Genome-wide association study of the backfat thickness trait in two pig populations

Abstract

Backfat thickness is a good predictor of carcass lean content, an economically important trait, and a main breeding target in pig improvement. In this study, the candidate genes and genomic regions associated with the tenth rib backfat thickness trait were identified in two independent pig populations, using a genome-wide association study of porcine 60K SNP genotype data applying the compressed mixed linear model (CMLM) statistical method. For each population, 30 most significant single-nucleotide polymorphisms (SNPs) were selected and SNP annotation implemented using Sus scrofa Build 10.2. In the first population, 25 significant SNPs were distributed on seven chromosomes, and SNPs on SSC1 and SSC7 showed great significance for fat deposition. The most significant SNP (ALGA0006623) was located on SSC1, upstream of the MC4R gene. In the second population, 27 significant SNPs were recognized by annotation, and 12 SNPs on SSC12 were related to fat deposition. Two haplotype blocks, M1GA0016251-MARC0075799 and ALGA0065251-MARC0014203-M1GA0016298-ALGA0065308, were detected in significant regions where the PIPNC1 and GH1 genes were identified as contributing to fat metabolism. The results indicated that genetic mechanism regulating backfat thickness is complex, and that genome-wide associations can be affected by populations with different genetic backgrounds.

Keywords

backfat thickness / SNP chip / genome-wide association study / compressed mixed linear model / pig

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Acknowledgements

This study was supported by the National Science Foundation of China (31172192), New Century Excellent Talents (NCET-11-0646) and Fundamental Research Funds for the Central Universities (2011JQ009, 2012PY009).

Compliance with ethics guidelines Dandan Zhu, Xiaolei Liu, Rothschild Max, Zhiwu Zhang, Shuhong Zhao and Bin Fan declare that they have no conflict of interest or financial conflicts to disclose.ƒAll applicable institutional and national guidelines for the care and use of animals were followed.

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Higher Education Press and Springer-Verlag Berlin Heidelberg