Uzzaman Md Rasel, Park Jong-Eun, Lee Kyung-Tai, Cho Eun-Seok, Choi Bong-Hwan, Kim Tae-Hun
Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Wanju 55365, Korea.
Asian-Australas J Anim Sci. 2018 Apr;31(4):473-479. doi: 10.5713/ajas.17.0178. Epub 2017 Oct 20.
The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig.
After screening with the following criteria: minor allele frequency, MAF≤0.01; Hardy-Weinberg equilibrium, HWE≤0.000001, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study.
The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were 0.22±0.05, 0.16±0.05, 0.10±0.03 and 0.08±0.03 on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs.
The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.
本研究旨在利用Illumina公司的猪SNP60芯片进行全基因组关联分析（GWA）和基因组划分，以鉴定约克夏猪乳头总数的变异并确定其可解释的遗传力。
按照以下标准进行筛选：次要等位基因频率，MAF≤0.01；哈迪-温伯格平衡，HWE≤0.000001，利用42,953个单核苷酸多态性（SNP）构建成对基因组关系矩阵。进行基于全基因组混合线性模型的关联分析（MLMA）。在本研究中，为了用全基因组或染色体组SNP估计可解释的遗传力，采用了通过最大似然法进行遗传相关性估计。
MLMA分析和错误发现率p值确定了两个不同染色体上的三个显著SNP（SSC8上的rs81476910和rs81405825；SSC13上的rs81332615）与乳头总数有关。此外，我们估计该性状常染色体上所有常见SNP可解释30%的变异。通过对基因组进行划分获得的最大遗传力分别为：SSC7上0.22±0.05，SSC13上0.16±0.05，SSC1上0.10±0.03，SSC8上0.08±0.03。其中，SSC7与本研究中在经验p值显著性水平为2.35E-05时通过全基因组关联研究鉴定的一个SNP（rs80805264）一起解释了估计的遗传力。有趣的是，在最近一项研究中确定的SSC7上与乳头数性状相关的一个附近数量性状位点（QTL）中发现了rs80805264。此外，所有其他显著SNP均位于与猪卵巢重量、产活仔总数和初情期年龄相关的一些QTL内和/或附近。
我们鉴定出的SNP无疑代表了猪基因组中一些重要的QTL区域以及与各种繁殖生理功能相关的感兴趣基因。
