Next-generation sequencing and physical mapping of wheat chromosome 5D and comparison with its wild progenitor
Akpınar, Bala Anı (2015) Next-generation sequencing and physical mapping of wheat chromosome 5D and comparison with its wild progenitor. [Thesis]
Wheat is a staple grain crop, essential to human nutrition and animal feed. Despite its agronomic importance, wheat genomics research has long lagged behind its counterparts, due to its genome attributes. Bread wheat genome is almost six times as large as the human genome at a size of ~17 Gigabases, and is composed of >80% repetitive elements. The hexaploid genome is organized into three related sub-genomes, giving rise to numerous paralogous and homeologous loci. In this study, we characterized the flow-sorted 5D chromosome of bread wheat, Triticum aestivum, through survey sequencing and physical mapping, including its repeat landscape, gene content and conservation and putative tRNA repertoire. The virtual gene order of 5D chromosome suggested several perturbations in synteny, in addition to a number of putatively wheat-specific genome rearrangements. The 5DS physical map revealed that its gene space is largely organized into gene islands with an increasing gradient towards the telomere. Physical size estimates on the physical map indicated that cytogenetic estimates may considerably underestimate the 0.63-0.67 deletion bin interval. Comparative analyses of its wild progenitor, Aegilops tauschii 5D chromosome shed light into wheat genome evolution. The high density 5DS physical map at ~10.5 markers/Mb and 1.34x-1.61x survey sequences of the entire chromosome provides the foundation of the reference sequencing of this chromosome and presents a valuable genomics resource that the breeders and the researchers should benefit from.
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