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.

Keywords: SLAF-seq; SNPs; genes; genome-wide association study; growth traits; pigs.

Figure 1

Frequency distribution histogram for ten growth traits. (A) Live backfat thickness (LBT), (B) Average daily gain from 30 to 60 kg (ADG30–60), (C) Average daily gain from 60 to 100 kg (ADG60–100), (D) Average daily gain from 30 to 100 kg (ADG30–100), (E) Body length (BL), (F) Body height (BH), (G) Back height (BAH), (H) Chest circumference (CC), (I) Chest depth (CD), (J) Rump circumference (RC).

Figure 2

The filtered SNP density distributions on Sscrofa chromosomes. The horizontal axis (x-axis) shows the chromosome length (Mb). Color index indicates the number of labels.

Figure 3

Manhattan plots and QQ plots for LBT, ADG30–60, ADG60–100, and ADG30–100 using MLM. (A) LBT, (B) ADG30–60, (C) ADG60–100, (D) ADG30–100. Negative log₁₀ p-values 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.

Figure 4

Manhattan plots and QQ plots for BL, BH and BAH using MLM. (A) BL, (B) BH, (C) BAH. Negative log₁₀ p-values 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.

Figure 5

Manhattan plots and QQ plots for CC, CD and RC using MLM. (A) CC, (B) CD, (C) RC. Negative log₁₀ p-values 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.