|03-430 Project Manager: D. C. Jones|
SAMPLING NUCLEOTIDE DIVERSITY IN COTTON
Allen Van Deynze, University of California, Davis and David M. Stelly, Texas Agricultural Experiment Station
The long-term objectives of this research are to develop and deploy novel genomic resources that can be directly applied to breeding cotton. Specific objectives are: 1) enhance TM-1 assembly with additional available Illumina data, 2) annotation of transcriptome for genome annotation and assembly, and 3) bioinformatics support for SNP validation for Gossypium species.
By refining our filters for sequences for presence of introns, homozygosity, and taking into account presence of paralogs or homoeologs, we were able to increase this efficiency from 15% to 54% validation. In doing so we are able to identify single copy gene loci from paralogous ones.
We have mapped all species datasets to the TM-1 reference assembly. This includes generation of additional SNP candidates form the enhanced TM-1 assembly and G. hirsutum and cross-referencing datasets with the Udall lab. We have mapped datasets to the D-genome sequence. The transcriptome dataset played an important role in annotating the D-genome (Anderson et al 2012). The results of the SNP discovery from transcriptomes and RAD were presented at the ICGI Conference in NC.
|Project Year: 2012|
Search 2012 Projects:|
▸ New Mexico
▸ North Carolina
▸ South Carolina
▸ Cotton Incorporated Fellow
▸ Crop Improvement
▸ Production Efficiency
▸ Sustainable Cotton
▸ Variety Improvement
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