Abstract
Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content.
Highlights
For several years, selection performed in most of the pig breeding schemes increased the efficiency of lean tissue deposition at the expense of back fat (BF) and intramuscular fat (IMF) content (De Vries and Kanis, 1994)
QTL DETECTION The total number of SNPs contained in the PorcineSNP60 Genotyping Bead Chip and potentially located in SSC12 was around 1,200 SNPs, following Sscrofa10 annotation
Seven out of the 63 SNPs associated with UI reached a q-value lower than 0.10 (Table A4 in Appendix) and six out of them match the SNPs showing association with double bound index (DBI) (q-value < 0.05). They included again the ASGA0054041 SNP located in the Phosphatidylcholine transfer protein (PCTP) gene, which showed a significant effect on this index as well consistently with the effect observed on palmitic fatty acid
Summary
Selection performed in most of the pig breeding schemes increased the efficiency of lean tissue deposition at the expense of back fat (BF) and intramuscular fat (IMF) content (De Vries and Kanis, 1994). We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle.
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