“Bio-informatic Applications in Genomics and Plant Breeding”

UNIVERSITY OF AGRICULTURAL SCIENCES, GKVK, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

SEMINAR – GPB 581 (0+1)

“Bio-informatic Applications in Genomics and Plant Breeding”

Information technology has been used in biosciences for a long time. The growth in importance of information technology is exemplified by the growth of several new interdisciplinary subfields of biology. One is “bioinformatics,” defined as the application of computers, databases, and computational methods to the management and analysis of biological information. Bioinformatics has become essential for almost every aspect of data management in modern biology. Bioinformatics is an interdisciplinary area of science and technology encompassing a systematic development and application of information technology solutions to handle biological information by addressing biological data collection and warehousing, data mining, database searches, analyses and interpretation, modelling, and product design.¹

The 3D coordinates of a protein are more useful if combined with data about the protein’s function, occurrence in different genomes, and interactions with other molecules. The biggest excitement currently lies with the availability of complete genome sequences for different organisms. The GenBank, EMBL, and DDBJ databases contain DNA sequences for individual genes that encode protein and RNA products. Bioinformatics plays an essential role in today’s plant breeding with regards to the development of new plant diagnostic tools, sequence analysis, clustering analysis, identification of disease resistance genes, and comparative genomics.² ⁴

The computational analysis of biological data is helpful in the prediction of 3D structure of proteins based on linear genomic information, elucidating the function of a molecule based on structure, stimulating metabolism from the biochemical functions of an organism, understanding genomic changes that result in inherited diseases, and discovering new drug molecules.³ Multiple sequence alignments are an essential tool for protein structure and function prediction, phylogeny inference, and other common tasks in sequence analysis.

BLAST is a sequence similarity search program that can be used via a web interface or as a stand-alone tool to compare a user’s query to a database of sequences. BLAST performs comparisons between pairs of sequences, searching for regions of local similarity. CLUSTALW is the most popular alignment tool to date; recent methods offer significantly better alignment quality and, in some cases, reduced computational cost. A phylogenetic tree or evolutionary tree is an illustration viewing the evolutionary relationships between diverse biological species or other entities.

A genome-wide association study on Horse gram with powdery mildew identified 10 significant associations similar to the MLO and RPW8.2 genes.³ Comparison of the gene coding sequences of the six legume species to determine their phylogenetic relationships was also conducted. The Ramachandran plot has provided a potent validation check on protein structure models, whether experimentally or computationally determined.

Bioinformatics faces multiple challenges, such as handling Big Data, dependency on others for primary data, ensuring the reproducibility of results, and achieving proper integration into academics. The application of graph databases to genomics is still in its infancy. The standard tabular design of traditional databases does not efficiently manage the diverse interactions between data or facilitate broad queries. The high degree of synteny among diverse plant species, commonality in traits, and the availability of expression and functional information of sequences have enabled the discovery of many useful traits for crop improvement.⁶

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REFERENCES

1. Blätke, M.A., Beier, S., Scholz, U., Gladilin, E., & Szymanski, J.J., 2021, Advances in applied bioinformatics in crops. Front. Res. Topics. Frontiers Media SA.

2. Luscombe, N.M., Greenbaum, D., & Gerstein, M., 2001, What is bioinformatics? An introduction and overview. Yearbook of Medical Informatics, 10(01): 83–100.

3. Mahesh, H.B., Prasannakumar, M.K., Manasa, K.G., Perumal, S., Khedikar, Y., Kagale, S., Soolanayakanahally, R.Y., Lohithaswa, H.C., Rao, A.M., & Hittalmani, S., 2021, Genome, transcriptome, and germplasm sequencing uncovers functional variation in the warm-season grain legume Horsegram (Macrotyloma uniflorum (Lam.) Verdc.). Front. Plant Sci., 12: 758119.

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