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
Rice Geo-referenced database on extent of inland valley lowlands In Burkina Faso, Mali, and the Niger and Kaduna states of Nigeria Database This database provides an estimate of the total area available for lowland rice production using geo-spatial modelling and elevation maps. An innovative algorithm was developed to assess inland valle (read more) The validated maps of inland valleys will be published on the spatial rice web portal of AfricaRice once finalized. All information will be available for unrestricted download online.

For more deta (read more)
4
Sorghum Aluminum tolerance diversity data Dataset Phenotyping dataset for aluminum tolerance for 255 accessions Refer to: Caniato, Fernanda F., Claudia T. Guimarães, Martha Hamblin, Claire Billot, Jean-François Rami, Barbara Hufnagel, Leon V. Kochian, et al. “The Relationship Between Population Structure and (read more) 3
Sorghum Gene for sorghum Al tolerance Gene ALTsb confirmed and cloned as a major aluminum tolerance gene in sorghum. Refer to: Magalhaes JM, Liu J, Guimares CT, Lana UGP, Alves VM, Wang Y-H, Schaffert RE, Hoekenga OA, Shaff JE, Pineros MA, Klein PE, and LV Kochian. 2007. A gene in the multidrug and toxic compound ex (read more) 3
Cassava A microsatellite kit for the GCP cassava reference germplasm set Genomic Resources Reference kit of 36 SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks Contact M. Ferguson, International Institute of Tropical Agriculture, Ibadan, Nigeria

m.ferguson@cgiar.org
2
Maize Total transcriptome of smoke and butenolide treated germinating maize kernels Genomic Resources Microarray data describing the total
transcriptome of smoke and
butenolide-induced germinating
maize seeds and seedlings
Transcriptome data has been deposited in the GEO database (http://www.ncbi.nlm.ni.gov/geo) under accession number GSE17484.

3
Maize Publication: A synthesis all known previous rice and maize disease resistance QTL studies Genomic Resources A publication demonstrating that
disease resistance QTLs are not
randomly distributed in the maize genome.
Wisser, R. J., Balint-Kurti, P. J. and Nelson R. J., 2006. The genetic architecture of disease resistance in maize: a synthesis of published studies. Phytopathology 96:120-129.

3
Maize QTL maps for maize diseases Genomic Resources QTL maps for maize diseases in a number of segregating populations Contact: Rebecca Nelson, Cornell University, USA
jmn99@cornell.edu

Also refer to:
1) Balint-Kurti, P.J., Krakowsky, M. D., Jines, M. P., Robertson, L. A., Molnár, T. L., Goodman M. M. and Hollan (read more)
3
Rice Dataset of non-host genes for rice varieties IR64 and Nipponbare. Genomic Resources 488 rice IR64 potential non-host genes, 492 rice Nipponbare potential non-host genes. jean-benoit Morel (CIRAD), jbmorel@cirad.fr 3
Rice An array of SNP markers for rice Genomic Resources 250 SNP markers developed for rice: 60 in the Xa7 region on chromosome 6, 60 around Xa13 on chromosome 8, and 130 around the cluster Xa4/Xa22/Xa26 on chromosome 11. Contact Susan McCouch, Cornell University, Ithaca, NY USA

srm4@cornell.edu
3
Rice A SNP data set for rice Genomic Resources Data set of SNP calls at 259,721 unique sites by a model-based approach across 20 varieties for development and discovery. Genome-wide SNP discovery was undertaken by re-sequencing multiple, diverse (read more) Available on-line at:
http://www.oryzasnp.org/
2
Rice Anchor markers for inter-specific crosses with Oryza sativa Genomic Resources A set of 125 SSR anchor markers along the rice genome that provides wide identification of polymorphisms across wild rice species (AA genome). Each anchor is represented by 3 SSR loci each. Orjuela J., A. Garavito, M. Bouniol, J.D. Arbelaez, L. Moreno, J. Kimball, G. Wilson, J.F. Rami, J. Tohme, S.R. McCouch, M. Lorieux. 2010. A Universal Core Genetic Map for rice. Theoretical and Applie (read more) 2
Wheat Validated SSR marker kit for diversity analysis of wheat germplasm collections Genomic Resources Reference kit of 19 SSRs with primer sequence list used to define the Wheat Germplasm Reference Set composed of a core set of 330 accessions representing the genetic diversity of the entirety of the (read more) Available from Generation Challenge Program, CIMMYT, Texcoco, Mexico
info@generationcp.org
2
Sorghum A validated Sorghum germplasm reference collection Genomic Resources The Sorghum Reference Set is composed of a core set of 384 accessions representing the genetic diversity of a composite set of 3384 accessions germplasm from the ICRISAT bank collection genotyped with (read more) see: http://www.icrisat.org/crop-sorghum-genebank-reference.htm

Available from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Germplasm Bank, Patancheru, India

