Next Article in Journal
Association Study between the Polymorphisms of Matrix Metalloproteinase (MMP) Genes and Idiopathic Recurrent Pregnancy Loss
Previous Article in Journal
Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome
Article

Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs

1
Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding/National Engineering Research Centre for Breeding Swine Industry/College of Animal Science, South China Agricultural University, Guangzhou 510642, China
2
Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(5), 346; https://doi.org/10.3390/genes10050346
Received: 28 February 2019 / Revised: 28 April 2019 / Accepted: 2 May 2019 / Published: 7 May 2019
(This article belongs to the Section Animal Genetics and Genomics)
South China indigenous pigs are famous for their superior meat quality and crude feed tolerance. Saba and Baoshan pigs without saddleback were located in the high-altitude area of Yunnan Province, while Tunchang and Ding’an pigs with saddleback were located in the low-altitude area of Hainan Province. Although these pigs are different in appearance, the underlying genetic differences have not been investigated. In this study, based on the single-nucleotide polymorphism (SNP) genotypes of 124 samples, both the cross-population extended haplotype homozygosity (XP-EHH) and the fixation index (FST) statistic were used to identify potential signatures of selection in these pig breeds. We found nine potential signatures of selection detected simultaneously by two methods, annotated 22 genes in Hainan pigs, when Baoshan pigs were used as the reference group. In addition, eleven potential signatures of selection detected simultaneously by two methods, annotated 24 genes in Hainan pigs compared with Saba pigs. These candidate genes were most enriched in GO: 0048015~phosphatidylinositol-mediated signaling and ssc00604: Glycosphingolipid biosynthesis—ganglio series. These selection signatures were likely to overlap with quantitative trait loci associated with meat quality traits. Furthermore, one potential selection signature, which was associated with different coat color, was detected in Hainan pigs. These results contribute to a better understanding of the underlying genetic architecture of South China indigenous pigs. View Full-Text
Keywords: signatures of selection; South China indigenous pigs; SNP; XP-EHH; FST signatures of selection; South China indigenous pigs; SNP; XP-EHH; FST
Show Figures

Figure 1

MDPI and ACS Style

Diao, S.; Huang, S.; Chen, Z.; Teng, J.; Ma, Y.; Yuan, X.; Chen, Z.; Zhang, H.; Li, J.; Zhang, Z. Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs. Genes 2019, 10, 346. https://doi.org/10.3390/genes10050346

AMA Style

Diao S, Huang S, Chen Z, Teng J, Ma Y, Yuan X, Chen Z, Zhang H, Li J, Zhang Z. Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs. Genes. 2019; 10(5):346. https://doi.org/10.3390/genes10050346

Chicago/Turabian Style

Diao, Shuqi, Shuwen Huang, Zitao Chen, Jinyan Teng, Yunlong Ma, Xiaolong Yuan, Zanmou Chen, Hao Zhang, Jiaqi Li, and Zhe Zhang. 2019. "Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs" Genes 10, no. 5: 346. https://doi.org/10.3390/genes10050346

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop