Identification of genes associated with chapatti quality using transcriptome analysis

Analysis of gene expression in developing grains of 20 diverse wheat genotypes was used to identify genes differentially expressed in genotypes with good chapatti quality. The genes that were identified as potentially playing an important role in chapatti quality included both annotated genes and genes of unknown function. Genes of known function differentially expressed in wheat genotypes with good chapatti quality included those associated with cell wall polysaccharide biosynthesis (upregulated) and protein synthesis (upregulation of many gliadins and down regulation of many LMW glutenins and other storage proteins). The expression of many other genes was associated with chapatti quality. The wbm gene that was upregulated in good bread wheats was not highly expressed in wheats known for good chapatti quality. This confirms that in wheat genotypes, the expression of some of the transcripts associated with good bread and chapatti quality characteristics are negatively correlated. This RNAseq analysis provides wheat breeders with an insight into the genes found to be associated with good chapatti quality. The large differences in the quality requirements for bread and chapatti make it difficult for breeders to breed wheat for both good bread and chapatti quality in the same genotype.