Welcome to the GCP proto-catalogue product list, which is sorted by 1) crop and 2) type (of product). The designation of “Global” refers to products such as learning modules, informatics tools/applications and others that facilitate the implementation of modern breeding methods for a wide range of crops. Additional searching may be performed by using a key word of your choice by use of your computer’s “Find” application (press Control and “f”).
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Oil crops |
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Potatoes |
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Beans |
Chickpeas |
Cowpeas |
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Groundnuts |
Lentils - coming soon |
Pigeonpeas |
| Soya beans - coming soon |
| Coconut |
Global
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
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 models for rice leaf growth |
Genetic basis of drought tolerance studies and study of common genetic basis for leaf growth. |
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 conditions. Plant Cell and Environment 30, 135-146 |
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2 |
NGS Data Analysis Pipe Line |
Genomic Resources |
This pipeline is capable in identifying the SNPs between the parental genotypes using different algorithms |
For analysis of Chickpea and Pigeonpea NGS data |
Contact T. Shah, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India (TM.shah@cgiar.org) |
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3 |
iMAS, an integrated marker-assisted selection system |
Informatics Application/Tool |
The Integrated Marker-Assisted Selection System (iMAS) software is an integrated molecular breeding analysis platform. The GCP supported the development of the iMAS. The iMAS provides simple-to-follow guidelines to assist users with the selection of the most appropriate experimental design and data analysis methods. It offers the users a regularly updated selection of the currently most appropriate options. The iMAS performs the required reformatting of datasets for all included software |
marker data analysis by plant breeders |
Downloadable from Generation Challenge Programme website, |
http://www. |
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4 |
A Central Registry application for registration and storage of project datasets |
Informatics Application/Tool |
A fully functional Central Registry application developed to allow registration of datasets, uploading of data files and registration of web service entry points. Section on GCP wiki site on assessments of analysis tools for SP1, SP2 and SP3; Technical Management of Central Registry, Strengthening the Central Registry�s resource collection, Development of the Central Registry, Content Management, Help desk, User survey |
Registration and storage of data sets from GCP projects. |
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5 |
iMAS, an integrated decision support system |
Informatics Application/Tool |
The Integrated Marker-Assisted Selection System (iMAS) software is an integrated molecular breeding analysis platform. The GCP supported the development of the iMAS. The iMAS provides simple-to-follow guidelines to assist users with the selection of the most appropriate experimental design and data analysis methods. It offers the users a regularly updated selection of the currently most appropriate options. The iMAS performs the required reformatting of datasets for all included software |
marker data analysis by plant breeders |
Direct download from Generation Challenge Programme |
http://www. |
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6 |
Dayhoff: A catalogue of plant gene orthologs and paralogs |
Informatics Application/Tool |
The GCP has developed Dayhoff, the ortholog gene catalogue. (http://202.123.56.214:8080/DayhoffWeb2/) Dayhoff documents stress-responsive genes comparatively across plant species. It is a compendium of protein families, phylogenetic trees and multiple sequence alignments with the associated experimental evidence. It serves to elucidate orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress, mainly abiotic stresses such as water deficit (‘drought'). For example, the comparison of microarray data about drought stress obtained across diverse crop species can be analysed in a comparative manner to identify common gene expression profiles under similar stresses. The web site includes query and visualization tools and allows searches and browsing of the underlying project database. |
On-line catalogue for the elucidation of orthologous and paralogous relationships between plant genes that may be involved in response to environmental stress |
Viewable and downloadable from the Generation Challenge Programme website |
http://www. |
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7 |
QuLine: Software for optimizing marker-assisted breeding systems for drought tolerance in cereals |
Informatics Application/Tool |
QuLine module, maintenance and update of the breeding simulation tool (QuLine) (version 1.4 released in July 2006; a new version will be released in late 2007) can simulate all aspects of conventional and marker-assisted selection for inbreeding crops; QugMan editor, completion of a prototype editor (QugMan) for the QU-GENE input files, allows marker and QTL maps to be used as direct inputs to the simulation platform. LER module, development of a QU-Gene plug-in module (LER) for a physiological model of leaf elongation rate in response to drought, enables direct input of gene information to a physiological model to allow the simulation of complex phenotypes in response to drought; QTL Mapping software, using the QU-GENE software library, developed a modified algorithm for improving the traditional composite interval mapping and associated software, i.e. ICIM, and simulates populations of genotypes for testing of QTL mapping tools and will allow integration of QTL mapping as an important step in recurrent breeding strategies; QuHybrid module, preliminary design and development of the hybrid breeding application module for application in hybrid crops (i.e. QuHybrid), allow simulation of breeding systems of hybrid crops including topcross testing and reciprocal selection schemes. |
Modeling to facilitate marker-assisted breeding decisions |
http://www.isbreeding.net |
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8 |
Laboratory Information Management System (LIMS) for high-throughput molecular genotyping |
Informatics Application/Tool |
