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 CAR3 an aromatic rice variety improved for submergence tolerance and brown planthopper resistance Germplasm BC2F4 selection of CAR3 an aromatic rice variety in Mekong improved for submergence tolerance (flash flooding type) and brownplanthopper resistance Contact: Jonaliza L. Siangliw, Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology at
jsiangliw@gmail.com
1
Rice Promising genotypes with high yield under rainfed lowland and drought conditions Germplasm Eleven rice genotypes which were identifed for high grain yield, drought tolerance and well adapted inr rainfed lowland conditions in the Mekong region. Among these, six genotypes were photoperiod in (read more) Contact :
Thailand - Boonrat Jongdee): boonrat@brrd.mail.go.th

Cambodia - Ouk Makara ou.makara@cardi.org.th

Laos - Phetmanyseng Xangsayasane: phetmanyseng@gmail.com
2
Beans SNP detection protocol for evaluation of TILLING population for common bean Protocol • A SNP detection technique was developed based on heteroduplex digestion with CelI enzyme that is useful for mutation detection Galeano CH, Gomez M, Rodriguez LM, Blair MW (2009) CEL I nuclease for SNP discovery and marker development in common bean (Phaseolus vulgaris L.) Crop Science 49 381-394 (DOI: 10.2135/cropsci2008.07.0 (read more) 3
Pigeonpeas A Pigeon Pea germplasm reference collection Genomic Resources The Pigeon Pea Reference Set is composed of a core set of 298 accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a cri (read more) The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Germplasm Bank

Contact: H. Upadhyaya, Head, Genebank, ICRISAT, India
h.upadhyaya@cgiar.org
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
Cassava A cassava germplasm reference set Germplasm A reference set derived from a cassava composite set of 2494 accessions from CIAT, IITA and EMBRAPA genotyped using 22 SSR at CIAT and 8 SSR at IITA Contact M. Ferguson, International Center for Tropical Agriculture(IITA), Ibadan, Nigeria

m.ferguson@cgiar.org
2
Cassava A cassava mapping population for drought tolerance in South America Germplasm A cassava mapping population genotyped with SSR markers for drought tolerance QTL. Contact. A. Alves, USDA-ARS National Center for Genetic Resources Preservation, Ft. Collins, CO, USA

Alfredo.Alves@ars.usda.gov
3
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
Rice A CSSL population of Oryza sativa x O. glaberrima Germplasm A Chromosome Segment Substitution Line working population of 62 BC3DH interspecific lines bearing introgressed genome segments from the AA genome of the cultivated species, Oryza glaberrima, in a O. (read more) Available through IRRI rice genebank, Los Banos, The Philippines
Contact Ruaraidh Sackville Hamilton
r.hamilton@cgiar.org

For additional information contact
M. Lorieux, CIAT/IRD, Cali, Colombia
(read more)
2
Rice A CSSL population of Oryza sativa x O. glumaepatula Germplasm A Chromosome Segment Substitution Line working population of about 60 interspecific lines bearing introgressed genome segments from the AA genome of the wild species, Oryza glumaepatula Contact M.Lorieux, CIAT/IRD, Cali, Colombia

m.lorieux@cgiar.org
2
Rice A CSSL population of Oryza sativa x O. meridonalis Germplasm A Chromosome Segment Substitution Line working population of 32 BC3DH interspecific lines bearing introgressed genome segments from the AA genome of the wild species, Oryza meridionalis Available through IRRI rice genebank, Los Banos, The Philippines
Contact Ruaraidh Sackville Hamilton
r.hamilton@cgiar.org

For additional information contact
M. Lorieux, CIAT/IRD, Cali, Colombia
(read more)
2
Rice A CSSL population of Oryza sativa x O. rufipogon Germplasm A Chromosome Segment Substitution Line working population of 60 BC3DH interspecific lines bearing introgressed genome segments from the AA genome of the wild species, Oryza rufipogon Available through IRRI rice genebank, Los Banos, The Philippines
Contact Ruaraidh Sackville Hamilton
r.hamilton@cgiar.org

For additional information contact
M. Lorieux, CIAT/IRD, Cali, Colombia
(read more)
2
Rice A data base of datasets for over 420,000 SNPs in rice Genomic Resources A publicly accessible database with the SNPs datasets annotated relative to the IRGSP and TIGR psuedomolecules and gene models for their annotation and visualization on the rice genome.This database s (read more) Publicly assessible on-line.

