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United States Department of Agriculture

Agricultural Research Service

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Research Project: A Physical, Genetic, and Functional Sequence Assembly of Chromosomes 12 and 26 Gossypium Hirsutum L. Cv. Tm-1 Using Mapped Bacs (#13-603)

Location: Genomics and Bioinformatics Research Unit

2013 Annual Report


1a.Objectives (from AD-416):
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.


1b.Approach (from AD-416):
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.


3.Progress Report:

The goal of this project is to develop genomics resources specifically in relation to testing procedures towards sequencing and assembling the cultivated cotton genome.

In a related National Science Foundation funded project, Bacterial Artificial Chromosomes (BACs) clones were generated and used to develop a physical map and establish their relative placement on the 26 cotton chromosomes. BACs from chromosomes 12 and 26 were pooled in specific set and DNA isolated. The DNA is being subject to high throughput DNA sequencing. This work is being done in conjunction with Clemson University.

Participants converse through mainly emails, quarterly reports, face to face meetings or phone conversations.


Last Modified: 12/19/2014
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