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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.


Unrooted phylogenetic tree depicting the genetic relationships among desi and kabuli genotypes. The tree was generated based on Nei’s genetic distance using genotyping data of 160 informative SSR markers in 31 desi and 15 kabuli chickpea genotypes. Molecular classification clearly differentiated genotypes into six different clusters, which corresponded to their cultivar-specific origin and parentage/known pedigree relationships.
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Figure 6: Unrooted phylogenetic tree depicting the genetic relationships among desi and kabuli genotypes. The tree was generated based on Nei’s genetic distance using genotyping data of 160 informative SSR markers in 31 desi and 15 kabuli chickpea genotypes. Molecular classification clearly differentiated genotypes into six different clusters, which corresponded to their cultivar-specific origin and parentage/known pedigree relationships.

Mentions: The pair-wise distance matrix among 46 desi and kabuli chickpea genotypes based on genotyping information of 160 validated polymorphic SSR markers revealed a broad range of genetic distance that varied from 0.16 (kabuli cv. BGD1105 – kabuli cv. Pusa1088) to 0.94 (desi cv. Vishal – desi cv. ICC4958) with an average of 0.68. Maximum average genetic distance was observed particularly among the accessions belonging to desi chickpea (0.65) in contrast to that detected within kabuli (0.57). The phylogenetic relationship among 31 desi and 15 kabuli chickpea genotypes has been depicted in an unrooted dendrogram (Figure 6). This set of informative genome-wide physically mapped SSR markers (160) clearly discriminated all 46 genotypes from each other and resulted in definite desi and kabuli cultivar-specific groupings. Most of the desi and kabuli genotypes were grouped in separate clusters (I and II), which further corresponded well with their known pedigree relationships and parentage with slight deviations. However, desi genotypes included under cluster I were further grouped into four different sub-clusters (Ia, Ib, Ic, and Id), while kabuli genotypes belonging to cluster II classified into two different sub-clusters (IIa and IIb; Figure 6).


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)

Unrooted phylogenetic tree depicting the genetic relationships among desi and kabuli genotypes. The tree was generated based on Nei’s genetic distance using genotyping data of 160 informative SSR markers in 31 desi and 15 kabuli chickpea genotypes. Molecular classification clearly differentiated genotypes into six different clusters, which corresponded to their cultivar-specific origin and parentage/known pedigree relationships.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: Unrooted phylogenetic tree depicting the genetic relationships among desi and kabuli genotypes. The tree was generated based on Nei’s genetic distance using genotyping data of 160 informative SSR markers in 31 desi and 15 kabuli chickpea genotypes. Molecular classification clearly differentiated genotypes into six different clusters, which corresponded to their cultivar-specific origin and parentage/known pedigree relationships.
Mentions: The pair-wise distance matrix among 46 desi and kabuli chickpea genotypes based on genotyping information of 160 validated polymorphic SSR markers revealed a broad range of genetic distance that varied from 0.16 (kabuli cv. BGD1105 – kabuli cv. Pusa1088) to 0.94 (desi cv. Vishal – desi cv. ICC4958) with an average of 0.68. Maximum average genetic distance was observed particularly among the accessions belonging to desi chickpea (0.65) in contrast to that detected within kabuli (0.57). The phylogenetic relationship among 31 desi and 15 kabuli chickpea genotypes has been depicted in an unrooted dendrogram (Figure 6). This set of informative genome-wide physically mapped SSR markers (160) clearly discriminated all 46 genotypes from each other and resulted in definite desi and kabuli cultivar-specific groupings. Most of the desi and kabuli genotypes were grouped in separate clusters (I and II), which further corresponded well with their known pedigree relationships and parentage with slight deviations. However, desi genotypes included under cluster I were further grouped into four different sub-clusters (Ia, Ib, Ic, and Id), while kabuli genotypes belonging to cluster II classified into two different sub-clusters (IIa and IIb; Figure 6).

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.