http://oryzasnp.plantbiology.msu.edu/
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
Rice A database storing the data from several rice microarray systems Informatics Application/Tool A database storing the data from several rice microarray systems established, and a pipeline system developed for the cis-element search in the promoter region of the genes which turned out to be the (read more) Contact S. Kikuchi,National Institute of Agrobiological Sciences (NIAS), Japan

skikuchi(0)nias.affrc.go.jp

online at: http://www.dna.affrc.go.jp/database/
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
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
Musa A genotyped set of Musa plantlets Germplasm A set of 561 Musa accessions genotyped with 22 SSRs Most of the plantlets corresponding to the genotyped accessions are available at, the International Transit Centre (ITC) hosted by the Katholieke Universiteit Leuven in Belgium.
Contact: Nicholas Rou (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 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
Rice A laboratory manual for use of low-cost, low tech genotyping for rice breeding programs Publication A laboratory manual developed for low-cost, low tech and low cost, high throughput technologies for breeders or researchers interested in applying these technologies for marker assisted selection. Fil (read more) Contact: Casiana (Nollie) M. Vera Cruz, IRRI

c.veracruz@cgiar.org

Manual URL:
Vera Cruz C.M., Reveche M.Y.V., Mercado E.F.L., Chen J., Skinner D.J., Bernardo M., Chin J.H., Collard B.C.Y. 2007 (read more)
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
Maize A low-cost QPM detection assay for maize Protocol One low cost, low tech technology – dot blot detection assay – developed with reduced cost for QPM in maize. Breeders have relied on seed phenotyping for QPM selection and some errors occur. The (read more) Contact: Susanne Dreisigacker, CIMMYT, Mexico

s.dreisigacker@cgiar.org
1
Rice A MAGIC analysis pipeline for rice Informatics Tools/Applications A pipeline to analyse GBS and phenotype data from MAGIC population using GWAS (from TASSEL) and mpMAP, leading to identifcation of SNP markers flanking target QTLs. Contact Chitra Raghavan, IRRI, Philippines at C.Raghavan@irri.org

3
Beans A MAGIC population of common bean Germplasm • An 8 parental MAGIC population was produced combining sources of tolerance to drough, low P, pathogens with interspecific hybridisation progeny. Seeds will soon be available in F4:6 generation.
• (read more)
Contact S. Beebe, CIAT, Cali, Colombia s.beebe@cgiar.org 2
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
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
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
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
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
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
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
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
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
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
Beans A molecular genetic map of common bean Genomic Resources A Genetic map based on 592 SNP markers for Conserved Orthologous Genes. Contact: Dr. Douglas Cook, University of California, Davis

drcook@ucdavis.edu
3
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
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
Beans A mutant population of common bean for TILLING. Germplasm • A mutant population of over 1000 common bean lines (BAT93) advanced to the M3:4 generation.
• Phenotyping data was obtained for several morphological traits, and can be accessed at: http://g (read more)
Phenotyping data can be accessed at: http://gcpcr.grinfo.net/index.php?app=datasets&inc=dataset_details&dataset_id=454,
TGPorch, MW Blair, P Lariguet, C Galeano, CE Pankhurst, WJ Broughton, Gener (read more)
2
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
Potatoes A Potato Germplasm Identification Kit of SSR markers Genomic Resources A set of SSR markers selected for potato genetic identification consisting of the most discriminatory 24 SSR markers covering all chromosomes, 2 per chromosome at a map distance of >10cM. Contact Marc Ghislain, CIP - Nairobi, Kenya
M.Ghislain@cgiar.org
3
Potatoes A potato germplasm reference set Germplasm A set of 1027 potato accessions virus free and available for international distribution Contact International Potato Center (CIP), Lima, Peru

www.cippotato.org
2
Rice A purified set of 20 lines for standardized genotyping Germplasm Genetic stocks of a genotyping reference set of 20 purified lines chosen by the rice breeding community for genome sequencing, SNP discovery, association mapping and phenotyping. Contact: R. Sackville Hamilton, International Rice Genebank, IRRI, The Philippines

r.hamilton@cgiar.org
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
Wheat A reference set of emmer (Triticum dicoccum) Germplasm A subset of 108 emmer wheat accessions with good agronomic potential and captures most ( ~80%) of the genetic diversity of the emmer collection Available from the CIMMYT Genebank, Texcoco, Mexico

Also contact Tom Payne, Head, Wheat Germplasm Resources, CIMMYT, Mexico
t.payne@cgiar.org
2
Wheat A selection wheat/barley introgression lines with drought tolerance Germplasm Wheat - barley translocation line, 3HS.3BL, and the addition lines, 3H, 4H Mv9kr1/lgri, showing the best drought resistance index in the field under a rainout shelter. The 3H Mv9kr1/Igri, the 4 (read more) Contact: Marta Molnar-Lang, Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary

molnarm@mail.mgki.hu
3
Wheat A set emmer(Tricticum dicoccum)/Aegilops Tauschii synthetic wheats Germplasm A collection of synthetic wheats derived from crosses of 70 good performing emmer wheat accessions from geographically diverse origins with three Aegilops tauschii accessions. Available from the CIMMYT Genebank, Texcoco, Mexico

Also contact Tom Payne, Head, Wheat Genebank, CIMMYT, Texcoco, Mexico
t.payne@cgiar.org
2
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
Maize A SNP array for drought candidate genes in maize. Genomic Resources 1536 SNP array for Drought Candidate Genes. GCP Central Registry http://gcpcr.grinfo.net/

http://www.panzea.org/db/gateway?file_id=2007_candidate_snp

Contact: Sarah Hearne, CIMMYT, Mexico
s.hearne@cgiar.org
2
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

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