Genomic Resource Development for European Hazelnut (Corylus avellana L.) Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/gq67jv47b

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  • European hazelnut (Corylus avellana L.) is an important crop Oregon's Willamette Valley, producing 99% of the hazelnuts grown in North America and brings over US $60 million dollars to the region annually. Hazelnuts are rich in fiber and vitamins, as well in demand by consumers due to their popularity as the predominant flavor in a multitude of confectionary pastes and chocolate spreads. Breeding efforts are focused on developing hazelnut cultivars with enhanced agronomic traits of interest including size, blanching ability, and resistance to disease. Molecular markers have been developed for hazelnut and placed on a genetic linkage map, linking DNA marker sequences that segregate with phenotypic traits of interest. The objective of this study was to utilize highthroughput sequencing technologies to sequence the hazelnut genome, allowing for trait and marker discovery on a genome-wide scale. We have established genomic resources for hazelnut, including genomic and transcriptomic sequences to allow breeders the opportunity to exploit the wealth of genetic diversity when choosing germplasm for crosses. We chose the Eastern Filbert Blight (EFB) resistant diploid hazelnut cultivar 'Jefferson' (OSU 703.007) as the reference. The 'Jefferson' transcriptome assembly is represented by 28,255 transcript contigs, having an average length of 532bp, and an N50 of 961bp. These transcripts were characterized using both BLASTX protein homology and gene ontology (GO) classifications, with the majority of the predicted proteins to have high conservation with the most closely related plant sequences of Vitis, Populus, and Ricinus. A survey of gene classes enriched among tissue types further validates the assembly and transcript models. The draft genome assembly for 'Jefferson' was assembled de novo using Illumina short read technology into 36,641 contigs and scaffolds, with half of the assembly contained in scaffolds and contigs greater than 21.5 Kb. We captured approximately 91% (345 Mb) of the flow-cytometrydetermined genome size and identified 34,910 putative gene loci which were functionally annotated to identify candidates for future molecular validation. The majority of the annotated genes share homology with the best annotated and related genera Vitis, Prunus, Populus, and Ricinus. We also resequenced seven additional European hazelnut cultivars, detecting millions of variants between one of more of these genomes and that of 'Jefferson'. These variants were annotated based on the functional consequence each polymorphism on the affected loci. In addition, we utilized Genotyping-by-Sequence (GBS) technologies to produce a high-density genetic map within 138 individuals of an F1 hazelnut mapping population, representing a five-fold increase in marker density over the previous maps. Hazelnut genome sequencing has provided new resources to the scientific community and promises to accelerate trait discovery and enhance future breeding efforts, and serve as a tool for gene discovery and functional studies.
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  • description.provenance : Submitted by Erik Rowley (rowleye@oregonstate.edu) on 2016-06-17T15:38:06Z No. of bitstreams: 1 RowleyErikR2016.pdf: 10826931 bytes, checksum: 0ac5a10d5b6bdb40bad332554fd0895a (MD5)
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