Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-006-032-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2024
End Date: Jul 31, 2026
Objective:
The collaborator will harvest and prepare roots for planned cytology analysis. Data obtained from that analysis will be used by the collaborator to guide development of method to perform cytology-informed scaffolding of intra-specific (S. spontaneum x S. officinarum) sugarcane genome assemblies.
Approach:
The ARS PI has generated sequence data for the sugarcane cultivars for which genome assemblies will be developed and performed initial assembly of the sequence data. The collaborator will obtain cytology services to characterize allele numbers per basic chromosome, total chromosome count and chromosomal location of S. spontaneum introgresssions. The Collaborator and/or collaborator's postdoc will align draft assemblies to publicly available progenitor species assemblies and read alignments will be compared to cytology results to develop in-silico pseudo-reference assemblies. These 'pseudo-references' will be used to scaffold draft assemblies by the collaborator.
