Plant Functional Genomics: Approaches and Applications

 

 

 Deployment of next generation sequencing tools has made it possible to sequence the whole genome within limited time period. At the moment, good number of crop plants genomes have been sequenced. Next challenge is to define function to these sequences (genes) and their regulation and interaction with the other genes. Though the effort towards the identification of genes function were started in early 1990s, however, after the sequencing of Arabidopsis thaliana (a model plant species), a mega project towards the exploration of genes function was initiated. Both the reverse (gene to phenotype) and forward genetics (phenotype to gene) approaches were used3. The functional genomics involves the attempts to understand function of genes through various approaches and platforms, which mainly includes, in-Silico analysis which is a genome annotation based approach involving prediction and comparison with existing DNA sequence information and data base through bioinformatic tools. Apart from in-Silico analysis functional genomics constitutes – expression analysis performed at protein and RNA level, down regulation through knock out (T-DNA and Transposon Tagging)/ knock down (RNAi) and over expression by activation tagging.

Manimaran et al. (2017) screened 70 Ac/Ds plants for salinity tolerance and identified one activation-tagged salt tolerant DS plant (DS-16, T3 generation) that showed enhanced expression of a novel ‘histone-like transcription factor’ belonging to rice NF-Y Subfamily C and named it as NF-YC 13. Kumari et al. (2018) developed the transgenic soybean plant conferring RNAi‑mediated resistance to yellow mosaic viruses using the intron-spliced hairpin construct encoding the coat protein sequence of MYMIV in the control of 35S promoter.

Thus functional genomics tools are mainly used in unravelling the functions of unknown genes – a huge genetic resource that can be utilized for improving the crop varieties using conventional breeding methods or by means of DNA markers assisted breeding.

References 

1. KUMARI, A., HADA, A., SUBRAMANYAM, K., THEBORAL, J., MISRA, S., GANAPATHI, A. AND MALATHI, V. G., 2018, RNAi-mediated resistance to yellow mosaic viruses in soybean targeting coat protein gene. Acta Physiologiae Plantarum, 40(2): 32.

 2. MANIMARAN, P., REDDY, S. V., MOIN, M., REDDY, M. R., YUGANDHAR, P., MOHANRAJ, S. S., BALACHANDRAN, S. M. AND KIRTI, P. B., 2017, Activation-tagging in indica rice identifies a novel transcription factor subunit, NF-YC13 associated with salt tolerance. Sci. Rep., 7(1): 9341.

3. MEHBOOB-UR-RAHMAN, Z. R., GUL, M. AND ZAFAR, Y., 2016, Plant functional genomics: Approaches and applications. App. Mol. Biotech., pp-172-201