Relationship of runs of homozygosity with adaptive and production traits in a paternal broiler line
J.A.P. Marchesi,
M.E. Buzanskas,
M.E. Cantão,
A.M.G. Ibelli,
J.O. Peixoto,
L.B. Joaquim,
G.C.M. Moreira,
T.F. Godoy,
A.P. Sbardella,
E.A.P. Figueiredo,
L.L Coutinho,
D.P. Munari,
M.C. Ledur
Affiliations
J.A.P. Marchesi
Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N – Vila Industrial, Jaboticabal, São Paulo 14884-900, Brazil
M.E. Buzanskas
Departamento de Zootecnia, Centro de Ciências Agrárias – Campus II, Universidade Federal da Paraíba (UFPB), Rodovia BR 079 – Km 12, Areia, Paraíba 58397-000, Brazil
M.E. Cantão
Embrapa Suínos e Aves, Rodovia BR 153, Km 110, Distrito de Tamanduá, Caixa Postal 321, Concórdia, Santa Catarina 89715-899, Brazil
A.M.G. Ibelli
Embrapa Suínos e Aves, Rodovia BR 153, Km 110, Distrito de Tamanduá, Caixa Postal 321, Concórdia, Santa Catarina 89715-899, Brazil
J.O. Peixoto
Embrapa Suínos e Aves, Rodovia BR 153, Km 110, Distrito de Tamanduá, Caixa Postal 321, Concórdia, Santa Catarina 89715-899, Brazil
L.B. Joaquim
Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N – Vila Industrial, Jaboticabal, São Paulo 14884-900, Brazil
G.C.M. Moreira
Departamento de Zootecnia, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, São Paulo 13419-900, Brazil
T.F. Godoy
Departamento de Zootecnia, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, São Paulo 13419-900, Brazil
A.P. Sbardella
Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N – Vila Industrial, Jaboticabal, São Paulo 14884-900, Brazil
E.A.P. Figueiredo
Embrapa Suínos e Aves, Rodovia BR 153, Km 110, Distrito de Tamanduá, Caixa Postal 321, Concórdia, Santa Catarina 89715-899, Brazil
L.L Coutinho
Departamento de Zootecnia, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, São Paulo 13419-900, Brazil
D.P. Munari
Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N – Vila Industrial, Jaboticabal, São Paulo 14884-900, Brazil
M.C. Ledur
Embrapa Suínos e Aves, Rodovia BR 153, Km 110, Distrito de Tamanduá, Caixa Postal 321, Concórdia, Santa Catarina 89715-899, Brazil
Genomic regions under high selective pressure present specific runs of homozygosity (ROH), which provide valuable information on the genetic mechanisms underlying the adaptation to environment imposed challenges. In broiler chickens, the adaptation to conventional production systems in tropical environments lead the animals with favorable genotypes to be naturally selected, increasing the frequency of these alleles in the next generations. In this study, ~1400 chickens from a paternal broiler line were genotyped with the 600 K Affymetrix® Axiom® high-density (HD) genotyping array for estimation of linkage disequilibrium (LD), effective population size (Ne), inbreeding and ROH. The average LD between adjacent single nucleotide polymorphisms (SNPs) in all autosomes was 0.37, and the LD decay was higher in microchromosomes followed by intermediate and macrochromosomes. The Ne of the ancestral population was high and declined over time maintaining a sufficient number of animals to keep the inbreeding coefficient of this population at low levels. The ROH analysis revealed genomic regions that harbor genes associated with homeostasis maintenance and immune system mechanisms, which may have been selected in response to heat stress. Our results give a comprehensive insight into the relationship between shared ROH regions and putative regions related to survival and production traits in a paternal broiler line selected for over 20 years. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the chicken genome.
