Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole-genome resequencing in Japanese Black cattle
Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole-genome resequencing in Japanese Black cattle
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DOI：
10.1111/asj.13335
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发表时间：
2020-01-01
影响因子：
2
通讯作者：
Mannen, Hideyuki
中科院分区：
文献类型：
--
作者：
Sasazaki, Shinji;Kawaguchi, Fuki;Mannen, Hideyuki
在我们之前的研究中，我们进行了全基因组关联研究（GWAS），以确定与脂肪面积与肋眼面积（FAR）之比相关的基因组区域，并在10-30 Mbp的BTA 7中检测到候选基因。本研究旨在利用全基因组重测序数据全面检测候选区域的所有多态性。基于8只动物的全基因组重测序，我们在该区域内检测到127，090个多态性。其中31,945个位于基因内。我们进一步将多态性缩小到6，044个，其中位于179个基因内的高FAR组和低FAR组之间的等位基因差异超过5个。我们随后调查了这些基因的功能，并选择了8个基因的170个多态性作为可能的候选多态性。我们集中在SLC 27 A6 K81 M作为一个假定的候选多态性。我们在日本黑人人群（n = 904）的SNP基因分型，以调查对FAR的影响。方差分析显示，SLC 27 A6 K81 M的p值（p =.0009）低于GWAS中最显著的SNP（p =.0049）。虽然在本研究中仅验证了SLC 27 A6 K81 M，但随后对其余候选基因和多态性的验证可能导致对FAR负责的基因和多态性的鉴定。
In our previous study, we performed genome-wide association study (GWAS) to identify the genomic region associated with Fat area ratio to rib eye area (FAR) and detected a candidate in BTA7 at 10-30 Mbp. The present study aims to comprehensively detect all polymorphisms in the candidate region using whole-genome resequencing data. Based on whole-genome resequencing of eight animals, we detected 127,090 polymorphisms within the region. Of these, 31,945 were located within the genes. We further narrowed the polymorphisms to 6,044 with more than five allele differences between the high and low FAR groups that were located within 179 genes. We subsequently investigated the functions of these genes and selected 170 polymorphisms in eight genes as possible candidate polymorphisms. We focused on SLC27A6 K81M as a putative candidate polymorphism. We genotyped the SNP in a Japanese Black population (n = 904) to investigate the effect on FAR. Analysis of variance revealed that SLC27A6 K81M had a lower p-value (p =.0009) than the most significant SNP in GWAS (p =.0049). Although only SLC27A6 K81M was verified in the present study, subsequent verification of the remaining candidate genes and polymorphisms could lead to the identification of genes and polymorphisms responsible for FAR.