Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

SIMPLE SUMMARY: In Ecuador, the production of Ecuadorian Creole chicken is of crucial importance in the economy and for the nutrition of families. These chickens represent a focal point in scientific research for three main reasons: (1) they are an unknown genetic resource derived from 500 years of environmental and human selection and represent an important reservoir of genetic variability and adaptability; (2) Ecuadorian Creole chicken production is normally familiar, in a marginal dimension, and it is an important source of economic input for medium–low income communities; and (3) being a local genetic resource, it is available to local communities without intermediary international enterprises and represents the starting point for food sovereignty. We aimed to measure the level of genetic diversity and its phylogenetic position compared with other outgroup breeds using information from microsatellite and mitochondrial markers. Our results showed that these chicken populations represent a great reservoir of genetic variability; however, the genetic fragmentation owing to the high geographical diversity of the country could compromise the conservation status and, therefore, the establishment of an official breeding program is needed for the conservation and valuation of these avian populations, with this genetic characterization being a first step. ABSTRACT: Latin American Creole chickens are generally not characterized; this is the case in Ecuador, where the lack of scientific information is contributing to their extinction. Here, we developed a characterization of the genetic resources of Ecuadorian chickens located in three continental agroecosystems (Pacific coastal, Andean, and Amazonian). Blood samples of 234 unrelated animals were collected in six provinces across Ecuador: Bolívar, Chimborazo, Cotopaxi, Guayas, Morona Santiago, and Tungurahua, in order to perform a genetic characterization and population structure assessment using the AVIANDIV project microsatellites panel (30 loci) and D-loop sequences of mitochondrial DNA and comparing with reference data from other breeds or genetic lines. The results indicate that Ecuadorian Creole chickens are the result of the admixture of different genetic groups that occurred during the last five centuries. While the influence of South Spanish breeds is demonstrated in the colonial age, genetic relationships with other breeds (Leghorn, Spanish fighter cock) cannot be discarded. The geographical configuration of the country and extreme climate variability have influenced the genetic isolation of groups constituting a homogeneous genetic status into the whole population. This is not only a source of genetic variation, but also a critical point because genetic drift produces a loss of genetic variants.