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

doi:10.15302/J-FASE-2014005

Frontiers of Agricultural Science and Engineering

2014, Vol. 1

Issue (2): 91-95 https://doi.org/10.15302/J-FASE-2014005

本期目录

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

Dandan ZHU¹,Xiaolei LIU¹,Rothschild MAX²,Zhiwu ZHANG³,Shuhong ZHAO¹,Bin FAN^1,^*(

)

1. Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
2. Department of Animal Science, Iowa State University, Ames, IA 50011, USA
3. Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA

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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.

Key words： backfat thickness SNP chip genome-wide association study compressed mixed linear model pig

收稿日期: 2014-03-15 出版日期: 2014-10-10

Corresponding Author(s): Bin FAN

引用本文:

. [J]. Frontiers of Agricultural Science and Engineering, 2014, 1(2): 91-95.
Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN. Genome-wide association study of the backfat thickness trait in two pig populations. Front. Agr. Sci. Eng. , 2014, 1(2): 91-95.

链接本文:

https://academic.hep.com.cn/fase/CN/10.15302/J-FASE-2014005
https://academic.hep.com.cn/fase/CN/Y2014/V1/I2/91

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