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United States Department of Agriculture

Agricultural Research Service


Location: Crop Germplasm Research

2013 Annual Report

1a. Objectives (from AD-416):
The objective of this cooperative research project is to advance cotton genomics by developing the resources for the genome sequence of the Upland cotton (Gossypium hirsutum) genetic standard, TM-1.

1b. Approach (from AD-416):
Large DNA-insert BAC libraries of the highly inbred genetic standard, TM-1, will be constructed and assembled into contigs to create a physical map. Minimum tiling path (MTP) BAC clones from selected contigs will be sequenced, and the assembled and annotated data will provide the complete cotton genome sequence with the gene content and distribution.

3. Progress Report:
The goal of this project is to develop resources for genome sequencing of the Gossypium hirsutum cotton standard, TM-1, and to sequence this genetic standard for enhanced cotton improvement. Work in FY 2013 focused on finalization of data analysis and interpretation. Over the life of this project, ARS scientists and their collaborators made major progress in sequence analysis and validation of 362 large-insert MTP BAC clones selected from chromosomes 12 and 26 of the AD1 (Gossypium hirsutum) Upland cotton genome. The work accomplished structural, functional, evolutionary, and comparative analyses of about 28 million base pairs (Mb); and assembled nuclear DNA sequence data, including sequence-based markers and repeat DNA elements. Detailed annotation of the sequence data revealed the genome complexity of Upland cotton and identified 1,070 important genes of interest. The most significant accomplishment of the project was the sequencing and analysis of a D-genome cotton diploid species, G. raimondii. The progenitor of G. raimondii is considered to be the contributor of the D-subgenome of the economically important fiber-producing tetraploid cotton species, G. hirsutum and G. barbadense. The sequence data were analyzed in detail for structural, functional, and comparative genomics to reveal genome complexity and to identify 40,976 protein-coding genes. Scientifically significant discoveries were submitted for publication in prestigious journals. The cotton genome sequence data were released worldwide via global community databases, including GenBank and CottonGen. The DNA sequence information developed from the AD1 tetraploid chromosomes, as well as from the probable D subgenome progenitor, will provide foundational data and direction to ongoing efforts to sequence the entire genome of the Upland cotton genome G. hirsutum. Exploitation of the knowledge gained through detailed sequencing and definition of the cotton genome will greatly facilitate development of new, more productive, and environmentally adapted cotton varieties for use by U.S. cotton farmers.

4. Accomplishments

Last Modified: 07/21/2017
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