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 Phosphorus deficiency-tolerant rice breeding lines Germplasm A set of BC2F3 and BC3F2 introgression lines with the phosphorus efficiency uptake gene, Pup1, in rice varieties IR64 and IR74 Available from Genetic Resources Center, IRRI, The Philippines

Contact Ruaraidh Hamilton, Head, GRC, IRRI, The Philippines
r.hamilton@irri.org
1
Rice Indonesian upland phosphorus deficiency-tolerant rice breeding lines Germplasm A set of BC2F3 rice introgression lines with the phosphorus efficiency uptake gene,Pup1, in Indonesian upland varieties (Dodokan, Situ Begendit and Batur) Available from IRRI Genetic Resources Center, IRRI, The Philippines

Contact Ruaraidh Hamilton, Head, GRC, IRRI
r.hamilton@irri.org


1
Rice OryGenesDB: an interactive tool for rice reverse genetics Informatics Application/Tool The original aim of the Orygenes database was to display sequence information resulting from the activities of the CIRAD group such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the fr (read more) On-line at http://orygenesdb.cirad.fr/

3
Rice Markers for submergence tolerance, blast resistance and bacterial blight Informative Markers Gene and SSR markers for bacterial blight resistance; SSR markers for broad-spectrum blast resistance and a gene marker for submergence tolerance Contact: Jonaliza L. Siangliw, Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology (jsiangliw@gmail.com) Available on-line at http:// (read more) 1
Rice PaddyMap: a data base for selection of rice genetic markers Informatics Application/Tool Paddy Map provides means to easily and quickly choose a series of genetic markers to be used to genotype a population derived from a specific cross. available online

http://mapdisto.free.fr/PaddyMap/
3
Rice Markers for salt tolerance in rice. Informative Markers Linked SSR and SNP markers identified for introgression of the Saltol QTL into elite rice varieties. https://www.integratedbreeding.net/markers-saltol-major-salt-tolerance-qtl-rice

Also contact Abdelbagi Ismael, International Rice Research Institute (IRRI), Los Banos, Philippines

abdelbagi.isma (read more)
1
Rice Training materials for trait phenotyping in rice Training materials Materials documenting the use of phenotyping techniques to validate traits that were introgressed into rice materials in the Mekong region Contact: Jonaliza L. Siangliw, Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology (jsiangliw@gmail.com) Available on-line at http:// (read more) 3
Rice Rice Blast resistance markers for rice Informative Markers Gene-specific molecular markers for candidate defence genes associated with resistance to rice blast
1) Thirty-three markers for 11 defence response candidate genes
2) Thirty SSR markers co-localizi (read more)
Contact R. Nelson,Cornell University, Ithaca, NY USA

jmn99@cornell.edu
2
Rice Molecular markers linked to field and isolate-specific blast resistance genes Informative Markers Three SSR markers linked to field blast resistance at the IRRI blast nursery, two SSR markers linked to field blast resistance in Sukabumi, one SSR marker linked to field blast resistance in Lampung, (read more) Contact R. Nelson,Cornell University, Ithaca, NY USA

jmn99@cornell.edu
1
Rice QTL for Aluminum tolerance in Rice Informative Markers Markers for major rice Al tolerance QTL with major effects on tolerance populations and to use for breeding for improved Al tolerance. L. Kochian, USDA/ARS, Cornell University, Ithaca, NY USA

lvk1@cornell.edu
2
Rice Markers for phosphorous uptake in rice. Informative Markers Validated markers for a major QTL for phosphate uptake in rice (PUP1). https://www.integratedbreeding.net/diagnostic-markers-major-phosphorous-uptake-qtl-pup1

Contact: Joong Hyoun Chin, International Rice Research Institute (IRRI), Los Banos, The Philippines
j.chin@c (read more)
1
Rice Markers for resistance to Bacterial Leaf Blight Informative Markers Informative markers for recessive resistance previously identified in Asian strain studies and found resistant as well to African strains of Bacterial Leaf Blight in rice (Oryzae sativa) Contact Marie Noelle Ndjiondjop, AfricaRice, Benin

M.NDJIONDJOP@cgiar.org
2
Rice Yield sensitivity module for a crop modeling system for cereals Informatics Application/Tool A new module developed in APSIM to account for yield sensitivity near flowering and formalize genetic control similarities of leaf and silk expansion in well-watered and stressed treatments; Ecomerist (read more) D. Luquet, International Center for Research for Agricultural Development (CIRAD), Montpellier, France

