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
Global Training materials on plant genetic diversity analysis Training Materials Training materials focusing on how to detect traits in diverse sources related to domestication for further uses in a perspective of breeding strategy. CD in English with support available on request from the Generation Challenge Programme (www.generationcp.org)
a.okono@cgiar.org
2
Global Course materials for germplasm data analysis Training Materials The objective of this project is to generate training materials and a curriculum for a course in assocation analysis/Linkage Disequilibrium mapping for collections of diverse crop germplasm. These ma (read more) Accessible soon from the GCP website.
2
Global Training materials: genomics and comparative genomics Training Materials An on-line course consisting of 2 learning modules, Volume 1: Using Molecular Marker Technology in Studies on Plant Genetic Diversity and Volume 2: Genetic Diversity Analysis with Molecular Marker Da (read more) Available on-line at:
https://www.integratedbreeding.net/genomics-and-comparative-genomics-learning-module
CDs on request at www.generationcp.org
3
Global A learning module: The use of molecular markers in efficient crop improvement: Marker-Assisted Breeding. Training Materials This learning module was designed to be used either as the basic material for a course or as a self-tutorial. It is geared towards scientists or upper-level students with a good background of biology, (read more) Viewable and downloadable at:

https://www.integratedbreeding.net/use-molecular-markers-efficient-crop-improvement-marker-assisted-breeding-learning-module
1
Global Crop Ontology Tool Informatics Application/Tool Crop Ontology (CO) compiles validated concepts along with their inter-relationships on anatomy, structure and phenotype of Crops, on trait measurement and methods as well as on Germplasm with the mult (read more) Available on-line.

http://genesys.cgxchange.org/gcp-crop-ontology/m-crop-ontology-curation-tool
1
Global The International Treaty on Plant Genetic Resources for Food and Agriculture: Implementing the Multilateral System - Learning Module Training Materials The module contains practical exercises to reinforce an understanding of the impact and working of International Treaty law in the types of situations that professionals in plant genetic resources can (read more) Bioversity International, Rome, Italy

http://www.bioversityinternational.org/training/training_materials/international_treaty.html
4
Global Training materials for project design and data analysis Training Materials Training materials encompassing data quality, general statistical theory, experimental design, analysis of single and multiple trials, GxE analysis, QTL and association mapping, diversity analysis, an (read more) Available on-line from:

https://www.integratedbreeding.net/analysis-field-trials
2
Global ParentChecker, a user-friendly tool to automate inference of parental genotypes Informatics tool/application ParentChecker is a user-friendly tool to automate inference of parental genotypes used to construct recombinant inbred line (RIL) populations particularly for cases where precise parental genotypic in (read more) See: Hu et al., BMC Genetics 2012, 13:9 doi:10.1186/1471-2156-13-9
or
Contact Philip Roberts, University of California - Riverside, USA

philip.roberts@ucr.edu
1
Global KBio Converter Informatics application/tool A data translation tool which relates KBioscience (LGC Genomics) KASP data output to a reference SNP source sequence. This conversion tool enables the user to input a standard KBio SNP Viewer input f (read more) Contact: Timothy Close, University of California - Riverside, USA, timothy.close@ucr.edu 3
Global Conserved orthologous markers in various crops for biotic and abiotic traits in common. Genomic Resources Sets of sequenced COS (conserved orthologous set) markers within and across crop families for biotic and abiotic traits including potato, tomatoe, legumes and Musa... These include:
• 100 COS ll pr (read more)
Contact Generation Challenge Program, Mexico

