Genetic Architecture of Feeding Behavior and Feed Efficiency in a Duroc Pig Population

Abstract

Increasing feed efficiency is a major goal of breeders as it can reduce production cost and energy consumption. However, the genetic architecture of feeding behavior and feed efficiency traits remains elusive. To investigate the genetic architecture of feed efficiency in pigs, three feeding behavior traits (daily feed intake, number of daily visits to feeder, and duration of each visit) and two feed efficiency traits (feed conversion ratio and residual feed intake) were considered. We performed genome-wide association studies (GWASs) of the five traits using a population of 1,008 Duroc pigs genotyped with an Illumina Porcine SNP50K BeadChip. A total of 9 genome-wide (P < 1.54E-06) and 35 suggestive (P < 3.08E-05) single nucleotide polymorphisms (SNPs) were detected. Two pleiotropic quantitative trait loci (QTLs) on SSC 1 and SSC 7 were found to affect more than one trait. Markers WU_10.2_7_18377044 and DRGA0001676 are two key SNPs for these two pleiotropic QTLs. Marker WU_10.2_7_18377044 on SSC 7 contributed 2.16 and 2.37% of the observed phenotypic variance for DFI and RFI, respectively. The other SNP DRGA0001676 on SSC 1 explained 3.22 and 5.46% of the observed phenotypic variance for FCR and RFI, respectively. Finally, functions of candidate genes and gene set enrichment analysis indicate that most of the significant pathways are associated with hormonal and digestive gland secretion during feeding. This study advances our understanding of the genetic mechanisms of feeding behavior and feed efficiency traits and provide an opportunity for increasing feeding efficiency using marker-assisted selection or genomic selection in pigs.

Keywords: Duroc; GWAS; feed conversion ratio; feed efficiency; feeding behavior; pigs; residual feed intake.

FIGURE 1

Manhattan plots of genome-wide association studies for feeding behavior and feed efficiency in male Duroc pigs. In the Manhattan plots, negative log10 P-values of the quantified SNPs were plotted against their genomic positions. Different colors indicate various chromosomes. The solid and dashed lines indicate the 5% genome-wide and chromosome-wide Bonferroni-corrected thresholds, respectively. On the vertical axis, Manhattan plot for (A) residual feed intake (RFI), (B) total daily feed intake (DFI), (C) feed conversion ratio (FCR), (D) total daily time spent in feeder (TBD), and (E) number of visits to feeder (NVD), respectively.

FIGURE 2

Regional association plot of the primary signal (WU_10.2_7_18377044) associated with DFI and RFI at SSC7. For each plot, negative log10 P-values of SNPs (y-axis) are presented according to their chromosomal positions (x-axis). The red line and green line indicate the genome-wide significance level (P < 1.54E-06) and the suggestive level (P < 3.08E-05), respectively. The primary SNP are denoted by large blue circles. SNPs are represented by colored circles according to the target SNP with which they were in strongest LD. The left panel of the figure shows the association results for DFI (A) before and (B) after conditional analysis on WU_10.2_7_18377044. The right panel of the figure shows the association results for RFI (C) before and (D) after conditional analysis on WU_10.2_7_18377044. The P-value of association results for (B) DFI and (D) RFI after conditional analysis on WU_10.2_7_18377044 fell below the predicted threshold.

FIGURE 3

Regional association plot of the primary signal (DRGA0001676) associated with FCR and RFI at SSC1. For each plot, negative log10 P-values of SNPs (y-axis) are presented according to their chromosomal positions (x-axis). The red line and green line indicate the genome-wide significance level (P < 1.54E-06) and the suggestive level (P < 3.08E-05), respectively. The primary SNP are denoted by large blue circles. SNPs are represented by colored circles according to the target SNP with which they were in strongest LD. The left panel of the figure shows the association results for FCR (A) before and (B) after conditional analysis on DRGA0001676. The right panel of the figure shows the association results for RFI (C) before and (D) after conditional analysis on DRGA0001676. The P-value of association results for (B) FCR and (D) RFI after conditional analysis on DRGA0001676 fell below the predicted threshold.

FIGURE 4

The LD block in the significantly associated region on SSC1. LD blocks are marked with triangles. Values in boxes are LD (r²) between SNP pairs and the boxes are colored according to the standard Haploview color scheme: LOD > 2 and D′ = 1, red; LOD > 2 and D′ < 1, shades of pink/red; LOD < 2 and D′ = 1, blue; LOD < 2 and D′ < 1, white (LOD is the log of the likelihood odds ratio, a measure of confidence in the value of D′). Annotated genes in the chromosomal region retrieved from the Ensemble genome browser (www.ensembl.org/Sus_scrofa/Info/Index).