拷贝数变异全基因组关联分析及数量性状基因座定位联合鉴定猪体高性状候选基因

doi:10.11843/j.issn.0366-6964.2020.07.005

Abstract

Abstract: The purpose of this study was to screen candidate genes affecting pig body height traits by using genome-wide copy number variation regions (CNVRs) association analysis and genome-wide quantitative trait loci (QTLs) mapping. CNVcaller software was used for rapid detection of genome copy number variations based on resequencing data of the Large White×Min pig F2 population constructed. Mixed-linear model (MLM) with gender and parity as fixed effects was used to perform copy number variation genome-wide association study (CNVR-GWAS) of body height traits. The software R/qtl was used for QTL analysis and the permutation test (PT) was used for inspection. The results of CNVR-GWAS and QTL were jointly annotated, combined with GO enrichment and KEGG pathway analysis, the loci and genes affecting pig body height were excavated. Candidate genes were verified by real-time quantitative polymerase chain reaction (qPCR) method. The results showed that there were 3 099 CNVRs in the whole genome of the population. Among them, two CNVRs were significantly associated with body height trait in the whole genome level, and they located at 25 358 001-26 696 400 bp (CNVR1) and 54 087 201-54 090 000 bp(CNVR2) on chromosome 7, respectively. The results of mixed linear model analysis showed that the increase of copy number of CNVR1 (P<0.01) and the loss of copy number of CNVR2 (P<0.01) had significant effects on pig body height. Two significant QTLs (BH-1 and BH-2, respectively)affecting pig body height were also found at genomic level, of which BH-2 had a greater impact on body height trait. There were one olfactory receptor gene OR12D3 and 18 unannotated genes in the overlap region of CNVR1 and BH-2. And the verification results of qPCR indicated that the copy number variation of OR12D3 was consistent with the results inferred by mixed linear model statistics. The copy number variation of the OR12D3 gene was inferred to be associated with pig body height trait.

Key words: Large White×Min pig F2 population, copy number variation, quantitative trait loci, body height, genome-wide association study

CLC Number:

S828.2

OUYANG Fengzheng, WANG Ligang, YUE Jingwei, YAN Hua, ZHANG Longchao, HOU Xinhua, LIU Xin, WANG Lixian. Genome-wide Association Study of Copy Number Variations and Quantitative Trait Loci Mapping to Identify Candidate Genes for Body Height Trait in Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(7): 1515-1524.

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Genome-wide Association Study of Copy Number Variations and Quantitative Trait Loci Mapping to Identify Candidate Genes for Body Height Trait in Pigs

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