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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.


Identification and analysis of polymorphic SSRs between desi and kabuli chickpea. (A) Distribution of polymorphic SSRs in different classes. (B) Number of SSRs with different motif length (2 to >20) differences. (C) Frequency of selected (most abundant) motifs in the polymorphic SSRs. (D) Distribution of polymorphic SSRs in in different genomic features (various gene components and intergenic regions).
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Figure 3: Identification and analysis of polymorphic SSRs between desi and kabuli chickpea. (A) Distribution of polymorphic SSRs in different classes. (B) Number of SSRs with different motif length (2 to >20) differences. (C) Frequency of selected (most abundant) motifs in the polymorphic SSRs. (D) Distribution of polymorphic SSRs in in different genomic features (various gene components and intergenic regions).

Mentions: We identified 1835 genome-wide SSRs showing polymorphism between desi and kabuli chickpea based on their expansion/contraction of SSR repeat-length (ranged from 2 to >20 bp; Figures 3A,B). Among the polymorphic SSRs obtained, the di-nucleotide repeat-motifs (1425 SSRs, 77.6%) were most abundant followed by tri-nucleotide motifs (388, 21.1%) (Figure 3B). With the increase of SSR repeat-length variation, the number of SSRs showing polymorphism decreased, which indicates inverse correlation between fragment length polymorphism and frequency of polymorphic SSRs identified in desi and kabuli chickpea (Figure 3A). Maximum number of polymorphic SSRs showed ≥2-bp repeat-unit variation and 287 SSRs with >20-bp variation between desi and kabuli chickpea were identified. The AT/TA di-nucleotide repeats (1339, 73%) were maximum followed by TTA/TAA (132, 7.2%), AAT/ATT (128, 6.8%), and TAT/ATA (104, 5.7%) (Figure 3C). All the identified 1835 polymorphic SSRs were structurally annotated in intergenic regions, and coding and non-CDS components of genes. Maximum number of polymorphic SSR repeats were identified in the intergenic regions (1453 SSRs, 79.2%), (Figure 3D). The polymorphic SSRs identified within genes included highest number in the upstream sequences (190, 10.4%) followed by introns (143, 7.8%), exons (31, 1.7%) and minimum in 3′-UTRs (3, 0.16%) of genes. All classes of polymorphic SSR repeats including di- to hexa-nucleotide motifs were maximum in the intergenic sequences (Figure 3D). The di-nucleotide followed by tri-nucleotide SSR repeats were abundant in the upstream regions (139 di- and 49 tri-nucleotide) and intronic (126 di- and 15 tri-nucleotide) sequences of genes, whereas tri-nucleotide repeats were maximum in the coding regions. About 85% of the polymorphic SSRs were present on the eight chickpea chromosomes, whereas other 15% were located on the scaffolds of kabuli chickpea genome (Supplementary Figure S1). A complete list of polymorphic SSRs along with their motifs and genomic location in both genomes is given in the Supplementary Table S1.


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)

Identification and analysis of polymorphic SSRs between desi and kabuli chickpea. (A) Distribution of polymorphic SSRs in different classes. (B) Number of SSRs with different motif length (2 to >20) differences. (C) Frequency of selected (most abundant) motifs in the polymorphic SSRs. (D) Distribution of polymorphic SSRs in in different genomic features (various gene components and intergenic regions).
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Related In: Results  -  Collection

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Figure 3: Identification and analysis of polymorphic SSRs between desi and kabuli chickpea. (A) Distribution of polymorphic SSRs in different classes. (B) Number of SSRs with different motif length (2 to >20) differences. (C) Frequency of selected (most abundant) motifs in the polymorphic SSRs. (D) Distribution of polymorphic SSRs in in different genomic features (various gene components and intergenic regions).
Mentions: We identified 1835 genome-wide SSRs showing polymorphism between desi and kabuli chickpea based on their expansion/contraction of SSR repeat-length (ranged from 2 to >20 bp; Figures 3A,B). Among the polymorphic SSRs obtained, the di-nucleotide repeat-motifs (1425 SSRs, 77.6%) were most abundant followed by tri-nucleotide motifs (388, 21.1%) (Figure 3B). With the increase of SSR repeat-length variation, the number of SSRs showing polymorphism decreased, which indicates inverse correlation between fragment length polymorphism and frequency of polymorphic SSRs identified in desi and kabuli chickpea (Figure 3A). Maximum number of polymorphic SSRs showed ≥2-bp repeat-unit variation and 287 SSRs with >20-bp variation between desi and kabuli chickpea were identified. The AT/TA di-nucleotide repeats (1339, 73%) were maximum followed by TTA/TAA (132, 7.2%), AAT/ATT (128, 6.8%), and TAT/ATA (104, 5.7%) (Figure 3C). All the identified 1835 polymorphic SSRs were structurally annotated in intergenic regions, and coding and non-CDS components of genes. Maximum number of polymorphic SSR repeats were identified in the intergenic regions (1453 SSRs, 79.2%), (Figure 3D). The polymorphic SSRs identified within genes included highest number in the upstream sequences (190, 10.4%) followed by introns (143, 7.8%), exons (31, 1.7%) and minimum in 3′-UTRs (3, 0.16%) of genes. All classes of polymorphic SSR repeats including di- to hexa-nucleotide motifs were maximum in the intergenic sequences (Figure 3D). The di-nucleotide followed by tri-nucleotide SSR repeats were abundant in the upstream regions (139 di- and 49 tri-nucleotide) and intronic (126 di- and 15 tri-nucleotide) sequences of genes, whereas tri-nucleotide repeats were maximum in the coding regions. About 85% of the polymorphic SSRs were present on the eight chickpea chromosomes, whereas other 15% were located on the scaffolds of kabuli chickpea genome (Supplementary Figure S1). A complete list of polymorphic SSRs along with their motifs and genomic location in both genomes is given in the Supplementary Table S1.

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.