A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

Jie Yang,Rongrong Ding,Qian Geng,Enqin Zheng,Shenping Zhou,Xingwang Wang,Jie Wu,Zhanwei Zhuang,Jianhui Yang,Fanming Meng,Zhenfang Wu,Jianping Quan

doi:10.1186/s12864-020-07288-1

Jie Yang, Rongrong Ding + Show 10 more

Open Access

https://doi.org/10.1186/s12864-020-07288-1

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Abstract

BackgroundAverage daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs.ResultsIn the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development.ConclusionsWe performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Highlights

Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs
This study showed a positive correlation between ADG and LMP in American and Canadian Duroc pigs
Through the Venn plot (Additional file 6: Figure S4), we found that there were many significant single nucleotide polymorphism (SNP) detected by the meta-analysis than the mixed-population genome-wide association studies (GWAS) in the two traits (ADG: 17 vs 12; LMP: 37 vs 22), and the proportion of significant SNPs detected by the single population GWAS verified by the meta-analysis is higher than the mixed population GWAS (ADG: 7/17 vs 1/12; LMP: 17/37 vs 9/22), which implies that the meta-analysis may be more suitable

Summary

Introduction

Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Average daily gain (ADG) and lean meat percentage (LMP) are considered as growth and carcass traits of pigs and are important indicators of pig production performance, which directly affect the profit of the farm. ADG and LMP are complex quantitative traits regulated by multiple genes and improving these two traits through conventional breeding is time-consuming and expensive. Considering pigs as an example, 1916 and 16,147 QTLs are associated with growth traits and meat and carcass traits, including 692 and 172 QTLs associated with ADG and LMP in the pig QTL database (https://www.animalgenome.org/cgi-bin/QTLdb/SS/index, April 23, 2020) [3], respectively. Poor resolution in QTL mapping experiments and complicated genetic architecture of many QTLs result in an unavoidable challenge for identifying causative mutations [4]

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