Genetic diversity and population structure of Yucatan black hairless pig using SNP50K chip
Keywords:
genetic diversityAbstract
In the present study, the Population structure and genetic diversity of 104 Yucatan black hairless pigs (YBH) and 8 Duroc breeds were by using an SNP50K chip characterized. The population structure was obtained, as well as the calculation of Principal Component Analysis (PCA), Minor Allele Frequency (MAF), observed heterozygosity (oH), consanguinity (F), Fixation index of individuals within subpopulations (Fis), the t (outcrossing rate or alogamia index) was made, also the association analysis to identify SNP with population differences. The genetic component of Duroc in YBH subpopulations is low, from 0.00363 to 0.03532, THUS, IT WAS OBSERVED (appreciating) a subpopulation with greater genetic diversity and lower values of F and Fis, as well as higher oH and t. SNPs were identified (p<1.213E-50 to p< 6.4E-20), associated with genes and biological processes. Genes EHF, DST, PDE8A, FOXA1 and VCL are related to epithelial cell differentiation, morphogenesis, and development of epithelium. Other 30 SNPs are to nutrient metabolism related, 23 SNPs to nutrient transport, 11 SNPs to immunity, 10 SNPs to muscle, skeletal and embryonic, and 7 SNPs to synapses and receptors. YBH is distant from Duroc with different population structure and genetic diversity with different genes that involve important biological processes.
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