Current status and future perspectives for sequencing livestock genomes

As the new genomics era matures, with large-scale genome research and the development of sophisticated bioinformatics tools that can be applied to the agricultural field, agricultural researchers should take advantage of and benefit from new sequencing and mapping technologies. In recent years, the genomes of several domesticated livestock animals (chicken, pig, cow, sheep, and horse) have been partially or completely sequenced. In this review, we first examine the current sequencing status for several sequenced agricultural species. Next, we discuss the different platforms used for genome sequencing, tools available for mapping sequences to the genome, and several additional applications for which next generation sequencing can be used. We also list tools available for analyzing data from these additional applications.Due to the high recombination rate of its micro-chromosomes, the chicken is an ideal model for studying genetic linkage [1]. The chicken genome sequence of Red Junglefowl (RJF) was the first livestock species to be sequenced. The first draft of the chicken genome was built from an assembly with 6.6-fold whole-genome shotgun coverage, although sex chromosomes were poorly annotated in the initial assembly [1,2]. The updated version of NCBI build 2.1 was released recently with a significant improvement on the annotation of the sex chromosomes. Roughly 2.8 million SNPs for chicken were identified [1,3,4] between the base (wild type) RJF sequence assembly and a partial genome scan of three chicken breeds: a female layer (White Leghorn); a male broiler (Cornish); and a female Silkie. A moderate density (60 k) Illumina SNP BeadChip for commercial chicken (broilers and layers) containing 352,303 SNPs was designed and additional SNPs not covered by the current chicken genome assembly (Gallus_gallus-2.1) were identified and selected recently [5]. The BBSRC ChickenEST Database (http://www.chick.manchester.ac.uk/ webcite) provides the most comprehensive database