Location: Sugarbeet Research
Project Number: 3060-21000-045-008-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2023
End Date: Oct 31, 2024
Objective:
1. Obtain high quality whole genome sequences in cultivated beet types (sugarbeet, fodder beet, leaf beet, table beet) and wild beet relatives (Beta. vulgaris ssp. maritima)
2. Identify genes specific in sugarbeet by comparing genomic sequences of different beet types
3. Identify pathways of gene expression regulation related to sugar production in sugarbeet expression
4. Development of pan-genomic reference of Beta. vulgaris species.
Approach:
1. Using ovary culture method to induce haploid tissue or plants for all beet types and Beta vulgaris ssp. maritima.
2. Extract high quality DNA from haploid tissue or plants for easy whole genome sequence assembly.
3. Using PacBio HiFi sequencing to get long reads covering whole genome with a depth of 40X, and assemble the long reads to obtain the high quality whole genome sequence in each beet type.
4. Sequence compare to identify genomic variations specific to sugarbeet.
5. RNA-seq to compare gene expression between sugarbeet and other beet types to identify genes related to sugar production pathways.
6. Combining RNA-seq and comparative genomics to annotate genes related to sugar production
