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CicArMiSatDB: the chickpea microsatellite database

Dadakhalandar Doddamani, Mohan AVSK Katta, Aamir W Khan, Gaurav Agarwal, Trushar M Shah, Rajeev K Varshney
2014 BMC Bioinformatics  
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  ...  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  ...  This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium.  ... 
doi:10.1186/1471-2105-15-212 pmid:24952649 pmcid:PMC4230034 fatcat:hpjdfqppurhhvmtbcn6mqot7rm

Plant Molecular Biology Databases

Zubir Awan
2019 Highlights in BioScience  
We are here targeting to review and rank some of the plant databases according to their use and feature.  ...  Information in biological databases involves the role of genes, composition, chromosomal location, clinical impacts of mutations, and similarity of biological sequences and characteristics.  ...  CicArMiSatDB Doddamani et al. (11) reported a user-friendly relational database called the Chickpea Microsatellite Database to support genetic research and apps for reproduction.  ... 
doi:10.36462/h.biosci.20191 fatcat:56ptwcsu7ngqljfstdfgcrvu6i

CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

Mohit Verma, Vinay Kumar, Ravi K. Patel, Rohini Garg, Mukesh Jain, Nicholas James Provart
2015 PLoS ONE  
Furthermore, the CTDB represents a resource for the discovery of functional molecular markers (microsatellites and single nucleotide polymorphisms) between different chickpea types.  ...  A catalog of transcription factor families and their expression profiles in chickpea are available in the database.  ...  Acknowledgments RG acknowledges the INSPIRE Faculty Award from the Department of Science and Technology, New Delhi. Author Contributions  ... 
doi:10.1371/journal.pone.0136880 pmid:26322998 pmcid:PMC4556341 fatcat:rukrwsgduvgqniau34pn3slx34

Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource

Swarup K. Parida, Mohit Verma, Santosh K. Yadav, Supriya Ambawat, Shouvik Das, Rohini Garg, Mukesh Jain
2015 Frontiers in Plant Science  
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  ...  A total of 1470 polymorphic SSR markers from diverse coding and noncoding regions of the chickpea genome were developed.  ...  Acknowledgments This work was financially supported by the core grant from NIPGR and the Department of Biotechnology  ... 
doi:10.3389/fpls.2015.00645 pmid:26347762 pmcid:PMC4543896 fatcat:j46or7dpgjfrpitii7eczmqbzy

нут; селекция; сорт; образец; засухоустойчивость; раннеспелость; крупносемянность; аскохитоз

Л. Н. Кобизєва, Н. О. Вус
2016 Plant Breeding and Seed Production  
CicArMiSatDB: the chickpea microsatellite database/BMC Bioinformatics. 2014. URL:http://www.biomedcentral.com/1471-2105/15/212. 17. Doddamani D., Khan A. W., Katta M. A. V. S.  ...  CicArMiSatDB: the chickpea microsatellite database. URL: http://cicarmisatdb.icrisat.org. 16. Doddamani D., Katta M.A.V.S.K., Khan A. W., Agarwal G., Shah T. M., Varshney R. K.  ...  Yuriev of NAAS, Ukraine The aim and tasks of the study. To summarize and organize achievements of the world chickpea breeding to evaluate prospects of the crop production expansion.  ... 
doi:10.30835/2413-7510.2016.87609 fatcat:u6vatmte55ahxpmfey2yd5y2km

Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses

Rajesh Kumar Singh, Charul Singh, Ambika, B. S. Chandana, Rohit K. Mahto, Ranjana Patial, Astha Gupta, Vijay Gahlaut, Gayacharan, Aladdin Hamwieh, H. D. Upadhyaya, Rajendra Kumar
2022 Frontiers in Genetics  
These altogether have helped in broadening the narrow genetic base of chickpeas.  ...  identification and development of QTLs and high-density trait mapping of the global chickpea germplasm.  ...  /)CicArMiSatDB is a web resource for learning about Chickpea microsatellite (Simple Sequence Repeat) markers.It gives the chickpea breeding community useful marker information.This database can be used  ... 
doi:10.3389/fgene.2022.905771 fatcat:vejpbym5xreprfkuhzu7v4owwe

CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

Morad M. Mokhtar, Alsamman M. Alsamman, Haytham M. Abd-Elhalim, Achraf El Allali, Khalil Kashkush
2021 PLoS ONE  
In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome.  ...  Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers.  ...  Acknowledgments The authors acknowledge the African Supercomputing Center at Mohamed VI Polytechnic University for the supercomputing resources (https://ascc.um6p.ma/) made available for conducting the  ... 
doi:10.1371/journal.pone.0259540 pmid:34762703 pmcid:PMC8584679 fatcat:6oltugaqvbffdbcf7ulq6fzh6e

Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses

L. Ali, S. Azam, J. Rubio, H. Kudapa, E. Madrid, R. K. Varshney, P. Castro, W. Chen, J. Gil, T. Millan
2015 Euphytica  
Acknowledgments This work has been supported by the project INIA contract RTA2010-00059, co-financed by EU funds (FEDER).  ...  Ali L. acknowledges Ph.D. fellowship from Syrian Ministry of High Education and ICRISAT for supporting six months stay at the Center of Excellence in Genomic (ICRISAT, Patancheru, India).  ...  Also chickpea data base (http://cicarmisatdb. icrisat.org/index.html) was used to select five microsatellite markers into the targeted genomic regions of Ca3 and Ca1 (Supplementary file 2).  ... 
doi:10.1007/s10681-015-1369-4 fatcat:5noyhi77bfcmfifp7acnvaqvo4

Development of Highly Informative Genome-Wide Single Sequence Repeat Markers for Breeding Applications in Sesame and Construction of a Web Resource: SisatBase

Komivi Dossa, Jingyin Yu, Boshou Liao, Ndiaga Cisse, Xiurong Zhang
2017 Frontiers in Plant Science  
Although the importance of microsatellites markers or simple sequence repeats (SSR) in crop genotyping, genetics, and breeding applications is well established, only a little information exist concerning  ...  Furthermore, we have developed an online user-friendly database, SisatBase (http://www.sesame-bioinfo.org/SisatBase/), which provides free access to SSRs data as well as an integrated platform for functional  ...  More importantly, there is no database to search for sesame SSR information at the whole genome level and to perform functional analyses, as developed in other crops such as chickpea (CicArMiSatDB: Doddamani  ... 
doi:10.3389/fpls.2017.01470 pmid:28878802 pmcid:PMC5572293 fatcat:5gvhzbpnsrdahp3pxi3x3btdzm

Next generation breeding in pulses: Present status and future directions

Ashish Kumar, Abhishek Bohra, Reyazul Rouf Mir, Radheshyam Sharma, Abha Tiwari, Mohd Anwar Khan, Rajeev K. Varshney
2021 Crop Breeding and Applied Biotechnology  
During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources in pulse crops including high-throughput DNA markers, candidate gene  ...  The present review discusses current status and future scope of using next-generation breeding approaches in pulses that will cause not only an increase in the rate of developing climateresilient superior  ...  Melinda Gates Foundation (#OPP1114827, OPP1130244) for financial support and Science & Engineering Research Board (SERB) of Department of Science & Technology (DST), Government of India for providing the  ... 
doi:10.1590/1984-70332021v21sa26 fatcat:syxih7ofvzg6zcbgat3sj2rlqa

Genomic resources in plant breeding for sustainable agriculture

Mahendar Thudi, Ramesh Palakurthi, James C. Schnable, Annapurna Chitikineni, Susanne Dreisigacker, Emma Mace, Rakesh K. Srivastava, C. Tara Satyavathi, Damaris Odeny, Vijay K. Tiwari, Hon-Ming Lam, Yan Bin Hong (+11 others)
2020 Journal of plant physiology  
resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea  ...  In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants  ...  aspx Pipemicrodb Microsatellite database and primer generation tool for pigeonpea genome http://webapp.  ... 
doi:10.1016/j.jplph.2020.153351 pmid:33412425 pmcid:PMC7903322 fatcat:xujybmnnbrdnfnueet55wsb25i