Identification of Genes Differentially Expressed In Elongating Fiber In a Cotton Chromosome Substitution Line CS-B25

Recently 17 interspecific chromosome substitution lines (CS-B lines) of upland cotton in G. hirsutum TM-1 background containing whole chromosomes or chromosome arms of G. barbadense (line 3-79) chromosomes have been developed and released to the public from the collaborative project of Dr. Stelly (Texas A & M University, College Station) and Dr. Jenkins’s ARS group (USDA/ARS at Mississippi State, MS). These 17 CS-B lines carry alleles with positive effects on fiber traits and some with negative effects. For example, the CS-B25 line, which has chromosome 25 from G. barbadense substituted into TM-1, exhibits fiber with increased fiber length, strength, and lower micronaire which are all positive traits for fiber quality.  Additionally CS-B25 yields are similar to TM-1. These results form a solid base that allows us to compare gene expression between CS-B25 and TM-1 lines during different stages of fiber development. In this study Affymetrix cotton genome arrays and subtraction hybridization have been used to identify up- and down-regulated genes in elongating fiber in CS-B25 in comparison to TM-1. This approach will ultimately allow us to identify cotton genes on the chromosome 25 of G. barbadense 3-79 which are associated with fiber quality traits.