delphine.luquet@cirad.fr
3
Rice A strategy for detection of deleted regions in rice mutants Protocol Three methods tested for detection and characterization of deletion mutants. See on-line publication of technique: Diaz, G., M. Ryba, R. Nelson, H. Leung, J. Leach*. 2007. Detection of deletion mutants in rice via overgo hybridization onto membrane spotted arrays. Plant Mol. (read more) 4
Rice Training materials: Marker Assisted Selection (MAS) Training Materials The use of MAS in rice for introgressing useful traits (quality, disease resistance) in well-adopted drought tolerant background Available on-line
http://dna.kps.ku.ac.th/
3
Rice Markers for a major drought tolerance QTL for rice and stable in high-yielding backgrounds. Informative Markers Markers for a previously undefined QTL, qDTY1.1, obtained from the highly tolerant Indian donor variety Moroberekan and found stable effect in different high yielding genetic backgrounds. Under droug (read more) Contact: Arvind Kumar, IRRI, Los Banos, The Philippines
a.kumar@cgiar.org
1
Rice Markers for a major drought tolerance QTL for upland rice. Informative Markers Markers for a major QTL, qDTY12.1, found conferring significant yield gains under upland drought stress in an IR64 background. Under lowland conditions, qDTY12.1 did not show any effect. However, qDT (read more) Contact: Arvind Kumar, IRRI, Los Banos, The Philippines
a.kumar@cgiar.org
1
Rice TDK1 an aromatic rice variety improved for submergence tolerance Germplsm F4 selection of TDK1 an aromatic rice variety with submergence tolerance improved for submergence tolerance (flash flooding type) Contact: Jonaliza L. Siangliw, Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology at
jsiangliw@gmail.com
1
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 SNP markers developed for bacterial blight resistance in rice Informative Markers Gene-based SNP markers developed for bacterial blight resistrance genes Xa21, xa5 and xa13 Contact: Casiana (Nollie) M. Vera Cruz, IRRI, The Philippines

c.veracruz@cgiar.org
1
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
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
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
Rice Arrays for SNP discovery in rice. Genomic Resources High densitiy oligonucleotide arrays using Affymetrix technology for 100 Mb of the rice genome developed by Perlegen Sciences, Inc., USA Contact: K.McNally, IRRI, The Philippines

k.mcnally@cgiar.org
3
Rice Rice transcriptome dataset for drought stress. Genomic Resources A high-quality transcriptome dataset (~44K genes) for two genotypic backgrounds under control, mild and severe drought stress providing a rich resource for data mining. Contact: Dr. Soshi Kikuchi, NIAS - National Institute of Agrobiological Sciences, Japan

skikuchi@nias.affrc.go.jp
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
Rice Nested Association Mapping (NAM) population of rice Germplasm A meta-population of 4,000 recombinant lines suitable for Nested Association Mapping studies, with a focus on African constraints for rice production. On request from IRRI Genebank, IRRI, Los Banos, The Philippines beginning September 2012
r.hamilton@cgiar.org

Also contact Mathia Lorieux, Principal Investigator, IRD/CIAT, Cali, Colombia
m.lori (read more)
3
Rice Manawthukha, an improved rice variety released in Myanmar, 2011 Germplasm Manawthuka, an elite non-fragrant cultivar with high amylose content (AC), intermediate gel consistency (GC) and gelatinisation temperature (GT), occupies the largest number of acres in Myanmar and wa (read more) Contact Theerayut toojinda, Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology at theerayuttoojinda@gmail.com or theerayut@dna.kps.ku.ac.th 1
Rice ‘Sinthu Latt’, a rice variety improved for salt tolerance Germplasm Sinthu Latt is a rice variety improved for salt tolerance by the Mekong Rice Community of Practice by introgression techniques using MAS, released in Myanmar, 2011 Contact Theerayut Toojinda, Rice Gene Discovery Unit, National Center for Genetic Engineering and Biotechnology,
Thailand
theerayut@dna.kps.ku.ac.th or theerayuttoojinda@gmail.com
1
Rice A validated rice germplasm reference collection Germplasm The rice reference set is a collection of 256 accessions the genetic composition of which is representative of the genetic diversity of the entire composite genebank collection (IRRI). Available from the IRRI Gene Bank, Los Banos, The Philippines
Contact R. Hamilton, IRRI
r.hamilton@cgiar.org
2
Rice Salt tolerant introgression lines Germplasm BRRI dhan28-Saltol lines with clean backgrounds by using donor FL378. Contact: Dr. Zeba I. Seraj, University of Dhaka, Dhaka, Bangladesh

zebai@univdhaka.edu
1
Rice Markers for reproductive stage salt tolerance in rice Informative markers One fine-mapped reproductive stage tolerance QTL from Boilam background with flanking SNP markers:
Contact: Zeba I Seraj, University of Dhaka, Dhaka, Bangladesh

zebai@univdhaka.edu

2
Rice Markers for locus accounting for interspecific sterility in rice Informative markers Confirmed SSR markers for the S1 locus conferring male sterility in interspecific crosses (Oryza sativa X O. glaberrima). These were determined at the peak of the segregation distortion showing clea (read more) Contact: Alain Ghesquière, Institute of Research for Development, IRD, Montpellier, France

alain.ghesquiere@ird.fr
2
Rice Markers for drought tolerance QTLs in lowland rice. Informative markers SNP markers for three large-effect QTLs (DTY3.1, DTY2.1, DTY2.2) for grain yield under lowland drought stress in the background of mega-varieties IR64 and Swarna and QTLs/regions on chromosome 1 (RM (read more) Contact: Arvind Kumar, IRRI, Los Banos, The Philippines

