title: Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance.
abstract: In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.
authors.forename: Izinara C
authors.initials: IC
authors.lastname: Rosse
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.|Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Juliana G
authors.initials: JG
authors.lastname: Assis
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.|Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Francislon S
authors.initials: FS
authors.lastname: Oliveira
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil.|Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Laura R
authors.initials: LR
authors.lastname: Leite
authors.affiliation: Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Flávio
authors.initials: F
authors.lastname: Araujo
authors.affiliation: Embrapa Informática Agropecuária, Campinas, SP, Brazil.
authors.forename: Adhemar
authors.initials: A
authors.lastname: Zerlotini
authors.affiliation: Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Angela
authors.initials: A
authors.lastname: Volpini
authors.affiliation: Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Anderson J
authors.initials: AJ
authors.lastname: Dominitini
authors.affiliation: EPAMIG, Belo Horizonte, MG, Brazil.
authors.forename: Beatriz C
authors.initials: BC
authors.lastname: Lopes
authors.affiliation: Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
authors.forename: Wagner A
authors.initials: WA
authors.lastname: Arbex
authors.affiliation: Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
authors.forename: Marco A
authors.initials: MA
authors.lastname: Machado
authors.affiliation: Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
authors.forename: Maria G C D
authors.initials: MG
authors.lastname: Peixoto
authors.affiliation: Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
authors.forename: Rui S
authors.initials: RS
authors.lastname: Verneque
authors.affiliation: Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
authors.forename: Marta F
authors.initials: MF
authors.lastname: Martins
authors.affiliation: Neurogenômica, Centro de Pesquisa René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
authors.forename: Roney S
authors.initials: RS
authors.lastname: Coimbra
authors.affiliation: Embrapa Gado de Leite, Juiz de Fora, MG, Brazil.
authors.forename: Marcos V G B
authors.initials: MV
authors.lastname: Silva
authors.affiliation: Grupo de Genômica e Biologia Computacional, Centro de Pesquisas René Rachou - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.|Vale Technology Institute, Belém, PA, Brazil.
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
authors.affiliation: Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais - UFMG, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31901-207, Brazil. ma.raquel.carvalho@gmail.com.
authors.forename: Maria Raquel S
authors.initials: MR
authors.lastname: Carvalho
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle; D060467:Disease Resistance / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D054643:INDEL Mutation / Q000235:genetics; D058977:Molecular Sequence Annotation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D000071436:Thermotolerance / Q000235:genetics*; D000073336:Whole Genome Sequencing / Q000379:methods*