In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle.

中文翻译：

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全基因组测序揭示了法国夏洛来牛对古巴热带气候适应的见解

在20世纪初期，古巴农民直接从法国进口夏洛来牛（CHFR）。这些动物现在被称为Chacuba（CHCU），已经适应古巴的恶劣热带环境条件。这些条件包括长期干旱和粮食短缺，以及欧洲牛磺酸牛难以应对的极端温度。在这项研究中，我们使用了来自12个CHCU个体的全基因组序列数据，以及来自六个另外的牛磺酸，标记和杂交品种的60个全基因组序列，以估计CHCU动物的遗传多样性，结构和准确的祖先起源。尽管假定CHCU动物形成了封闭种群，但我们混合分析的结果表明，印度s牛的渗入能力有限。我们使用扩展的单倍型纯合性（EHH）方法来鉴定基因组中可能在CHCU适应热带环境中起重要作用的区域。推定的选择事件发生在Bos indicus比例较高的基因组区域，但仅靠Bos indicus渗入不足以解释CHCU对热带气候的适应性。EHH建议在基因组窗口中进行潜在适应的信号，这些信号包括与生热有关的牛磺酸基因（ATP9A，GABBR1，PGR，PTPN1和UCP1）和头发发育（CCHCR1和CDSN）。在这些基因中，我们确定了可能具有功能影响并促成CHCU和CHFR动物之间某些表型差异的单核苷酸多态性（SNP）。全基因组数据证实CHCU牛与法国（CHFR）和加拿大的夏洛来牛密切相关，但也表明CHCU中Bos indicus基因的基因渗入有限。我们观察到CHCU和CHFR创建者群体之间最近适应热带气候的可能信号，这些信号很大程度上与Bos indicus渗入无关。最后，我们报告了可能具有功能影响的候选基因和变体，并解释了CHCU和CHFR牛之间观察到的某些表型差异。