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.
Highlights
Brazil has the world’s largest commercial cattle herd with around 215.2 million head in 2015 according to the agricultural census [1], from which about 80% is estimated to be composed of purebred and crossbreed Bos primigenius indicus animals
We presented an extensive genome analysis of Gyr, Girolando, Guzerat and Holstein breeds following whole-genome re-sequencing using an Illumina HiSeq 2000 sequencing platform, which lead to identification of 27,441,279 single nucleotide variations (SNVs) and 3,828,041InDels in the cattle genome
The high number of genetic variants identified for each breed is important to monitoring genetic diversity and for developing strategies to prevent an eventual loss of genetic variability
Summary
Brazil has the world’s largest commercial cattle herd with around 215.2 million head in 2015 according to the agricultural census [1], from which about 80% is estimated to be composed of purebred and crossbreed Bos primigenius indicus animals. Guzerat and Gyr, which were introduced from India, are important indicine cattle breeds for milk and meat production in Brazil. The Guzerat breed is recognized for traits such as resistance to parasites, heat tolerance and willingness to consume forage with low nutritional value, all of which are important to its adaptation to adverse tropical environments. This breed was included in the FAO list of domestic animal genetic resources to be conserved by management [4] due to their potential for production in the tropics and their small effective population size
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