A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population

Abstract

Background Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs. Results Firstly, we performed a genome-wide analysis for CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 pigs. A total of 11,100 CNVs were detected, which were aggregated by overlapping 695 CNV regions (CNVRs). Next, we investigated CNVs of pigs from the same population by whole-genome resequencing. A genome-wide analysis of 21 pigs revealed 23,856 CNVRs that were further divided into three categories (851 gain, 22,279 loss, and 726 mixed), which covered 190.8 Mb (~ 8.42%) of the pig autosomal genome. Further, the identified CNVRs were used to determine an overall validation rate of 68.5% for the CNV detection accuracy of chip data. CNVR association analyses identified one CNVR associated with LMA, one with LMD and eight with LMP after applying stringent Bonferroni correction. The wssGWAS identified eight, six and five regions explaining more than 1% of the additive genetic variance for LMA, LMD and LMP, respectively. The CNVR analyses and wssGWAS identified five common regions, of which three regions were associated with LMA and two with LMP. Four genes (DOK7, ARAP1, ELMO2 and SLC13A3) were highlighted as promising candidates according to their function. Conclusions We determined an overall validation rate for the CNV detection accuracy of low-density chip data and constructed a genomic CNV map for Duroc pigs using resequencing, thereby proving a value genetic variation resource for pig genome research. Furthermore, our study utilized a composite genetic strategy for complex traits in pigs, which will contribute to the study for elucidating the genetic architecture that may be influenced and regulated by multiple forms of variations.

Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle

“…Among them, there were 153 genes shared by cis-eQTL and gene-based GWAS, while 23 genes were shared among cis-eQTL, gene-based GWAS and selection signatures. Among 23 genes, six genes ( SLC13A3 , ATG7 , ETFDH , GADL1 , PRKG1 and ACAD11 ) were observed to be related to carcass yield traits, and SLC13A3 was highlighted as a promising candidate for carcass traits in pigs [ 36 ]. In another study, increasing the expression of ATG7 in M. longissimus was highly correlated with the ultrasonic M. longissimus area and body weight in cattle [ 37 ].…”

Genome-wide association studies for economically important traits in mink using copy number variation

“…Similar to SNPs, CNVs can be applied to detect associations with traits of economic interest in livestock species, and therefore, are considered complementary sources to explain genetic variation contributing to differences in phenotypes 18 . Over the past decade, multiple studies have been carried out to examine the association between CNVs with several important phenotypes in livestock species, such as reproduction 19 , 20 , health 21 – 23 , feed efficiency and growth 24 – 26 , and performance traits 27 – 29 .…”

Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing

“…With the development of large-scale human CNV research, substantial progress has been made in CNV detection in livestock and poultry species, including cattle ( Bos taurus ) [ 5 , 6 ], pigs ( Sus scrofa ) [ 7 ], goats ( Capra hircus ) [ 8 ], sheep ( Ovis aries ) [ 9 ], dogs ( Canis familaris ) [ 10 ], and chickens ( Gallus gallus ) [ 4 ]. To date, CNV overlapping genes screened in numerous animal models have been shown to be related to coat color [ 10 , 11 ], meat quality [ 12 ], reproduction [ 13 ], immune response [ 14 ], disease [ 15 ], and environmental adaptations [ 16 ].…”