Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.
Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.
Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil.
Nedenia Bonvino
NB
Stafuzza
Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil.
Adhemar
A
Zerlotini
Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil.
Francisco Pereira
FP
Lobo
Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil.
Michel Eduardo Beleza
ME
Yamagishi
Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil.
Tatiane Cristina Seleguim
TC
Chud
Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.
Alexandre Rodrigues
AR
Caetano
Departamento de Ciências Exatas, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil.
Danísio Prado
DP
Munari
Department of Animal Science, Iowa State University, Ames, Iowa, United States of America.
Dorian J
DJ
Garrick
Embrapa Gado de Leite, Juiz de Fora, Minas Gerais, Brazil.
Marco Antonio
MA
Machado
Embrapa Gado de Leite, Juiz de Fora, Minas Gerais, Brazil.
Marta Fonseca
MF
Martins
Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
Maria Raquel
MR
Carvalho
United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, Maryland, United States of America.
John Bruce
JB
Cole
Embrapa Gado de Leite, Juiz de Fora, Minas Gerais, Brazil.
Marcos Vinicius Gualberto
MV
Barbosa da Silva
D000818:Animals; D001938:Brazil; D001947:Breeding; D002417:Cattle / Q000145:classification / Q000235:genetics*; D005260:Female; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000662:veterinary; D054643:INDEL Mutation; D008297:Male; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis / Q000662:veterinary; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000662:veterinary; D013045:Species Specificity