GWAS for Meat and Carcass Traits Using Imputed Sequence Level Genotypes in Pooled F2-Designs in Pigs

Abstract

In order to gain insight into the genetic architecture of economically important traits in pigs and to derive suitable genetic markers to improve these traits in breeding programs, many studies have been conducted to map quantitative trait loci. Shortcomings of these studies were low mapping resolution, large confidence intervals for quantitative trait loci-positions and large linkage disequilibrium blocks. Here, we overcome these shortcomings by pooling four large F2 designs to produce smaller linkage disequilibrium blocks and by resequencing the founder generation at high coverage and the F1 generation at low coverage for subsequent imputation of the F2 generation to whole genome sequencing marker density. This lead to the discovery of more than 32 million variants, 8 million of which have not been previously reported. The pooling of the four F2 designs enabled us to perform a joint genome-wide association study, which lead to the identification of numerous significantly associated variant clusters on chromosomes 1, 2, 4, 7, 17 and 18 for the growth and carcass traits average daily gain, back fat thickness, meat fat ratio, and carcass length. We could not only confirm previously reported, but also discovered new quantitative trait loci. As a result, several new candidate genes are discussed, among them BMP2 (bone morphogenetic protein 2), which we recently discovered in a related study. Variant effect prediction revealed that 15 high impact variants for the traits back fat thickness, meat fat ratio and carcass length were among the statistically significantly associated variants.

Genome-Wide Association Study for Body Length, Body Height, and Total Teat Number in Large White Pigs

“…Zhou et al reported the BMP2 gene as a candidate gene associated with body length and body height traits in Chinese Shushan pigs ( Zhou et al, 2019 ). Moreover, BMP2 as a candidate gene was discovered and associated with carcass length in pigs ( Falker-Gieske et al, 2019 ). BMP2 was also associated with the distal midpiece reflex for sperm traits in a Duroc boar population ( Zhao et al, 2020 ).…”

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

“…GWAS were performed with the Genome-wide Complex Trait Analysis (GCTA) software version 1.92.3 beta3 using the imputed sequence level genotype data filtered for MAF (> 0.01). In order to correct for relatedness between animals and stratification [ 6 ], a random genetic term was included based on a genomic relationship matrix calculated only from SNP-chip-data and following a leave one chromosome out (LOCO) approach as described here [ 10 ]. Briefly, a model of the form y = Wα + Xβ + u + ϵ is fitted, where y is an n × 1 vector of phenotypes n hens (a summary of the phenotype data is shown in Table 5 ).…”

“…Here we present an approach in which we performed whole-genome sequencing (WGS) on selected animals, in order to impute low-level chip genotype data to sequencing level. We have already successfully applied this strategy in a porcine F2 design [10]. In the present study, we combined the results of GWAS from two resource populations: an F2 design and one half-sib (HS) population divergently selected for feather pecking behavior.…”

Identification of SNPs and Candidate Genes for Milk Produce Ability in Yorkshire Pig

“…Genome-wide association study (GWAS) is an effective strategy to examine the underlying genetics of complex traits [12]. Many studies have identified candidate markers associated with important economic traits in pigs, such as meat quality [13] and growth [14] . For litter weight gain trait in Yorkshire sow lactation, the GWAS has been performed to detect two quantitative trait locus (QTLs) on Sus scrofa Chromosome (SSC) 7 (126Mb and 101Mb) [15].…”