info@generationcp.org
3
Global The McClintock introductory course for crop bioinformatics Training Materials This is a largely self-study introductory course in crop bioinformatics targeting crop scientists who wish to apply bioinformatics techniques to their work, but don't yet have any specialized training (read more) Direct on-line access at:
https://www.integratedbreeding.net/mcclintock-introductory-course-crop-bioinformatics
3
Global Learning materials for statistical methods for linkage disequilibrium analysis Training Materials Capacity building materials addressing statistical methods for linkage disequilibrium analysis Available on-line from GCP website
https://www.integratedbreeding.net/linkage-disequilibrium-mapping-ld-mapping
2
Global A mixed model linkage disequilibrium (LD) mapping methodology Training Materials A mixed model LD mapping methodology using different sources of information: kinship/coancestry, population stratification, or other methods of diversity analysis, addressing issues of LD mapping in r (read more) Available on-line from: https://www.integratedbreeding.net/linkage-disequilibrium-mapping-ld-mapping
Also refer to:
Paper : Pswaray, A; van Eeuwijk FA, Ceccarelli S, Grando S, Comadran J, Russel JR (read more)
3
Global Guidelines for the design of linkage disequilibrium (LD) studies Training Materials Guidelines for the design of LD studies (number of markers, number of genotypes, which marker systems, etc) Available on-line from: https://www.integratedbreeding.net/linkage-disequilibrium-mapping-ld-mapping 3
Global A statistical strategy for the choice of reference genotypes and marker sets Training Materials Exploitation of the available genetic resources around the world requires information about the relationships and genetic diversity present among genebank collections. These relations can be establish (read more) On-line publication:
Statistical Techniques for Defining Reference Sets of Accessions and Microsatellite Markers
T. L. Odong,* J. van Heerwaarden, J. Jansen, T. J. L. van Hintum, and F. A. van Eeuwi (read more)
3
Global Drought phenotyping in crops: from theory to practice Training materials This book, published under a Creative Commons licence, to ensure the widest possible dissemination, is a detailed description and analysis of the complex work of drought phenotyping in crops, simultan (read more) Available on-line: https://www.integratedbreeding.net/drought-phenotyping-crops-theory-practice
or:
http://www.generationcp.org/communications/research-publications/phenotyping-book-methods-applicat (read more)
2
Global GreenPhylDB: a bioinformatics tool facilitating comparative functional genomics for plants Informatics tool/appliation GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on complete genomes, covering a broad taxonomy of gre (read more) Available on-line at:
http://www.greenphyl.org/cgi-bin/index.cgi

Also see:
Rouard,M., Guignon,V., Aluome,C., Laporte,M.-A., Droc,G., Walde,C., Zmasek,C.M., Perin,C. et Conte,M.G. (2010) GreenPhy (read more)
3
Global GreenPhyl Orthologous Search Tool (GOST): online phylogenomic analysis tool. Informatiics tool/application GOST allows biologists to perform online phylogenomic analysis. This tool is intended to provide a reliable means of sequence annotation, gene functional analysis and candidate gene search for any pla (read more) In process. LInk to come. 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 validated Groundnut germplasm reference collection Germplasm The Groundnut 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 crit (read more) See: http://www.icrisat.org/crop-groundnut-genebank-Referenceset.htm

Available from: The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Gene Bank

Contact H. Upadhyaya, (read more)
2
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 Sources of resistance to Groundnut Rosette Virus Germplasm From 300 genotypes screened from the GCP reference collection, four sources of resistance to Groundnut Rosette Virus were identified: ICG 14705, ICG 13099, ICGV-SM 03701, ICGV-SM 03710 Available from: The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Gene Bank

Contact H. Upadhyaya, Head, Genebank, ICRISAT, India
h.upadhyaya@cgiar.org
2
Groundnuts Sources of resistance to Groundnut Early Leaf Spot Germplasm From 300 genotypes screened from the GCP reference collection, six sources of resistance to Early Leaf Spot were identified: ICGV-SM 95741, ICGV-SM 07543, ICG 405, ICG 12276, ICG 12672, ICGV-SM 06684, (read more) Available from: The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Gene Bank

Contact H. Upadhyaya, Head, Genebank, ICRISAT, India
h.upadhyaya@cgiar.org
2
Groundnuts Sources of resistance to Groundnut Rust Germplasm From 300 genotypes screened from the GCP reference collection, five sources of resistance to Groundnut Rust were identified: ICG 1703, ICG 10010, ICG 4729, ICG 6022, ICG 7897 Available from: The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Gene Bank