The LIMS developed by ICRISAT meets the needs of a moderately high-throughput molecular genotyping facility. The ICRISAT LIMS is being used at the genomics laboratory facilities in ICRISAT-Patancheru. During 2005, the existing ICRISAT MS-Windows based LIMS was recoded as a platform independent, multi-user LIMS that manages workflow and information in the Applied Genomics Laboratory (AGL) at ICRISAT-Patancheru. The LIMS was developed as modules, thus any number of modules can be added depending upon the laboratory using the application. The goal of the LIMS transfer project was to transfer this application to the Biosciences Eastern and Central Africa (BecA) laboratories in Nairobi, Kenya and IITA in Ibadan, Nigeria for use by the scientists and technical staff at these locations. Both ICRISAT and IITA already have scientists based in BecA and have on-going research projects in genomics of sorghum and cassava, as well as other crops. |
Laboratory information management at ICRISAT and BeCA |
Contact Trushar Shah, International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) |
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9 |
QU-GENEUI software for simulation of conventional and marker-assisted breeding |
Informatics Application/Tool |
QU-GENE User Interface genetic simulation software providing tools for simulation of breeding programmes from simple back-crossing strategies to complex marker-assisted breeding scenarios. |
Decision tool for marker assisted breeding |
From Software page at http://www.uq.edu.au/lcafs/qugene/ |
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10 |
Generation Atlas |
Informatics Application/Tool |
Generation Atlas is online maps and tools for researchers, students, policy analysts and others interested in crop improvement. Developed by the Generation Challenge Programme, it uses map server technology to allow users to explore constraints and opportunities of agricultural production throughout the world. |
Locating and comparison of agricultural constraints to crop improvement throughout the world |
Viewable and usable from the Generation Challenge Programme website (www.generationcp.org) |
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11 |
HaploPhyle |
Informatics Application/Tool |
Haplophyle is a pipeline for the analysis of genotyping data which includes haplotype definition, haplotype network analysis and connection with external data, such as geographic origin or genetic group assessment. |
On-line genotyping analysis for haplotypes |
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12 |
Genetics and Breeding Simulation Tools |
Informatics Application /Tool |
Tools that can be used to simulate and compare different breeding methods for both self- and cross-pollinated crops |
QuHybrid has been used in CIMMYT's Maize Breeding Program (i) to optimize breeding strategies in improving pro-Vitamin A content, and (i) to compare the one-stage versus two-stage testcrossing. More than 200 people have been trained in China to use the breeding simulation tools. |
Contact Mark Dieters, UQ, Australia (m.dieters@uq.edu.au) |
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13 |
QTL Mapping Software |
Informatics Application /Tool |
A softare helps to build the genetic linkage map and conduct QTL mapping for many genetic populations |
The novel QTL mapping method ICIM has received more than 40 citations according to Google Scholar. More than 200 people have downloaded the integrated software QTL IciMapping from the webpage http://www.isbreeding.net. More than 200 people have been trained in China to use the novel method and the integrated software. |
Jiankang Wang, CIMMYT/CAAS, Beijing, China |
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14 |
GCP Molecular Marker Toolkit |
Informatics Application /Tool |
The Toolkit is a publicly available and easy accessible database for currently available and validated markers for 19 food security crops. The 19 crops currently covered are Musa spp., barley, beans, cassava, chickpea, coconut, cowpea, faba bean, groundnut, lentils, maize, millet, pigeonpea, potato, rice, sorghum, sweet potato, wheat, and yam. This first version of the tool includes only STS, SSR, SNP, and SCAR markers. This toolkit is a compilation of information available via internet sources, public databases and papers that has been verified against plant breeders' experiences. |
Access to informative markers for abiotic and biotic traits by breeders. |
Viewable and accessible from Generation Challenge Programme website (www.generationcp.org) |
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15 |
Molecular Marker Toolbox |
Informative Markers |
A searchable database on molecular markers useful for marker-assisted selection in 19 food security crops. Information on molecular markers for MAS is often scattered in often difficult accessible information sources. Molecular Marker Toolkit(MM Toolkit) was developed to provide that kind of information on those molecular markers that are effectively used in breeding programmes of 19 crops essential to food security. |
Improved compilation of all existing information on molecular markers useful for marker-assisted selection in 19 food security crops |
Viewable and accessible from Generation Challenge Programme website (www.generationcp.org) |
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16 |
Publication: Targeting and Impact Analysis of Generation Challenge Programme Technologies |
Publication |
A final technical report on GCP project no. G4006.13, Targeting and Impact Analysis of Generation Challenge Programme Technologies. Geographic distribution and the magnitude of poverty in the 14 GCP priority farming systems; Crop-specific modelling of drought severity and type; Analysis of GCP priority farming systems and their patterns of technology adoption at disaggregated levels within each region; Economic assessment of the potential market-scale impacts of a variety of household-level adoption scenarios |
Information used in the GCP Strategic Framework |
Summary available from the Generation Challenge Programme, Brief no. 1, Where in the world do we start? (www.generationcp.org) |
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17 |
Publication: Ex Ante Impact Analysis of Marker-Assisted Selection Technologies Supported by the Generation Challenge Programme (GCP) |
Publication |
A final technical report for GCP project no. G4006.14,Ex Ante Impact Analysis of Marker-Assisted Selection Technologies Supported by the Generation Challenge Programme (GCP). Construct technology-impact pathways for rice and cassava molecular-assisted breeding projects; gather secondary data on prices, production, area, and trade for the two crops in the target countries; gather crop loss data. |
GCP strategic framework |
Summary of report available from the Generation Challenge Programme as Pathways to Impact, Brief no.3, Molecular and conventional breeding through an economic lens.(www.generationcp.org) |
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18 |
Quantitative PCR assays for key pathogens |
Publication |
RT-PCR assays for Setosphaeria turcica and Aspergillus flavus |
