**6. Transcriptome studies in cotton**

The technique of isolating and characterizing the Spatio-temporal pool of mRNA to study the differential gene expression patterns between contrasting genotypes and understanding underlying alternative pathways for specific trait supremacy has been well implemented in cotton. Many characters have been targeted to find the key responsible genes and pathways, especially fiber initiation, and elongation being highly focused up on [61–68]. Other characters like Green and Brown colored cotton [69–71], Cadmium tolerance [72], Cold stress [73], Drought stress [74], Nematode resistance [75], Semigamy in Pima cotton [76], Whitefly mediated cotton leaf curl infection transcriptome [77], the transcriptome of Mepiquat chloride-induced compact types using in cotton [78] have also been done in cotton. Many studies have been carried out to identify genes that are differentially expressed, however paucity of the causes of the differential expression, hints us towards epigenetic regulations and transcription factors as the probable cause. Very few methylation studies have been carried out in cotton for fiber quality [79], male sterility [80], cold stress [81], salt tolerance [82], fruiting branch development [83]. Thus, there is huge scope for studies like differential methylation, studies on transcription factor, and correlating them with the differential expression patterns.
