Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

Abstract

Background: Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray analysis were taken as phenotypes in a linkage analysis to map eQTL. Moreover, expression levels were correlated with traits related to meat quality and principle components with high loadings of these traits. By using an up-to-date annotation and localization of the respective probe-sets, the integration of eQTL mapping data and information of trait correlated expression finally served to point to candidate genes for meat quality traits.

Results: Genome-wide transcriptional profiles of M. longissimus dorsi RNAs samples of 74 F2 animals of a pig resource population revealed 11,457 probe-sets representing genes expressed in the muscle. Linkage analysis of expression levels of these probe-sets provided 9,180 eQTL at the suggestive significance threshold of LOD > 2. We mapped 653 eQTL on the same chromosome as the corresponding gene and these were designated as 'putative cis-eQTL'. In order to link eQTL to the traits of interest, probe-sets were addressed with relative transcript abundances that showed correlation with meat quality traits at p ≤ 0.05. Out of the 653 'putative cis-eQTL', 262 transcripts were correlated with at least one meat quality trait. Furthermore, association of expression levels with composite traits with high loadings for meat quality traits generated by principle component analysis were taken into account leading to a list of 85 genes exhibiting cis-eQTL and trait dependent expression.

Conclusion: Holistic expression profiling was integrated with QTL analysis for meat quality traits. Correlations between transcript abundance and meat quality traits, combined with genetic positional information of eQTL allowed us to prioritise candidate genes for further study.

Figure 1

Graphical scheme of eQTL across 18 chromosome obtained by eQTL analysis of 11457 probe-set. Y-axis shows P-values, expressed on the -log10 scale, and X-axis shows position of eQTL in cM though18 chromosome. The genome-wide significant threshold (p ≤ 0.05) is shown with the dot line.

Figure 2

Position of eQTL of probe-sets that show trait-correlated expression and that are located on the same chromosome (SSC1 to 4) as the corresponding genes. Left: physical map with positions of microsatellite markers (red) and genes (black) represented by the probe-sets in Mb according to the Sscrofa9 genome sequence; Right: sex-averaged linkage maps of SSC 1 to 4 with positions of microsatellite markers and eQTL of corresponding probe-sets in cM; Both maps are linked based on the microsatellite marker positions (red and bold). Meat quality traits, with which the expression levels of probe-sets are correlated, are presented in brackets. Trait abbreviations are given at table 2.

Figure 3

Position of eQTL of probe-sets that show trait-correlated expression and that are located on the same chromosome (SSC5 to 8) as the corresponding genes. Left: physical map with positions of microsatellite markers (red) and genes (black) represented by the probe-sets Mb according to the Sscrofa9 genome sequence; Right: sex-averaged linkage maps of SSC 1 to 4 with positions of microsatellite markers and eQTL of corresponding probe-sets in cM; Both maps are linked based on the microsatellite marker positions (red and bold). Meat quality traits, with which the expression levels of probe-sets are correlated, are presented in brackets. Trait abbreviations are given at table 2.

Figure 4

Position of eQTL of probe-sets that show trait-correlated expression and that are located on the same chromosome (SSC9 to 12) as the corresponding genes. Left: physical map with positions of microsatellite markers (red) and genes (black) represented by the probe-sets Mb according to the Sscrofa9 genome sequence; Right: sex-averaged linkage maps of SSC 1 to 4 with positions of microsatellite markers and eQTL of corresponding probe-sets in cM; Both maps are linked based on the microsatellite marker positions (red and bold). Meat quality traits, with which the expression levels of probe-sets are correlated, are presented in brackets. Trait abbreviations are given at table 2.

Figure 5

Position of eQTL of probe-sets that show trait-correlated expression and that are located on the same chromosome (SSC12 to 16) as the corresponding genes. Left: physical map with positions of microsatellite markers (red) and genes (black) represented by the probe-sets Mb according to the Sscrofa9 genome sequence; Right: sex-averaged linkage maps of SSC 1 to 4 with positions of microsatellite markers and eQTL of corresponding probe-sets in cM; Both maps are linked based on the microsatellite marker positions (red and bold). Meat quality traits, with which the expression levels of probe-sets are correlated, are presented in brackets. Trait abbreviations are given at table 2.

Figure 6

Position of eQTL of probe-sets that show trait-correlated expression and that are located on the same chromosome (SSC17 and 18) as the corresponding genes. Left: physical map with positions of microsatellite markers (red) and genes (black) represented by the probe-sets Mb according to the Sscrofa9 genome sequence; Right: sex-averaged linkage maps of SSC 1 to 4 with positions of microsatellite markers and eQTL of corresponding probe-sets in cM; Both maps are linked based on the microsatellite marker positions (red and bold). Meat quality traits, with which the expression levels of probe-sets are correlated, are presented in brackets. Trait abbreviations are given at table 2.