GCP Product Catalogue

The Product Catalogue is an evolving  compilation of  a diverse array of  products derived from tangible outputs of projects supported in whole or in part by the CGIAR Generation Challenge Programme.  As projects mature, more products are added. Products are listed under the specific project crop or ‘Global’.   Under each crop, you will find diverse types of products, such as  germplasm, markers, genomics resources and informatics applications.  ‘Global’ includes products  applicable to several or all crops and generally includes informatics tools and learning materials. We consider all catalogued products as useful. However, our user base is highly varied and includes upstream as well as downstream plant scientists. Not all products will be of direct interest to breeders. Consequently, a BUL (Breeding Use Level) rating has been provided to indicate the direct usefulness of products to breeders:

Breeding Use Levels
BULDescription
1 Ready to use for breeding
 (I.e. predictive markers, germplasm of acceptable agronomic type containing a well-defined and characterized trait, and etc.).
2 Qualified use for breeding
 (i.e germplasm in which trait genetics have not been well defined or markers that may be informative but not necessarily predictive).
3 Indirectly useful for breeding
 (i.e. genomic resources from which downstream products for breeding are developed and many informatics applications).
4 Not developed for breeding, per se
 (i.e. miscellaneous information as socio-economic reports).


How to use this table:

  • With the exception of BUL, you can sort by column by clicking on the title of each column
  • You can search for any term, word, or keyword by typing it into the search box above the table
  • You can export data by clicking on the CSV link above the table

CSV
Crop/Area Product Type Description Access BUL
Cassava F1S1 genetic stocks for starch, beta carotene, DM, starch and CBSD Germplasm Agronomically good materials fixed for pest and disease resistance and have different quality or other desirable breeding attributes. Making intercrosses between these F1S1 provides a quick way to de (read more) Contact: Chiedozie Egesi, National Root Crops Research Institute, Umdike, Nigeria
cegesi@yahoo.com
1
Chickpea A microsatellite kit for the GCP chickpea reference germplasm set Genomic Resources Reference kit of 35 SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks Available on-line from ICRISAT, Patancheru, India

http://www.icrisat.org/bt-genomics-chickpea.htm
2
Chickpea DaRT marker array for chickpea Genomic Resources An array of 15,360 DArT markers for chickpea discovered by screening a library of several thousand fragments from a genomic representation prepared from a pool of DNA samples that encompass the divers (read more) Available through Diversity Arrays Technology Pty Ltd (DArT P/L)

http://www.diversityarrays.com
3
Chickpea A validated Chickpea germplasm reference collection Germplasm The Chickpea Reference Set is composed of a core set of 300 accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a criti (read more) Available from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Germplasm Bank
refer to: http://www.icrisat.org/chickpea-genebank-reference-set.htm
Contact: H D Upadhy (read more)
2
Chickpea A SNP dataset for chickpea Genomic Resources A set of 2,005 SNPs validated and optimzed by KASPar assays Refer to: http://europepmc.org/articles/PMC3437486/reload=0;jsessionid=Cf1PzJomW0EHSzgJz4O3.10

Contact Rajeev Varshney, ICRISAT

r.k.varshney@cgiar.org
3
Chickpea SSR markers for chickpea Genomic Resources A total of 1655 SSR markers (Table 1) were developed from enriched libraries (311; Nayak et al, 20092010, Theor Appl Genet 120: 1415-1441) and BAC-end sequences (1344, Varshney et al, 2009aThudi et al (read more) Contact R. K. Varshney, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
r.k.varshney@cgiar.org

Also refer to: 1) Nayak S, Zhu H, Varghese N, Choi H- (read more)
3
Chickpea A reference genetic map for chickpea Genomic Resources A comprehensive genetic map comprising 1,291 marker loci including SSRs, DArTs and SNPs on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed The number of markers per lin (read more) Contact R. K. Varshney, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India

r.k.varshney@cgiar.org

Also refer to: Thudi M, Bohra A, Nayak SN, Varghese N (read more)
3
Chickpea Drought and salinity reponsive ESTs in the chickpea genome Genomic Resources A total of 20,162 (18,435 high quality) drought- and salinity- responsive ESTs were generated from ten different root tissue cDNA libraries of chickpea. Sequence editing, clustering and assembly analy (read more) Open Access - http://www.biomedcentral.com/1471-2164/10/523

