De Novo transcriptome sequencing explored cultivar specific sequence variation and differential expression of pigment synthesis genes in turmeric (Curcuma longa L.)

Turmeric contains a yellow color pigment that is curcumin, based on which different cultivars of turmeric have been released so far. Limited molecular studies on different pigment synthesis genes and lack of cultivar specific SSRs and SNPs in turmeric have confined the scope of identification of turmeric and establishment of their genetic makeup. In this study de novo transcriptome assembly of four turmeric cultivars i.e. Suroma, Roma, Lakadong and Megha was done. From the transcriptome analysis, cultivar specific SSRs, SNPs and transcripts encoding pigment synthesis genes were derived. A total of 113,862 contigs for Suroma, 125,762 for Roma, 113,021 for Lakadong and 116,711 for Megha were obtained. Multiple databases were used to acquire a complete annotation and the transcripts were functionally categorized using GO, KOG, KEGG and PlantCyc database. While presenting a large repertoire of cultivar specific quality SNPs and variations in SSRs, we have also demonstrated the functional basis of differentially expressed pigment synthesis genes among the four cultivars. The results of this study have clearly indicated their different genetic makeup. This report would enable authentic identification of these morphologically similar elite cultivars through use of cultivar specific SSRs and SNPs and to understand the molecular mechanisms behind differential expression of specific pigment synthesis genes in turmeric while providing scope for overall improvement of the taxa.