Mapping phenotypic traits in swine

The Illinois Meat Quality Pedigree (IMQP), a three-generation Berkshire x Duroc resource population, was created to discover quantitative trait loci (QTL) influencing carcass composition, growth, and meat quality traits in pigs. Each animal in the IMQP population was genotyped for 137 microsatellite markers and 43,486 single-nucleotide polymorphisms (SNP). Two different analyses were performed to detect QTL in this population. For the first analysis, a linkage map consisting of 137 microsatellite markers was used to perform a regression interval analysis with QTLexpress, a publicly available web-based software. In the second analysis, the SOLAR software package was used to perform a variance component analysis with a physical map created from the 43,486 SNP markers. Ninety-five QTL were detected using the QTLexpress software while 787 QTL were detected using the SOLAR software. Of these QTL, 40 of the QTL detected by QTLexpress were located in the same position as 119 of the QTL detected by SOLAR. One of the QTL identified by the regression interval analysis was highly significant and associated with a relatively large effect on loin eye area. The QTL is located between microsatellite markers SW1129 and SW1647 on chromosome 6 encompassing a span of 73.2 million base pairs (Mb) with a 95% confidence interval spanning 98 Mb. To reduce the size of this interval and identify positional candidate genes, 1,600 SNP markers from the Illumina?? PorcineSNP60 Genotyping BeadChip that were located within the 95% confidence interval were analyzed using available analysis software programs. Software included QTLexpress, Qxpak, R/qtl, SOLAR, PLINK and Bayes-C. Results from each analysis were consolidated and a consensus region was identified between 85.67 and 85.68 Mb. To examine the power of high-density SNP genotyping platforms for the mapping of specific phenotypes, a unique coat color phenotype observed during the development of the IMQP was selected for analysis. Individuals of the F2 generation displayed a diverse set of coat color phenotypes including several (n=9) solid white individuals. In pigs, a dominant mutation in the KIT gene has been shown to be responsible for white coat color, however neither of the founder breeds are known to have dominant white mutations. Based on matings between white F2 sows with Duroc, Berkshire and white F2 boars, it was concluded that the white coat color observed in this population is inherited as a recessive phenotype. A whole genome association study was performed to identify regions of the genome controlling recessive white coat color. Regions with significant associations were identified on chromosomes 1, 2, and 6. The locus on chromosome 6 contained melanocortin receptor 1 (MC1R), a gene known to control pigmentation in mammals. Each animal in the population was genotyped for the MC1R recessive e/MC1R*4 allele (A240T mutation), and all white F2 animals genotyped as homozygous 240T, or e/e. Tyrosine hydroxylase was identified as a candidate gene for the region on chromosome 2. Genomic sequence for tyrosine hydroxylase was generated and the population was genotyped for an A159T mutation. All solid white individuals except two genotyped as homozygous 159T for this mutation. Two significant regions associated with white coat color were identified on chromosome 1 and several positional candidate genes were identified but remain to be investigated