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. 2022 Jul 19;12(14):1839.
doi: 10.3390/ani12141839.

Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis

Bing Pan  1 , Haoyuan Long  1 , Ying Yuan  1 , Haoyuan Zhang  1 , Yangyang Peng  1 , Dongke Zhou  1 , Chengli Liu  1 , Baiju Xiang  2 , Yongfu Huang  1 , Yongju Zhao  1 , Zhongquan Zhao  1 , Guangxin E  1
Affiliations

Identification of Body Size Determination Related Candidate Genes in Domestic Pig Using Genome-Wide Selection Signal Analysis

Bing Pan et al. Animals (Basel). .

Abstract

This study aimed to identify the genes related to the body size of pigs by conducting genome-wide selection analysis (GWSA). We performed a GWSA scan on 50 pigs belonging to four small-bodied pig populations (Diannan small-eared pig, Bama Xiang pig, Wuzhishan pig, and Jeju black pig from South Korea) and 124 large-bodied pigs. We used the genetic parameters of the pairwise fixation index (FST) and π ratio (case/control) to screen candidate genome regions and genes related to body size. The results revealed 47,339,509 high-quality SNPs obtained from 174 individuals, while 280 interacting candidate regions were obtained from the top 1% signal windows of both parameters, along with 187 genes (e.g., ADCK4, AMDHD2, ASPN, ASS1, and ATP6V0C). The results of the candidate gene (CG) annotation showed that a series of CGs (e.g., MSTN, LTBP4, PDPK1, PKMYT1, ASS1, and STAT6) was enriched into the gene ontology terms. Moreover, molecular pathways, such as the PI3K-Akt, HIF-1, and AMPK signaling pathways, were verified to be related to body development. Overall, we identified a series of key genes that may be closely related to the body size of pigs, further elucidating the heredity basis of body shape determination in pigs and providing a theoretical reference for molecular breeding.

Keywords: body size; domestic pigs; genome wide; skeletal muscles.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Wide-genome selective signal analysis of 174 pigs by SNP dataset. (a) The distribution of θπ ratio (−Log10[θπ ratio(θπcase/θπcontrol)]) on the autosomal chromosome calculated by 40k sliding window size with 20k step. (b) The distribution of FST on the autosomal chromosomes calculated by 40k sliding window size with 20k step.
Figure 2
Figure 2
Annotation and functional enrichment of candidate genes of pig body size determination. Note: (A) Circle graphic of gene ontology (GO) enrichment. (B) Network graphic pattern of top 25 significant enriched molecular signaling pathways (KEGG).
See this image and copyright information in PMC

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