Rodrigues Julia Lisboa, Braga Larissa Graciano, Watanabe Rafael Nakamura, Schenkel Flávio Schramm, Berry Donagh Pearse, Buzanskas Marcos Eli, Munari Danísio Prado
Departamento de Ciências Exatas, Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Brazil.
Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada.
J Appl Genet. 2025 Jan 30. doi: 10.1007/s13353-025-00941-z.
Natural and artificial selection in domesticated animals can cause specific changes in genomic regions known as selection signatures. Our study used the integrated haplotype score (iHS) and Tajima's D tests within non-overlapping windows of 100 kb to identify selection signatures, in addition to genetic diversity and linkage disequilibrium estimates in 9498 sheep from breeds in Ireland (Belclare, Charollais, Suffolk, Texel, and Vendeen). The mean observed and expected heterozygosity for all the sheep breeds were 0.353 and 0.355, respectively. Suffolk had the least genetic variation and, along with Texel, had slower linkage disequilibrium decay. iHS and Tajima's D detected selection signatures for all breeds, with some regions overlapping, thus forming longer segments of selection signatures. Common selection signatures were identified across iHS and Tajima's D methods for all breeds, with Belclare and Texel having several common regions under positive selection. Several genes were detected within the selection signature regions, including ITGA4, TLR3, and TGFB2 related to the immune system against endoparasites; DLG1, ROBO2, MXI1, MTMR2, CEP57, and FAM78B related to reproductive traits; WDR70 related to milk traits; SCHM1 and MYH15 related to meat traits; and TAS2R4, TAS2R39, and TAS2R40 related to adaptive traits. In conclusion, our results demonstrated moderate genetic diversity in the sheep breeds and detected and characterized selection signatures harboring genes associated with reproductive traits, milk production, meat production, and adaptive traits such as endoparasite resistance.
家畜中的自然选择和人工选择会导致基因组区域发生特定变化，即所谓的选择印记。我们的研究在100 kb的非重叠窗口内使用综合单倍型评分（iHS）和 Tajima's D 检验来识别选择印记，此外还对来自爱尔兰品种（贝尔克莱尔、夏洛来、萨福克、特克塞尔和旺丁）的9498只绵羊进行了遗传多样性和连锁不平衡估计。所有绵羊品种的平均观察杂合度和期望杂合度分别为0.353和0.355。萨福克的遗传变异最少，与特克塞尔一样，连锁不平衡衰减较慢。iHS和Tajima's D检验检测到了所有品种的选择印记，其中一些区域重叠，从而形成了更长的选择印记片段。通过iHS和Tajima's D方法在所有品种中都识别出了共同的选择印记，贝尔克莱尔和特克塞尔有几个处于正选择下的共同区域。在选择印记区域内检测到了几个基因，包括与抗内寄生虫免疫系统相关的ITGA4、TLR3和TGFB2；与繁殖性状相关的DLG1、ROBO2、MXI1、MTMR2、CEP57和FAM78B；与产奶性状相关的WDR70；与肉质性状相关的SCHM1和MYH15；以及与适应性状相关的TAS2R4、TAS2R39和TAS2R40。总之，我们的结果表明绵羊品种具有适度的遗传多样性，并检测和表征了包含与繁殖性状、产奶、产肉以及诸如抗内寄生虫等适应性状相关基因的选择印记。
