Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data

Abstract

BackgroundPorcine fatty acid composition is a key factor for quality and nutritive value of pork. Several QTLs for fatty acid composition have been reported in diverse fat tissues. The results obtained so far seem to point out different genetic control of fatty acid composition conditional on the fat deposits. Those studies have been conducted using simple approaches and most of them focused on one single tissue. The first objective of the present study was to identify tissue-specific and tissue-consistent QTLs for fatty acid composition in backfat and intramuscular fat, combining linkage mapping and GWAS approaches and conducted under single and multitrait models. A second aim was to identify powerful candidate genes for these tissue-consistent QTLs, using microarray gene expression data and following a targeted genetical genomics approach.ResultsThe single model analyses, linkage and GWAS, revealed over 30 and 20 chromosomal regions, 24 of them identified here for the first time, specifically associated to the content of diverse fatty acids in BF and IMF, respectively. The analyses with multitrait models allowed identifying for the first time with a formal statistical approach seven different regions with pleiotropic effects on particular fatty acids in both fat deposits. The most relevant were found on SSC8 for C16:0 and C16:1(n-7) fatty acids, detected by both linkage and GWAS approaches. Other detected pleiotropic regions included one on SSC1 for C16:0, two on SSC4 for C16:0 and C18:2, one on SSC11 for C20:3 and the last one on SSC17 for C16:0. Finally, a targeted eQTL scan focused on regions showing tissue-consistent effects was conducted with Longissimus and fat gene expression data. Some powerful candidate genes and regions were identified such as the PBX1, RGS4, TRIB3 and a transcription regulatory element close to ELOVL6 gene to be further studied.ConclusionsComplementary genome scans have confirmed several chromosome regions previously associated to fatty acid composition in backfat and intramuscular fat, but even more, to identify new ones. Although most of the detected regions were tissue-specific, supporting the hypothesis that the major part of genes affecting fatty acid composition differs among tissues, seven chromosomal regions showed tissue-consistent effects. Additional gene expression analyses have revealed powerful target regions to carry the mutation responsible for the pleiotropic effects.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-845) contains supplementary material, which is available to authorized users.

Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny

“…Multiple regions were found that had a high frequency of ROH across both the maternal breeds whereas one region was detected across all three breeds. The regions on SSC1 (248.7–264.2 Mb), SSC4 (42.1–61.3 Mb) and SSC14 (98.0–111.7 Mb) detected in LW and LA were previously shown to impact meat and carcass quality [48–51], multiple production and meat quality traits [52, 53], and reproduction [54], respectively. Four regions were found to have a higher frequency of ROH5 and/or ROH10 across the terminal DU breed and both the maternal breeds.…”

“…Four regions were found to have a higher frequency of ROH5 and/or ROH10 across the terminal DU breed and both the maternal breeds. The regions on SSC3 (36.4–59.5 Mb) and SSC14 (121.0–132.5 Mb) were found to be associated with meat and carcass quality traits [52, 55, 56], and with carcass quality [57] and fitness traits [58], respectively.…”

Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs

“…The efforts from the Pig Genome Sequencing Consortia in assembling the pig genome materialized in a new and efficient tool in the form of genome browsers that can help to identify positional candidate genes underlying these relevant genomic regions. The latest GWAS studies in IMF composition have confirmed the relevance of regions in SSC4, 8 and 14 across most breeds and identified other breed-specific fragments [20,40,41]. On the whole, GWAS regions explain in most cases a relatively small fraction (<8%) of the phenotypic variation.…”

“…This limits the application of these markers in a pig breeding system that has lean content, among other traits, as a selection objective. Similarly, genomic regions associated with fat composition are mostly shared between muscle and fat traits [41], indicating that common fatty acid enzymatic/transport pathways take place in these two fat depots [45]. In terms of fatty acid composition this is not a limitation, as long as the lean content remains the same.…”

“…For instance, several promoter mutations in the ELOVL fatty acid elongase 6 ( ELOVL6 ) gene have been associated with C16 (16:0 and 16:1) to C18 (18:0 and 18:1) content in longissimus dorsi muscle and backfat [43,44]. This enzyme elongates saturated and monounsaturated C12 to C18 fatty acids and it was a strong positional candidate gene for several compositional QTL at SSC8 in backfat [41,63] and muscle [40,64]. The mutations in the promoter have been linked to the disruption of several transcription factor binding sites and also to differential methylation of local CpG islands which correlate with gene expression.…”