International Publisher of Science, Technology and Medicine

Journal of Applied Bioinformatics & Computational Biology

Research Article

Computational Analysis of Short Tandem Repeat (STR) Markers from Genome Wide Expression Regions of Sugar Beet (Beeta vulgaris)

Virupaksh U Patil1*, Vanishree G1, Vivek Hegde2, Chaturvedi KK3 and Chakrabarti SK1
1ICAR-Central Potato Research Institute, Shimla-171001 (Himachal Pradesh), India
2ICAR-Central Tuber Crop Research Institute, Thiruvananthapuram – 695017 (Kerala), India
3ICAR-Indian Agriculture Statistical Research Institute, Pusa, New Delhi-110012 (Delhi), India
Corresponding author : Virupaksh U Patil
ICAR-Central Potato Research Institute, Shimla-171001 (Himachal Pradesh), India
Tel: 9418284300
E-mail: [email protected], [email protected]
Received: June 01, 2016 Accepted: June 27, 2016 Published: June 30, 2016
Citation: Patil VU, Vanishree G, Hegde V, Chaturvedi KK, Chakrabarti SK. (2016) Computational Analysis of Short Tandem Repeat (STR) Markers from Genome Wide Expression Regions of Sugar Beet (Beeta vulgaris). J Appl Bioinform Comput Biol 5:2. doi:10.4172/2329-9533.1000125

Abstract

Computational Analysis of Short Tandem Repeat (STR) Markers from Genome Wide Expression Regions of Sugar Beet (Beeta vulgaris)

Using transcriptome and expressed sequence tags (EST) data to extract short Tandem Repeats (STRs) also called Simple Sequence Repeats (SSRs) or microsatellites and develop markers has progressively become prevalent as number of sequencing data for various crops under public domain is mounting astonishingly. In the present study we have explored the genome-wide expression/genic STRs from sugar beet. Our in silico analysis results showed that among the 225,152 STRs present in the genome, only 12,881 were identified as transcript/genic markers. Of the total 27,421 predicted protein coding genes, 9,817 genes found to be carrying at least one STR marker and as many as 1,785 genes carried multiple STRs. Tri mer repeats were found to be abundantly present on the coding region and tetra mer was the least. Further, motif A/T was found to be more abundant than C/G in exons of sugar beet genes. The knowledge of these functional markers can directly be used for the molecular breeding of the crop as they are quickly obtained by electronic sorting, and present in expressed regions of the genome. .

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