Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers.
Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers.
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DOI：
10.1186/s12864-017-3610-0
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发表时间：
2017-03-14
期刊：
影响因子：
4.4
通讯作者：
Schenkel FS
中科院分区：
文献类型：
--
作者：
Brito LF;Kijas JW;Ventura RV;Sargolzaei M;Porto-Neto LR;Cánovas A;Feng Z;Jafarikia M;Schenkel FS
选择标记的检测有可能阐明与家畜物种重要的表型性状相关的基因和突变的身份。调查一个种群的遗传多样性水平也是非常相关的，因为遗传多样性是育种所必需的原材料，对基因组选择的实施具有实际意义。共1151动物从9个山羊种群选择不同的育种目标和基因型与Illumina山羊50 K单核苷酸多态性（SNP）微珠芯片被列入这项调查。多态性SNPs的比例范围从0.902（努比亚）到0.995（牧场）。总体平均HO和HE分别为0.374 ± 0.021和0.369 ± 0.023。平均遗传距离（D）为0.263（Toggenburg）~ 0.323（Rangeland）。近交指标FEH、FVR、FLEUT、FROH和FPED的总体平均值分别为0.129、-0.012、-0.010、0.038和0.030。位于19条染色体上的几个区域在至少一个山羊品种中可能受到选择。利用所有SNPs构建的基因组群体树基于选择目的区分了品种，而仅利用最显著区域的SNPs构建的基因组群体树显示了拉曼查与其他品种之间的巨大差异。我们推测这一区域与耳的形态发生有关。此外，我们还发现了与繁殖性状、成年体质量、食物转化效率、腹部脂肪沉积、构象性状、肝脏脂肪代谢、乳脂肪酸、体细胞评分、乳蛋白、耐热性和耳形态发生可能相关的基因。一般来说，中度到高度水平的遗传变异，观察到所有的品种和纯合性运行的表征提供了深入了解品种的发展历史。这些信息将有助于山羊基因组选择和其他基因组研究的实施。我们还确定了各种基因组区域的积极选择使用平滑FST和hapFLK统计和建议的基因，这是潜在的选择。这些结果现在可以提供一个基础，制定生物学假说有关的选择过程中的山羊。本文的在线版本（doi：10.1186/s12864-017-3610-0）包含补充材料，可供授权用户使用。
The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.