Project Summaries

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.
Thus far we have established an assembly of TM-1 based on long read 454 and Sanger sequences to map and compare all transcriptome datasets to. This includes datasets from our labs and enhanced by the Udall lab. All datasets have been mapped to the reference TM-1 assembly and SNP genotypes extracted for all polymorphic positions across species and lines. Furthermore we have compared the new dataset obtained from Floragenex using RAD technology (also known as GBS-genotype by sequencing). The RAD dataset for Maxxa and TM-1 is from genomic DNA. Approximately 1500 SNPs were identified with this technology of which 185 overlapping with current transcriptome datasets indicating its complementarity. Validation of the RAD dataset has been only 10% which has lead us to abandon the current assembly by Floragenex. Reads will be mapped to D-genome and A -genome assembly in the Van Deynze/Stelly lab (see Stelly 08-386).

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
 

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CORE PROGRAM
▸ Cotton Incorporated Fellow
▸ Cottonseed
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▸ Production Efficiency
▸ Sustainable Cotton
▸ Variety Improvement

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