The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.

中文翻译：

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全面的全基因组扫描检测与地中海家养羊局部适应和气候适应能力相关的基因组区域

家畜遗传资源的管理和动物对气候变化的适应可能会对畜牧业的长期可持续性产生重大影响。基因组数据包含有用的相关信息，需要利用这些信息来有效管理遗传资源。在本文中，我们报告了高产地中海希俄斯奶羊的基因组特征，并重点关注与当地适应和选择相关的遗传多样性措施，以及作为与气候变化相关的新型适应特性的动物对天气波动的适应能力的遗传结构。我们检测到纯合性 (ROH) 和杂合性 (ROHet) 的运行，揭示了 Chios 绵羊基因组中的多个高度纯合和杂合热点。在 13 号染色体上鉴定出一个特别高度纯合的区域，作为与牛奶性状相关的定向遗传选择的候选者，其中包括以前被证明与局部适应恶劣环境条件有关的注释基因。在绵羊染色体 3、10、13 和 19 上杂合丰富的区域揭示了与对家畜疾病的潜在保护作用和增强的整体适应性相关的有利杂合性。此外，对显示牛奶产量变化的绵羊弹性表型进行了基因组分析。对天气变化的反应。绵羊对热应激的抵抗力是一种显着的遗传性状 (h2 = 0.26)，并且在遗传上对产奶量具有拮抗作用。全基因组关联和区域遗传力图分析揭示了 5 号染色体上新的基因组标记和区域，它们与绵羊对气候变化的适应能力显着相关。随后，注释分析在 5 号染色体上检测到一组与嗅觉受体复合物相关的基因，这些基因可以通过呼吸率和呼吸蒸发的变化参与缓解热应激。其他基因在先前报道的与牲畜散热相关的生物过程中分组，包括压力和免疫反应。我们的结果可能有助于绵羊遗传资源的最佳管理，并为旨在减轻未来环境挑战的现代选择性育种计划提供信息，以实现可持续农业，同时更好地平衡动物适应和生产力。我们的结果与所研究的品种和各自的环境条件直接相关；然而，该方法可以扩展到其他感兴趣的牲畜物种。