Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits.
Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits.
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DOI：
10.3389/fgene.2021.612492
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发表时间：
2021
影响因子：
3.7
通讯作者：
Larkin DM
中科院分区：
文献类型：
--
作者：
Sweet-Jones J;Lenis VP;Yurchenko AA;Yudin NS;Swain M;Larkin DM
应用于牲畜育种的遗传工具的进步促使人们对以前被忽视的适应恶劣当地环境的品种进行了研究。其中一个群体是威尔士山羊品种，该品种可以在海拔 300 m 的海拔地区饲养，但由于羊毛质量较差且胴体尺寸较小，因此被认为生产价值较低。这与低地品种相反，低地品种更适合羊毛和肉类生产品质，但在高地牧场上表现不佳。在此，使用来自代表 15 个威尔士绵羊品种的 317 只个体的中密度基因分型数据以及来自同一组的 14 个品种的全基因组重测序数据，使用基于单倍型和 SNP 的方法扫描选择和候选遗传变异的特征。对基因分型数据进行的基于单倍型的选择扫描表明，高地品种中的 GBA3、PPARGC1A、APOB 和 PPP1R16B 基因区域以及低地品种中的 RNF24、PANK2 和 MUC15 基因区域存在强选择。对重测序数据进行的基于 SNP 的选择扫描指出，假定选择下存在错义突变，这些突变与高地品种的局部适应有关，具有血管生成 (VASH1)、抗氧化 (RWDD1)、细胞应激 (HSPA5)、膜运输（ABCA13 和 SLC22A7）和胰岛素信号传导（PTPN1 和 GIGFY1）等功能。相比之下，低地品种中含有候选错义突变的基因与细胞周期（CDK5RAP2）、细胞粘附（CDHR3）和毛色（MC1R）有关。我们发现了新的基因变异，对威尔士当地绵羊适应环境具有潜在的功能影响。了解这些变异对于通过标记辅助选择提高英国和世界绵羊品种的适应性品质非常重要。
Advances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches. Haplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R). We found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection.
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影响因子：
3.7
作者：
Heaton MP;Leymaster KA;Kalbfleisch TS;Kijas JW;Clarke SM;McEwan J;Maddox JF;Basnayake V;Petrik DT;Simpson B;Smith TP;Chitko-McKown CG;International Sheep Genomics Consortium
通讯作者：
International Sheep Genomics Consortium
影响因子：
20.1
作者：
Chen, Christina Yingxian;Salomon, Alexander K.;Prosser, Benjamin L.
通讯作者：
Prosser, Benjamin L.
影响因子：
7.1
作者：
Fernandez-Marcos, Pablo J.;Auwerx, Johan
通讯作者：
Auwerx, Johan
影响因子：
4.8
作者：
Giovannone, B;Lee, E;Smith, RJ
通讯作者：
Smith, RJ
影响因子：
3.7
作者：
Fariello MI;Servin B;Tosser-Klopp G;Rupp R;Moreno C;International Sheep Genomics Consortium;San Cristobal M;Boitard S
通讯作者：
Boitard S