2012 Annual Report 1a.Objectives (from AD-416): The overall objective is to identify molecular markers associated with quantitative trait loci (QTL) controlling fiber quality traits and yield, and eventually apply the identified markers in breeding. The specific objectives of this agreement are:. 1)to identify molecular markers associated with fiber quality traits (length, strength, micronaire, uniformity, elongation) and yield;. 2)to determine the effects of random mating on breaking adverse linkage such as between fiber quality and yield. 1b.Approach (from AD-416): ARS scientists at Mississippi State have developed a unique random mated germplasm population of Upland cotton (Gossypium hirsutum L.) involving six cycles of random mating beginning with an 11 parent half diallel. This germplasm designated RMUP-C5 (Random Mated Upland Population Cycle. 5)(Reg. No. GP-893, PI 652942) was released in 2008. The 11 parents used in development represented nonrelated or distantly related cultivars or breeding lines from across the U.S. Cotton Belt. Two hundred thirty three recombinant inbred lines (RILs) from this population are being evaluated for fiber quality traits (strength, length, micronaire, uniformity, etc) and yield. Twenty mapped simple sequence repeat (SSR) markers will be selected from each chromosome based on a high density linkage map. In addition, only markers known to be polymorphic within Upland cotton will be selected. A total of 520 polymorphic SSR markers will be used to scan the genomes of 233 RILs and their 11 parents. Associations between SSR markers and trait of interests will be determined using statistical analysis and other appropriate softwares. 3.Progress Report: Recombinant inbred lines (RILs) derived from random-mating are made to increase the cotton germplasm gene base so that cotton breeders will have the maximum available genes and traits to work with in cotton germplasm improvement for any trait of interest. The 550 RILs derived from random mating of 11 cotton varieties demonstrated wide range of variations in fiber quality and yield. ARS scientists at New Orleans, LA, analyzed 275 RILs with 798 DNA molecular markers. These markers revealed more than 1,300 loci. The RILs were planted in Mississippi in 2009-2012 to collect yield and fiber data. We analyzed the associations between molecular markers and fiber quality traits using JMP Genomics 5.1 and Trait Analysis by Association Evaluation and Linkage (TASSELL) softwares. Potential marker-fiber quality traits (length, strength, fineness) were identified. These candidate marker-trait associations are being validated using the remaining 275 RILs. Future work will be to enrich the population with more molecular markers, and obtain more trait data, validate the marker-fiber trait associations in different populations, and transfer the markers to cotton breeders to assist cotton breeding.