Molecular Cytogenetics and Gene Mapping in Sheep (<i>Ovis aries, </i>2n = 54)

Abstract

The development of a completely annotated sheep genome sequence is a key need for understanding the phylogenetic relationships and genetic diversity among the many different sheep breeds worldwide and for identifying genes controlling economically and physiologically important traits. The ovine genome sequence assembly will be crucial for developing optimized breeding programs based on highly productive, healthy sheep phenotypes that are adapted to modern breeding and production conditions. Scientists and breeders around the globe have been contributing to this goal by generating genomic and cDNA libraries, performing genome-wide and trait-associated analyses of polymorphism, expression analysis, genome sequencing, and by developing virtual and physical comparative maps. The International Sheep Genomics Consortium (ISGC), an informal network of sheep genomics researchers, is playing a major role in coordinating many of these activities. In addition to serving as an essential tool for monitoring chromosome abnormalities in specific sheep populations, ovine molecular cytogenetics provides physical anchors which link and order genome regions, such as sequence contigs, genes and polymorphic DNA markers to ovine chromosomes. Likewise, molecular cytogenetics can contribute to the process of defining evolutionary breakpoints between related species. The selective expansion of the sheep cytogenetic map, using loci to connect maps and identify chromosome bands, can substantially contribute to improving the quality of the annotated sheep genome sequence and will also accelerate its assembly. Furthermore, identifying major morphological chromosome anomalies and micro-rearrangements, such as gene duplications or deletions, that might occur between different sheep breeds and other Ovis species will also be important to understand the diversity of sheep chromosome structure and its implications for cross-breeding. To date, 566 loci have been assigned to specific chromosome regions in sheep and the new cytogenetic map is presented as part of this review. This review will also summarize the current cytogenomic status of the sheep genome, describe current activities in the sheep cytogenomics research sector, and will discuss the cytogenomics data in context with other major sheep genomics projects.

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

“…The different stages of the reference genome assemblies of the two species may also have played a role. The sheep genome has been the subject of several improvements and refinements (Maddox et al, 2001;Goldammer et al, 2009), including the development of a virtual genome map based on bovine, dog and human genome assemblies (Dalrymple et al, 2007). These efforts culminated in the first draft of the ovine reference genome (Archibald et al, 2010), which has been improved further and the current released reference assembly, Oar v3.1, has a contig N50 length of~40 Kb and a total assembled length of 2.61 Gb, with~99% anchored onto the 26 autosomes and the X chromosome (Jiang et al, 2014).…”

Genome-Wide Genetic Diversity and Differentially Selected Regions among Suffolk, Rambouillet, Columbia, Polypay, and Targhee Sheep

“…Based on BAC (bacterial artificial chromosome) end sequences, Dalrymple and colleagues [1] first reported a virtual sheep genome by painting a total of 84,624 sheep BACs (about 5.4-fold genome coverage) to orthologous regions in the human genome, which were assembled into 1,172 sheep BAC comparative genome contigs that covered 91.2% of the human genome. In 2009, Goldammer and coworkers [2] constructed a cytogenetic map of the sheep genome with 566 loci, which helped link and order genome regions, such as sequence contigs, genes, and polymorphic DNA markers to ovine chromosomes. Approximately two years ago, the International Sheep Genomics Consortium (ISGC) began assembly of a draft reference genome of sheep ( Ovis aries ) using both Sanger sequencing and the next-generation sequencing platforms [3].…”

Fluorescence in situ hybridization mapping of six loci containing genes involved in the dioxin metabolism of domestic bovids

“…Corresponding human locations HGNC ( http:// www.genenames.org/) of the six genes are in agreement with comparative mapping data between bovids and humans (Table 1). This study adds further information to the previous cytogenetic maps of the domestic bovids (BOVMAP (http://dga.jouy.inra.fr/cgi-bin/lgbc/main.pl?BASE=); Goldammer et al 2009;Schibler et al 2009;Di Meo et al 2008) and assigns, for the first time, six loci containing genes which are strongly involved in the metabolism of a variety of xenobiotics, including polycyclic aromatic hydrocarbons (PAHs) and halogenated aromatic hydro-carbons, in chromosomes of cattle, sheep, river buffalo and goat. Although assembled genome sequences are available for several species, especially for cattle, and chromosome gene location can be predicted based on available comparative maps of Bovids, FISHmapping, especially applied on R-banded chromosome preparations, is still useful to construct precise genomic maps.…”