A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits.
A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits.
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DOI：
10.1371/journal.pone.0177014
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Folch JM
中科院分区：
文献类型：
--
作者：
Revilla M;Puig-Oliveras A;Castelló A;Crespo-Piazuelo D;Paludo E;Fernández AI;Ballester M;Folch JM
拷贝数变异（拷贝数变异）是与snp互补的重要遗传变异，可以被认为是家畜一些重要经济性状的生物标志物。本研究基于下一代测序数据对猪CNVs进行了基因组分析，以确定在伊比利亚与长白猪回交群体中分离的CNVs，并研究它们与脂肪酸组成和生长相关性状的关系。共检测到1,279个CNVs，包括重复和缺失，整个样本的CNVs从106到235不等，平均每个样本有183个CNVs。此外，我们还检测到包含245个基因的540个CNV区域（CNVRs）。功能注释表明，这些基因具有多种分子功能，可能在商品品种的生产性状中发挥作用。部分已鉴定的cnvr含有相关功能基因（如CLCA4、CYP4X1、GPAT2、MOGAT2、PLA2G2A和PRKG1等）。其中4个基因（CLCA4、GPAT2、MOGAT2和PRKG1）在150只BC1_LD动物（25%伊比利亚和75%长白种）中通过qPCR验证了拷贝数的变化。此外，还分析了它们对背脂肪和肌内脂肪酸组成以及生长相关性状的贡献。CNVR112 （GPAT2）与C18:2(n-6)/C18:3（n-3）比例在背膘和胴体长度等方面的相关性具有统计学意义。值得注意的是，gpat是催化甘油三酯和甘油磷脂生物合成第一步的酶，这表明这种CNVR可能有助于脂肪酸组成和生长性状的遗传变异。这些发现为进一步鉴定影响猪经济上重要性状的性状相关cnvr提供了有用的基因组信息。
Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace backcross population and study their association with fatty acid composition and growth-related traits. A total of 1,279 CNVs, including duplications and deletions, were detected, ranging from 106 to 235 CNVs across samples, with an average of 183 CNVs per sample. Moreover, we detected 540 CNV regions (CNVRs) containing 245 genes. Functional annotation suggested that these genes possess a great variety of molecular functions and may play a role in production traits in commercial breeds. Some of the identified CNVRs contained relevant functional genes (e.g., CLCA4, CYP4X1, GPAT2, MOGAT2, PLA2G2A and PRKG1, among others). The variation in copy number of four of them (CLCA4, GPAT2, MOGAT2 and PRKG1) was validated in 150 BC1_LD (25% Iberian and 75% Landrace) animals by qPCR. Additionally, their contribution regarding backfat and intramuscular fatty acid composition and growth–related traits was analyzed. Statistically significant associations were obtained for CNVR112 (GPAT2) for the C18:2(n-6)/C18:3(n-3) ratio in backfat and carcass length, among others. Notably, GPATs are enzymes that catalyze the first step in the biosynthesis of both triglycerides and glycerophospholipids, suggesting that this CNVR may contribute to genetic variation in fatty acid composition and growth traits. These findings provide useful genomic information to facilitate the further identification of trait-related CNVRs affecting economically important traits in pigs.