Expression data from 10 DPA fibers

Upland cotton (Gossypium hirsutum L.) is the most important fiber crop, and its lint yield improvement is impeded due to its narrow genetic base and the lack of understanding of the genetic basis of yield. Backcross inbred lines (BILs) or near-isogenic lines (NILs) in the same genetic background differing in lint yield, developed through advanced backcrossing, provide an important genomic resource to study the molecular genetic basis of lint yield. We used a microarray-based comparative transcriptome analysis on developing fibers at 10 days post-anthesis (DPA) between a high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense, and identified differentially expressed genes (DEGs) during this process. Fibers were selected at rapidly elongation stages of fiber development for RNA extraction and hybridization on Affymetrix microarrays. A high-yield (HY) group and a low-yield (LY) group each with three BILs were selected from a BIL population between G. hirsutum and G. barbadense. We identified a number of yield and yield component QTL- co-localizing DEGs and developed several DEG-based SSCP-SNP markers for the traits, thereby providing a set of candidate genes for molecular breeding and the genetic manipulation of lint yield in cotton. Three BILs (i.e., NMGA-026, NMGA-017 and NMGA-144, designated HY1, HY2, and HY3, respectively) were high-yielding (HY); and three other BILs (i.e., NMGA-066, NMGA-095 and NMGA-023, designated LY1, LY2 and LY3, respectively) were low-yielding (LY).