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/

Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach

“…It has the advantage being specific to the location over the targeted chromosome and hence can be used as the marker of any specific genes. Similar density of 341–671 SSRs/Mb has been reported in case of sugar beet (Iquebal et al, 2015 ).…”

OUP accepted manuscript

“…Similar higher abundance of di-nucleotide is also reported in other crops (44, 45). SSR relative density across all three species and their genotypes was found in 291–573 markers per Megabase, which is within the range of other reported crops like rice (370–490 markers per Megabase) and sugarbeet (341–671 markers per Megabase) (46).…”

Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

“…Although their importance in gene mapping and MAS, only few SSR markers are available for sesame research and the available ones fail to adequately represent the entire genome ( Dossa, 2016 ). More importantly, there is no database to search for sesame SSR information at the whole genome level and to perform functional analyses, as developed in other crops such as chickpea (CicArMiSatDB: Doddamani et al, 2014 ), (CMsDB: Parida et al, 2015 ), Cucumis melo (CmMDb: Bhawna et al, 2015 ), tomato (TomSatDB: Iquebal et al, 2013 ), sugar beet (SBMDb: Iquebal et al, 2015 ), brassicas ( Shi et al, 2014 ), etc.…”