Resistance studies research |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
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19 |
Presentations of four workshop courses on phenotypic and marker-based analysis of multi-environment data. |
Training Materials |
Workshop courses to explore methodology based on mixed models to perform QTL mapping using multiple traits and multiple environments simultaneously. The approach allows investigating issues related to: a) the causes underlying GxE (QTLxE), b) the causes of genetic correlations between traits (pleiotropic and linked QTLs), and c) the causes of changing genetic correlations between environments. Workshops held in various years in various venues(October 2005, Zaragoza (Sp), September 2006, Sao Paulo (Br), July 2007, Colonia del Sacramento (Uruguay) / Piracicaba (Brazil). |
Instructional material |
Viewable and downloadable from the Generation Challenge Programme website |
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20 |
A document describing the GCP product delivery strategy. |
Training Materials |
The Delivery Strategy Document resulted from a workshop following an e-forum that took place on line from April 11th to May 6th, 2005.The results of the e-forum were then synthesized and used as a starting point for the Working Group that met in Cali, Colombia, from 5-7 July 2005, to discuss the delivery strategy and provide input into the work plan. Among the 20 participants were plant breeders; social scientists with backgrounds in rural innovation, agricultural economists with a background in impact assessment, agricultural anthropologists; an intellectual property attorney and farmer leaders from the three regions (Africa, Asia and Latin America). In addition to IPGRI and GCP-SP5 staff members, the participants represented the perspectives of the CG Centres, NARS, ARIs, the HarvestPlus Challenge Programme, universities, the private sector and the stakeholders. |
Instructional material |
Viewable and downloadable from the Generation Challenge Programme website |
http://www. |
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21 |
Powerpoint presentations on the use of plant genetic diversity and molecular marker assisted breeding - Chile |
Training Materials |
A training workshop commissioned by the Generation Challenge Programme was held in Santiago, Chile to provide both conceptual and hands-on training in the use of plant genetic diversity and molecular marker assisted breeding. Emphasis was placed on practical applied usage and improving the links between plant breeding, germplasm management and utilization, and molecular biology methods, with a particular focus on the use of microsatellite markers. Sessions included DNA-based markers, PCR-based markers, comparing molecular marker techniques, diversity analyses, population genetics, phenotyping and statistical analyses, linkage mapping and QTL discovery & analysis, marker-assisted breeding strategies, and practical applications. Laboratory practicals included DNA extractions, PCR, electrophoresis, and the use of microsatellites. Computer practicals included SSR diversity, mapping and breeding software, and the use of public databases. |
Capacity building on use of molecular markers. |
Viewable and downloadable from GCP web-site - Capacity Building Corner |
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22 |
Powerpoint presentations on the use of plant genetic diversity and molecular marker assisted breeding - Pretoria, SA |
Training Materials |
The objectives of this workshop were to provide both conceptual and hands-on training in the use of plant genetic diversity and molecular marker assisted breeding, with emphasis on practical applied usage and improving the links between plant breeding, germplasm management and utilization, and molecular biology methods, with a particular focus on the use of microsatellite markers; Powerpoint presentations (with the permission of the presenters), along with a list of participants names and contact information posted on the GCP SP5 website. |
On-line capacity building on use of plant diversity and molecular markers |
Viewable and downloadable from GCP website - Capacity Building Corner |
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23 |
Powerpoint presentations on the use of plant genetic diversity and molecular marker assisted breeding - Thailand |
Training Materials |
All final materials used and powerpoint presentations for Plant Genetic Diversity and Molecular Marker Assisted Breeding Workshop, along with a list of participants names and contact information posted on the GCP SP5 website |
On-line capacity building on use of plant diversity and molecular markers |
Viewable and downloadable from GCP website, Capacity Building Corner |
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24 |
Presentations on scientific project proposal writing |
Training Materials |
Workshops held in Cotonou, Benin, Kuala Lumpur, Malaysia and Quito, Ecuador. These workshops were designed to help scientists who are planning, writing, or reviewing concept notes and proposals to submit to international donors. The Generation Challenge Programme sponsored the development of the training material and the organization of three regional training workshops in 2005. The objective was to increase the capacity of the Generation Challenge Programme (GCP) African, Latin American and Asian partners (NARS) in proposal development that leads to more effective distribution of research outputs and results, and to an increased fund raising ability. The Principal Investigator and main trainer was Karine Malgrand, formerly Programmeme Specialist-Fund Raising at the International Plant Genetic Resource Institute (IPGRI), now an independent consultant. Karine can be contacted at karine@malgrand.org. |
On-line capacity building on scientific project proposal writing |
Viewable and downloadable on GCP website, Capacity Building Corner |
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25 |
Training materials on plant genetic resource policy issues |
Training Materials |
