P5028 A genome-wide association study for growth rate in commercial pigs

Abstract

Growth and related traits (e.g., average daily gain) are of main interest in pig breeding ensuring progress toward a reduced number of days to market. Hence, the objective of this study was to identify genomic regions associated with growth rates in pigs represented by the trait ‘Days to 110 kg (D110)’. A total of 952 commercial line Maxgro boars (Hermitage Genetics) were genotyped using Illumina Porcine SNP60 BeadChips. After quality control, the remaining 51,661 SNPs were tested for an association with estimated breeding values (EBV) for D110. In total 124 SNPs reached the threshold of suggestive significance (p-value ≤ 5 × 10−5) for an association with EBV of D110. The largest number of associated SNPs was located on SSC1 (16 SNPs), SSC4 (15 SNPs), SSC3 and 15 (14 SNPs), followed by SSC13 (12 SNPs), and SSC5, 10, and 11 (6 SNPs). Moreover, 12 of these SNPs mapping to 7 porcine autosomes crossed the Bonferroni-adjusted genome-wide significance threshold (p-value ≤ 1 × 10−6). A list of positional candidate genes, closest to significantly associated SNPs, was created allowing a maximum distance of 1 Mb between the marker and genes. Subsequently, the list of genes was used to identify enriched pathways and biological functions for D110. Most promising QTLs were detected on SSC 10 and 15. On SSC10, association analyses revealed AKR1C3 as the positional candidate gene. On SSC15, 5 SNPs reaching the genome-wide significance were located within a 682 Kb segment between 2.64 and 3.32 Mb. Three of these SNPs mapped within intronic regions of KIF5C. The two remaining SNPs were located next to MBD5 and LYPD6B. A number of positional candidate genes for EBV of D110 (AKR1C3, MBD5, ACVR2A, AKR1C1/AKR1C2 and AKR1C4) were clustered in an endocrine system function and development category. Additionally, these genes were significantly overrepresented in lipid metabolism and energy production. In summary, the present study demonstrated a number of chromosomal regions significantly associated with EBV for D110 in pigs. The identified positional candidate genes indicate for a complex functional basis of growth traits comprising endocrine regulations, resource allocation and cellular metabolism.