ORCID Profile
0000-0003-1242-4401
Current Organisation
URUS Group LP
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Publisher: American Dairy Science Association
Date: 09-2016
Publisher: Oxford University Press (OUP)
Date: 03-2020
DOI: 10.1093/GIGASCIENCE/GIAA021
Abstract: Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is & × more continuous than the original assembly, with contig N50 & Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.
Publisher: Frontiers Media SA
Date: 29-01-2015
Publisher: Oxford University Press (OUP)
Date: 11-2017
DOI: 10.2527/JAS2017.1752
Publisher: Springer Science and Business Media LLC
Date: 11-08-2022
DOI: 10.1038/S41588-022-01153-5
Abstract: Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) s les. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
Publisher: Springer Science and Business Media LLC
Date: 2014
Publisher: Public Library of Science (PLoS)
Date: 18-02-2014
Publisher: Elsevier BV
Date: 08-2014
Publisher: Elsevier BV
Date: 2015
Publisher: Springer Science and Business Media LLC
Date: 13-06-2013
Abstract: Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle ( Bos primigenius indicus ) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs). The most significant SNP (rs133012258, P GC = 1.34 × 10 -9 ), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1 , CHCHD7 , MOS , RPS20 , LYN , RDHE2 ( SDR16C5 ) and PENK . The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length. This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle ( Bos primigenius taurus ) also affect birth weight and size in zebu cattle ( Bos primigenius indicus ).
Location: United States of America
No related grants have been discovered for John Cole.