a.kumar@cgiar.org
1
Rice Drought tolerant rice introgression lines. Germplasm IR64 introgressed lines with four, three, and two confirmed drought tolerance QTL combination. Contact: Arvind Kumar, IRRI, Los Banos, The Philippines

a.kumar@cgiar.org
1
Rice Drought tolerant rice introgression lines in Vandana background. Germplasm Vandana introgressed lines developed with a major QTL for drought, qDTY12.1. Contact: Arvind Kumar, IRRI, Los Banos, The Philippines

a.kumar@cgiar.org
1
Rice Rice breeding lines for drought tolerance in agronomically acceptable backgrounds. Germplasm Breeding lines evaluated from drought tolerance in multi-locational trials. Four breeding lines released as varieties for cultivation in different provinces of India: in Tamil Nadu, PMK3; in Orissa (read more) Contact: Arvind Kumar, IRRI, Los Banos, The Philippines

a.kumar@cgiar.org
1
Rice Rice drought responsive genes. Genomic Resources The drought responsive transcriptome changes in the leaves of two contrasting rice cultivars Apo (drought tolerant) and IR64 (drought sensitive) were analyzed and contrasted. More than hundred rice d (read more) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5978 3
Rice SNPs for identifying haplotype structure Genomic Resources A set of SNPs developed with Golden Gate Illumina chemistry curated for their annotation and visualization on the rice genome. Data allowed definition of haplotype structure and differentiation of (read more) SNP data available on-line in the TropGenes database at http://gendiversity.cirad.fr/GenDiversity/GenotypingStudies.do
3
Rice Rice MAGIC populations Germplasm Four MAGIC populations (indica, indica Plus, japonica, and Global (indica x japonica). These are being used to different degrees. Over 2000 MAGIC lines have been distributed to multiple countries and (read more) Contact:
Hei Leung, IRRI, Philippines at h.leung@irri.org,
or
Glenn Gregoiro, IRRI, Philippines at g.gregorio@irri.org
2
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
Rice Markers for a major salt-tolerance QTL, Saltol, in rice Informative markers 10 SSR foreground markers across the Saltol region including gene-based markers. Also 80 robust background markers identified that are polymorphic between FL478/Fl378 and Bangladesh varieties, BR11 a (read more) Contact Abdelbagi M. Ismail, International Rice Research Institute (IRRI), The Philippines
abdelbagi.ismail@cgiar.org
1
Rice Validated SSR marker kit for diversity analysis of rice germplasm collections Genomic Resources Reference kit of 20 SSRs with primer sequence list used to define the Rice Germplasm Reference Set composed of a core set of 256 accessions representing the genetic diversity of the entirety of the I (read more) Available from Generation Challenge Program, CIMMYT, Texcoco, Mexico
info@generationcp.org
2
Rice IR57514 an IRRI rice variety improved for grain quality Germplasm BC3 selection of IR57514 improved for good grain quality and submergence tolerance (flash flooding type) 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
Rice Drought tolerace QTLs for lowland and upland rice Informative Markers qDTY1.1: effective in upland and lowland ecosystem; Donors Swarna, IR64, MTU1010, Sabitri and Sambha Mahsuri. Phenotypic variance explained 13%
qDTY2.3: effective in upland and lowland ecosystem; Don (read more)
For markers contact: Contact : Arvind Kumar, IRRI, Philippines, a.kumar@cgiar.org

For donors contact Ruaraidh Sackville Hamilton, IRRI, Philippines, r.hamilton@cgiar.org
1
Rice Upland and lowland rice varieties introgressed with drought tolerance QTL. Germplasm 1- Vandana variety introgessed with qDTY12.1. The introgressed line identity is IR 84984-83-15-481-B.
2- IR64 variety introgressed with qDTY2.2 and qDTY4.1. The identity of the most promising lines i (read more)
Contact : Arvind Kumar, IRRI, Philippines a.Kumar@cgiar.org 1
Rice MAGIC Indica Germplasm 1831 S6:8 lines drived from intercrossing of 8 Indica founder lines according to MAGIC schema. The founder lines are [Fedearroz 50, Shan?Huang Zhan?2 (SHZ?2), IRRI 123 (PSBRc82), IR77186?122?2?2?3, I (read more) IRRI, working collection available for distribuion upon requests. MTA required as institutional policy. Contact Hei Leung, hleung@irri.org 2
Rice MAGIC Plus Germplasm 2200 S6:8 lines drived from intercrossing of 8 Indica founder lines according to MAGIC with two additional rounds of 8-way F1 intercrossing.
The founder lines are [Fedearroz 50, Shan?Huang Zhan?2 (SH (read more)
IRRI, working collection available for distribuion upon requests. MTA required as institutional policy. Contact Hei Leung, hleung@irri.org 2
Rice MAGIC Japonica Germplasm 400 S4:6 lines drived from intercrossing of 8 japonica founder lines according to Multi-parent Advanced Generation Inter-Crosses (MAGIC) schema [CSR30, Cypress, IAC165, Jinbubyeo, WAB56?125, IR73571?3 (read more) IRRI, working collection available for distribuion upon requests. MTA required as institutional policy. Contact Hei Leung, hleung@irri.org 2

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