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 | |
| BUL | Description |
| 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
| 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | |
