Sequencing and annotated analysis of full genome of Holstein breed bull

Abstract

In the present study, we describe the deep sequencing and structural analysis of the Holstein breed bull genome. Our aim was to receive a high-quality Holstein bull genome reference sequence and to describe different types of variations in its genome compared to Hereford breed as a reference. We generated four mate-paired libraries and one fragment library from 30 μg of genomic DNA. Colour space fasta were mapped and paired to the reference cow (Bos taurus) genome assembly from Oct. 2011 (Baylor 4.6.1/bosTau7). Initial sequencing resulted in the 4,864,054,296 of 50-bp reads. Average mapping efficiency was 71.7 % and altogether 3,494,534,136 reads and 157,928,163,086 bp were successfully mapped, resulting in 60 × coverage. This is the highest coverage for bovine genome published so far. Tertiary analysis found 6,362,988 SNPs in the bull's genome, 4,045,889 heterozygous and 2,317,099 homozygous variants. Annotation revealed that 4,330,337 of all discovered SNPs were annotated in the dbSNP database (build 137) and therefore 2,032,651 SNPs were novel. Large indel variations accounted for the 245,947,845 bp of the variation in entire genome and their number was 312,879. We also found that small indels (number was 633,310) accounted for the total variation of 2,542,552 nucleotides in the genome. Only 106,768 small indels were listed in the dbSNP. Finally, we identified 2,758 inversions in the genome of the bull covering in total 23,099,054 bp of genome's variation. The largest inversion was 87,440 bp in size. In conclusion, the present study discovered different types of novel variants in bull's genome after high-coverage sequencing. Better knowledge of the functions of these variations is needed.

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

“…Given the large number of novel variants, these results indicate that a high number of genetic variants remain to be identified in the bovine genome. It is important to note that the lower proportion of novel variants discovered in the Holstein breed was expected, because its genome has already been extensively re-sequenced [10, 12, 17, 34]. …”

The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows

“…Despite the fact that a continuously growing number of whole-genome sequences are available for cattle, the knowledge of the bovine genome is still limited (Kõks et al 2014 ). Up to now, most of the published results were based on the analysis of genomes of single (Eck et al 2009 ; Kõks et al 2013 , 2014 ) or only a few individuals (Larkin et al 2012 ; Lee et al 2013 ; Stothard et al 2011 ).…”

“…Despite the fact that a continuously growing number of whole-genome sequences are available for cattle, the knowledge of the bovine genome is still limited (Kõks et al 2014 ). Up to now, most of the published results were based on the analysis of genomes of single (Eck et al 2009 ; Kõks et al 2013 , 2014 ) or only a few individuals (Larkin et al 2012 ; Lee et al 2013 ; Stothard et al 2011 ). Recently, a few studies in which a larger number of animals were sequenced (Baes et al 2014 ; Brøndum et al 2014 ; Daetwyler et al 2014 ; Höglund et al 2015 ; Jansen et al 2013 ) were published.…”

Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

“…Previous studies reported a significant rate of false positive calls among deleterious missense and loss-of-function variants [3, 44]. Thus, the efficiency of our calling approach and the relevance of the resulting variants were assessed by genotyping a selected panel containing 304 heterozygous deleterious missense and loss-of-function mutations for which no homozygous individual for the alternative allele was observed in our population.…”