The cattle genome reveals its secrets

Abstract

MinireviewT Th he e c ca at tt tl le e g ge en no om me e r re ev ve ea al ls s i it ts s s se ec cr re et ts s Cattle belong to an ancient group of mammals, the Cetartiodactyla, that first appeared around 60 million years ago. Domesticated cattle (Bos taurus and Bos taurus indicus) diverged from a common ancestor 250,000 years ago, and have had a long and rich association with human civilization since Neolithic times 8,000-10,000 years ago. All modern cattle breeds originate from large populations of the ancestral aurochs (Bos taurus primigenius; Figure 1) through thousands of years of domestication. During this time, more than 800 cattle breeds have been established, representing an important resource for understanding the genetics of complex traits in ruminants. More than a billion cattle are raised annually worldwide for beef and dairy products, as well as for hides. Cattle therefore represent significant scientific opportunities, as well as an important economic resource.Sequencing of the cattle genome began in December 2003, led by Richard Gibbs and George Weinstock at the Baylor College of Medicine's genome sequencing center in Houston, Texas, USA. The first draft sequence of the bovine genome was based on DNA taken from a Hereford dam, L1 Dominette 01449 (Figure 2), a cattle breed used in beef production. In parallel, a large number of single-nucleotide polymorphisms (SNPs) have also been generated from the partial sequence of six breeds (Holstein, Angus, Jersey, Limousin, Norwegian Red and Brahman). Taken together with the sequence of L1 Dominette 01449 (the reference bovine genome [1]) these represent a valuable resource for marker-assisted selection of genetic traits in commercial breeding programs.The Bovine Genome Project represents a complex collaborative effort between multiple groups and funding from the United States, Canada, France, United Kingdom, New Zealand and Australia.Undoubtedly the current bovine genome sequence will be improved in both its sequence coverage and its annotation, but this draft sequence will form the basis for cattle genetics and genomics for the next 20 years or more. So what have we learned?T Th he e g ge en no om me e a as ss se em mb bl ly y p pr ro ob bl le em m --s st ti il ll l n no ot t s so ol lv ve ed d? ?The technology for generating raw sequence data has advanced rapidly over the past 35 years, starting with Sanger sequencing in the 1970s, automated fluorescent Sanger sequencing in the 1980s and, recently, ultra-high-A Ab bs st tr ra ac ct t throughput methods based on the parallel sequencing platforms produced by 454, Illumina, and ABI. However, the scale of these advances has not been matched by new algorithms and tools for sequence assembly, particularly for large genomes. Common problems associated with large genomes have been repetitive sequences (generally around 50% of a vertebrate genome), gene families and genetic polymorphisms, all of which can cause errors in assembly. Genome assembly is still a problem, requiring a combination of parallel computing...

On the performance of tests for the detection of signatures of selection: a case study with the Spanish autochthonous beef cattle populations

“…Among the genes included in these regions, some of them may be good candidates for being affected by selection i.e. : (1) genes that are related to energy balance and homeostasis: R3HGM1 ( R3H domain containing 1 ) on BTA2 [48]; CAMK1D ( calcium/calmodulin - dependent protein kinase ID ) on BTA13 [49]; and SLC25A33 ( solute carrier family 25 ( pyrimidine nucleotide carrier ) , member 33 ) and SLC2A5 ( solute carrier family 2 ( facilitated glucose/fructose transporter ), member 5 ) on BTA16 [49, 50]; (2) PLIN5 ( perilipin 5 ) on BTA7, which is involved in the regulation of lipid metabolism in rat and pigs [51, 52]; (3) SCAPER ( s - phase cyclin A - associated protein in the endoplasmic reticulum ) on BTA21, which regulates cell cycle progression [53]; and (4) there are two other signatures of selection that are worth noting i.e. one detected for the RG population on BTA19 (between 27,941,270 and 28,571,032 bp) where ALOX15B ( arachidonate 15 - lipoxygenase, type B ) and ALOX12B ( arachidonate 12 - lipoxygenase, 12R type ) are located and are involved in immune response [54], and one for the ANI population on BTA20 (between 40,854,136 and 40,996,384 bp) where the NPR3 ( natriuretic peptide receptor 3 ) gene is located, which is related with cattle stature [55].…”

A Meta-Assembly of Selection Signatures in Cattle

“…Access to bovine genome sequence assemblies ( S2 Fig ) and high-density genotyping panels ( S3 Fig ) have provided researchers with remarkable resources to study the effects of domestication and selection on the architecture of the bovine genome. Subsequent investigations have revolutionized our understanding of mammalian evolution, domestication and devised strategies for enhancing genetic improvement for dairy and beef production [ 23 , 29 ]. Organized breeding systems that have large well characterized cattle populations also provide pivotal resources for the discovery of genes contributing to complex traits such as milk production, fertility, muscle formation, energy partitioning and disease resistance [ 10 , 12 , 30 , 31 ].…”

A clone-free, single molecule map of the domestic cow (Bos taurus) genome

“…Their strategy leveraged paired-end BAC sequence information, mapping data and, most notably, syntenic relationships to the human genome that allowed 91 % of the UMD2 contigs to be anchored to bovine chromosomes, based on the integrated bovine genome map [ 4 , 11 ]. Comparisons between these two assemblies revealed substantial differences that appear as assembly errors, genome segmental inversions, chromosomal placements, sequence gap numbers, and discrepancies of the sequence coverage across the bovine genome [ 11 – 13 ]. Two updated bovine genome sequence assemblies (Btau4.6 and UMD3.1) were released from these groups featuring additional BAC sequence data, corrected assembly errors and additional gap filling.…”