Chromosome Substitution Line: Useful Genetic Resource for Targeted Exploitation of the Beneficial Alleles from Wild and Unadapted Germplasm in Cotton Genetic Improvement.

Upland cotton has been domesticated through intensive selection process to produce specific types of fibers for textile industries. Recent studies revealed that germplasm pool of Upland cotton (G. hirsutum) in the US has been eroded seriously during the domestication process by excessive exploitation of a few elite lines over time.  Previous attempts by cotton breeders documented that gene retention and genetic recombinations are very difficult to broaden the germplasm base of Upland cotton from alien species.   To help overcome barriers to effective introgression, we have developed a number of alien chromosome substitution (CS) lines from G. barbadense (CS-B), G. mustelinum (CS-M) and G. tomentosum (CS-T). Most of the CS lines are nearly isogenic to the inbred ‘Texas Marker-1’ (TM-1, G. hirsutum).  Comparative analysis of the CS lines have provided means to identify and associate important traits with specific substituted chromosome or chromosome segments.  We released a set of 17 disomic CS-B lines through hypoaneuploid-based backcrossing in a near-isogenic genetic background of TM-1 line. We also developed near-isogenic chromosome-specific recombinant inbred lines (CS-RILs) by crossing specific CS lines with the common recurrent, inbred TM-1, then inbreeding via single-seed decent.  Analysis of CS-RILs for traits and SSR and/or SNP markers enable markers to be associated with genes with marked effects on important fiber traits. By creating and analyzing various types of CS-derived near isogenic families, the chromosome-specific genetic effects were determined for various agronomic and fiber properties. Results have validated CS-B11sh, CS-B16, and CS-B17 harboring RKN, FOV1 and FOV4 resistance genes associated with SSR markers, respectively. Preliminary results based on various morpho-physiological traits suggest that CS-T04 has higher tolerance against drought and low temperature.  CS-B25 was associated with improved fiber traits including high fiber strength, length and low micronaire.