Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population

Abstract

Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.

Identification of New Genes and Genetic Variant Loci Associated with Breast Muscle Development in the Mini-Cobb F2 Chicken Population Using a Genome-Wide Association Study

“…The Pearson’s correlation coefficient is able to assess the linearity of the relationship between continuous variables, while the Spearman’s correlation coefficient evaluates their monotonic relationship [ 32 ]. In most studies, the Pearson’s correlation coefficient is usually used to describe the correlation between traits [ 28 , 33 ], but in this study, the relationship between these traits, such as breast muscle weight and breast depth ( Figure 1 ), did not show complete linearity. Although they showed the same trend, they did not have a stable rate of change, which is more consistent with monotony.…”

Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population

“…A four-way crossbred pig population was established as described previously ( Wang et al, 2022a ; Wang et al, 2022b ). In short, 223 four-way crossbred pigs (115 females and 108 males, DSYLS) investigated were offspring of seven hybrid boars (Duroc × Saba, DS) and 37 hybrid sows (Yorkshire × (Landrace × Saba), YLS) from the pigs and broilers breeding farm in Chuxiong City, Yunnan Province, China ( Supplementary Figure S1 ).…”

“…SLAF library construction and sequencing were performed as described previously ( Wang et al, 2022a ; Wang et al, 2022b ). In short, using the phenol-chloroform extraction procedure, genomic DNA was isolated from ear tissue samples.…”

“…SNP throughout the entire genome were generated as described previously ( Wang et al, 2022a ; Wang et al, 2022b ). In short, SNP loci were found based on information from polymorphic SLAF tags using predominantly GATK ( McKenna et al, 2010 ).…”

“…SLAF-seq has also been successfully used for genotyping of pigs and detected abundant novel mutation sites ( Li et al, 2017 ; Qin et al, 2020 ). Furthermore, we also identified some genomic regions and several candidate genes for porcine fatness-related and growth-related traits using GWAS based on SLAF-seq technology in our previous studies ( Wang et al, 2022a ; Wang et al, 2022b ).…”