Genome-wide association studies for growth and meat production traits in sheep.

Li Zhang,Fuping Zhao,Lingyang Xu,Jiasen Liu,Caihong Wei,Guobin Lu,Youmin Zheng,Lixin Du,Xiaoning Zhang,Shifang Zhang,Hangxing Ren,Jian Lu,Marinus F.W Te Pas

doi:10.1371/journal.pone.0066569

Li Zhang, Fuping Zhao + Show 11 more

Open Access

https://doi.org/10.1371/journal.pone.0066569

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Abstract

BackgroundGrowth and meat production traits are significant economic traits in sheep. The aim of the study is to identify candidate genes affecting growth and meat production traits at genome level with high throughput single nucleotide polymorphisms (SNP) genotyping technologies.Methodology and ResultsUsing Illumina OvineSNP50 BeadChip, we performed a GWA study in 329 purebred sheep for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers, chest girth, and shin circumference). After quality control, 319 sheep and 48,198 SNPs were analyzed by TASSEL program in a mixed linear model (MLM). 36 significant SNPs were identified for 7 traits, and 10 of them reached genome-wise significance level for post-weaning gain. Gene annotation was implemented with the latest sheep genome Ovis_aries_v3.1 (released October 2012). More than one-third SNPs (14 out of 36) were located within ovine genes, others were located close to ovine genes (878bp-398,165bp apart). The strongest new finding is 5 genes were thought to be the most crucial candidate genes associated with post-weaning gain: s58995.1 was located within the ovine genes MEF2B and RFXANK, OAR3_84073899.1, OAR3_115712045.1 and OAR9_91721507.1 were located within CAMKMT, TRHDE, and RIPK2 respectively. GRM1, POL, MBD5, UBR2, RPL7 and SMC2 were thought to be the important candidate genes affecting post-weaning gain too. Additionally, 25 genes at chromosome-wise significance level were also forecasted to be the promising genes that influencing sheep growth and meat production traits.ConclusionsThe results will contribute to the similar studies and facilitate the potential utilization of genes involved in growth and meat production traits in sheep in future.

Highlights

With the increasing popularity of meat production in sheep industry, geneticists and breeders pay more attention to sheep growth and meat production traits
The results will contribute to the similar studies and facilitate the potential utilization of genes involved in growth and meat production traits in sheep in future
A small number of quantitative trait loci (QTL) have been identified in sheep with only 789 reported from a genome scan based on marker-QTL linkage analysis [5](updated on May 15th,2013)

Summary

Introduction

With the increasing popularity of meat production in sheep industry, geneticists and breeders pay more attention to sheep growth and meat production traits. A mass of quantitative trait loci (QTL) were found by candidate gene approach and genome scanning technology in livestock. Numerous QTL studies for different quantitative traits have been performed in pig, cattle, chicken and sheep [1,2,3,4]. With the development of high throughput SNP genotyping technologies, genome-wide association studies (GWAS) have been widely applied to detect and localize candidate genes for quantitative traits in different species, which brings more ideas to increase the efficiency of animal breeding and selection [6,7,8]. The aim of the study is to identify candidate genes affecting growth and meat production traits at genome level with high throughput single nucleotide polymorphisms (SNP) genotyping technologies

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