven (socio-cultural) pressure. Our study highlights the role played by population admixture for driving rapid adaptive response to tropical constraints.

基因混合（Admixture）是一种可实现短期适应性演化的进化过程。来自瓜德罗普岛的克里奥尔牛是一类热带适应型家畜品种。该群体的三方基因混合与长期隔离特性，为解析家畜适应性基因混合的遗传决定机制提供了独特研究契机。本研究对23头瓜德罗普克里奥尔牛（GUA）进行了基因组测序，并将该数据与涵盖欧洲、非洲及瘤牛（indicine）类群的25个代表性品种的99头牛的测序基因组进行整合，从而实现了迄今为止最为全面的该群体遗传变异模式解析，并检测了其选择信号。本研究共鉴定出17228983个单核苷酸多态性位点（SNPs），并证实瓜德罗普克里奥尔牛基因组中非洲血统与瘤牛血统的占比高于欧洲血统。研究表明，与克里奥罗牛不同，瓜德罗普克里奥尔牛群体直接起源于西非，其瘤牛血统通过西非祖先传递而来。本研究基于单倍型纯合性过剩、等位基因频率差异以及局部血统的过剩/缺失，结合多种方法的信号一致性，鉴定出5个瘤牛血统富集的强候选区域。这些区域包含与免疫、耐热及运动相关的功能基因。此外，本研究发现此前已报道的角相关基因RXFP2在瓜德罗普克里奥尔牛基因组中受到强烈选择压力，这一现象可能源于人类驱动的社会文化层面的选择压力。本研究揭示了群体基因混合在驱动家畜快速响应并适应热带环境胁迫中发挥的关键作用。