The quality of meat products is strongly influenced by pH. This trait is influenced by environmental factors and is also under genetic control. Up to now only two major genes related to pig meat pH (RYR1 and PRKAG3) have been identified and QTL regions (QTLRs) influencing it are reported in at least 10 porcine chromosomes. With the aim to fine maps some of these regions and to locate genes responsible of the QTL effects, three relevant QTLRs (SSC1 60-80 cM, SSC2 55-66 cM, SSC3 42-60 cM) were chosen and SNPs were searched in silico in transcribed sequences. We analysed 1822 porcine UniGene clusters located in the three QTLRs and chosen comparing pig and homologous human chromosomes through the NCBI map viewer tool. The clusters with a minimum of four sequences were aligned with MegaBLAST for the in silico search of SNPs. We marked as putative SNP a mutation detected in at least two sequences to avoid inconsistent results. The presence of some in silico identified SNPs was confirmed by an HRM analysis testing a panel of Italian Large White pigs divergent for pig meat pH. On the whole we found more than 400 SNPs that we will genotype by the high-throughput Illumina GoldenGate system to perform an association study with the considered trait and to identify the most interesting positional candidate genes located in these regions.
Zambonelli P., Davoli R., De Paolis L.F., Buttazzoni L., Russo V. (2009). In silico SNP detection in transcribed sequences mapping in QTL regions for pork pH and localisation of the SNP on porcine genomic sequence. HINXTON HALL, CAMBRIDGE : Consortium and European Network for Pig Genomics.
In silico SNP detection in transcribed sequences mapping in QTL regions for pork pH and localisation of the SNP on porcine genomic sequence
ZAMBONELLI, PAOLO;DAVOLI, ROBERTA;DE PAOLIS, LUIGI FRANCESCO;RUSSO, VINCENZO
2009
Abstract
The quality of meat products is strongly influenced by pH. This trait is influenced by environmental factors and is also under genetic control. Up to now only two major genes related to pig meat pH (RYR1 and PRKAG3) have been identified and QTL regions (QTLRs) influencing it are reported in at least 10 porcine chromosomes. With the aim to fine maps some of these regions and to locate genes responsible of the QTL effects, three relevant QTLRs (SSC1 60-80 cM, SSC2 55-66 cM, SSC3 42-60 cM) were chosen and SNPs were searched in silico in transcribed sequences. We analysed 1822 porcine UniGene clusters located in the three QTLRs and chosen comparing pig and homologous human chromosomes through the NCBI map viewer tool. The clusters with a minimum of four sequences were aligned with MegaBLAST for the in silico search of SNPs. We marked as putative SNP a mutation detected in at least two sequences to avoid inconsistent results. The presence of some in silico identified SNPs was confirmed by an HRM analysis testing a panel of Italian Large White pigs divergent for pig meat pH. On the whole we found more than 400 SNPs that we will genotype by the high-throughput Illumina GoldenGate system to perform an association study with the considered trait and to identify the most interesting positional candidate genes located in these regions.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