A course curriculum and training materials have been developed for international/regional workshops to train research managers and scientists on plant genetic resource policy issues, with special focus on the development of institutional policies and tools for Freedom to Operate, i.e. IPR and ABS. The training materials consist of PowerPoint presentations, assignments and exercises and reference materials. Depending on the specific course objectives and course setting they can be used for regional courses. The purpose of this project was to create a curriculum and training materials for regional courses on genetic resource policies. The objectives of these courses are to create awareness, extend relevant knowledge and share experiences among scientists and science managers, enhancing their capacity to develop or strengthen institutional policies for handling Intellectual Property Rights and Access and Benefit Sharing. The primary beneficiaries are scientists and science managers from GCP partner organizations. The design of the curriculum on genetic resources issues with special focus on institutional policies and tools for Freedom to Operate, IPR and ABS, has been based on experiences of courses in Sweden, Germany/Bioversity International, but differs from these in specifically addressing the institutional context. The training materials have been developed by Wageningen UR with inputs from Bioversity International and Embrapa. Training materials were first used in two-week international course with similar objectives in Wageningen in June 2005 and June 2006 (outside the responsibilities of GCP), and finally tested in a regional workshop in Karaj, Iran in 2006, with a group of 22 professionals from Central West Asia and Africa. Participants worked in biotechnology, crop improvement, seed supply and genetic resources conservation and were coming from both NARS and civil society. |
Capacity building on plant genetic resource policy issues |
The training materials are available on CD by request to the Generation Challenge Programme |
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26 |
Training materials on plant genetic diversity analysis |
Training Materials |
This course refers to dynamics of genetic diversity in cultivated plants. It is dedicated to persons interested in the study of genetic diversity for domesticated plants. It is organised following the evolution point of view of domestication, and focusing on how to detect traits related to domestication for further uses in a perspective of breeding strategy. It is mostly taking into consideration genetic diversity. |
Capacity building in plant genetic diversity analysis |
CD in English with support available on request from the Generation Challenge Programme (www.generationcp.org) |
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27 |
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 materials were developed in such a way as to be useful either as a self-tutorial, or as a basis for a course of approximately 1 week duration. |
Capacity building for association analysis and mapping |
Viewable and downloadable from Generation Challenge Programme Website (www.generationcp.org) |
http://www. |
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28 |
Proceedings: The Molecular Markers for Allele Mining Workshop |
Training Materials |
The summaries copy edited by a professional English editor and adapted to the IPGRI Style Guide v 2.1 (Oct. 2005). Publication of the Proceedings by IPGRI was completed on September 10, 2006, with 1,000 copies printed. The publication was distributed to genebank managers and curators, plant breeders and other colleagues as well as the authors and contributors; a CD containing all the presentations was also provided for all participants; The purposes of the workshop were to: (1) convey knowledge gained through GCP SubprogrammeÊ1 activities in year 1 to CG and non-CG scientists involved with germplasm management so that a wider community can benefit; (2) record the views of various actors in the field of germplasm conservation, management and use worldwide; and (3) promote a sense of ownership and develop a community of practitioners within various institutions to expand the impact of the GCP. |
Capacity building for germplasm management |
Viewable and downloadable from the Generation Challenge Programme website, Capacity Corner |
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29 |
Training materials: genomics and comparative genomics |
Training Materials |
Comparative genomics is a relatively new field of research that has developed due to increasing technological capabilities, particularly in the area of DNA sequencing, and an increased understanding of the conservation of biology. The potential benefits of this new field are extensive, not only on the academic level of an increased understanding of biological organisms, but also including many practical applications. In the field of plant breeding and crop improvement the promise of comparative genomics holds special potency as it has implications on global hunger, nutrition, conservation, and environmental protection. Information that once seemed particular to only one species or limited group of species can now often be useful across many species, genera or even further. One result of comparative genomics has been the increasing speed at which new data, information, discoveries and technologies are now developing. This is exciting and promises many benefits; however, it also means that it has become increasingly difficult to keep abreast of current research and technologies. This is particularly true for researchers in developing countries who have limited access to scientific publications or extended academic communities. Thus, the very researchers who could most benefit from comparative genomics are those least able to, due at least in part to the lack of know-how (together with infrastructure insufficiencies, etc.). This project aims to begin to solve this problem by creating materials to be used in training global scientists in the use of genomics and comparative genomics. A recent collaboration of IPGRI and the Institute of Genomic Diversity at Cornell University resulted in 2 learning modules, Volume 1: Using Molecular Marker Technology in Studies on Plant Genetic Diversity and Volume 2: Genetic Diversity Analysis with Molecular Marker Data. These learning modules (available as a CD in several languages and downloadable as pdf) have been used as the basis of molecular marker training workshops, and more than 700 copies have been requested by researchers worldwide. Similar training materials covering genomics and comparative genomics are now in great demand to follow and complement the concepts covered in the previous learning modules. |
Capacity building and access to educational resources for comparative genomics. |
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30 |
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, genetics and plant breeding. It is expected that readers have some understanding of molecular markers (a number of resources are given throughout, if not). It is meant to complement other learning modules available, such as those available or in progress for molecular markers, genetic diversity, phenotyping, and plant breeding |
Capacity building for the use of marker assisted breeding for crop improvement. |
Viewable and downloadable at www.generationcp.org Capacity Corner |
Barley
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
Barley stress tolerant genes |
Genomic Resources |
Fourteen new barley genes presumably involved in stress tolerance identified in a microarray study and sequenced. |
