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. 2023 Feb 6:14:1001352.
doi: 10.3389/fgene.2023.1001352. eCollection 2023.

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

Huiyu Wang  1   2 , Xiaoyi Wang  1 , Mingli Li  1 , Hao Sun  3 , Qiang Chen  1 , Dawei Yan  1 , Xinxing Dong  1 , Yuchun Pan  4 , Shaoxiong Lu  1
Affiliations

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

Huiyu Wang et al. Front Genet. .

Abstract

Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07-0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.

Keywords: GWAS; SLAF-seq; candidate genes; crossbred pigs; meat quality.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Manhattan plots and QQ plots for pH45, MC and MA using MLM. (A) pH45 (B) MC (C) MA. Negative log10 p-value of the filtered high-quality SNPs were plotted against their genomic positions; The dashed lines of green, orange and blue correspond to the Bonferroni-corrected thresholds of p = 1.00 × 10−5 (−log10 p = 5), p = 4.39 × 10−7 (−log10 p = 6.36), and p = 4.39 × 10−8 (−log10 p = 7.36), respectively; λ, Genomic inflation factor.
FIGURE 2
FIGURE 2
Manhattan plots and QQ plots for WL, CL and DL using MLM. (A) WL (B) CL (C) DL. Negative log10 p-value of the filtered high-quality SNPs were plotted against their genomic positions; The dashed lines of green, orange and blue correspond to the Bonferroni-corrected thresholds of p = 1.00 × 10−5 (−log10 p = 5), p = 4.39 × 10−7 (−log10 p = 6.36) and p = 4.39 × 10−8 (−log10 p = 7.36), respectively; λ, Genomic inflation factor.
FIGURE 3
FIGURE 3
Haploview plots of linkage disequilibrium (r2) between SNPs on pig chromosome. (A) A region on SSC10 (106.40 kb) contained a haploview block with two significant SNPs related to CL (B) A region on SSC2 (31.45 kb) contained a haploview block with two significant SNPs related to DL. Values in the diamond are r 2 values between SNPs. The darker the color, the stronger the correlation between two SNPs.
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