Also refer to:Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Jayashree B, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KH (read more)
3
Chickpea Markers for major drought tolerance QTL for in chickpea Informative Markers Predictive markers for QTL associated with a ‘hotspot' harbouring several for root-related traits for drought tolerance contributing about 30 percent of phenotypic variation as well as for CID (60 (read more) Contact R. K. Varshney,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India for markers..

r.k.varshney@cgiar.org
1
Chickpea MAGIC lines for trait mapping Germplasm A total of 1200 MAGIC lines were developed by using eight desi chickpea elite lines/cultivars (ICC 4958, ICCV 10, JAKI 9218, JG 11, JG 130, JG 16, ICCV 97105 and ICCV 00108) from Ethiopia, Kenya and (read more) Send request to: Dr Pooran Gaur, Principal Scientist (Chickpea Breeding), ICRISAT, Patancheru, Hyderabad 502 324, AP, India; Email: P.Gaur@cgiar.org; Fax: +91-40-30713074/30713075.
Note: The recipie (read more)
2
Chickpea The chickpea genome sequence Genomic Resources The draft genome sequence of chickpea (CDC Frontier, a kabuli chickpea variety) adds to the genomic resources available for leg¬ume research. The Papilionoideae subfamily now has the draft or complet (read more) Genome sequence analysis is available as an Open Access article from Nature Biotechnology (doi:10.1038/nbt.2491). Sequence data as international public good is available at NCBI under Genome: PRJNA175 (read more) 3
Chickpea A transcriptome assembly and SNP dataset for chickpea Genomic resources A total of 103 215 tentative unique sequences (TUSs) have been produced from 435 018 Roche/454 reads and 21 491 Sanger expressed sequence tags (ESTs). Alignment of ?37 million Illumina/Solexa tags gen (read more) Contact R.K. Varshney, ICRISAT, Patancheru, India
r.k.varshney@cgiar.org

http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2011.00625.x/abstract; http://cicar.comparative-legumes.org/data/
(read more)
3
Chickpea Root QTL introgressed drought tolerant chickpea breeding lines Germplasm A genomic region from Linkage Group 4 that affects root traits and several other drought tolerance traits was introgressed into three well-adapted cultivars (JG 11 and KAK 2 from India and Chefe from (read more) The seed of root QTL intogressed drought tolerant chickpea breeding lines will be available to researchers globally on signing of material transfer agreements of the institutes supplying the breeding (read more) 1
Chickpea Integrated QTL and physical maps of chickpea Genomic Resources Physical map available in public domain to provide opportunities to chickpea geneticists and breeders for identifying the markers and genes in desired QTL region for both basic and applied aspects. Online in public domain at: http://probes.pw.usda.gov:8080/chickpea/ 3
Chickpea Drought tolerant chickpea breeding lines Germplasm Promising drought tolerant chickpea breeding lines selected based on the yield performance under terminal moisture stress conditions. There are 18 fixed (F7+) breeding lines, which include 16 lines d (read more) Anyone can receive seed by sending request to: Dr Pooran Gaur, Principal Scientist (Chickpea Breeding), ICRISAT, Patancheru, Hyderabad 502 324, AP, India; Email: P.Gaur@cgiar.org; Fax: +91-40-30713074 (read more) 2
Coconut A validated reference set for coconut Germplasm The Coconut Reference Set is composed of a core set of accessions representing the entirety of the genetic diversity of coconut. The reference set represents a critical resource for plant scientists t (read more) Available through Bioversity International, Rome, Italy