14 genes used in the ADOC project |
Contact M. Baum, International Center for Agriculture Research in Dry Areas (ICARDA), Aleppo, Syria |
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2 |
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 |
Reference kit of 20 SSRs and EST-SSRs for barley |
Contact Jean-Francois Rami, CIRAD, Montpellier France |
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3 |
A validated Barley germplasm reference collection |
Genomic Resources |
The Barley Reference Set is composed of a core set of accessions representing the genetic diversity of the entirety of the ICARDA germplasm bank collection. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for prebreeding crosses. |
The Associated Marker kits are a set of markers that has been used to characterize the corresponding reference set collection. Using this same set of markers, any scientist will be able to compare the diversity of his/her own deversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germplasm. |
The International Center for Agriculture Research in Dry Areas (ICARDA) Germplasm Bank |
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4 |
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 |
Mapping and association studiesfor drought tolerance in wild barley . |
Contact Professor Robbie Waugh, SCRI, Scotland, UK (Robbie.Waugh@scri.ac.uk). Also see site at following URL. |
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5 |
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. |
Genetic studies for drought tolerance in cereals. |
Contact Professor Robbie Waugh, SCRI, Scotland, UK (Robbie.Waugh@scri.ac.uk). Also see site at following URL. |
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6 |
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 . |
Genetic studies of drought tolerance in barley. |
Contact Professor Robbie Waugh, SCRI, Scotland, UK |
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7 |
A barley germplasm reference set |
Germplasm |
A reference set of barley (about 300 lines) representing 10% of the whole collection. The composite set of 3000 accessions genotyped with 50 SSR. The composite set consisted of the following germplasm: H. vulgare ssp. spontaneum (15%) The barley wild progenitor is represented by 445 accessions, 65 % of this total are original accessions from GRU collection missions. Hyper-arid, arid and semi-arid collection sites represent 1%, 20% and 63% of the total, respectively. The set originates from 20 countries and collection sites belong to 58 ecological clusters. Landraces (65%):Landraces are a major part of the set with 1935 accessions. A significant part (20 %) is original material collected by ICARDA. Hyper-arid, arid and semi-arid collection sites are present with 3%, 33% and 43%, respectively. The landrace set originates from 85 countries and 78% is of CWANA origin. Collection sites belong to 255 ecological clusters. Improved germplasm (20%): This category includes cultivars, unfinnished breeders' materials and genetic stocks, which represent 13%, 6% and 1% of the CP barley set, respectively. |
Comparative genomics studies and introduction of diversity and selected traits in barley breeding programmes. |
Contact M. Baum, International Center for Agriculture Research in Dry Areas, Allepo, Syria |
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8 |
SNP markers for drought tolerance QTLs in barley recombinant chromosome substitution lines |
Informative Markers |
A set of SNP markers designed via an Illumina and GoldenGate assay (Close et al., 2009*) of barley recombinant chromosome substitution lines These SNPs are based on ESTs; HarvEST 35 unigene number can be supplied by access contact person as noted below. |
Association and QTL mapping studies for drought tolerance in barley |
Contact Professor Robbie Waugh, SCRI, Scotland, UK (Robbie.Waugh@scri.ac.uk). Also see site at following URL. |
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9 |
SNP markers for drought tolerance QTLs in landrace barleys |
Informative Markers |
A set of SNP markers designed via an Illumina and GoldenGate assay (Close et al., 2009*) of the Syrian and Jordanian Landrace Collection of barley. These SNPs are based on ESTs; HarvEST 35 unigene number can be supplied by access contact person as noted below. |
Association and QTL mapping studies for drought tolerance in barley |
Contact Professor Robbie Waugh, SCRI, Scotland, UK |
Maize
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
A microsatellite kit for the GCP maize reference germplasm set |
Genomic Resources |
Reference kit of 35 SSRs for maize with |
Assessment of diversity in maize collections |
Contact Jean-Francois Rami, CIRAD, Montpellier France |
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2 |
Total transcriptome of smoke and butenolide treated germinating maize kernels |
Genomic Resources |
Microarray data describing the total |
genetic studies to elucidate physiological and biochemical pathways to induce increased germination and vigor of maize seeds under drought stress |
Transcriptome data has been deposited in the GEO database (http://www.ncbi.nlm.ni.gov/geo) under accession number GSE17484. |
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3 |
Publication: A synthesis all known previous rice and maize disease resistance QTL studies |
Genomic Resources |
A publication demonstrating that |
Reference |
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. |
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4 |
A maize germplasm reference set |
Germplasm |
A reference set of maize composed |
Comparative genomics studies and introduction of diversity and selected traits in maize breeding programs. |
Contact J. Cairns, International Center for Maize and Wheat Development (CIMMYT), El Batan, Mexico |
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5 |
NILs for Southern Leaf Blight resistance in maize |
Germplasm |
A set of ~15 NILs carrying SLB QTL |
Resistance and genomics studies. See: |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
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6 |
NILs for Northern Leaf Blight resistance in maize |
Germplasm |
For CML52-derived NILs, 61 SSR |
Resistance and genomics studies. |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
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7 |
Disease resistance maize lines |
Germplasm |
Elite lines from the Kenya Agriculture |
Four best hybrids identified for nomination to the Kenyan National Performance trials |
Contact S. Gethi, Kenya Agriculture Research Institute (Kari), |
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8 |
A SNP array for drought candidate genes in maize |
Informative Markers |
1536 SNP array for Drought Candidate |
Introgression of drought tolerant traits into maize |
