The Local South American Chicken Populations Are a Melting-Pot of Genomic Diversity.

Juan Carlos Aguirre-Pabón,Marcelo Vallinoto,Galo Escudero-Sánchez,Michael R. Miller,Agusto Luzuriaga-Neira,Gustavo Villacís-Rivas,Lucía Pérez-Pardal,Makarena Rubilar-Quezada,Freddy Cueva-Castillo,Sean M. O’Rourke,Albano Beja-Pereira,Amarilis Ulloa-Núñez

doi:10.3389/fgene.2019.01172

Abstract

Chicken have a considerable impact in South American rural household economy as a source of animal protein (eggs and meat) and a major role in cultural traditions (e.g., cockfighting, religious ceremonies, folklore). A large number of phenotypes and its heterogeneity are due to the multitude of environments (from arid to tropical rain forest and high altitude) and agricultural systems (highly industrialized to subsistence agriculture). This heterogeneity also represents the successive introduction of domestic chicken into this continent, which some consider predating Columbus’ arrival to South America. In this study, we have used next-generation restriction site-associated DNA sequencing to scan for genome-wide variation across 145 South American chickens representing local populations from six countries of South America (Colombia, Brazil, Ecuador, Peru, Bolivia, and Chile). After quality control, the genotypes of 122,801 single nucleotide polymorphisms (SNPs) were used to assess the genomic diversity and interpopulation genetic relationship between those populations and their potential sources. The estimated population genetic diversity displayed that the gamefowl has the least diverse population (θπ = 0.86; θS = 0.70). This population is also the most divergent (FST = 0.11) among the South American populations. The allele-sharing analysis and the admixture analysis revealed that the current diversity displayed by these populations resulted from multiple admixture events with a strong influence of the modern commercial egg-layer chicken (ranging between 44% and 79%). It also revealed an unknown genetic component that is mostly present in the Easter Island population that is also present in local chicken populations from the South American Pacific fringe.

Highlights

The domestic chicken, Gallus gallus domesticus, is a major source of animal protein and owes its popularity to lowcost production and the inexistence of any cultural or religious prohibition to its consumption
Regarding the South American continental populations, the lowest number of private variants was observed in the Chilean continental populations, while the highest value was obtained in the Bolivian population
We used reduced representation library sequencing, in this case, RADseq, to interrogate a medium-high number of single nucleotide polymorphisms (SNPs) (122,801). The comparison of this set with those SNPs identified in the NCBI dbSNP database revealed that 91% of our SNPs match with others previously identified and 97% of them are located in intergenic or intronic regions, showing great potential to be used in genetic diversity studies

Summary

Introduction

The domestic chicken, Gallus gallus domesticus, is a major source of animal protein (eggs and meat) and owes its popularity to lowcost production and the inexistence of any cultural or religious prohibition to its consumption. It is widely accepted that the red junglefowl (Gallus gallus) from jungles in South and Southeast Asia is considered the most probable ancestor of the domestic chicken (Fumihito et al, 1994; Fumihito et al, 1996). Several recent genetic studies based on the mitochondrial DNA (mtDNA) variation have suggested the additional contributions of the red junglefowl from the Indian Subcontinent, South and East of China, Thailand, Myanmar, and Indonesia (e.g., see for more detail Liu et al, 2006; Miao et al, 2013)

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Conclusion