A genomewide association study of feed efficiency and feeding behaviors at two fattening stages in a White Duroc × Erhualian F2 population1

Abstract

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 × Erhualian F2 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.

Identification of loci affecting teat number by genome-wide association studies on three pig populations

“…the effect of QTL detected in a previous round was treated as a fixed effect in the statistical model when searching for QTL in the next round. This approach has smaller error residuals and consequently has a stronger detection power than the linear mixed GWAS model [30]. Third, only additive effect were included in our GWAS model while both additive and dominant effects were considered in the QTL model.…”

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

“…On BTA18, CMIP (C-Maf inducing protein), a candidate gene for reading-related traits, was also associated with plasma lipoprotein levels [56]. Moreover, WSCD1 (WSC domain containing 1), which encodes a protein with sulfotransferase activity that participates in the metabolism of glucose, was a candidate gene for feed efficiency and feeding behaviors in the White Duroc × Erhualian F2 population [57].…”

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

“…On BTA18, CMIP (C-Maf inducing protein), a candidate gene for reading-related traits, was also associated with plasma lipoprotein levels [58]. Moreover, WSCD1 (WSC domain containing 1), which encodes a protein with sulfotransferase activity that participates in the metabolism of glucose, was a candidate gene for feed efficiency and feeding behaviors in the White Duroc × Erhualian F2 population [59].…”