GCP Central Registry http://gcpcr.grinfo.net/ |
http:// |
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9 |
QTL maps for maize diseases |
Informative Markers |
QTL maps for maize diseases in a |
Reference for genomics studies |
1) Balint-Kurti, P.J., Krakowsky, M. D., Jines, M. P., Robertson, L. A., Molnár, T. L., Goodman M. M. and Holland J. B. (2006) Identification of Quantitative Trait Loci for Resistance to Southern Leaf Blight and Days to Anthesis in a Maize Recombinant Inbred Line Population. Phytopathology 96:1067-1071 |
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10 |
QTL for Aluminum tolerance in Maize |
Informative Markers |
Markers for novel maize Al tolerance |
Aluminum tolerance studies and improvement of maize breeding lines |
Contact L. Kochian, USDA/ARS, Cornell University, Ithaca, NY USA |
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11 |
Getting the focus right: a GCP socio-economic study to determine production constraints specific to maize |
Publication |
This study organized the systematic |
On-line socio-economic study |
Viewable and downloadable from Generation Challenge Program Website (www.generationcp.org) |
http://www |
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12 |
Genotypes of maize and sorghum identified with superior performance on acid soils |
Publication |
Genotypes of maize and sorghum |
Study of performance of QTLs in genotypes of maize and sorghum grown on acid soils. |
L. Kochian, USDA/ARS, Cornell University, Ithaca, NY USA |
Pearl millet
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
DaRT marker array for pearl millet |
Genomic Resources |
An array of DArT markers for pearl millet 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 species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in pearl millet. |
Diversity studies of pearl millet collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
Rice
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
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. |
Phenotypic and cytological characterisation of non-host interactions in rice and wheat with M. grisea and P. triticina, transcriptome analysis of non-host interaction in rice and wheat, validation of non-host genes in rice and wheat, non-host gene mapping in rice and wheat, |
jean-benoit Morel (CIRAD), jbmorel@cirad.fr |
jean-benoit Morel (CIRAD), jbmorel@cirad.fr |
|
2 |
An array of SNP markers for rice |
Genomic Resources |
250 SNP markers developed for rice. A total of 250 PCR primers were designed, 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; Sequences from 8 diverse Indonesian rice accessions generated for 215 primer pairs described above and there are 1720 sequences; all of the sequences from the 8 rice accessions aligned and SNPs called for all of them; information about SNP location and frequency in a limited set of indica and japonica germplasm; 125 SNP detection assays designed and carried out on 96 diverse Indonesian accessions at Genaissance Pharmaceuticals; A collection of 250 Indonesian landraces analyzed with a set of genome-wide simple sequence repeat (SSR) markers, LD measured in three genomic regions surrounding the bacterial blight resistance genes Xa7, Xa13, and the cluster of Xa4/Xa22/Xa26, single nucleotide polymorphism (SNP) markers developed across each region by sequencing PCR products from a subset of eight landraces, and genotyped across a larger subset of accessions using a high-throughput SNP assay; SNP data used to measure the LD across each region and define the haplotype block structure found in this set of rice germplasm. |
Rice genomics and mapping studies. |
Contact S. McCouch, Cornell University, Ithaca, NY (The products not been shared with other GCP projects nor with projects outside the GCP yet.They will be as soon as paper is accepted for publication.) |
|
|
3 |
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 rice varieties through DNA-DNA hybridization on high density oligonucleotide arrays . |
comparative genomics studies in rice |
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|
|
4 |
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. |
Development of a Universal Core Genetic Map for rice |
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 Applied Genetics, 120:563-572 |
m. lorieux@cgiar.org |
|
5 |
Chinese rice hybrids with drought tolerance. |
Germplasm |
A new hybrid cultivar, Liaoyou 5224, derived from the cross between a selected DT IL, C5224 and a CMS line - Liao5216A approved to be released to farmers in the Liaoning province and recommended for multilocal testing in North China; Another new hybrid cultivar, Liaoyou 5249 derived from the cross between an IL (C5249) and Liao99A is tested in the Liaoning province; A high yield DT japonica IL, HR95 is recommended for multilocal testing in the Ningxia Province. |
Multi-locational testing and release in China. |
Contact Z.K. Li, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China |
lizhk@caas.net.cn |
|
6 |
Advanced blast resistant rice lines |
Germplasm |
Six Vandana-like lines with added blast resistance from Morobereken ready for testing in upland sites in India (Vandana is a drought tolerant upland variety but deficient in disease resistance in the upland environment) |
Breeding lines for rice blast resistance |
Contact Rebecca Nelson, Cornell University, Ithaca, NY USA |
|
|
7 |
Bacterial Blight resistant rice accessions |
Germplasm |
Rice accessions with relatively high resistance to most known pathogen races of bacterial blight in the Philippines |
Genomic studies; pre-breeding materials |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
|
|
8 |
Disease and drought resistance rice lines |
Germplasm |
Elite progenies from Moroberekan/Vandana cross showing resistance to blast, drought and, in some cases, ShB were identified in India and the Philippines. |
Drought and disease resistance breeding programs in Indonesia |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
|
|
9 |
Interspecific rice line (Oryzae sativa x O. glaberrima) resistant to rice blast and drought in Africa |
Germplasm |
One interspecific line (SIK400-b-56-1-361-18)with good performance in terms of leaf rolling and reduced leaf burning, ability to recover from drought, and resistance to leaf blast |
Research: study of feasibility of introgression of drought tolerance O. glaberrima to African rice |
Contact Marie Noelle Ndiondjop, AfricaRice, Benin |
|
|
10 |
Oryzae glaberrima accessions resistant to Bacterial Leaf Blight |
Germplasm |
20 accessions of O. glaberrima found resistant to one of three new African races of Bacterial Leaf Blight |
Genetic studies and introgression of Bacterial Leaf Blight resistance into interspecific lines of O. oryzae |
Contact Marie Noelle Ndjiondiop, AfricaRice, Benin |
Marie Noelle Ndjiondjop @ M.NDJIONDJOP |
|
11 |