Contact H. Upadhyaya, Head, Genebank, ICRISAT, India
h.upadhyaya@cgiar.org
2
Groundnuts Sources of drought tolerance in Groundnut Germplasm Highly contrasting drought tolerant germplasm identified from 300 genotypes screened for the GCP reference collection H. Upadaya, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India

h.upadhyaya@cgiar.org
2
Groundnuts Groundnut synthetics for drought tolerance Germplasm (A. batizocoi K9484 x A. stenosperma V10309)4x and (A. gregoryii V6389 x A. stenosperma V10309)4x

Contact David Bertioli, Unversity of Brasilia, Brazil
davidbertioli@unb.br

Refer to:
Supplementary information:

Foncéka D, Hodo-Abalo T, Rivallan R, Faye I, Sall MN, Ndoye O, Fávero AP, Bert (read more)
2
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
Groundnuts New groundnut synthetics for drought tolerance Germplasm Four new synthetic amphidiploids (c.5) incorporating the the nenomes of wild Arachis spp. selected for their drought tolerance:

(A. batizocoi K9484 x A. stenosperma V10309)4x , (A. batizocoi K9484 (read more)
Contact:

José Valls, EMBRAPA, Brazil or David Bertioli, Universidade Catolica de Brasilia, Brazil

valls@cenargen.embrapa.br davidbertioli@unb.br
2
Groundnuts Improved gene-rich reference maps for groundnut Genomic Resources Improved gene-rich reference maps for the component, AA and BB diploid and the tetraploid AABB genomes of groundnut. All maps available through published studies. Contact: José Valls, EMBRAPA, Brazil or David Bertioli, Universidade Catolica de Brasilia, Brazil or Marcio C. Moretzsohn, EMBRAPA, Brazil

valls@cenar (read more)
3
Groundnuts A genetic map for disease resistance genes in groundnut Genomic Resources A genetic map with 34 sequence-confirmed candidate disease resistance genes and five Late Leaf Spot QTLs mapped. Map available through a published study.

Leal-Bertioli et al., 2009. Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biology, 9:112.

Additional f (read more)
3
Groundnuts An analysis of genome synteny of Arachis with other legumes Genomic Resources A genome synteny of Arachis analysed with L. japonicus, M. tuncatula and common bean derived from an analysis based on more than 100 genic markers. Analysis results available through a published study.
Contact: José Valls, EMBRAPA, Brazil or
David Bertioli, Universidade Catolica de Brasilia, Brazil or Jens Stougaard, Univesity of Aahus, Denm (read more)
3
Groundnuts Genotyping system for incorporation of wild Arachis genes in groundnut breeding programs Protocol A genotyping system (c. 10 markers per chromosome) based on genic markers suitable for use in breeding programs to introgress wild Arachis spp. genes into cultivated groundnut. Contact: José Valls, EMBRAPA, Brazil or
David Bertioli, Universidade Catolica de Brasilia, Brazil

valls@cenargen.embrapa.br
davidbertioli@unb.br marciocm@cenargen.embrapa.br
3
Groundnuts BAC libraries for wild species of Arachis representing component gemomes of A. hypogea. Genomic Resources Two large-insert libraries in Bacterial Artificial Chromosome (BAC) vector constructed and characterized for each of the diploid ancestral species. Libraries include a set of characterized probes for (read more) Details can be obtained from the publication Guimarães et al., 2008. BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut. BMC Plant Biology 8:14

C (read more)
3
Groundnuts Protocol for reducing the complexity of groundnut DNA sequencing Protocol The protocol will be described as part of a tetraploid groundnut transcriptome publication The protocol can be obtained at any time from Peggy Ozias-Akins, University of Georgia
pozias@uga.edu
Also refer to the following open-access citations:
BMC Genomics 2012, 13:608 doi:10.1186/1471-2 (read more)
3
Groundnuts cDNA Sequence assembly for groundnut Genomic Resources Assembly of cDNA sequences from 21 tetraploid groundnut genotypes. Assembly is available as a fasta file upon request and will be made available for password protected download from http://nespal.org/oziasakinslab/?page_id=1400
The password can be obtained by e-mai (read more)
3
Groundnuts GoldenGate SNP array for groundnut Genomic Resources SNP file used for constructing the GoldenGate array Assembly is available as a fasta file upon request and will be made available for password protected download from http://nespal.org/oziasakinslab/?page_id=1400
The password can be obtained by e-mai (read more)
3
Groundnuts A molecular genetic map of groundnut Genomic Resources A genetic map based on 498 SNP markers for Conserved Orthologous Genes. Contact: Dr. Douglas Cook, University of California, Davis

