Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population.

Donglin Ruan,Cineng Xu,Shenping Zhou,Zhanwei Zhuang,Yibin Qiu,Jie Yang,Linjun Hong,Jie Wu,Sixiu Huang,Enqin Zheng,Zhenfang Wu,Rongrong Ding,Gengyuan Cai

doi:10.3390/genes12010117

Donglin Ruan, Cineng Xu + Show 11 more

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https://doi.org/10.3390/genes12010117

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Abstract

Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

Highlights

Pork is the primary source of protein for humans, with global pork consumption exceeding 110 metric kilotons per year [1]
This study aims to identify genomic regions and candidate genes associated with growth traits such as days adjusted to 100 kg (AGE), average daily gain adjusted to 100 kg (ADG), backfat thickness (BF) and predicted lean meat percentage (LMP) adjusted to 100 kg in a Duroc pig population using the weighted single-step genome-wide association study (GWAS) (wssGWAS) methodology
Previous studies reported that the average AGE phenotype of Duroc and other western commercial pig breeds was between 150 and 162 days, ADG was between 610 and 820 g/day, BF was between 11.69 and 18.19 mm, and LMP was between 56% and 62% [6,14,24,25,26]

Summary

Introduction

Pork is the primary source of protein for humans, with global pork consumption exceeding 110 metric kilotons per year [1]. The age to 100 kg, average daily gain, backfat thickness, and lean meat percentage for a specific stage are vital indicators to measure the growth rate and carcass fat content of pigs due to their significant impact on production efficiency [2] Both genetic and non-genetic effects can affect growth traits, including pig breed, feeding behavior, and nutrition level. 2036 QTL for growth traits have been reported in the pig QTL database (https://www.animalgenome.org/cgi-bin/QTLdb/SS/summary, release 27 August 2020) These findings have provided a certain number of molecular markers to porcine breeding for growth traits—for instance, Jiang et al [6] performed a GWAS in a total of 2025 American and British Yorkshire pigs using PorcineSNP80 bead chip and detected five significant SNPs for days to 100 kg and the other five significant SNPs for 10th rib backfat thickness. To overcome the limitation of the traditional GWAS approach, the weighted single-step GWAS (wssGWAS) proposed by Wang et al [8] is preferable for livestock breeding, for which phenotypic and genealogical information is available for the vast majority of individuals and the small size of individuals genotyped

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