Fertile interspecific (Oryzae sativa x O. glaberrima) lines |
Germplasm |
Seed of five new fully fertile interspecific (Oryzae sativa x O. glaberrima) lines with desirable agronomic traits available for crossing |
Genetic studies and introgression of desirable traits from O. glaberrima into breeding lines of O. sativa |
Contact Marie Noelle Ndjiondjop, AfricaRice, Benin |
|
|
12 |
A CSSL population of Oryza sativa x O. rufipogon |
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 rufipogon |
Genetic studies and search for beneficial genes from O. rufipogon that may be introgressed into O. sativa |
Contact M. Lorieux, CIAT/IRD, Cali, Colombia |
m.lorieux@cgiar.org |
|
13 |
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 |
Genetic studies and search for beneficial genes from O. glumaepatula that may be introgressed into O. sativa |
Contact M.Lorieux, CIAT/IRD, Cali, Colombia |
m. lorieux@cgiar.org |
|
14 |
A CSSL population of Oryza sativa x O. meridonalis |
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 meridionalis |
Genetic studies and search for beneficial genes from O. meridionalis that may be introgressed into O. sativa |
Contact M. Lorieux, CIAT/IRD, Cali, Colombia |
m. lorieux@cgiar.org |
|
15 |
A CSSL population of Oryza sativa x O. glaberrima |
Germplasm |
A Chromosome Segment Substitution Line working population of about 60 interspecific lines bearing introgressed genome segments from the AA genome of the cultivated species, Oryza glaberrima, in a O. sativa subspecies japonica background |
Genetic studies and search for beneficial genes from O. glaberrima that may be introgressed into O. sativa |
Contact M. Lorieux, CIAT/IRD, Cali, Colombia |
m. lorieux@cgiar.org |
|
16 |
Interspecific rice lines (Oryza sativa x O. glaberrima) with drought tolerance |
Germplasm |
A set of interspecific, Oryza sativa x O. glaberrima, chromosome segment substitution lines identified with superior drought tolerance in Africa |
Identification of genes conferring drought adaptive traits. |
Contact B. Manneh, AfricaRice, Benin |
b.manneh@cgiar.org |
|
17 |
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 |
Quantifying the effects of Pup1 on phosphorus uptake in irrigated, elite rice varieties |
Contact Sigrid Heuer, IRRI, Los Banos, Philippines [NOT AVAILABLE UNTIL 2012] |
S.HEUER@cgiar.org |
|
18 |
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 Gagendit and Batur) |
Testing effect of Pup1 on phosphorus uptake efficiency of three Indonesan upland varieties |
Contact S. Heuer, IRRI, Los Banos, Philippines [NOT AVAILALBLE UNTIL 2012] |
S.HEUER@cgiar.org |
|
19 |
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 same cluster after the microarray experiments |
comparative genomics studies in rice |
Contact S. Kikuchi,National Institute of Agrobiological Sciences (NIAS), Japan |
|
|
20 |
OryGenesDB: an interactive tool for rice reverse genetics |
Informatics Application/Tool |
The OryGenesDB CIRAD-based webservice originated from the the Oryza sativa database. |
comparative genomics studies for rice researchers |
Viewable and downloadable at the Generation Challenge Program website (www.generationcp.org) and at http://orygenesdb.cirad.fr/ |
http://www. |
|
21 |
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. |
comparative genomics studies in rice |
available online |
|
|
22 |
Saltol markers for rice |
Informative Markers |
Three markers identified for introgression of Saltol into elite varieties. At Dhaka University, three varieties bred for the salinity affected areas in Satkhira for Boro (dry winter season) are being tested again in the saline zone in Satkhira for the 3rd consecutive year, three markers identified for introgression of Saltol into elite varieties by student from BRRI (Sazzzadur Rahman) used in MAS program starting August, 2007 (background and foreground marker information were provided by IRRI) and popular varieties Identified as recipients of Saltol , crosses made with Saltol donors and are being advanced for further analysis using MAS; at IRRI and UCD, progress made in identifying tightly linked as well as flanking markers at the two loci, background markers also identified and MAB system initiated to introgress the two QTLs into popular varieties; Further precision mapping of the Saltol locus, Development and validation of genetic markers for MAS, Identification and validation of candidate genes and Functional confirmation of Saltol and impact assessment; for phosphorus deficiency, Development and validation of genetic markers for MAS, Build the capacity of participating NARES partners in MAB and other needed molecular techniques. |
Introgression of the salt tolerance gene, Saltol, into breeding lines of rice |
Contact Abdelbagi Ismael, International Rice Researach Institute (IRRI), los Banos, Philippines |
|
|
23 |
Rice Blast resistance markers for rice |
Informative Markers |
Gene-specific molecular markers for candidate defence genes associated with resistance to rice blast |
Genomics studies; breeding for blast resistance |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
|
|
24 |
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, four SSR markers linked to resistance to blast isolate 033, three SSR markers linked to resistance to blast isolate 173, three SSR markers linked to resistance to blast isolate 123 |
Rice Blast resistance studies; breeding for blast resistance |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
|
|
25 |
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. |
Aluminum tolerance studies and improvement of rice breeding lines. |
L. Kochian, USDA/ARS, Cornell University, Ithaca, NY USA |
|
|
26 |
Pup1, a major QTL for phosphorus uptake in rice |
Informative Markers |
A validated major QTL for phosphate uptake in rice (PUP1) |
Improving phosphorus uptake in rice breeding lines. Comparative genomics studies for searches for homologs in sorghum and maize. |
Sigrid Heuer, International Rice Research Institute (IRRI), Los Banos, The Philippines |
|
|
27 |
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) |
Marker assisted selection of resistance to Bacterial Leaf Blight of rice in AfricaRice breeding programs |
Contact Marie Noelle Ndjiondjop, AfricaRice, Benin |
|
|
28 |
Molecular markers for the phosphorus uptake QTL, Pup1, in rice. |
Informative Markers |
A set of foreground markers for the phosphorus uptake QTL, Pup1, in rice |
Introgression of the Pup1 QTL into different rice varieties |
Contact S. Heuer, IRRI, Los Banos, Philippines |
|
|
29 |
Yield sensitivity module for a crop modeling system for cereals |
Publication |
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; Ecomeristem model adapted to simulate cereals behaviour under drought conditions. |
Crop modeling for drought studies in rice and maize. |
D. Luquet, International Center for Research for Agricultural Development (CIRAD), Montpellier, France |
|
