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CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.

- PLoS ONE (2015)

Bottom Line: Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family.We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family.CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

View Article: PubMed Central - PubMed

Affiliation: National Bureau of Plant Genetic Resources, Genomics resources div., New Delhi-12, India.

ABSTRACT
Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

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A segment of comparative map displayed through CMap interface showing the syntenic correspondences (in blue lines) between (A) Cucumis melo chromosome 1 and Cucumis sativus chromosome 7, (B) Cucumis melo chromosome 2 and Citrullus lanatus chromosome 16.
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pone.0118630.g006: A segment of comparative map displayed through CMap interface showing the syntenic correspondences (in blue lines) between (A) Cucumis melo chromosome 1 and Cucumis sativus chromosome 7, (B) Cucumis melo chromosome 2 and Citrullus lanatus chromosome 16.

Mentions: The result of the respective query will be presented in a tabular format with marker ID, motif sequence, motif repeat, chromosomal location, start and end positions along with hyperlinks to corresponding primer information and physical map (Fig 4A). The hyperlink provided for ‘Primers’ under 'Get' column redirects to the primer data page that lists information about the corresponding primer which include forward and reverse primer sequences, respective melting temperatures (Tm), lengths and expected product size (Fig 4B). The 'Position' hyperlink under 'Physical' column redirects to CMap interface [39] where the physical locations of the markers in the melon genome can be viewed interactively (Fig 4C). The 'Map' tab gives CMap [39] based interactive physical map of all the microsatellite markers on the twelve chromosomes of the melon genome (Fig 5). This interactive map allows the user to study the syntenic relationships among any chromosome or all the chromosomes of the melon genome and cucumber and/or watermelon chromosomes by drawing interactive comparative maps (Fig 6).


CmMDb: a versatile database for Cucumis melo microsatellite markers and other horticulture crop research.

- PLoS ONE (2015)

A segment of comparative map displayed through CMap interface showing the syntenic correspondences (in blue lines) between (A) Cucumis melo chromosome 1 and Cucumis sativus chromosome 7, (B) Cucumis melo chromosome 2 and Citrullus lanatus chromosome 16.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401682&req=5

pone.0118630.g006: A segment of comparative map displayed through CMap interface showing the syntenic correspondences (in blue lines) between (A) Cucumis melo chromosome 1 and Cucumis sativus chromosome 7, (B) Cucumis melo chromosome 2 and Citrullus lanatus chromosome 16.
Mentions: The result of the respective query will be presented in a tabular format with marker ID, motif sequence, motif repeat, chromosomal location, start and end positions along with hyperlinks to corresponding primer information and physical map (Fig 4A). The hyperlink provided for ‘Primers’ under 'Get' column redirects to the primer data page that lists information about the corresponding primer which include forward and reverse primer sequences, respective melting temperatures (Tm), lengths and expected product size (Fig 4B). The 'Position' hyperlink under 'Physical' column redirects to CMap interface [39] where the physical locations of the markers in the melon genome can be viewed interactively (Fig 4C). The 'Map' tab gives CMap [39] based interactive physical map of all the microsatellite markers on the twelve chromosomes of the melon genome (Fig 5). This interactive map allows the user to study the syntenic relationships among any chromosome or all the chromosomes of the melon genome and cucumber and/or watermelon chromosomes by drawing interactive comparative maps (Fig 6).

Bottom Line: Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family.We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family.CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

View Article: PubMed Central - PubMed

Affiliation: National Bureau of Plant Genetic Resources, Genomics resources div., New Delhi-12, India.

ABSTRACT
Cucumis melo L. that belongs to Cucurbitaceae family ranks among one of the highest valued horticulture crops being cultivated across the globe. Besides its economical and medicinal importance, Cucumis melo L. is a valuable resource and model system for the evolutionary studies of cucurbit family. However, very limited numbers of molecular markers were reported for Cucumis melo L. so far that limits the pace of functional genomic research in melon and other similar horticulture crops. We developed the first whole genome based microsatellite DNA marker database of Cucumis melo L. and comprehensive web resource that aids in variety identification and physical mapping of Cucurbitaceae family. The Cucumis melo L. microsatellite database (CmMDb: http://65.181.125.102/cmmdb2/index.html) encompasses 39,072 SSR markers along with its motif repeat, motif length, motif sequence, marker ID, motif type and chromosomal locations. The database is featured with novel automated primer designing facility to meet the needs of wet lab researchers. CmMDb is a freely available web resource that facilitates the researchers to select the most appropriate markers for marker-assisted selection in melons and to improve breeding strategies.

Show MeSH