Fine Mapping Of The Major QTL For Glycolytic Potential On Porcine Chromosome3

Glycolytic potential (GP) reflects the muscle’s capacity for glycogen and glucose glycolysis at postmortem in pigs. GP can be calculated by the equation:GP (μmol/g)=2×(glycogen+glucose-6-phosphate+glucose)+lactate. GP strongly influences the ultimate pH which, in turn, affects other quality traits such as meat color and dry-cured ham production. Thus, it is regarded as an important indicator of pork quality. In a previous study, a whole genome scan for quantitative trait loci (QTL) for GP traits was performed with194microsatellites covering19porcine chromosomes in a large-scale White Duroc×Erhualian resource population. The most significant QTL for GP was located between markers SW2021and SE47329on pig chromosome3, with a confidence interval of13cM. This QTL explained6.36%of the phenotypic variance in the F2population.In this study, we attempted to refine the location of the QTL for GP on SSC3via the increase in marker density, population size and integration of statistical tools. First, QTL for GP was remapped by a genome-wide association study (GWAS) using the genotype data of porcine60K chips. The results of GWAS demonstrate that the strongest association with GP and one of its components,the residual glycogen content, as at ALGA124306(P=4.46×10-11, at15.35Mb on physical map) within the initial interval of the SSC3QTL. In contrast, no significant associations were observed for other components of GP (including glucose6-phosphate and lactate determined on longissimus muscles taken at postmortem30min) at this region. These findings may suggest that the QTL plays a predominant role in glycogen synthesis or breakdown rather than glycolysis. The results of GWAS also indicated that the most significant SNP explained19.56%of the phenotypic variance in the F2population.Linkage disequilibrium (LD) analysis with an arbitrary threshold of R2>0.8showed that ALGA124306lies in the haplotype (or LD) block H3GA0008906-SIRI0001253(13.87Mb-16.27Mb), with a size of2.4Mb. As the causal mutation(s) underlying the GP QTL must be in strong LD with ALGA124306, the QTL is very likely to locate in the above-mentioned haplotype block.The QTL genotypes of6F1boars from the resource population were deduced by the marker-assisted segregation analysis, of which three are heterozygotes (Qq) and the other three are homozygotes (qq). Based on the inheritance of F1haplotypes from F0animals, we inferred that2White Duroc boars have the Qq genotype and all Erhualian sows carry the qq genotype. The "Q" chromosomes of White Duroc share an IBD (identical-by-decent) haplotype spanning the ALGA0119970-ALGA0116808interval (14.3Mb-16.8Mb). However, two IBS (identical-by-state) haplotypes shared by "Q" and "q" chromosomes were identified at the two ends of the ALGA0119970-ALGA0116808region, after22additional SNPs within these haplotypes were genotyped for the F0boars. Excluing the Q/q IBS regions, the QTL interval was narrowed to the Q-specific IBD region of1.06Mb between markers IBD2-2and IBD2-5.Finally, the GWAS study in a Sutai half-sib population also evidence the SSC3harbors QTL affecting residual glycogen content, with the strongest statistical association observed at ALGA0123314(P=8.8×10-44). This locus accounted for53.6%of phenotypic variance in this population. Then, we identified that the LD block containing ALGA0123314was flanked by markers ASGA0094824and H3GA0008937. This block spans about860kb.From this study, the confidence interval of the major QTL for GP on SSC3interval was significantly reduced from13Mb to less than900kb, which will contribute to the identification of causal gene underlying the QTL in the future.