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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.


Distribution of SSRs identified from desi and kabuli chickpea genomes in different regions of the chickpea genome. The bar graph displays the number of SSRs of different classes located in different genomic features (various gene components and intergenic regions) of the chickpea genome.
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Figure 2: Distribution of SSRs identified from desi and kabuli chickpea genomes in different regions of the chickpea genome. The bar graph displays the number of SSRs of different classes located in different genomic features (various gene components and intergenic regions) of the chickpea genome.

Mentions: A total of 519.8 and 522.3 Mb sequences of desi and kabuli chickpea genomes, respectively, were utilized for mining and characterization of SSR motifs. Based on these analyses, 74941 and 81845 perfect SSRs (excluding mono-nucleotides) were identified in desi and kabuli chickpea with an average density of 0.144 SSR/kb and 0.157 SSR/kb, respectively (Table 1). The overall frequency of compound SSRs identified in desi (2563, 0.005 SSRs/kb) and kabuli (2470, 0.004 SSRs/kb) chickpea was almost comparable with each other. In both the genomes, di-nucleotide repeat-motifs (desi: 41457, 55.3% and kabuli: 47127, 57.6%) were most prevalent followed by tri- and tetra-nucleotides (Table 1). In terms of proportion of total number of SSRs identified, the long hyper-variable class I repeats varied from 49.8% (40789) in kabuli to 50.3% (37737) in desi chickpea. The class I and class II di-nucleotide repeat-motifs were present in maximum fraction varying from 49.1 (18537) to 62.3% (25568) in desi and kabuli chickpea (Figure 1A). Next, the tri-nucleotide SSR repeat-motifs were most abundant (varied from 34.2 to 38.4%) in both class I and class II SSRs, while tetra-, penta-, and hexa-nucleotide motifs were completely absent in case of class II SSRs. The frequency of AT-rich di-nucleotide repeat-motifs (32354 SSRs in desi, 43.2% and 37977 SSRs in kabuli, 46.4%) was maximum in both desi and kabuli chickpea followed by AAT/ATT-rich tri-nucleotide SSRs (21113 SSRs, 28.2% in desi and 22003, 26.9% in kabuli) and AAAT/ATTT-rich tetra-nucleotide SSRs (3095, 4.1% and 2924, 3.6%) (Figure 1B). The structural annotation of identified SSRs in desi genome revealed their highest frequency in intergenic regions (64961 SSRs) followed by introns (6762), exons (3218), CDS (1816), and upstream regions (3289) (Figure 2). All five different classes of SSR repeat-motifs (di- to hexa-nucleotides) were predominant particularly in the intergenic regions as compared to various coding and non-CDS components of genes. However, within genes, the frequency of di- (4191), tetra- (462), and penta-nucleotide (84) SSR repeat-motifs were maximum in the intronic and upstream sequences, whereas tri- (2100) and hexa-nucleotide (76) motifs were abundant in the exons (Figure 2). Maximum number of tri-nucleotide SSR repeat-motifs was found in the CDS (1673 SSRs), whereas upstream regions (3029), and 5’- (703) and 3’-UTRs (168) were rich in di-nucleotide repeat-motifs.


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)

Distribution of SSRs identified from desi and kabuli chickpea genomes in different regions of the chickpea genome. The bar graph displays the number of SSRs of different classes located in different genomic features (various gene components and intergenic regions) of the chickpea genome.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 2: Distribution of SSRs identified from desi and kabuli chickpea genomes in different regions of the chickpea genome. The bar graph displays the number of SSRs of different classes located in different genomic features (various gene components and intergenic regions) of the chickpea genome.
Mentions: A total of 519.8 and 522.3 Mb sequences of desi and kabuli chickpea genomes, respectively, were utilized for mining and characterization of SSR motifs. Based on these analyses, 74941 and 81845 perfect SSRs (excluding mono-nucleotides) were identified in desi and kabuli chickpea with an average density of 0.144 SSR/kb and 0.157 SSR/kb, respectively (Table 1). The overall frequency of compound SSRs identified in desi (2563, 0.005 SSRs/kb) and kabuli (2470, 0.004 SSRs/kb) chickpea was almost comparable with each other. In both the genomes, di-nucleotide repeat-motifs (desi: 41457, 55.3% and kabuli: 47127, 57.6%) were most prevalent followed by tri- and tetra-nucleotides (Table 1). In terms of proportion of total number of SSRs identified, the long hyper-variable class I repeats varied from 49.8% (40789) in kabuli to 50.3% (37737) in desi chickpea. The class I and class II di-nucleotide repeat-motifs were present in maximum fraction varying from 49.1 (18537) to 62.3% (25568) in desi and kabuli chickpea (Figure 1A). Next, the tri-nucleotide SSR repeat-motifs were most abundant (varied from 34.2 to 38.4%) in both class I and class II SSRs, while tetra-, penta-, and hexa-nucleotide motifs were completely absent in case of class II SSRs. The frequency of AT-rich di-nucleotide repeat-motifs (32354 SSRs in desi, 43.2% and 37977 SSRs in kabuli, 46.4%) was maximum in both desi and kabuli chickpea followed by AAT/ATT-rich tri-nucleotide SSRs (21113 SSRs, 28.2% in desi and 22003, 26.9% in kabuli) and AAAT/ATTT-rich tetra-nucleotide SSRs (3095, 4.1% and 2924, 3.6%) (Figure 1B). The structural annotation of identified SSRs in desi genome revealed their highest frequency in intergenic regions (64961 SSRs) followed by introns (6762), exons (3218), CDS (1816), and upstream regions (3289) (Figure 2). All five different classes of SSR repeat-motifs (di- to hexa-nucleotides) were predominant particularly in the intergenic regions as compared to various coding and non-CDS components of genes. However, within genes, the frequency of di- (4191), tetra- (462), and penta-nucleotide (84) SSR repeat-motifs were maximum in the intronic and upstream sequences, whereas tri- (2100) and hexa-nucleotide (76) motifs were abundant in the exons (Figure 2). Maximum number of tri-nucleotide SSR repeat-motifs was found in the CDS (1673 SSRs), whereas upstream regions (3029), and 5’- (703) and 3’-UTRs (168) were rich in di-nucleotide repeat-motifs.

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.