GENETIC STRUCTURE AND COMPOSITION OF THE MEXICAN HAIRLESS PIG

Abstract

The objective of this study was to analyze the genetic variability and structure of the Mexican hairless pig (CPM) within a conservation and sustainable development framework. The genotypes of 35,584 SNPs from 107 CPM individuals were analyzed. Observed (Ho) and expected (He) heterozygosity, polymorphic information content (PIC), potential Hardy-Weinberg disequilibrium, effective number of breeders (Ne), and the FIS statistic were estimated; additionally, the inbreeding coefficient (F) was determined for each individual. A population structure analysis was performed to identify the number of lines or genotypes (k) comprising the CPM, along with an identity-by-state analysis. The number of SNPs per chromosome ranged from 919 to 3,134, with an average of 1,872. He, Ho and PIC levels ranged from 0.358 to 0.384, 0.293 to 0.388, and 0.286 to 0.303, respectively. For F, 65.4% of individuals exhibited values below 1%, 15.9% ranged from 1 to 10%, 8,4% from 10 and 20%, and 10.2% exceeded 20%. The optimal k was two, with average genetic contributions of 70.5 and 29.5%. The He > Ho ratio was consistent across all chromosomes, indicating a deficit of heterozygtes. The FIS values across chromosomes ranged from -0.008 to 0.216, with an average of 0.027. The Ne was estimated at 60; as an indicator of the inbreeding rate, an increase of 0.833% per generation was observed. The genetic variability in CPM reflects its population history and provides key information for the design of conservation sustainable development strategies.