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Front. Genet. | doi: 10.3389/fgene.2019.01172

South American chicken populations are a melting-pot of genomic diversity

 Agusto Luzuriaga-neira1,  Lucía Perez-Pardal1, Sean M. O’Rourke2, Gustavo Villacís-Rivas3, Freddy Cueva-Castillo3, Gallo Escudero-Sánchez4, Juan Carlos Aguirre-Pabón1, A Ulloa-Nuñez5, M Rubilar-Quezada5*,  Marcelo Vallinoto6, Michael R. Miller7* and  Albano Beja-Pereira1, 8*
  • 1Center for Research on Biodiversity and Genetic Resources, Abel Salazar Institute of Biomedical Sciences, University of Porto, Portugal
  • 2Center for Watershed Sciences, University of California, Davis, United States
  • 3Biotechnology Center, National University of Loja, Ecuador
  • 4National University of Loja, Ecuador
  • 5Faculty of Veterinary Sciences, University of Concepción, Chile
  • 6Institute of Coastal Studies, Federal University of Pará, Brazil
  • 7Department of Animal Science, University of California, Davis, United States
  • 8Departamento de Geociências, Ambiente e Ordenamento do Território (DGAOT), Faculty of Sciences, University of Porto, Portugal

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 manifestations (e.g. cockfighting, religious ceremonies, folklore). A large number of phenotypes and its heterogeneity are representative to the rusticity of the 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 subcontinent, which some consider predating Columbus arrival to South America. In this study, we have used next-generation sequencing of restriction site associated DNA to scan for genome-wide variation across 145 South American chicken 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 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 to 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.

Keywords: Gallus gallus, RADseq, Population Genetics, Local resources, snps

Received: 30 Jul 2019; Accepted: 23 Oct 2019.

Copyright: © 2019 Luzuriaga-neira, Perez-Pardal, O’Rourke, Villacís-Rivas, Cueva-Castillo, Escudero-Sánchez, Aguirre-Pabón, Ulloa-Nuñez, Rubilar-Quezada, Vallinoto, Miller and Beja-Pereira. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. M Rubilar-Quezada, Faculty of Veterinary Sciences, University of Concepción, Chillán, Chile,
Dr. Michael R. Miller, Department of Animal Science, University of California, Davis, Davis, California, United States,
Dr. Albano Beja-Pereira, Faculty of Sciences, University of Porto, Departamento de Geociências, Ambiente e Ordenamento do Território (DGAOT), Porto, 4169-007, Porto, Portugal,