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中国细毛羊周岁羊毛性状的全基因组重测序关联研究。

Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep.

机构信息

Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.

Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China.

出版信息

J Anim Sci. 2021 Sep 1;99(9). doi: 10.1093/jas/skab210.

Abstract

To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the "HIBLUP" package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h2) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.

摘要

为了研究与细毛羊周岁羊毛性状相关的单核苷酸多态性(SNP)位点,优化标记辅助选择和解析羊毛性状的遗传结构,我们在中国的四个细毛羊品种(阿尔卑斯美利奴羊(AMS)、中国美利奴羊(CMS)、青海细毛羊(QHS)和敖汉细毛羊(AHS))中,基于固定和随机模型循环概率统一(FarmCPU),对周岁毛长(YSL)、周岁平均纤维直径(YFD)、周岁毛绒重(YGFW)和周岁净绒率(YCFR)进行了全基因组关联研究(GWAS),使用了全基因组重测序数据(总计 577 只羊)。总共在全基因组显著阈值(P = 5.45E-09)以上检测到 16 个 SNP,在 GWAS 结果中,79 个 SNP 位于提示显著阈值(P = 5.00E-07)以上。对于 YFD 和 YGFW 性状,有 7 个和 9 个 SNP 达到全基因组显著阈值,而对于 YSL 和 YCFR 性状,没有 SNP 达到全基因组显著阈值,而有 57 个 SNP 超过提示显著阈值。我们记录了位于全基因组显著 SNP 附近 ±50-kb 区域的 14 个基因和位于提示显著 SNP 附近 ±50-kb 区域的 59 个基因。同时,我们使用“HIBLUP”包中的平均信息受限最大似然算法(AI-REML)来估计四个期望的周岁羊毛性状的遗传力和方差分量。YSL、YFD、YGFW 和 YCFR 的估计遗传力值(h2)分别为 0.6208、0.7460、0.6758 和 0.5559。我们注意到,本研究中的遗传参数可用于细毛羊育种。本研究中新发现的显著 SNP 和新鉴定的候选基因将增强我们对周岁羊毛形成的理解,显著 SNP 可应用于细毛羊育种的基因组选择。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2eb2/8418636/dc3e722f0daa/skab210f0001.jpg

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