C (read more)
2
Wheat A microsatellite kit for the GCP wheat reference germplasm set representive of the diversity of the CIMMYT wheat collection Genomic Resources A reference kit of 35 SSRs giving maximum polymorphism across a subset of wheat lines, with a sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks Contact Larry Butler,GCP

l.butler@cgiar.org

Also found in following publication: http://en.cnki.com.cn/Article_en/CJFDTOTAL-XBZW200612000.htm
2
Wheat Database for a CIMMYT wheat composite set Genomic Resources A database of a wheat composite set of 2600 accessions genotyped with 49 SSRs and composed of 1) bread wheat cultivars, breeding lines, and landraces; 2) durum wheat cultivars and landraces; and 3) w (read more) Contact S. dreisigacker, International Center for Maize and Wheat Improvement (CIMMYT) El Batan, Mexico

s.dreisigacker@cgiar.org
3
Beans A microsatellite kit for the GCP common bean reference germplasm set Genomic Resources • Reference kit of 34 SSRs with sequence list and allele sizes.
• These microsatellites were applied to many different germplasm collections. Reports of genetic diversity were widely published. T (read more)
Contact Lucy Diaz, CIAT, l.m.diaz@cgiar.org.

References:
MWBlair, LMDiaz,JA Acosta-Gallegos, Race Structure in the Mexican Collection of Common Bean Landraces, Crop Sci. 2013 53: 517-528

(read more)
2
Beans Microsatellite primers for multiple purposes in common bean Genomic Resources • Primers for over 1,500 microsatellites were designed. Sequences and protocols are available.
• Microsatellites were based on 417 simple sequence repeat (SSR) loci from non-enriched genomic libra (read more)
Submitted to IBP,
Contact Bodo Raatz, CIAT, Colombia, b.raatz@cgiar.org
Also refer to: Refer to: 1)Blair MW, Munoz-Torres M, Giraldo MC, Pedraza F (2009b). Development and diversity of Andean-der (read more)
3
Beans Kaspar markers for gene expression of common bean under drought Genomic Resources A set of qPCR primer pairs for 25 AP2 transcription factors was used in parental surveys to determine polymorphism and develop gene-based genetic markers. To analyse other candidate genes, a subtracti (read more) Contact B. Raatz, CIAT, Cali, Colombia at b.raatz@cgiar.org 3
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 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
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 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 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
Groundnuts DaRT marker array for groundnut Genomic Resources An array of DArT markers for groundnut discovered by screening a library of several thousand fragments from a genomic representation prepared from a pool of DNA samples that encompass the diversity o (read more) Available through Diversity Arrays Technology Pty Ltd (DArT P/L)

http://www.diversityarrays.com
3
Groundnuts A groundnut genetic map Genomic Resources The first cultivated groundnut (Arachis hypogaea L.) map derived from a RIL population between TAG24 and ICGV86031 Open access publication:
Varshney RK, Bertioli DJ, Moretzsohn MC, Vadez V, Krishnamurthy L, Aruna R, Nigam SN, Moss BJ, Seetha K, Ravi K, He G, Knapp SJ, Hoisington DA (2008).
The first SSR-base (read more)
3
Groundnuts A groundnut BAC library Genomic Resources A Bacteria Artificial Chromosome (BAC) groundnut library with approximately 80,000 clones Guimarães PM, Garsmeur O, Proite K, Leal-Bertioli SCM, Seijo G, Chaine C, Bertioli DJ, D`Hont A. (2008) BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated (read more) 3
Groundnuts Gene markers for peanut Genomic Resources Markers were developed as genomic resources necessary for molecular breeding of peanut, and for the incorporation of wild genes into cultivated peanut to produce improved varieties of groundnut. Details can be found at http://www.biomedcentral.com/content/supplementary/1471-2229-7-7-S1.xls

http://cgi-www.daimi.au.dk/cgi-chili/phyfi/go

Proite et al., 2007. ESTs from a wild Arachis specie (read more)
3
Groundnuts QTL map for disease resistance in groundnut Genomic Resources 34 sequence-confirmed candidate disease resistance genes and five QTL mapped on the reference AA-genome population. Detials can be found in the following publication: Leal-Bertioli et al., 2009. Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biology, 9:112.

