Abstract
BackgroundA robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species.ResultsThe turkey genome physical map was constructed based on 74,013 BAC fingerprints (11.9 × coverage) from two independent libraries, and it was integrated with the turkey genetic map and chicken genome sequence using over 41,400 BAC assignments identified by 3,499 overgo hybridization probes along with > 43,000 BAC end sequences. The physical-comparative map consists of 74 BAC contigs, with an average contig size of 13.6 Mb. All but four of the turkey chromosomes were spanned on this map by three or fewer contigs, with 14 chromosomes spanned by a single contig and nine chromosomes spanned by two contigs. This map predicts 20 to 27 major rearrangements distinguishing turkey and chicken chromosomes, despite up to 40 million years of separate evolution between the two species. These data elucidate the chromosomal evolutionary pattern within the Phasianidae that led to the modern turkey and chicken karyotypes. The predominant rearrangement mode involves intra-chromosomal inversions, and there is a clear bias for these to result in centromere locations at or near telomeres in turkey chromosomes, in comparison to interstitial centromeres in the orthologous chicken chromosomes.ConclusionThe BAC-based turkey-chicken comparative map provides novel insights into the evolution of avian genomes, a framework for assembly of turkey whole genome shotgun sequencing data, and tools for enhanced genetic improvement of these important agricultural and model species.
Highlights
A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis
Turkey BAC contig physical map A total of 85,208 clones were fingerprinted for physical map assembly, randomly selected from two large-insert turkey BAC libraries, CHORI-260 and TKNMI, the latter of which was generated in this study
We sequenced 43,238 BAC ends randomly selected from the two BAC libraries and hybridized the libraries with over 3,500 overgo probes designed from turkey BAC-end sequences (BES), microsatellite markers and genes, chicken genes, and other regions of the chicken genome demonstrating high evolutionary conservation to facilitate map construction and comparative genomics
Summary
A robust bacterial artificial chromosome (BAC)-based physical map is essential for many aspects of genomics research, including an understanding of chromosome evolution, high-resolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait analysis. To facilitate turkey genetics research and better understand avian genome evolution, a BAC-based integrated physical, genetic, and comparative map was developed for this important agricultural species. An important step towards the comprehensive analysis of a large genome is the generation of high-quality, wellanchored physical maps [6,7,8,9]. Such maps have been widely used to effectively integrate genomic tools for highresolution genome mapping, marker-assisted breeding, positional cloning of genes, and quantitative trait locus (QTL) detection [10,11]. Gu et al [20] constructed a BACbased physical map of Brachypodium distachyon and compared it with the rice and wheat genomes, providing an important resource for the completion of the Brachypodium genome sequence and grass comparative genomics
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