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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.


Population genetic structure inferred best possible structure among desi and kabuli chickpea genotypes. The genotyping data of 160 informative genome-wide SSR markers in 31 desi and 15 kabuli chickpea genotypes was used for this analysis. These mapped markers assigned 46 chickpea genotypes into five populations that majorly grouped accordingly by their cultivar-specific origin and parentage/pedigree relationships. The accessions represented by vertical bars along the horizontal axis were classified into K color segments based on their estimated membership fraction in each K cluster. Five diverse colors represent different population groups based on optimal population number K = 5.
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Figure 7: Population genetic structure inferred best possible structure among desi and kabuli chickpea genotypes. The genotyping data of 160 informative genome-wide SSR markers in 31 desi and 15 kabuli chickpea genotypes was used for this analysis. These mapped markers assigned 46 chickpea genotypes into five populations that majorly grouped accordingly by their cultivar-specific origin and parentage/pedigree relationships. The accessions represented by vertical bars along the horizontal axis were classified into K color segments based on their estimated membership fraction in each K cluster. Five diverse colors represent different population groups based on optimal population number K = 5.

Mentions: The population genetic structure among 31 desi and 15 kabuli chickpea genotypes was determined using 160 validated polymorphic SSR markers with varying levels of population numbers (K = 2–10) with 20 replications. The optimization of K inferred that at K = 5, the average estimate of Ln P(D) across 20 independent replications plateaus and also best replicate giving maximum log likelihood values with sharp peak was obtained. All 46 chickpea genotypes were majorly classified into two distinct high resolution population groups (Figure 7). The population groups, I (31 desi and one kabuli chickpea) and II (14 kabuli chickpea) contained the genotypes mostly from desi and kabuli chickpea, respectively. The desi population group (I) was further classified into four sub-population groups; Ia (10 desi and one kabuli chickpea genotypes), Ib (10 desi), Ic (8 desi), and Id (3 desi) (Figure 7). The cultivar-specific classification and geographical origin of 46 chickpea genotypes belonging to all the five individual population groups are provided in the Supplementary Table S3. The population groupings obtained among 46 chickpea genotypes corresponded well with their origin and pedigree relationships/parentage. This was further consistent with the clustering patterns and genetic relationships as obtained by the NJ tree analysis. Further, molecular genetic variation among and within five populations was estimated using above 160 informative SSR markers. It revealed a wider level of quantitative genetic differentiation (FST varied from 0.16–0.91 with an average of 0.64) among five population groups. The genetic variation among the five population groups (mean FST: 0.62) was higher than that estimated within populations (0.53). Higher molecular diversity of population group I (mean FST: 0.86) as compared to group II (0.69) was evident. Within population groups I and II, maximum divergence was observed in population groups Ib (mean FST: 0.83) and IIb (0.65), respectively. All the 46 chickpea genotypes clearly belonged to a structured population of five distinct groups in which about 74.2% of inferred ancestry of each group was derived from one of the model-based population and remaining ∼25.8% contained admixed ancestry. Maximum admixtures (20.3%) of the three desi population groups (Ib, Ic, and Id) with kabuli population (II) were observed.


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)

Population genetic structure inferred best possible structure among desi and kabuli chickpea genotypes. The genotyping data of 160 informative genome-wide SSR markers in 31 desi and 15 kabuli chickpea genotypes was used for this analysis. These mapped markers assigned 46 chickpea genotypes into five populations that majorly grouped accordingly by their cultivar-specific origin and parentage/pedigree relationships. The accessions represented by vertical bars along the horizontal axis were classified into K color segments based on their estimated membership fraction in each K cluster. Five diverse colors represent different population groups based on optimal population number K = 5.
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Related In: Results  -  Collection

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Figure 7: Population genetic structure inferred best possible structure among desi and kabuli chickpea genotypes. The genotyping data of 160 informative genome-wide SSR markers in 31 desi and 15 kabuli chickpea genotypes was used for this analysis. These mapped markers assigned 46 chickpea genotypes into five populations that majorly grouped accordingly by their cultivar-specific origin and parentage/pedigree relationships. The accessions represented by vertical bars along the horizontal axis were classified into K color segments based on their estimated membership fraction in each K cluster. Five diverse colors represent different population groups based on optimal population number K = 5.
Mentions: The population genetic structure among 31 desi and 15 kabuli chickpea genotypes was determined using 160 validated polymorphic SSR markers with varying levels of population numbers (K = 2–10) with 20 replications. The optimization of K inferred that at K = 5, the average estimate of Ln P(D) across 20 independent replications plateaus and also best replicate giving maximum log likelihood values with sharp peak was obtained. All 46 chickpea genotypes were majorly classified into two distinct high resolution population groups (Figure 7). The population groups, I (31 desi and one kabuli chickpea) and II (14 kabuli chickpea) contained the genotypes mostly from desi and kabuli chickpea, respectively. The desi population group (I) was further classified into four sub-population groups; Ia (10 desi and one kabuli chickpea genotypes), Ib (10 desi), Ic (8 desi), and Id (3 desi) (Figure 7). The cultivar-specific classification and geographical origin of 46 chickpea genotypes belonging to all the five individual population groups are provided in the Supplementary Table S3. The population groupings obtained among 46 chickpea genotypes corresponded well with their origin and pedigree relationships/parentage. This was further consistent with the clustering patterns and genetic relationships as obtained by the NJ tree analysis. Further, molecular genetic variation among and within five populations was estimated using above 160 informative SSR markers. It revealed a wider level of quantitative genetic differentiation (FST varied from 0.16–0.91 with an average of 0.64) among five population groups. The genetic variation among the five population groups (mean FST: 0.62) was higher than that estimated within populations (0.53). Higher molecular diversity of population group I (mean FST: 0.86) as compared to group II (0.69) was evident. Within population groups I and II, maximum divergence was observed in population groups Ib (mean FST: 0.83) and IIb (0.65), respectively. All the 46 chickpea genotypes clearly belonged to a structured population of five distinct groups in which about 74.2% of inferred ancestry of each group was derived from one of the model-based population and remaining ∼25.8% contained admixed ancestry. Maximum admixtures (20.3%) of the three desi population groups (Ib, Ic, and Id) with kabuli population (II) were observed.

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.