Location: Northwest Irrigation and Soils Research
Title: Whole Genome Sequencing of Sugar Beet and Transcriptional Profiling of Beet Curly Top Resistance Authors
Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 12, 2013
Publication Date: N/A
Interpretive Summary: A simplified approach has been implemented to generate public sugarbeet (Beta vulgaris subsp. vulgaris) whole genome sequence data (WGS). Next generation sequencing (NGS) systems based on generating large number of short sequence data is suitable to achieve this approach. The objectives of this study, were to; identify a large number of single nucleotide polymorphic (SNP) markers to be shared among public and private sugar beet researchers and specifically target polymorphic SNP between beet curly top resistant and susceptible genotypes, in addition to enriching sugar beet public genomic sequence data. To establish a SNP panel for public genotyping and genetic mapping we used the Fluidigm® SNPtype assay coupled to the IFC and EP1 reader systems. This platform offers a flexible small scale genotyping system available in the following chip formats: 24.192, 48.48, and 96.96. We deployed the 96.96 format that allows for genotyping 96 individuals using 96 SNP markers and generated 9,216 data points.
Technical Abstract: The genome of the sugar beet (Beta vulgaris subsp. vulgaris) doubled haploid line (KDH13) has been sequenced using Illumina HiSeq2000 next generation sequencing platform. This line (PI663862) was released by USDA-ARS as a genetic stock resistant to beet curly top. Sequencing of a standard paired end and a 2kb-insert mate-pair genomic libraries, constructed from leaf sample yielded 82.9 Gb sequence data. The raw sequence data was filtered for mitochondria and chloroplasts nucleotides that accounted for less than 2%. A total of 51.5 Gb of nuclear sequence data with a 35.7% GC content was assembled into contigs that achieved 68X genome coverage. The assembly of KDH13 (BvvSeq-1) was generated from a total of 3,850,207 contigs of which 95,923 with 1.15 Kb length at N50. The contigs were assembled into 126,533 scaffolds of 1.8 Kb lengths at N50 that cover 238Mb which spans approximately 31% of the 758Mb sugar beet genome. BvvSeq-1 was aligned to the reference draft genome sequence of sugar beet (RefBeet-0.9), which was generated from the doubled haploid line (KWS2320) that is susceptible to beet curly top. A total of 404Mb of BvvSeq-1 were mapped to RefBeet-0.9 which accounts to 69%. A comprehensive array of nucleotide variants were identified between the curly top resistant and susceptible lines, including a selected thousand single nucleotide variants that will be used for developing a public genotyping platform in a 96X96 Fluidigm genotyping chip.