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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.


Diagrammatic representation of polymorphic SSRs present in different components of chickpea genes. Introns and exons are represented by lines and boxes, respectively. Different components of exons are represented in different shaded boxes. The SSR motifs present in different genic regions have been highlighted in gray texture. The motif and its frequency in both chickpea (desi/kabuli) types are also given. Gene ID and length (bp) are given on right side.
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Figure 4: Diagrammatic representation of polymorphic SSRs present in different components of chickpea genes. Introns and exons are represented by lines and boxes, respectively. Different components of exons are represented in different shaded boxes. The SSR motifs present in different genic regions have been highlighted in gray texture. The motif and its frequency in both chickpea (desi/kabuli) types are also given. Gene ID and length (bp) are given on right side.

Mentions: The forward and reverse primers from the flanking sequences of polymorphic 1835 SSR repeat-motifs were designed. The structural annotation and organization of selected SSR repeats located in different components of genes are presented in the Figure 4. We could design primers for 1470 (80.1%) polymorphic SSRs, which included 1151 (78.3%) in the intergenic regions, 150 (10.2%) in the upstream regulatory sequences, 125 (8.5%) in the introns, 31 (2.1%) in the exons, 17 (1.2%) in the 5′-UTRs, 11 (0.75%) in the CDS, and 3 (0.20%) in the 3′-UTRs (Supplementary Table S1). At least 85% of these genome-wide unique SSR markers were mapped on the chickpea chromosome pseudomolecules (Supplementary Figure S1). Maximum number of markers were mapped on chromosome 4 (224, 15.2%) followed by chromosome 5 (206, 14%), while minimum number of markers mapped on chromosome 8 (72, 4.9%).


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)

Diagrammatic representation of polymorphic SSRs present in different components of chickpea genes. Introns and exons are represented by lines and boxes, respectively. Different components of exons are represented in different shaded boxes. The SSR motifs present in different genic regions have been highlighted in gray texture. The motif and its frequency in both chickpea (desi/kabuli) types are also given. Gene ID and length (bp) are given on right side.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Diagrammatic representation of polymorphic SSRs present in different components of chickpea genes. Introns and exons are represented by lines and boxes, respectively. Different components of exons are represented in different shaded boxes. The SSR motifs present in different genic regions have been highlighted in gray texture. The motif and its frequency in both chickpea (desi/kabuli) types are also given. Gene ID and length (bp) are given on right side.
Mentions: The forward and reverse primers from the flanking sequences of polymorphic 1835 SSR repeat-motifs were designed. The structural annotation and organization of selected SSR repeats located in different components of genes are presented in the Figure 4. We could design primers for 1470 (80.1%) polymorphic SSRs, which included 1151 (78.3%) in the intergenic regions, 150 (10.2%) in the upstream regulatory sequences, 125 (8.5%) in the introns, 31 (2.1%) in the exons, 17 (1.2%) in the 5′-UTRs, 11 (0.75%) in the CDS, and 3 (0.20%) in the 3′-UTRs (Supplementary Table S1). At least 85% of these genome-wide unique SSR markers were mapped on the chickpea chromosome pseudomolecules (Supplementary Figure S1). Maximum number of markers were mapped on chromosome 4 (224, 15.2%) followed by chromosome 5 (206, 14%), while minimum number of markers mapped on chromosome 8 (72, 4.9%).

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.