Differentially expressed genes during fibre development in dipoid cotton ,Gossypium spp.

Functional Genomics

poster

Katageri, Ishwarappa; Hande, Atul; Dhandapani, G; Kanakachari, M; Vamadevaiah, H.M.; Khadi, Basavaraj,M; Solanke, AmolKumar; Reddy, V Shiva; Polumetla, Anandkumar

Katageri, Ishwarappa

Katageri, Ishwarappa

The goal of this work was to identify differentially expressed genes at two different stages during cotton fibre development i.e. 0 dpa and 10 dpa. The techniques like microarray, suppression substractive hybridization (SSH) and qRT-PCR were followed using the isogenics representing FL (Fuzzy linted) and Fl (Fuzzy-lintless) linesof G.arboreum. The scanning electron microscopy (SEM) revealed no difference in the fibre initials except for the fuzz development in Fl (Fuzzy-lintless) line which is due to the down-regulation of the some genes necessary for the fibre development. Microarrays identified transcripts which were either down-regulated or up-regulated in the fibre. Most of the genes up-regulated at 0 dpa but at 10 dpa large number of genes were down-regulated and out of total 278 transcripts 239 were showing matches with the Arabidopsis. The network covers broad processes like transcription factors. The transcription factors like AP2-EREBP, C2H2, WRKY were up-regulated at 0 dpa and during 10 dpa transcription factors coding AP2-EREBP, AUX/IAA, bHLH, C2H2, C3H, HB, MYB, NAC, Orphans, PLATZ and WRKY were down-regulated which may be the probale reason for the undergrowth of the fibre in the fuzzy-lintless line. Phytohormone signaling is also one of the important aspect in the fibre developmental process in the Fl (Fuzzy-lintless) line because most of the phytohormones like abscisic acid, auxin, brassinosteroid, ethylene, gibberellin, and salicylic acid were up-regulated at the 0 dpa and same were down-regulated at 10 dpa. This alteration in the regulation at the two stages might have led to the loss of co-ordination in the development process and ceased the fibre growth in the fuzzy-lintless line. In the Fl line, down-regulation of the transcript at 10 dpa coding for the trehalose-6-phosphate synthase (TPS), endo-xyloglucan hydrolase family proteins, UDP-glucose 4-epimerase (UGE), EXPANSINs, Arabinogalactan proteins (AGPs), β-galactosidase 13 (BGAL13), UDP-glucosyl transferase 74B1 (UGT74B1), Tubulins (TUBs) may the possible reason for the undergrowth of the fibre because these elements are necessary for the energy and cell wall metabolism. Fatty acids are essential for the fibre growth but in the Fl line acyl-CoA (ACO) oxidase 4 was down-regulated at the 10 dpa may have resukted in the undergrowth of the fibre due to loss in the VLCFA chains which interact with the other factors for normal fibre growth. The down-regulation of the genes like lipid transfer proteins (LPTs) and the hydrolases family representing from the fatty acid synthesis lead to undergrowth of the fibre in the Fl line at 10 dpa. Phosphatidylinositol (PtdIns) transfer proteins (PITPs) are signaling molecules in lipid metabolism and tip directed growth of the fibre and the down-ragulation of such gene may be the factor for the reduction of the fibre growth in developing fibres of fuzzy-lintless line.Transcripts related to the signaling including the Ca2+ and reactive oxygen species (ROS) which are the leading factors for fibre initation and cotton fibre growth itself is a kind of stress but their down-regulation resulted to the loss of co-ordination during the 0 dpa. Down-regulation of ROS scavenging factor peroxidase 2 (PA2) which has affected the ROS and led to the reduced fibre growth in fuzzy lintless line. Some miscellaneous factors like cellular and signal transcduction coding for MAPK cascade, Plant receptor-like kinases (RLKs) and LRR-family protein were down-regulation at 10 dpa. These factors have been involved in the cellular communication and the development of the fibre and down-regulation at 10 dpa may have resulted to loss of the function of such genes and reduced fibre growth in the Fl (fuzzy-lintless) line. Heat shock proteins (HSPs), which are the involved protein refolding and stabilizing the plant in response to the abiotic stress but such genes which are down-regulated at 10 dpa may be the on eof thereason for the reduction of the fibre growth and it is worth to mention that fibre development is itself a stress. Spermine synthase (SPDS3) was one of the genes down-regulated at both the stages in fuzzy-lintless line. It is considered as the SPDS gene which is responsible for the polyamine biosynthesis and in the Fl line it was down-regulation which may lead reduce fibre growth by modulating the concentration of polyamines. In SSH, based on the putative functions of genes preferentially or specifically expressed in fibre elongation stage in cotton fibre development BLAST results showed that many novel genes were contained in forward library and a few had been previously reported. On the basis of previous reports and the putative functions of the genes which are involved in fibre development and how those genes regulate fibre growth were reported in the database. This include actin depolymerizing factor 2 (ACT2), acyl- oxidase 1 (ACO1), beta-galactosidase (β-galactosidase) from Ricinus communis. There were contigs showing the homology to the beta-glucanase (β-glucanase), β-ketoacyl-Coa synthase family protein, beta-tubulin 19 (β-tubulin 19), elongation factor 1 (EF1), glucose-6-phosphate 1-epimerase, malate dehydrogenase, xyloglucan endotransglucosylase hydrolase protein 32 (XTH32/XET32). Genes like calcineurin b-like protein (CBL), calmodulin binding (CaM), mitogen-activated protein kinase 16 (MAPK/ MPK16), diacylglycerol acyltransferase (ACY) Phospholipase-C (PLC), phosphatidylcholine transferases (PCY), Phospholipase-C (PLC) were also found in the database and attempt was made for some of this genes to validate by the Quantitave real-time PCR which confirmed the chance of the undergrowth of the fibre in the Fl line. The microarray and the quantitave real-time PCR showed a good correlation between the expression levels. Quantitave real-time PCR confirmed the chance of the undergrowth of the fibre in the Fl line which evaluated the expression patterns of 32 genes, including 17 from microarray and 15 from SSH using quantitative RT-PCR.