Molecular markers from the transcribed/expressed region of the genome in higher plants

In recent years, molecular marker technology in higher plants has witnessed a shift from the so-called random DNA markers (RDMs), developed in the past arbitrarily from genomic DNA and cDNA, to the molecular markers representing the transcriptome and the other coding sequences. These markers have been described as gene targeted markers (GTMs). Another specific class of markers includes the so-called functional markers (FMs), which are supposed to have a cause and effect relationship with the traits of interest. In this review, we first describe the development of these markers representing the transcriptome or genes per se; we then discuss the uses of these markers in some detail and finally add a note on the future directions of research and the implications of the wider application of these markers in crop improvement programmes. Using suitable examples, we describe markers of different classes derived from cDNA clones, expressed sequence tags (ESTs), gene sequences and the unique (coding) sequences obtained through methyl filtration or genome normalization (high C(0) t fraction) from gDNA libraries. While we briefly describe RFLPs, SSRs, AFLPs and SNPs developed from the transcriptome (cDNA clones and EST databases), we have discussed in more detail some of the novel markers developed from the transcriptome and specific genes. These novel markers include expressed sequence tag polymorphisms (ESTPs), conserved orthologue set (COS) markers, amplified consensus genetic markers (ACGMs), gene specific tags (GSTs), resistance gene analogues (RGAs) and exon-retrotransposon amplification polymorphism (ERAP). Uses of these markers have been discussed in some detail under the following headings: development of transcript and functional maps, estimations of genetic diversity, marker-assisted selection (MAS), candidate-gene (CG) approach and map-based cloning, genetical genomics and identification of eQTLs, study of genome organization and taxonomic and phylogenetic studies. At the end, we also append a list of websites relevant to further studies on the transcriptome. For want of space, considerable information including voluminous data in the form of 12 tables, and a long list of references cited in these tables, has been placed on the Internet as electronic supplementary material (ESM), which the readers may find useful.