Structural and Functional Genomics Analyses of Two Near Isogenic Cottons (Gossypium hirsutum L.) Lines Differing in Fiber Maturity

Cotton fiber fineness and maturity are important properties of determining fiber grades in the textile market. To understand the genetic control and molecular mechanisms of fiber fineness and maturity, we studied two near isogenic lines, Gossypium hirsutum, Texas Marker-1 wild type (TM-1) and immature fiber (im) mutant showing a significant difference in micronaire values. The fibers from im mutant plants were finer and less mature with lower micronaire values than those from the recurrent parent, TM-1.  A comprehensive fiber property analysis of TM-1 and im mutant showed that the lower micronaire of fibers in im mutant was due to the lower fiber maturity as compared to the TM-1 fibers.  Structural genomics analysis showed that the immature fiber phenotype was controlled by one single recessive im gene located on chromosome 3.   Transcriptome analysis revealed that the expression levels of stress related genes were significantly changed in the im mutant fibers.   Consistent with the transcriptome data showing the elevated levels of alternative respiration induced in the im mutant fibers by stress, biochemical analyses showed that the reactive oxygen species levels of developing fibers from im mutant were lower than those from TM-1 fibers.  The results provide insight into how the molecular mechanisms involved in the stress responses regulate cotton fiber maturity.