Contact Nicolas Roux, Bioversity International, Rome, Italy
r.roux@cgiar
2
Coconut DaRT marker array for coconut Genomic Resources An array of DArT markers for coconut discovered by screening a library of several thousand fragments from a genomic representation prepared from a pool of DNA samples that encompass the diversity of t (read more) Available through Diversity Arrays Technology Pty Ltd (DArT P/L)

http://www.diversityarrays.com/
3
Cowpea Markers for major Fusarium resistance QTL in cowpea Informative Markers SNPs marking the genomic region conferring resistance to Fusarium wilt derived from phenotyping two RIL populations. A major gene for resistance to race 3 of Fusarium wilt was mapped from RIL analysis (read more) Contact Philip Roberts, Unversity of California - Riverside, Riverside, CA USA (philip.roberts@ucr.edu)
Refer to:
Pottorff M, Wanamaker S, Ma YQ, Ehlers JD, Roberts PA, and Close TJ. (2012) Genetic (read more)
1
Cowpea A physical map of cowpea Genomic Resources 60,000 BACs from African breeding genotype IT97K-499-35 were fingerprinted. The final physical map is an assembly of 43,717 BACs with a depth of 11x genome coverage. The clones were assembled into con (read more) Contact Timothy Close, University of California (Riverside) at timothy.close@ucr.edu
or
Dr. Ming-Cheng Luo, University of California (Davis) at mcluo@ucdavis.edu

Http://phymap.ucdavis.edu/cowpe (read more)
3
Cowpea HarvEST:Cowpea Informatics Application/Tool A Windows and online cowpea genomics browser Contact: Tim Close, University of California-Riverside, USA at timothy.close@ucr.edu.

Available for Windows from harvest.ucr.edu and on-line at http://www.harvest-web.org/hweb/bin/wc.dllhwebProces (read more)
3
Cowpea Map for Staygreen QTL in cowpea Genomic Resources A map of QTL for delayed drought stress-induced premature senescence and maturity in cowpea Contact: Philip Roberts, University of California-Riverside, USA at philip.roberts@ucr.edu

Refer to: Muchero W, Ehlers J, Close T and Roberts P (2009). Mapping QTL for drought stress-induced premat (read more)
3
Cowpea A validated cowpea germplasm reference set Germplasm The Cowpea Reference Set is composed of a core set of 370 accessions representing the entirety of the genetic diversity of cowpea. The reference set represents a critical resource for plant scientist (read more) Available from the IITA genebank, Ibadan, Nigeria
Contact Michael Abberton , International Institute of Tropical Agriculture, Ibadan, Nigeria
m.abberton@cgiar.org
2
Cowpea A microarray chip for expression analysis in cowpea. Genomic Resources 41949 EST sequences from drought stressed and non-stressed drought susceptible and tolerant cowpea materials generated, representing 16954 unigenes. Contact S. Hearne, CIMMYT, Mexico

s.hearne@cgiar.org
3
Cowpea Markers for Striga resistance in cowpea Informative Markers Gene-linked SCARs MahSe 2 marker for resistance to races SG1 and SG3 and SCARs AGG/CTT 200B for resistance to race SG5. Contact Jean-Baptiste Tignegre, INERA (Institut de L'Environnement et des Recherches Agricoles), Burkina Faso at racinetignegre@yahoo.com.

Refer to: Ouedraogo J.T, M. Ouedraogo, B.S. Gowda and M.P (read more)
1
Cowpea QTLs for resistance to root-knot nematode, flower and foliar thrips, bacterial blight and ashy-stem blight Informative Markers RIL populations were phenotyped for resistance to root-knot nematode, flower and foliar thrips, bacterial blight and ashy-stem blight. QTLs for resistance to these biotic stresses were identified from (read more) Contact Philip Roberts, Unversity of California - Riverside, Riverside, CA USA at philip.roberts@ucr.edu

Refer to: Muchero, W., J.D. Ehlers, T.J. Close and P.A. Roberts. 2011. Genic SNP markers and (read more)
2
Cowpea Validated SSR marker kit for diversity analysis of cowpea germplasm collections Genomic Resources Reference kit of 20 SSRs with primer sequence list used to define the Wheat Germplasm Reference Set composed of a core set of 338 accessions representing the genetic diversity of the entirety of the (read more) Available from Generation Challenge Program, CIMMYT, Texcoco, Mexico
info@generationcp.org
2
Cowpea An improved cowpea consensus genetic linkage map Genomic Resources The first version of the cowpea consensus genetic linkage map included 928 markers spanning 11 linkage groups over a total map size of 680 centimorgans (cM). Map refinement continued with the genotypi (read more) The current SNP-based cowpea consensus genetic linkage map is included in a publicly available browser called HarvEST:Cowpea, which can be downloaded as a Windows software from http://harvest.ucr.edu. (read more) 3
Cowpea BreedIt SNP Selector Informatics Application/Tool Facilitates selection of marker sets for customized genotyping. The application generates different polymorphic marker subsets according to the marker genome coverage specified and flanking markers (read more) Directly downloadable at http://breedit.org/
1
Cowpea A molecular genetic map of cowpea Genomic Resources A genetic map based on 527 SNP markers for Conserved Orthologous Genes. Contact: Dr. Douglas Cook, University of California, Davis

