Gaspar Daniel, Usié Ana, Leão Célia, Guimarães Sílvia, Pires Ana Elisabete, Matos Claudino, Ramos António Marcos, Ginja Catarina
Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), Beja, Portugal.
BIOPOIS/CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.
Front Genet. 2023 Jan 13;14:1109490. doi: 10.3389/fgene.2023.1109490. eCollection 2023.
As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ H ≤ .34; .30 ≤ H ≤ .35; 1.7 × 10 ≤ π ≤ 3.1 × 10) and the levels of inbreeding were negligible (.005 ≤ F ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.
随着全球变暖的影响变得越来越复杂且难以应对，本地适应的绵羊品种的保护和可持续利用正逐渐兴起。葡萄牙本土绵羊品种是重要的遗传多样性宝库，高度适应恶劣环境，且在低投入生产系统中饲养。然而，仍缺乏能够详细描述这些品种并加速选择更具适应能力以应对气候挑战的动物的基因组数据。在此，我们对来自四个葡萄牙本土绵羊品种（坎帕尼察、博尔代莱拉-埃斯特雷拉山脉、白美利奴和黑美利奴）的37只动物以及19只杂交绵羊的基因组进行了测序，以推断它们的基因组多样性和种群结构。这些品种的平均基因组多样性非常相似（0.30≤H≤0.34；0.30≤H≤0.35；1.7×10⁻³≤π≤3.1×10⁻³），近亲繁殖水平可忽略不计（0.005≤F≤0.038）。主成分分析、贝叶斯聚类分析和Treemix分析将葡萄牙品种分为两个主要群体，这与历史记录一致：一个群体包括坎帕尼察和埃斯特雷拉山脉品种以及其他欧洲和跨界奶牛品种；另一个群体是分化明显的多用途美利奴和与美利奴相关的品种。纯合子连续片段分析在所有个体的基因组中产生了1690个纯合子连续片段，平均覆盖2.27Gb。纯合子连续片段覆盖的全基因组范围从埃斯特雷拉山脉品种的27.75Mb到坎帕尼察品种的61.29Mb不等。绵羊线粒体基因组的系统发育分析将葡萄牙本土品种与来自土耳其的两只阿卡曼品种动物一起归入B1a亚单倍群。这一结果为西南亚绵羊对伊比利亚半岛本地品种的直接影响提供了额外支持。我们的研究是对葡萄牙绵羊品种进行基因组特征描述的第一步，结果强调了基因组数据作为指导本地适应绵羊品种保护工作的有效工具的潜力。此外，我们生成的基因组数据可用于识别品种鉴定标记和认证品种产品的可追溯性标记。
