Location: Genomics and Bioinformatics Research
Project Number: 6066-21310-004-19-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jan 1, 2013
End Date: Dec 31, 2013
The genome sequence of Gossypium raimondii has just been released. This represents a “D” genome which is believed to be the nearest relative of the D genome in tertraploid cotton. Thus it is possible to use the raimondii sequence as a reference genome for examining the D genome in cultivated cotton and as gene space is relatively conserved even the “A” genome of tetraploid cotton can be compared to the reference D genome. Resources have been developed to create a BAC physical map of cotton. These BACs and the related minimal tiling path are available and BACs have been assigned to specific chromosomes. This project will identify and sequence the BACs associated with chromosomes 12 and 26 of the cultivar Tm-1 which is a genetic standard for cultivated cotton. These chromosomes are known to have genes important for disease resistance.
Using the BAC physical map, BACs have been assigned to the 26 chromosomes of cultivated cotton (13 for each of the A and D genomes). BAC pools will be made consisting of 30-40 BACs per pool for a total of approximately 250 BACs per each of the chromosomes. These pools will be subject to high throughput sequencing technology and the DNA sequences will be assembled. Assembly strategies will test different numbers of BACs pooled together to see if an optimal pooling strategy can be developed. After assembly the sequences will be annotated.