Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data
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 backfat and intramuscular fat. In the presen...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2012-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00101/full |
| _version_ | 1818059817224241152 |
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| author | María eMuñoz Estefânia eAlves Jordi eCorominas Josep María Folch Joaquim eCasellas Joaquim eCasellas Jose Luis Noguera Luis eSilió Ana Isabel Fernández |
| author_facet | María eMuñoz Estefânia eAlves Jordi eCorominas Josep María Folch Joaquim eCasellas Joaquim eCasellas Jose Luis Noguera Luis eSilió Ana Isabel Fernández |
| author_sort | María eMuñoz |
| collection | DOAJ |
| description | 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 backfat and intramuscular fat. 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 intramuscular fat 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 backfat, 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. |
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| id | doaj.art-083fb8c7b16c4cfeba86f88ef9582afc |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-10T13:22:33Z |
| publishDate | 2012-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-083fb8c7b16c4cfeba86f88ef9582afc2022-12-22T01:47:16ZengFrontiers Media S.A.Frontiers in Genetics1664-80212012-01-01210.3389/fgene.2011.0010115975Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP dataMaría eMuñoz0Estefânia eAlves1Jordi eCorominas2Josep María Folch3Joaquim eCasellas4Joaquim eCasellas5Jose Luis Noguera6Luis eSilió7Ana Isabel Fernández8INIAINIAUniversidad Autónoma de BarcelonaUniversidad Autónoma de BarcelonaUniversidad Autónoma de BarcelonaIRTAIRTAINIAINIAFatty 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 backfat and intramuscular fat. 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 intramuscular fat 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 backfat, 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.http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00101/fullfatty acid compositionhigh-density SNP chipSSC12 |
| spellingShingle | María eMuñoz Estefânia eAlves Jordi eCorominas Josep María Folch Joaquim eCasellas Joaquim eCasellas Jose Luis Noguera Luis eSilió Ana Isabel Fernández Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data Frontiers in Genetics fatty acid composition high-density SNP chip SSC12 |
| title | Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data |
| title_full | Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data |
| title_fullStr | Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data |
| title_full_unstemmed | Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data |
| title_short | Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high density SNP data |
| title_sort | survey of ssc12 regions affecting fatty acid composition of intramuscular fat using high density snp data |
| topic | fatty acid composition high-density SNP chip SSC12 |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2011.00101/full |
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