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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #339234

Title: Single nucleotide variants and indels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds

Author
item STAFUZZA, NEDENIA - Universidade Estadual Paulista (UNESP)
item ZERLOTINI, ADHEMAR - Embrapa
item LOBO, FRANCISCO - Embrapa
item YAMAGISHI, MICHEL - Embrapa
item CHUD, TATIANE - Universidade Estadual Paulista (UNESP)
item CAETANO, ALEXANDRE - Embrapa
item MUNARI, DANISIO - Universidade Estadual Paulista (UNESP)
item MACHADO, MARTA - Embrapa
item CARVALHO, MARIA - Federal University Of Minas Gerais
item Cole, John
item DA SILVA, MARCOS - Embrapa

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2017
Publication Date: 3/21/2017
Citation: Stafuzza, N.B., Zerlotini, A., Lobo, F., Yamagishi, M., Chud, T., Caetano, A., Munari, D., Machado, M., Carvalho, M., Cole, J.B., Da Silva, M. 2017. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds. PLoS One. 12(3): e0173954.

Interpretive Summary: Most studies to identify structural variants in cattle DNA have focused on animals of European descent that are adapted to perform well in temperate climates. However, tropically adapted cattle are economically important in many part of the world, including Brazil. In this study, whole-genome DNA sequence data for 12 bulls of the Guzerat, Gyr, Girolando, and Holstein breeds were used to construct a catalog of known DNA variants in tropically adapted cattle, and compare them against cattle adapted to temperate environments. This study resulted in the identification of 2,557,670 novel single-nucleotide variants, as might be included on genotyping chips, and 883,219 insertions and deletions. These findings provide a resource for the construction of genotyping arrays for tropically adapted cattle, as well as for identifying genomic regions that have undergone changes in response to selection for performance in hot climates.

Technical Abstract: 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.