drcook@ucdavis.edu
3
Cowpea Drought tolerant cowpea reference lines for West Africa Germplasm Drought tolerant breeding lines selected for drought tolerance in three west African countries. In Burkina Faso three early-maturing lines (Mouride, IT85F-3139, and Yacine) and two medium-maturing lin (read more) Contact: Ousmane Boukar, (IITA) International Institute of Tropical Agriculture, Ibadan, Nigeria, o.boukar@cgiar.org or Phillip Roberts, University of California-Riverside, USA, philip.roberts@ucr.edu (read more) 1
Cowpea Heat tolerance QTL and associated markers Informative Markers A set of five heat tolerance QTL identified in the RIL population CB27/IT82E-18. These QTL each accounted for 11-18% of the phenotypic variance for heat response in this population on average over two (read more) Lucas, M.R., B. Huynh, N.N. Diop, P.A. Roberts, and T.J. Close, T.J. 2013. Markers for breeding heat tolerant cowpea. Molecular Breeding 31:529-536.

Also contact: Philip Roberts, University of Cali (read more)
2
Cowpea Markers for aphid resistance QTL Informative Markers Following three seasons of aphid tolerance screening of the RIL population CB27/UCR 779, a major QTL for aphid resistance was identified in this population and accounted for much of the phenotypic va (read more) All data and access will be made availabfle in publication in 2015. For more information contact Phil Robers, University of California, Riverside
philip.roberts@ucr.edu
1
Global Next Generation Sequencing (NGS) Data Analysis Pipe Line Informatics Application/Tool A data analysis pipeline capable of identifying the SNPs between the parental genotypes using different algorithms Available on-line
http://hpc.icrisat.cgiar.org/ngs/

Also contact T. Shah, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India (TM.shah@cgiar.org)

2
Global iMAS, an integrated decision support system for marker assisted selection Informatics Application/Tool The Integrated Marker-Assisted Selection System (iMAS) is an integrated molecular breeding analysis platform to facilitate an integrated system, based on freely available software. iMAS provides a sin (read more) Directly downloadable on-line
http://www.icrisat.org/bt-software-imas.htm
1
Global Dayhoff: A catalogue of plant gene orthologs and paralogs Informatics Application/Tool Dayhoff is a compendium of protein families, phylogenetic trees and multiple sequence alignments with the associated experimental evidence. It serves to elucidate orthologous and paralogous relationsh (read more) Available on-line from http://202.123.56.214:8080/DayhoffWeb2/
3
Global Laboratory Information Management System (LIMS) for high-throughput molecular genotyping Informatics Application/Tool A LIMS developed by ICRISAT to meet the needs of a moderately high-throughput molecular genotyping facility. The ICRISAT LIMS is being used at the genomics laboratory facilities in ICRISAT-Patancher (read more) Directly downloadable at http://www.icrisat.org/bt-bioinformatics-lims.htm

Contact: Trushar Shah, International Crops Research Institute for the Semi-Arid Tropics(ICRISAT)

TM.Shah@cgiar.org
3
Global QU-GENEUI software for simulation of conventional and marker-assisted breeding Informatics Application/Tool QU-GENEUI is a package of tools and includes QUGENE, and it's supporting applications, QuLine, QuHybrid, QuMARS and installation and usage manuals.QU-GENE is a simulation software to investigate the c (read more) Directly downloadable through https://www.integratedbreeding.net/ib-tools/breeding-decision 3
Global Generation Atlas: on-line interactive agriculture production map and tool Informatics Application/Tool The Generation Atlas uses map server technology to allow users to explore opportunities for and constraints to agricultural production throughout the world. Developed for the Generation Challenge Prog (read more) Viewable and usable from the Integrated Breeding Platform website under Support Services/On-line support for field trials
https://www.integratedbreeding.net/generation-atlas
3
Global HaploPhyle Informatics Application/Tool Haplophyle is a pipeline for the analysis of genotyping data which includes haplotype definition, haplotype network analysis and connection with external data, such as geographic origin or genetic gro (read more) Direct on-line access:

