title: SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
abstract: DNA marker plays important role as valuable tools to increase crop productivity by finding plausible answers to genetic variations and linking the Quantitative Trait Loci (QTL) of beneficial trait. Prior approaches in development of Short Tandem Repeats (STR) markers were time consuming and inefficient. Recent methods invoking the development of STR markers using whole genomic or transcriptomics data has gained wide importance with immense potential in developing breeding and cultivator improvement approaches. Availability of whole genome sequences and in silico approaches has revolutionized bulk marker discovery. We report world's first sugarbeet whole genome marker discovery having 145 K markers along with 5 K functional domain markers unified in common platform using MySQL, Apache and PHP in SBMDb. Embedded markers and corresponding location information can be selected for desired chromosome, location/interval and primers can be generated using Primer3 core, integrated at backend. Our analyses revealed abundance of 'mono' repeat (76.82%) over 'di' repeats (13.68%). Highest density (671.05 markers/Mb) was found in chromosome 1 and lowest density (341.27 markers/Mb) in chromosome 6. Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density. This will enable present linkage map having marker distance of ∼2 cM, i.e. from 200 to 2.6 Kb, thus facilitating QTL/gene mapping. We also report e-PCR-based detection of 2027 polymorphic markers in panel of five genotypes. These markers can be used for DUS test of variety identification and MAS/GAS in variety improvement program. The present database presents wide source of potential markers for developing and implementing new approaches for molecular breeding required to accelerate industrious use of this crop, especially for sugar, health care products, medicines and color dye. Identified markers will also help in improvement of bioenergy trait of bioethanol and biogas production along with reaping advantage of crop efficiency in terms of low water and carbon footprint especially in era of climate change. Database URL: http://webapp.cabgrid.res.in/sbmdb/.
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
authors.forename: Mir Asif
authors.initials: MA
authors.lastname: Iquebal
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
authors.forename: Sarika
authors.initials: S
authors.lastname: Jaiswal
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
authors.forename: U B
authors.initials: UB
authors.lastname: Angadi
authors.affiliation: Biotechnology Unit, Department of Botany, Jai Narain Vyas University, Jodhpur 342003, India, Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, PO Box 123 Broadway New South Wales 2007, Australia.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
authors.forename: Vasu
authors.initials: V
authors.lastname: Arora
authors.affiliation: National Bureau of Agriculturally Important Microorganisms, Kusmaur, Mau NathBhanjan, Uttar Pradesh 275101, India and Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, India.
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India.
authors.forename: Anil
authors.initials: A
authors.lastname: Rai
authors.affiliation: Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, PUSA, New Delhi 110012, India, dineshkumarbhu@gmail.com.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Kumar
mesh_terms: D027461:Beta vulgaris / Q000235:genetics*; D056804:Biofuels; D032461:Chromosomes, Plant / Q000235:genetics; D030541:Databases, Genetic; D005819:Genetic Markers; D018745:Genome, Plant; D007221:Industry; D018895:Microsatellite Repeats / Q000235:genetics*; D059372:Nucleotide Motifs / Q000235:genetics
chemical_list: D056804:Biofuels; D005819:Genetic Markers