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CicArMiSatDB: the chickpea microsatellite database.

Doddamani D, Katta MA, Khan AW, Agarwal G, Shah TM, Varshney RK - BMC Bioinformatics (2014)

Bottom Line: Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding.However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program.Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement.

View Article: PubMed Central - HTML - PubMed

Affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India. r.k.varshney@cgiar.org.

ABSTRACT

Background: Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program. Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement.

Description: In order to assist genetic studies and breeding applications, we have developed a user friendly relational database named the Chickpea Microsatellite Database (CicArMiSatDB http://cicarmisatdb.icrisat.org). This database provides detailed information on SSRs along with their features in the genome. SSRs have been classified and made accessible through an easy-to-use web interface.

Conclusions: This database is expected to help chickpea community in particular and legume community in general, to select SSRs of particular type or from a specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement.

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Database schema of CicArMiSatDB.
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Figure 1: Database schema of CicArMiSatDB.

Mentions: The information on SSRs was stored in five database tables (FigureĀ 1). Each SSR was represented with a unique identifier called SSR_ID. The description of database tables is as follows.


CicArMiSatDB: the chickpea microsatellite database.

Doddamani D, Katta MA, Khan AW, Agarwal G, Shah TM, Varshney RK - BMC Bioinformatics (2014)

Database schema of CicArMiSatDB.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230034&req=5

Figure 1: Database schema of CicArMiSatDB.
Mentions: The information on SSRs was stored in five database tables (FigureĀ 1). Each SSR was represented with a unique identifier called SSR_ID. The description of database tables is as follows.

Bottom Line: Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding.However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program.Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement.

View Article: PubMed Central - HTML - PubMed

Affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India. r.k.varshney@cgiar.org.

ABSTRACT

Background: Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program. Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement.

Description: In order to assist genetic studies and breeding applications, we have developed a user friendly relational database named the Chickpea Microsatellite Database (CicArMiSatDB http://cicarmisatdb.icrisat.org). This database provides detailed information on SSRs along with their features in the genome. SSRs have been classified and made accessible through an easy-to-use web interface.

Conclusions: This database is expected to help chickpea community in particular and legume community in general, to select SSRs of particular type or from a specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement.

Show MeSH