Identification of the genes and pathways associated with pigment gland morphogenesis in cotton by transcriptome profiling of near-isogenic lines

Cottonseed protein is underutilized due to the presence of pigment gland containing a toxic compound called gossypol. Cotton produces gossypol and related compounds in various tissues to protect itself against microbial, insect, and rodent attacks. Understanding the mechanism of cotton pigment gland formation and regulation of gossypol biosynthesis will greatly facilitate the research efforts in developing a cotton variety with a gossypol free seed and normally glanded foliage. In this study we make use of near-isogenic lines of cotton pigment gland to screen the genes related to gland morphogenesis applying both GeneChip and suppression subtractive hybridization (SSH) methods.We identified 880 differentially expressed genes associated with gland morphogenesis in cotton by comparing transcriptome profiles of cotton from glandless and glanded near-isogenic lines using a GeneChip. Gene ontology (GO) analysis showed that 880 genes were distributed mainly among the following GO categories: cellular process (14.45%), physiological process (14.23%), catalytic activity (9.21%), metabolism (8.99%), and cell parts (5.24%). Molecular pathway analysis revealed that these differentially expressed genes were involved in 58 KEGG pathways. Differentially expressed genes were also identified and isolated using suppression subtractive hybridization (SSH) with the same near-isogenic lines. A total of 147 ESTs were identified whose expression was either up- or down-regulated. Sequencing and BLAST analysis indicated that some of these genes were novel, while others were related to energy metabolism, transcription factors, and biotic responses. 13 genes were found to be differentially expressed both in SSH and GeneChip analysis. The expression pattern of these genes was verified by real-time PCR. The gene expression profiles produced in this study provide useful information on the molecular mechanism and regulation of gland formation and the related process in cotton. Of particular interest for future study are the genes identified by both SSH and GeneChip analysis. The outcomes are helping for our understanding of the development of specialised structures such as trichomes in plant species, from an applied and basic science perspective and promoting the application in molecular breeding.