drcook@ucdavis.edu
3
Groundnuts Wild introgression chromosome segment substitution lines (CSSL) for groundnut Germplasm ~80 CSSLs developed CSSLs with cultivated cultivar Fleur 11 crossed with the amphidiploid (A. ipaenesis x A. duranensis). Evaluated under drought conditions by ISRA (Senegal), ICRISAT (Niamey, Hydera (read more) Contact 1: ISRA Issa Faye (Institut Senegalais de Recherche Agricole - ISRA): Email contact: issafaye2001@yahoo.fr. Contact (II) CIRAD-Daniel Fonceka Email contact: daniel.fonceka@cirad.fr 2
Groundnuts A collection of Bolivian groundnut landraces Germplasm A collection of Bolivia with new accessions imported from USDA (375 accessions) and others collected in the Southern Bolivia (Chaco Boliviano) Contact: Antonio Gandarillas, Promotion and Research of Andean Products (Proinpa) Foundation, La Paz, Bolivia

gandaril@proinpa.org
3
Groundnuts A set of domestic x wild groundnut chromosomal segment substitution lines (CSSL) Germplasm ~80 CSSLs developed from crosses with the domestic variety Fleur 11 amphidiploid (A. ipaenesis x A. duranensis). Available from ICRISAT Genebank
http://www.genesys-pgr.org/

Also contact: h.upadhyaya@cgiar.org
2
Groundnuts A microsatellite kit for the GCP groundnut reference germplasm set Genomic Resources Reference kit of 20 SSRs with sequence list and allele sizes Available from CIRAD, France
Contact Jean-Francois Rami, CIRAD
rami@cirad.fr
2
Groundnuts KASP markers for groundnut Genomic Resources A set of 90 GKAM (Groundnut KASP Marker Assays) with sequence list KASPAR markers and assays are vailable through LGC, Genomics Ltd. https://www.lgcgenomics.com/. 3
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 A maize germplasm reference set Germplasm A reference set of maize composed of 137 inbred lines derived from the CIMMYT maize composite set of 987 inbred lines, genotyped with 47 SSRs, and 467 populations genotyped with 30 SSRs Available from Maize Genetic Resources, CIMMYT, Mexico

Contact S. Traschel, CIMMYT, Mexico
s.traschel@cgiar.org
or
Denise Kostich, CIMMYT, Mexico
d.kostich@cgiar.org
2
Maize NILs for Southern Leaf Blight resistance in maize Germplasm A set of ~15 NILs carrying SLB QTL
from the resistant lines Mo17 and
NC250 developed in a B73
background.
Contact R. Nelson,Cornell University, Ithaca, NY USA
jmn99@cornell.edu

Also Refer to:
Zwonitzer, J.C. , Balint-Kurti, P., et al. Use of backcross recurrent selection and QTL mapping to identify l (read more)
2
Maize NILs for Northern Leaf Blight resistance in maize Germplasm For CML52-derived NILs, eight NIL pairs showing differences in disease reaction to Northern Leaf Blight (NLB). For DK888-derived NILs,, Five NIL pairs showing differences in reaction to NLB. Contact R. Nelson,Cornell University, Ithaca, NY USA

jmn99@cornell.edu
2
Maize Grey Leaf Spot resistant Kenyan maize lines Germplasm Elite lines from the Kenya Agriculture
Research Institute resistant to Grey
Leaf Spot
Contact S. Gethi, Kenya Agriculture Research Institute (Kari)

jgethi@wananchi.com
1

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