BackgroundThe MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants.ResultsA genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5′ to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis.ConclusionA comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis identified several MYBs with potential role in development and stress response of plants.

SummaryGenetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stressresponsive transcriptome between drought-tolerant (DT) landraces ⁄ genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzymeencoding genes. Drought susceptibility of IR64 was attributable to significant downregulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis ⁄ gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant upregulation of a-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype.Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.