Data from: Demography and rapid local adaptation shape Creole cattle genome diversity in the tropics

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 Ne Slope (NeS) analysis. Third, we performed whole genome scans for selection signatures based on cross-population extended haplotype homozygosity (XP-EHH) and population differentiation (FST) 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 Ne 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 Ne with the attainment of the current small Ne 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 (GDNF), 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.

哥伦布抵达美洲后引入的伊比利亚牛，在短时间内对有限种群施加了高强度的选择压力。解析该过程中受选择的基因组区域，有助于提升畜禽的气候适应性与可持续畜牧生产效率。本研究首先明确了普通牛（taurine）与瘤牛（indicine）对现代克里奥尔牛基因组结构的遗传贡献比例；其次，通过近似贝叶斯计算（approximate Bayesian computation, ABC）、连锁不平衡（linkage disequilibrium, LD）及有效种群数量斜率（Ne Slope, NeS）分析，推断其种群演化历史动态；第三，基于交叉群体扩展单倍型纯合性（cross-population extended haplotype homozygosity, XP-EHH）与群体分化指数（FST）开展全基因组选择信号扫描，以解析快速剧烈的环境转变过程中参与适应性演化与表型改变的遗传机制。为解答上述科学问题，本研究整合了克里奥尔品种的单核苷酸多态性阵列（SNP array）数据（约54000个单核苷酸多态性位点）与其现代推定的伊比利亚祖先种群的遗传数据。对15世纪末以来克里奥尔牛种群历史的重建结果显示，其种群规模在约180年前引入瘤牛与商用品种前经历了显著扩张，随后有效种群数量（Ne）出现急剧收缩。NeS分析揭示了种群动态变化的短期复杂性，呈现出ABC推断的扩张末期的种群缩减-扩张事件，以及后续数次有效种群数量波动，直至20世纪末才达到当前的较小有效种群规模。针对热带适应性的选择信号定位到了参与体温调节的滑毛被毛区域，鉴定出一个新的候选基因（GDNF），同时发现了参与免疫功能、行为过程、铁代谢以及适应新型摄食条件的全新候选基因组区域。本研究成果可为农场动物遗传资源（farm animal genetic resources, FAnGR）的长远保护提供支撑，通过开发分子选育工具，助力在气候变化背景下培育性能更优、适应性更强且福利水平更佳的肉牛种群。