TAILIEUCHUNG - Tools and resources for SNP mining in crop plants

Molecular genetic markers correspond to highly potent source for the study of plant genomes and the association of inherited phenotypic traits with underneath genetic variation. Single Nucleotide Polymorphism (SNPs) are most abundant form of molecular genetic marker which represents a single nucleotide difference between two individuals at a defined location. Compare to others SNPs are direct sequence variation which offers the precise nature of the allelic variants among different genotypes. Further, it signify recurrent type of genetic polymorphism with high density genome coverage. Advent of Next generation sequencing technology drives the exploration of sequence diversity for various crops. These studies revealed abundance of SNPs in plant systems, with the frequency of 100-300bp per detection based on EST(expressed sequence tags) sequence data has been performed for crops like maize, barley, tomato and trees like pine and in Arabidopsis which is a model plant. Similarly SNP identification based on array analyses has been published for Arabidopsis, rice, barley and maize. Amplicon resequencing approach has been utilized for the identification of SNPs in maize, soybean, Arabidopsis, rice, tomato, sugarbeet, barley and spruce. There are two sets of data to perform SNP mining one is reference sequence data and other is de novo sequence data. This mining for various datasets mainly comprise of subsequent steps: in first step we have to group sequence reads on the basis of their sequence resemblance and confirm identity of reads whether they are covering similar part of genome or they have the same transcript origin. | International Journal of Current Microbiology and Applied Sciences ISSN 2319-7706 Volume 8 Number 01 2019 Journal homepage http Review Article https Tools and Resources for SNP Mining in Crop Plants Saurabh Pandey1 Sunidhi Mishra2 and Kailash Chandra3 National Institute of Plant Genome Research Aruna Asaf Ali Marg New Delhi-110067 India 2Department of Vegetable Sciences Indira Gandhi Agricultural University Krishak Nagar Raipur Chhattisgarh 492012 India 3College of Agriculture . Jobner Fatehpur Shekhawati Sikar-332301 Rajasthan India Corresponding author ABSTRACT Keywords Tools Resources SNP Mining Crop Plants Article Info Accepted 17 December 2018 Available Online 10 January 2019 Molecular genetic markers correspond to highly potent source for the study of plant genomes and the association of inherited phenotypic traits with underneath genetic variation. Single Nucleotide Polymorphism SNPs are most abundant form of molecular genetic marker which represents a single nucleotide difference between two individuals at a defined location. Compare to others SNPs are direct sequence variation which offers the precise nature of the allelic variants among different genotypes. Further it signify recurrent type of genetic polymorphism with high density genome coverage. Advent of Next generation sequencing technology drives the exploration of sequence diversity for various crops. These studies revealed abundance of SNPs in plant systems with the frequency of 100-300bp per detection based on EST expressed sequence tags sequence data has been performed for crops like maize barley tomato and trees like pine and in Arabidopsis which is a model plant. Similarly SNP identification based on array analyses has been published for Arabidopsis rice barley and maize. Amplicon resequencing approach has been utilized for the identification of SNPs in maize soybean Arabidopsis rice tomato sugarbeet barley and spruce. There

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• SNP mining
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• SNP mining in crop plants
• Tools and resources
• Genome level inside plant breeding