Genomewide study and validation of markers associated with production traits in German Landrace boars1

Abstract

We present results from a genomewide association study (GWAS) and a single-marker association study. The GWAS was performed with the Illumina PorcineSNP60 BeadChip from which 5 markers were selected for a validation analysis. Genetic effects were estimated for feed intake, weight gain, and traits of fat and muscle tissue in German Landrace boars kept on performance test stations. The GWAS was performed in a population of 288 boars and the validation study for another 432 boars. No statistically significant effect was found in the GWAS after adjusting for multiple testing. Effects of 2 markers, which were significant genomewide before correction for multiple testing (P < 0.00005), could be confirmed in the validation study. The major allele of marker ALGA0056781 on SSC1 was positively associated with both higher weight gain and fat deposition. The effect on live-weight gain was 2.25 g/d in the GWAS (P=0.0003) and 3.73 g/d in the validation study (P=0.01) and for back fat thickness was 0.15 mm in the GWAS (P < 0.0001) and 0.20 mm in the validation study (P=0.02). The marker had similar effects on test-day weight gain (GWAS: 3.85 g/d, P=0.001; validation study: 6.80 g/d, P=0.003) and back fat area (GWAS: 0.27 ㎠ , P < 0.0001; validation study: 0.35 ㎠ , P=0.03). Marker ASGA0056782 on SSC13 was associated with live-weight gain. The major allele had negative effects in both studies (GWAS: -4.88 g/d, P < 0.0001; validation study: -3.75 g/d, P=0.02). The effects of these 2 markers would have been excluded based on the GWAS alone but were shown to be significantly trait associated in the validation study indicating a false-negative result. The G protein-coupled receptor 126 (GPR126) gene approximately 200 kb downstream of marker ALGA0001781 was shown to be associated with human height and therefore might explain the association with weight gain in pigs. Several traits were affected in an economically desired direction by the minor allele of the markers, pointing to the possibility of improvement through further selection.