Genomic analysis of marker-associated fiber development genes in upland cotton (Gossypium hirsutum L)

Understanding genetic control of fiber development is essential for cotton improvement. This study analyzed several thousand fiber Unigenes in Upland cotton (Gossypium hirsutum). They included 2423 Unigenes for fiber initiation (IN), 1841 for fiber elongation (EL) and 86 for secondary cell wall deposition (SCWD). These Unigenes were located on recombination hotspots between At and Dt subgenomes with nearly equal frequency (51% vs. 49%). Sequence analysis with Upland cotton TM-1 genome assembly showed that 477 IN, 464 EL, 20 SCWD and 367 non-fiber Unigenes intersect with predicted coding sequences. There were 140 IN, 118 EL and one SCWD Unigenes that do not overlap between individual stages of fiber development. Annotation of top scoring Unigenes with Kyoto encyclopedia of genes and genomes indicated mitochondrial biogenesis for IN Unigene #18205, conversion of PRPP to histidine for IN #25329, and spliceosome pathways for IN #24380. EL Unigene #11669 appeared to be responsible for septum site-determining protein, EL #11916 for vacuolar protein, and EL #17251 for protein trichome birefringence-like 33. One SCWD Unigene #190099 was responsible for legumin A-like protein. In addition, Unigene #03070 overlapped three fiber development stages and involved in fatty acid biosynthesis. Unigenes that shared same genomic positions for all fiber stages are of particular interest as they may have possible pleiotropic function. On the other hand, Unigenes from one fiber development stage that did not share with any other stage may have stage-specific function. This information would be useful for plant breeders to exploit fiber genes in cotton breeding programs.