Journal of Environmental Biology

Genome wide identification of nucleotide-binding site leucine-rich repeat (NBS-LRR) gene encoding regions in Solanum lycopersicum resistant to environmental pathogens by computational methods

Paper received: 31.01.2019???????????????????? Revised received: 05.03.2019??????????????? Re-revised received: 16.03.2019????????????? Accepted: 25.03.2019

Authors Info

M.K. Chandraprakash*

and R.R. Thomas

Division of Social Sciences & Training, Indian Institute of Horticultural Research, Bengaluru-560 089, India

*Corresponding Author Email :

mkchandraprakash007@gmail.com 

Abstract

Aim: The nucleotide binding site leucine rich repeat (NBS-LRR) genes are responsive to pathogen strike in plants. This study focused on identifying the loci specific NBS-LRR gene encoding regions in tomato at whole genome level.    

Methodology: Major computational challenges in analyzing large genomic data using existing analytical tools were limited by the amount of memory used for reading large data. In this study, a specific algorithm was developed to identify a signature pattern associated with stress tolerant coding regions using stream readers for reading whole tomato genome, chromosome wise, to locate NBS-LRR coding sequences.

Results: The computer program reads chromosome wise data and extracts the potential stress tolerant coding regions. It was found that more than 300 disease resistance protein coding regions were found across all chromosome, specifically in chromosome 12 more NBS-LRR concentration were found and their respective locus were identified.

Interpretation: The identified disease resistance protein coding regions, specifically the NBS-LRR coding regions and their loci can be useful for plant breeders to select parental lines for developing plants tolerant to disease and pest invasion.

Key words: Computational methods, Environmental pathogens, NBS-LRR genes, Tomato genome

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