Laura Grapes

Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci.

Recently, a method for fine mapping quantitative trait loci (QTL) using linkage disequilibrium was proposed to map QTL by modeling covariance between individuals, due to identical-by-descent (IBD) QTL alleles, on the basis of the similarity of their marker haplotypes under an assumed population history. In the work presented here, the advantage of using marker haplotype information for fine mapping QTL was studied by comparing the IBD-based method with 10 markers to regression on a single marker, a pair of markers, or a two-locus haplotype under alternative population histories. When 10 markers were genotyped, the IBD-based method estimated the position of the QTL more accurately than did single-marker regression in all populations. When 20 markers were genotyped for regression, as single-marker methods do not require knowledge of haplotypes, the mapping accuracy of regression in all populations was similar to or greater than that of the IBD-based method using 10 markers. Thus for populations similar to those simulated here, the IBD-based method is comparable to single-marker regression analysis for fine mapping QTL.

Investigation of a QTL region for loin eye area and fatness on pig Chromosome 1

Previously, quantitative trait loci (QTL) for tenth-rib backfat (TENTHRIB) and loin eye area (LEA) were identified on pig Chromosome 1 (SSC 1) near microsatellite S0008 from a three-generation Berkshire × Yorkshire cross (BY). This work attempted to refine these QTL positions and identify genes associated with these QTL. Genotypes of BY (n = 555) were determined by PCR-RFLP or PCR tests for 13 polymorphisms identified in BY F0 individuals for candidate genes, BAC end sequences, and genomic clones. Using least-squares regression interval mapping, the LEA QTL was estimated at S0008; the TENTHRIB QTL position was shifted approximately 1 cM downstream from S0008. Of the genes/sequences mapped in the QTL region, CL349415 was significantly associated with TENTHRIB (p = 0.02) and solute carrier family 2, member 12 (SLC2A12) was significantly associated with LEA (p = 0.02). These results suggest that the gene(s) responsible for the LEA and TENTHRIB QTL effects are tightly linked to S0008 or that the high informativeness of S0008 relative to surrounding markers is influencing the QTL position estimates. In addition, janus kinase 2 (JAK2) was mapped to a suggestive LEA QTL region and showed association with LEA (p = 0.009), fatness, color, and pH traits in BY.

The pig platelet-activating factor receptor gene is expressed at the mRNA level in different tissues and is mapped to chromosome 6

After the pig platelet-activating factor receptor (PAFr) gene was cloned and sequenced, the chromosomal location of this gene was studied using a pig/rodent somatic cell hybrid panel containing 27 cell lines. The results indicated that the pig PAFr gene is located on SSC6q22-23. Platelet-activating factor (PAF, 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) is thought to be very important in the animal reproductive processes. Its function is mediated through a membrane-bound receptor. Pig PAFr mRNA distribution in different tissues was tested using reverse transcription and PCR (RT-PCR) reactions. All tissues examined expressed PAFr. Using a pig PAFr gene DNA competitor, PAFr expression was quantificated. The pig PAFr mRNA expression level was estimated to be from 1 x 10(2) to 1.2 x 10(4) copies of complementary DNA (cDNA) per 50 ng of total RNA. The highest level was found in lung, and the lowest in the skeletal muscle. These results demonstrated that PAFr was differentially expressed in pig tissues.