http://haplophyle.cirad.fr
3
Global QuHybrid: a genetics and breeding simulation tool Informatics Application/Tool QuHybrid can be used to simulate and compare different breeding methods for both self- and cross-pollinated crops Downloadable on-line from
http://www.uq.edu.au/lcafs/qugene/
Also Contact Mark Dieters, UQ, Australia (m.dieters@uq.edu.au)or Jiankang Wang, CIMMYT China / CAAS, China (jkwang@cgiar.org)
3
Global QTL IciMapping (ICIM): QTL Mapping Software Informatics Application/Tool An integrated software for building genetic linkage maps and mapping quantitative trait genes Available on-line
http://www.isbreeding.net/software/

Also contact
Jiankang Wang, CIMMYT/CAAS, Beijing, China
jkwang@cgiar.org wangjk@caas.net.cn
2
Global GCP Molecular Marker Toolkit Informatics Application/Tool The Toolkit is a publicly available and easy accessible database for currently available and validated STS, SSR, SNP, and SCAR markers for 19 food security crops (Musa spp., barley, beans, cassava, ch (read more) Available in due course via Integrated Breeding Platform at www.integratedbreeding.net 2
Global Publication: Targeting and Impact Analysis of Generation Challenge Programme Technologies Publication A report on: 1)geographic distribution and the magnitude of poverty in the 14 GCP priority farming systems; 2) crop-specific modeling of drought severity and type; 3) analysis of GCP priority farming (read more) http://www.generationcp.org/gcp-impact/gcp-socioeconomic-studies/targeting-and-impact-analysis-of-gcp-technologies/23-about-section/gcp-people/stakeholder 4
Global Publication: Ex Ante Impact Analysis of Marker-Assisted Selection Technologies Supported by the Generation Challenge Programme (GCP) Publication A final technical report for GCP project no. G4006.14,Ex Ante Impact Analysis of Marker-Assisted Selection Technologies Supported by the Generation Challenge Programme (GCP). Construct technology-imp (read more) Summary of report available from the Generation Challenge Programme as Pathways to Impact, Brief no.3, Molecular and conventional breeding through an economic lens.
(www.generationcp.org)

http://w (read more)
4
Global Presentations of four workshop courses on phenotypic and marker-based analysis of multi-environment data. Training Materials Workshop courses to explore methodology based on mixed models to perform QTL mapping using multiple traits and multiple environments simultaneously. The approach allows investigating issues related to (read more) Accessible soon from the GCP website. 3
Global Powerpoint presentations on the use of plant genetic diversity and molecular marker assisted breeding - Chile Training Materials A training workshop to provide both conceptual and hands-on training in the use of plant genetic diversity and molecular marker assisted breeding. Emphasis was placed on practical applied usage and im (read more) Accessible soon from the GCP website. 2
Global Powerpoint presentations on the use of plant genetic diversity and molecular marker assisted breeding - Pretoria, SA Training Materials Conceptual and hands-on training in the use of plant genetic diversity and molecular marker assisted breeding, with emphasis on practical applied usage and improving the links between plant breeding, (read more) Accessible soon from the GCP website. 2
Global Powerpoint presentations on the use of plant genetic diversity and molecular marker assisted breeding - Thailand Training Materials All final materials including powerpoint presentations for a Plant Genetic Diversity and Molecular Marker Assisted Breeding Workshop. Accessible soon from the GCP website. 2
Global Presentations on scientific project proposal writing Training Materials Materials of workshops designed to help scientists for planning, writing, or reviewing concept notes and proposals to submit to international donors. Accessible soon from the GCP website. 4
Global Training materials on plant genetic resource policy issues Training Materials Training materials developed for international/regional workshops to train research managers and scientists on plant genetic resource policy issues, with special focus on the development of institutio (read more) The training materials are available on CD by request to the Generation Challenge Programme a.okono@cgiar.org 4

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