Looking at the Genetic Structure of Mexican Chicken Population

Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems.

The aim of this study was to characterize the genetic variability of Mexican chicken’s population to reveal any underlying population structure carrying out a phylogenetic analysis, using individuals of indigenous unselected Mexican population.

A total of 213 chickens were sampling in different rural production units located in 25 states of Mexico. Genotypes were obtained using the Affymetrix Axiom® 600K Chicken Genotyping Array, containing 580,954 SNPs, distributed across the genome with an average spacing of 1.7 Kb.

Identity by Descent (IBD) estimation and the Principal Components Analysis (PCA) were performed using SVS Golden Helix 8.4 software. The ADMIXTURE v. 1.3.0 software was used to infer the most probable number of ancestral populations based on the SNP genotype data. Neighbor-Joining (NJ) tree, constructed based on the allele sharing distance (DAs) as the genetic distance between not-related individuals, was created. Run of homozygosity (ROH) analysis was performed for each individual, using the SVS software.

ADMIXTURE analyses identified three ancestors and the proportion of each of them has been determined in each individuals. The results of the NJ analysis resulted consistent with those obtained by the PCA. A total of 5,331 ROH were identified in this study. The average ROH length was longer compared to those estimated in another study in Italian chicken native breeds. Mexican chicken population showed the lowest average ROH length value (~1.9 Mb).