A genomewide association study of feed efficiency and feeding behaviors at two fattening stages in a White Duroc x Erhualian F-2 population

Feeding efficiency is a multifactorial and economically important trait in pigs. Genetic improvement of feeding efficiency will greatly benefit the pig industry. In the past decades, the hog market weight has increased worldwide. However, whether the genetic architecture of feeding efficiency is same or not at early and late fattening periods is unclear. To map genomic regions for feed efficiency and feeding behavior traits at early (n >= 384) and late (n >= 334) growth stages in pigs, we performed genomewide association studies for feed to gain ratio (FCR), residual feed intake (RFI), daily feed intake, daily visit times, daily feeding time (DFT), feed intake per second (FIPS), and feed intake per visit during 3 periods (2 stages and overall) in a White Duroc x Erhualian F-2 intercross population. Six chromosomal regions showed significant association with these traits, of which 4 loci were reported for the first time. Our results confirmed the QTL of FCR around 34 Mb on SSC7 and RFI around 134 Mb on SSC12. Of note, 2 regions were associated with more than 1 trait. One was around 36 Mb on SSC7, and there were 47 and 67 SNP associated with FCR from 120 to 210 and from 120 to 240 d, respectively. The top SNP is located in a 2.88-Mb linkage disequilibrium (LD) block that harbors 44 genes. We propose the high mobility group AT-hook 1 gene as a plausible candidate gene in this region. The other was evidenced around 53 Mb on SSC12, which had multiple association signals for DFT and FIPS. The top SNP is located in a 211-kb LD block that harbors only 1 annotated gene, WSCD1, which encodes a protein with sulfotransferase activity and involves the glucose metabolism and, therefore, appears to be a plausible candidate gene. Except the region on SSC12 associated with DFT at both stages, the rest of the regions associated with the traits at only 1 stage, so the genetic architectures of the 2 stages are not same.