Genome-wide association analysis reveals genetic loci and candidate genes for feeding behavior and eating efficiency in Duroc boars

<div><p>Efficient use of feed resources is a challenge in the pork industry because the largest variability in expenditure is attributed to the cost of fodder. Efficiency of feeding is directly related to feeding behavior. In order to identify genomic regions controlling feeding behavior and eating efficiency traits, 338 Duroc boars were used in this study. The Illumina Porcine SNP60K BeadChip was used for genotyping. Data pertaining to individual daily feed intake (DFI), total daily time spent in feeder (TPD), number of daily visits to feeder (NVD), average duration of each visit (TPV), mean feed intake per visit (FPV), mean feed intake rate (FR), and feed conversion ratio (FCR) were collected for these pigs. Despite the limited sample size, the genome-wide association study was acceptable to detect candidate regions association with feeding behavior and eating efficiency traits in pigs. We detected three genome-wide (<i>P</i> < 1.40E-06) and 11 suggestive (<i>P</i> < 2.79E-05) single nucleotide polymorphism (SNP)-trait associations. Six SNPs were located in genomic regions where quantitative trait loci (QTLs) have previously been reported for feeding behavior and eating efficiency traits in pigs. Five candidate genes (<i>SERPINA3</i>, <i>MYC</i>, <i>LEF1</i>, <i>PITX2</i>, and <i>MAP3K14</i>) with biochemical and physiological roles that were relevant to feeding behavior and eating efficiency were discovered proximal to significant or suggestive markers. Gene ontology analysis indicated that most of the candidate genes were involved in the development of the hypothalamus (GO:0021854, <i>P</i> < 0.0398). Our results provide new insights into the genetic basis of feeding behavior and eating efficiency in pigs. Furthermore, some significant SNPs identified in this study could be incorporated into artificial selection programs for Duroc-related pigs to select for increased feeding efficiency.</p></div

Tag SNPs and closest genes for feeding behavior and eating efficiency traits.

<p>Tag SNPs and closest genes for feeding behavior and eating efficiency traits.</p

Descriptive statistical analysis of feeding behavior and eating efficiency in a male Duroc population.

<p>Descriptive statistical analysis of feeding behavior and eating efficiency in a male Duroc population.</p

Comparative mapping of tag SNPs with previous QTLs reported in the pig QTL database (as of April 3, 2016) and previous GWAS results.

<p>Comparative mapping of tag SNPs with previous QTLs reported in the pig QTL database (as of April 3, 2016) and previous GWAS results.</p

Manhattan plots of genome-wide association studies for eating efficiency and feeding behavior in male Duroc pigs.

<p>The inserted quantile–quantile (Q–Q) plots in the right show the observed versus expected log p-values. In the Manhattan plots, negative log10 <i>P</i> 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 and Q-Q plot for the number of visits to the feeder per day (NVD), FPV, and feed conversion ratio (FCR), respectively.</p