2010 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 Upland cotton (Gossypium hirsutum) standard, TM-1, and to sequence selected chromosomes of this genetic standard. The work involves development of genomics tools known as large-insert bacterial artificial chromosome (BAC) libraries that are used in development of a physical map that records relative positions in the genome of specific genetic components or genes. Project work in FY 2010 analyzed and validated DNA sequences developed from portions of cotton chromosomes 12 and 26. Appropriate analysis of these sequences revealed informative and useful evolutionary features within the cotton genome, and allowed comparisons to be made and conclusions drawn concerning the genetic relationship of cotton with other plant species whose genome has been sequenced. Genetic comparisons made between cotton and poplar, grape, rice, maize (corn), and Arabidopsis (a model plant used in many aspects of molecular biology research) showed that cotton is more closely related to poplar than to the other species. As work under this project progresses, important new information will be discovered, and new tools developed, to facilitate sequencing of all chromosomes of the cotton genome. The knowledge gained from sequencing of the cotton genome will greatly facilitate the work of cotton breeders and geneticists to develop more productive and environmentally adapted cotton varieties for use by U.S. cotton farmers. The ADODR of this project monitors the cooperator's performance by frequent e-mail communications, periodic telephone conversations, and through critical review and analysis of shared data. More intensive interactions with the cooperator occur, usually on an annual basis, via face-to-face interactions that include appropriate discussions of work progress, problems, and priorities.