title: Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding.
abstract: The transcript pool of a plant part, under any given condition, is a collection of mRNAs that will pave the way for a biochemical reaction of the plant to stimuli. Over the past decades, transcriptome study has advanced from Northern blotting to RNA sequencing (RNA-seq), through other techniques, of which real-time quantitative polymerase chain reaction (PCR) and microarray are the most significant ones. The questions being addressed by such studies have also matured from a solitary process to expression atlas and marker-assisted genetic enhancement. Not only genes and their networks involved in various developmental processes of plant parts have been elucidated, but also stress tolerant genes have been highlighted. The transcriptome of a plant with altered expression of a target gene has given information about the downstream genes. Marker information has been used for breeding improved varieties. Fortunately, the data generated by transcriptome analysis has been made freely available for ample utilization and comparison. The review discusses this wide variety of transcriptome data being generated in plants, which includes developmental stages, abiotic and biotic stress, effect of altered gene expression, as well as comparative transcriptomics, with a special emphasis on microarray and RNA-seq. Such data can be used to determine the regulatory gene networks, which can subsequently be utilized for generating improved plant varieties.
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.
authors.forename: Pinky
authors.initials: P
authors.lastname: Agarwal
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
authors.forename: Arunima
authors.initials: A
authors.lastname: Mahto
authors.forename: Sweta
authors.initials: S
authors.lastname: Das
authors.forename: Iny Elizebeth
authors.initials: IE
authors.lastname: Mathew
authors.forename: Naveen
authors.initials: N
authors.lastname: Malik
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
mesh_terms: D001709:Biotechnology; D032621:DNA Shuffling / Q000379:methods*; D023281:Genomics / Q000379:methods*; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
keywords: Functional genomics; Microarray; NGS; RNA-seq; Transcriptome