|
30 |
A strategy for detection of deleted regions in rice mutants |
Publication |
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. Biol. Rep. in press. (online available: 10.1007/s11105-007-0002-7) |
Reference |
Contact R. Nelson,Cornell University, Ithaca, NY USA |
|
|
31 |
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 |
Capacity building for molecular breeders. |
|
Sorghum
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
AltSB: a major sorghum Al tolerance gene |
Gene |
Incontrovertible evidence that novel Al tolerance genes exist in the sorghum genome was obtained. Elite Al tolerant sorghum hybrids developed from the breeding program; AltSB confirmed as a major aluminum tolerance gene and cloned. As well, 6 preliminary candidate genes for maize Al tolerance via association analysis and verification of two of these by linkage analysis were identified. |
Study of genetic control of aluminum tolerance in sorghum and maize |
Contact Leon V. Kochian, USDA/ARS, Cornell University, Ihica, New York USA |
|
|
2 |
A microsatellite kit for the GCP sorghum reference germplasm set |
Genomic Resources |
Reference kit of 48 SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks |
Assessment of diversity in cassava collections |
Contact Jean-Francois Rami, CIRAD, Montpellier France |
|
|
3 |
A validated Sorghum germplasm reference collection |
Genomic Resources |
The Sorghum Reference Set is composed of a core set of accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for prebreeding crosses. |
The Associated Marker kits are a set of markers that has been used to characterize the corresponding reference set collection. Using this same set of markers, any scientist will be able to compare the diversity of his/her own deversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germpalsm. |
The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Germplasm Bank |
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|
4 |
A sorghum germplasm reference set |
Germplasm |
A sorghum reference set of 384 accessions derived from an ICRISAT sorghum composite set of 3384 accessions genotyped with 41 SSR |
Comparative genomics studies and introduction of diversity and selected traits in sorghum breeding programs. |
Contact H. Upadaya, International Center for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, India |
Wheat
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
A microsatellite kit for the GCP wheat reference germplasm set |
Genomic Resources |
A reference kit of 35 SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks |
Assessment of diversity in wheat collections |
Contact Jean-Francois Rami, CIRAD, Montpellier France |
|
|
2 |
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) wild relatives of hexaploid, tetraploid, and diploid wheats from around the world. |
CIMMYT wheat gene bank |
Contact S. dreisigacker, International Center for Maize and Wheat Improvement (CIMMYT) El Batan, Mexico |
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|
3 |
QTLs for yield, drought adaptive and agronomic traits |
Informative Markers |
Markers described for QTLs associated with yield, drought adaptive (GC, CT, CID and SSC) and agronomic traits discriminated from 800 genotypes of spring wheat |
Physiological and genetic studies of drought adaptive traits in spring wheat |
CIMMYT IWIS3 database. Contact Matthew Reynolds, Wheat Program, CIMMYT, Mexico |
|
|
4 |
Methodologies for large scale phenotyping in spring wheat |
Protocol |
Novel large-scale phenotyping methodologies for drought adaptive traits in spring wheat |
Phenotyping and discrimination of genotypes for drought adaptive traits in CIMMYT spring wheat nurseries |
CIMMYT IWIS3 database. Contact Matthew Reynolds, Wheat Program, CIMMYT, Mexico |
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|
5 |
Crossing plan for developing spring wheat populations with negligible diversity for flowering |
Protocol |
A crossing plan among complementary lines to develop spring wheat populations with negligible diversity for flowering across a range of environments. |
Crossing in breeding programs to produce drought-adaptive spring wheat genotypes |
CIMMYT IWIS3 database. contact Matthew Reynolds, Wheat Program, CIMMYT, Mexico |
|
|
6 |
Database for phenotypic expression in spring wheat |
Publication |
A database for 800 genotypes of the phenotypic expression for ground cover (GC), canopy temperature (CT), carbon isotope discrimination (CID), soluble stem carbohydrates (SSC) and yield and agronomic traits |
Selection and discrimination of spring wheat genotypes with drought tolerance |
CIMMYT IWIS3 database. Contact Matthew Reynolds, Wheat Program, CIMMYT, Mexico |
|
|
7 |
Report on estimation of drought-adaptive traits |
Publication |
Analysis and report identifying the degree to which a range of drought-adaptive traits can be reliable estimated in controlled environoments |
Estimation of traits exhibited by spring wheat plants assessed for drought-adaptation in controlled environment greenhouses |
CIMMYT IWIS3 database; Contact Matthew Reynolds, Wheat Program, CIMMYT, Mexico |
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
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 |
Assessment of diversity in cassava collections |
Contact M. Ferguson, International Institute of Tropical Agriculture, Ibadan, Nigeria |
|
|
2 |
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 |
Comparative genomics studies and introduction of diversity and selected traits in cassava breeding programmes. |
Contact M. Ferguson, International Center for Tropical Agriculture(IITA), Ibadan, Nigeria |
|
|
3 |
Cassava germplasm improved for physiological and biotic traits |
Germplasm |
BC2 progenies with excellent delayed PPD identified for establishment in vitro and shipment to partners in Africa; Several wild Manihot species and inter-specific hybrids with resistance to cassava green mites identified, accessions of M. esculenta sub spp flabellifolia with resistance to whiteflies identified; Development of a new set of CMD resistant materials with enhanced nutritional quality for shipment to partners in Africa; The main objective of project is to accelerate the process of introgression of useful genes from wild relatives into cassava via a modified Advance Back Cross QTL (ABC-QTL) breeding scheme. |
Germplasm to be used in a SP3 commissioned project 2003 (Cassava Nigeria) |
Contact A. Bellotti,International Center of Tropical Agriculture (CIAT), Cali, Colombia |
|
|
4 |
Drought tolerant contrasting cassava varieties |
Germplasm |
In order to elucidate the mechanisms of cassava which has remarkable tolerance to drought and to determine the best traits to be used in breeding programmes for drought tolerance, selected contrasting varieties have been screened and evaluated in four representative semi-arid environments in Brazil, Colombia, