Limits...
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.

Show MeSH
A GBrowse view displaying genomic features.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: A GBrowse view displaying genomic features.

Mentions: The search result could further be optionally customized. For example, one could restrict or filter the number of SSRs displayed within the range 25–100 results per page in a table. The table can be sorted depending on the unique SSR-ID and the chromosome in which SSR is present. BLAST search was integrated into the database to find the nearest genic and non-genic SSR available for the query sequence identified in the chickpea genome thereby enabling to discover linked SSRs. User can click on the marker information displayed on the BLAST result page to visualize the marker details in the configured genome browser (GBrowse). Additional details such as the sequence of the SSR could be obtained by clicking on the expanding icon (“+” symbol).GBrowse enables the user to graphically visualize different details (gene, CDS) present in the genome by extracting information from the GFF file. User can customize the tracks displayed by selecting the genomic features of their interest from the “select tracks” tab and type a search term or landmark into the text field at the top of the page. This fetches the region of the genome that spans the landmark, and displays it in an image panel called the “detailed view”. The detailed view consists of 3 horizontal tracks, each of which contains a particular type of sequence feature like gene, CDS and predicted SSR (Figure 4).


CicArMiSatDB: the chickpea microsatellite database.

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

A GBrowse view displaying genomic features.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: A GBrowse view displaying genomic features.
Mentions: The search result could further be optionally customized. For example, one could restrict or filter the number of SSRs displayed within the range 25–100 results per page in a table. The table can be sorted depending on the unique SSR-ID and the chromosome in which SSR is present. BLAST search was integrated into the database to find the nearest genic and non-genic SSR available for the query sequence identified in the chickpea genome thereby enabling to discover linked SSRs. User can click on the marker information displayed on the BLAST result page to visualize the marker details in the configured genome browser (GBrowse). Additional details such as the sequence of the SSR could be obtained by clicking on the expanding icon (“+” symbol).GBrowse enables the user to graphically visualize different details (gene, CDS) present in the genome by extracting information from the GFF file. User can customize the tracks displayed by selecting the genomic features of their interest from the “select tracks” tab and type a search term or landmark into the text field at the top of the page. This fetches the region of the genome that spans the landmark, and displays it in an image panel called the “detailed view”. The detailed view consists of 3 horizontal tracks, each of which contains a particular type of sequence feature like gene, CDS and predicted SSR (Figure 4).

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