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Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.

Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M - Front Plant Sci (2015)

Bottom Line: These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications.The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential.The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations.

View Article: PubMed Central - PubMed

Affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research New Delhi, India.

ABSTRACT
Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.

No MeSH data available.


Snapshots of the public web resource CMsDB showing its various utilities. The snapshots were taken from the database webpages.
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Figure 8: Snapshots of the public web resource CMsDB showing its various utilities. The snapshots were taken from the database webpages.

Mentions: We developed a public data resource, CMsDB, to provide a searchable interface to the SSR data reported in this study. CMsDB is publicly available at http://www.nipgr.res.in/CMsDB.html. The database provides browsable access to all the SSRs identified in desi and kabuli chickpea types, and polymorphic SSRs between them. CMsDB can be used to retrieve SSRs in desi and kabuli genomes using various simple [genomic location (chromosome number and position) and genomic feature (genic and/or inter-genic)] and advanced [motif type (di- to hexa-nucleotide), motif sequence, repeat number and repeat unit length] search parameters. Multiple parameters can be combined also to search for a specific set of SSRs as per user requirement. The output lists all the SSRs meeting the user-selected parameters(s) in tabulated format along with various information, including SSR identifier, chromosome number, motif type and length, genomic location (start and end position in bp) and location in the genomic features (genic/intergenic, gene identifier and intron/exon/upstream sequence). An option for downloading the flanking sequences (50–250 bp) of individual/multiple SSRs has also been provided. Polymorphic SSRs between desi/kabuli can also be searched/retrieved using similar parameters. Further, CMsDB provides information on the primers designed for the polymorphic SSRs. In addition to download the flanking sequences (50–250 bp), an option for viewing/downloading the designed primers for individual/multiple polymorphic SSRs has also been provided. Whole datasets have also been made available for download for high-throughput genotyping applications. We aim to update the database as the new versions of desi and kabuli reference genome sequence data set(s) will become available for chickpea. Figure 8 provides snapshots of various features and utilities of the CMsDB.


Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource.

Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M - Front Plant Sci (2015)

Snapshots of the public web resource CMsDB showing its various utilities. The snapshots were taken from the database webpages.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4543896&req=5

Figure 8: Snapshots of the public web resource CMsDB showing its various utilities. The snapshots were taken from the database webpages.
Mentions: We developed a public data resource, CMsDB, to provide a searchable interface to the SSR data reported in this study. CMsDB is publicly available at http://www.nipgr.res.in/CMsDB.html. The database provides browsable access to all the SSRs identified in desi and kabuli chickpea types, and polymorphic SSRs between them. CMsDB can be used to retrieve SSRs in desi and kabuli genomes using various simple [genomic location (chromosome number and position) and genomic feature (genic and/or inter-genic)] and advanced [motif type (di- to hexa-nucleotide), motif sequence, repeat number and repeat unit length] search parameters. Multiple parameters can be combined also to search for a specific set of SSRs as per user requirement. The output lists all the SSRs meeting the user-selected parameters(s) in tabulated format along with various information, including SSR identifier, chromosome number, motif type and length, genomic location (start and end position in bp) and location in the genomic features (genic/intergenic, gene identifier and intron/exon/upstream sequence). An option for downloading the flanking sequences (50–250 bp) of individual/multiple SSRs has also been provided. Polymorphic SSRs between desi/kabuli can also be searched/retrieved using similar parameters. Further, CMsDB provides information on the primers designed for the polymorphic SSRs. In addition to download the flanking sequences (50–250 bp), an option for viewing/downloading the designed primers for individual/multiple polymorphic SSRs has also been provided. Whole datasets have also been made available for download for high-throughput genotyping applications. We aim to update the database as the new versions of desi and kabuli reference genome sequence data set(s) will become available for chickpea. Figure 8 provides snapshots of various features and utilities of the CMsDB.

Bottom Line: These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications.The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential.The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations.

View Article: PubMed Central - PubMed

Affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research New Delhi, India.

ABSTRACT
Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.

No MeSH data available.