A Whole Genome Scanning for QTL Affecting Leg Weakness and Its Related Traits in a White Duroc × Erhualian Resource Population

Abstract

A linkage map comprising 194 microsatellite markers across the pig genome was constructed with a large scale White Duroc × Erhualian resource population. The marker order on this linkage map was consistent with the USDA-MARC reference map except for 2 markers on pig chromosome (SSC) 3, 2 markers on SSC13 and 2 markers on the X chromosome. The length of the sex-average map (2,344.7 cM) was nearly the same as those of the USDA-MARC and the NIAI maps. A highly significant heterogeneity in recombination rates between sexes was observed. The female autosomes had higher average recombination rates than the male autosomes except for SSC1 and SSC13. However, recombination rates in the pseudoautosomal region were greater in males than in females. These observations are consistent with the previous reports. The recombination events on each paternal and maternal chromosome of F2 animals were also inferred by SimWalk2. Recombination rates were not significantly affected by the age (in the unit of day) and the parity of F1 animals. However, the recombination rates on the paternal chromosomes were affected by the mating season of F1 animals. This could represent an effect of environmental temperature on spermatogenesis. To detect quantitative trait loci (QTL) for leg weakness in pigs, a total of 1,484 F2 pigs were recorded for their leg scores (at 76 d and 213 d) and gait scores (at 153 d and 223 d) in the White Duroc × Erhualian resource population. Moreover, the lengths of the limb bones, the areal mineral density of the femoral bone (aBMD) and the length and the weight of the biceps brachii muscle were recorded after these F2 animals were harvested at 240 d. A whole genome scan was performed with 194 microsatellite markers in the resource population to identify QTL for these traits. A total of 79 QTL were detected, including 35 at the 1% genome-wide significant level and 9 at the 5% genome-wide significant level. Seventy-two of the 79 QTL showed significant additive effects and 20 of the 79 QTL had significant dominance effects. At least two QTL were detected for each trait except for the leg score at 76 d, for which no QTL was identified. Some of QTL for leg scores, gait scores and lime bone lengths confirmed previous findings. Eighteen QTL for the weight and the length of the biceps brachii muscle and two QTL for the aBMD were detected in present study. To our knowledge, this was the first report about QTL for the three traits in pigs. Two chromosome regions each on SSC4 and SSC7 showed significant and multiple associations with leg weakness and the growth of the biceps brachii muscle and the lime bones, which are worthwhile for further investigation. Combined analysis of data from two or more resource populations can improve the power and accuracy of QTL mapping and allow some cross-validation of results. In this study, we performed a genome-wide scan using combined data from two F2 populations derived from a cross between Large White and Chinese Meishan pigs. A total of 739 pigs were included in the analysis. In total 187 markers were genotyped in the two populations, including 115 markers genotyped in both populations, and these markers covered 2,282 cM of the pig genome with an average of 13.58 cM between adjacent markers. Seven traits (teat number, birth weight, weaning weight, test-end weight, fat depth at shoulder, fat depth at mid back and fat depth at loin) were analyzed for both individual populations and the combined population. There were 9 (2, 10), 1 (4, 4) and 14 (5, 18) QTL that achieved 1% genome-wide, 5% genome-wide and suggestive significance levels, respectively, in population 1 (population 2, combined population). Additive effects of QTL detected in the two populations at all significance levels were largely consistent suggesting that the QTL represent real genetic effects, but this was not the case for dominance or imprinting effects. There were also a number of significant interactions between detected QTL effects and population.