2012 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. In FY 2012, project work made significant progress in sequencing the wild cotton species G. raimondii. The ancestor of G. raimondii is considered to be one of the parents of the modern economically important fiber producing tetraploid cotton species, G. hirsutum and G. barbadense. Detailed structural, functional, and comparative analyses of the DNA sequence data were conducted to reveal the genome complexity and to identify important genes of interest. As work by this project continues, the genome sequence and associated information developed will be made publicly available to other researchers and will be a highly useful tool for application in ongoing work to develop cottons with enhanced quantity and quality traits. Project work will ultimately lead to a high resolution map of the tetraploid cotton genome, which is much needed to support the work of the worldwide cotton research community.