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

doi:10.15302/J-FASE-2014005

Front. Agr. Sci. Eng.

2014, Vol. 1

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

LETTER

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.

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

Corresponding Author(s): Bin FAN

Online First Date: 22 September 2014 Issue Date: 10 October 2014

Cite this article:

Dandan ZHU,Xiaolei LIU,Rothschild MAX, et al. Genome-wide association study of the backfat thickness trait in two pig populations[J]. Front. Agr. Sci. Eng. , 2014, 1(2): 91-95.

URL:

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

Fig.1 Cluster analysis plotted by first versus second principal components (PC) for the two pig populations

Fig.2 Manhattan plots of genome-wide association studies with tenth rib backfat thickness in two pig populations. (a) Pots for population 1; (b)?plots for population 2. SNPs on each chromosome are labeled with a different color on the X-axis as indicated, and the Y-axis is the negative log base 10 of the P-values. SNPs with tighter associations with the trait will have a larger Y-coordinate value.

Fig.3 Haplotypes on a 1.78 Mb region on SSC12 containing all the significant SNPs associated with tenth rib backfat thickness for pigs in Population 2 obtained with the HAPLOVIEW program. The solid lines indicate the two blocks identified.

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