Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers

Abstract

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 México's chicken population to reveal any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of México. Genotypes were obtained using the Affymetrix Axiom® 600 K Chicken Genotyping Array. The Identity by Descent (IBD) and the principal components analysis (PCA) were performed by SVS software on pruned single nucleotide polymorphisms (SNPs).ADMIXTURE analyses identified 3 ancestors and the proportion of the genetic contribution of each of them has been determined in each individual. The results of the Neighbor-Joining (NJ) analysis resulted consistent with those obtained by the PCA. All methods utilized in this study did not allow a classification of Mexican chicken in distinct clusters or groups. A total of 3,059 run of homozygosity (ROH) were identified and, being mainly short in length (<4 Mb), these regions are indicative of a low inbreeding level in the population. Finally, findings from the ROH analysis indicated the presence of natural selective pressure in the population of Mexican chicken.The study indicates that the Mexican chicken clearly appear to be a unique creole chicken population that was not subjected to a specific artificial selection. Results provide a genetic knowledge that can be used as a basis for the genetic management of a unique and very large creole population, especially in the view of using it in production of hybrids to increase the productivity and economic revenue of family farming agriculture, which is widely present in México.

Sexual Dimorphism and Breed Characterization of Creole Hens through Biometric Canonical Discriminant Analysis across Ecuadorian Agroecological Areas

“…The high coefficient of variation observed in the results is similar to that reported in different populations of chickens in Mexico [64], and also in indigenous chickens in Nigeria [61], which demonstrates the variability of the morphometry in the birds studied, which may be due to genetic divergence processes followed by the populations, such as migration [65], which resulted in the morphological modification of the populations to adapt to the characteristics of the different environments and the orography to which the birds were introduced [63, [66][67][68].…”

Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens

“…Within-breed diversity and the population structure analyses in livestock species are fundamental for understanding environmental adaptation, implementing conservation programs and designing selection plans [ 10 , 17 , 18 ]. While a huge effort was expended to study cosmopolitan breeds in the past, a growing attention had been shifted to the local breeds which are important genetic resources for their potential to solving problems in agriculture related to environmental changes [ 19 , 20 ]. Local chickens in Tibet have evolved over centuries under extreme natural conditions.…”

Investigating inbreeding in the turkey (Meleagris gallopavo) genome

“…Long ROH are a consequence of more recent inbreeding and short ROH are indicative of more distant ancestral inbreeding where the short ROH may be a result of recombination events breaking long chromosomes into segments ( Browning and Browning, 2012 ; Mastrangelo et al, 2016 ). Other advantages are the ability to differentiate local versus genome-wide inbreeding, and the ability to reveal selection signatures that potentially harbor genes associated with economically important traits targeted for genetic improvement ( Strillacci et al, 2018 ; Almeida et al, 2019 ).…”