Corres (read more)
3
Maize QTL for leaf growth in maize, wheat and rice Genomic Resources QTLs of the P1P2 population for leaf growth and ASI, QTLs of leaf length in maize, wheat and rice for well watered and water deficient plants, Models of silk and leaf growth for maize, Elements of mod (read more) Sadok W, Naudin Ph, Boussuge B, Muller B, Welcker C, Tardieu F (2007) Leaf growth rate per unit thermal time follows QTL-dependent daily patterns in hundreds of maize lines under naturally fluctuating (read more) 3
Beans A data set of 1500 SNP scored in 96 common bean types Genomic Resources • 96 common bean types were genotyped with 1500 SNPs using the SNP platform at Kbio/LGC.
• More than 5000 SNPs are available at Genbank through a cooperation with BeanCAP.
GCP data base, Contact Bodo Raatz, CIAT, Cali, Colombia, b.raatz@cgiar.org. Full set of 5000 SNPs presumably submitted to CIAT Genebank 3
Beans Data on more than 200 genotypes from Africa evaluated with 800 SNP as part of forensics project. Genomic Resources • More than 200 genotypes from Africa were evaluated with 800 most informative SNPs to provide a basis for quality control and impact studies, as well as to have information on the genetic background (read more) Contact Chunlin He, C.He@cgiar.org 3
Beans A diversity analysis of the GCP reference collection for common bean Genomic Resources • A study of genetic diversity, seed size associations and population structure of a core collection of 604 genotypes of common bean.
• CIAT previously worked with a larger set of 1400 genotypes th (read more)
Blair MW, Diaz LM, Buendia HF, Duque MC (2009a). Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.). Theoretical and Applie (read more) 3
Barley Barley stress tolerant genes Genomic Resources Fourteen new barley genes presumably involved in stress tolerance identified in a microarray study and sequenced. Contact M. Baum, International Center for Agriculture Research in Dry Areas (ICARDA), Aleppo, Syria

m.baum@cgiar.org
3
Barley A microsatellite kit for the GCP barley reference germplasm set Genomic Resources reference kit of 20 SSRs and EST-SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks Contact Jean-Francois Rami, CIRAD, Montpellier France

rami@cirad.fr
2
Barley A barley germplasm reference collection Genomic Resources The Barley Reference Set is composed of a core set of 294 accessions representing the genetic diversity of the entirety of the ICARDA germplasm bank collection. The reference set represents a critical (read more) The International Center for Agriculture Research in Dry Areas (ICARDA) Germplasm Bank 2
Barley Small chromosomal regions of wild barley indicating increased yield under drought Genomic Resources Data set describing small chromosomal regions in wild barley conferring increased yields unders drought and identified by flanking SNP markers Contact Professor Robbie Waugh, SCRI, Scotland, UK (Robbie.Waugh@scri.ac.uk). Also see site at following URL.

http://barleyworld.org/GCP_RCSL.html
3
Barley Candidate drought-tolerance genes from homologous regions in rice Genomic Resources Chromosomal regions in rice homologous to regions conferring drought tolerance in barley. Regions are identified by SNP flanking markers. Contact Professor Robbie Waugh, SCRI, Scotland, UK (Robbie.Waugh@scri.ac.uk). Also see site at following URL.

http://barleyworld.org/GCP_RCSL.html
2
Barley Candidate genes for drought tolerance in barley landraces Genomic Resources Candidate genes for drought tolerance identified from the Syrian and Jordanian Landrace Collection of barley. Contact Professor Robbie Waugh, SCRI, Scotland, UK

Robbie.Waugh@scri.ac.uk
3
Maize Validated SSR marker kit for diversity analysis of maize germplasm collections Genomic Resources Reference kit of 20 SSRs with primer sequence list used to define the Maize Germplasm Reference Set composed of a core set of 234 accessions representing the genetic diversity of the entirety of the (read more) Available from Generation Challenge Program, CIMMYT, Texcoco, Mexico
info@generationcp.org
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
Musa DNA of the GCP germplasm reference set for Musa Genomic Resources DNA of Musa reference collection (52 accessions= GCP mini-core collection. For each of the accessions, ten extractions, each of three grams of frozen leaves were made with the Matab method (Risterucc (read more) Contact N. Roux, Bioversity, Rome
Up to 5 in vitro plantlets (proliferating or rooted) corresponding to the characterized accessions can be distributed for research purposes. Germplasm is available (read more)
3
Musa DaRT marker array for Musa spp. Genomic Resources An array of DArT markers for Musa 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 the (read more) Available through Diversity Arrays Technology Pty Ltd (DArT P/L)

http://www.diversityarrays.com/
3
Musa SSR markers for the BORLI (Musa) map Genomic Resources 180 SSR markers and 380 DArT markers for the BORLI (Musa) map and 41 BACs completely sequenced. 2 cDNA libraries from PKW leaves and roots produced. 5760 ESTs clones from these libraries sequenced.
(read more)
Direct on-line access:

http://www.musagenomics.org/
http://www.gnpannot.org/fr/content/musaceae-statistics
http://tropgenedb.cirad.fr/tropgene/?module=BANANA
http://esttik.cirad.fr/cgi-bin/publi (read more)
3
Potatoes A microsatellite kit for the GCP potato reference germplasm set Genomic Resources A Reference kit of 24 SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks Contact Rosario Herrera, International Potato Center (CIP), Lima, Peru

r.herrera@cgiar.org
3
Potatoes DaRT marker array for potato Genomic Resources An array of DArT markers for potato 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 th (read more) Available through Diversity Arrays Technology Pty Ltd (DArT P/L)

http://www.diversityarrays.com/
3
Yams DaRT marker array for yam Genomic Resources An array of DArT markers for yam 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 the s (read more) Available through Diversity Arrays Technology Pty Ltd (DArT P/L)

http://www.diversityarrays.com/
3

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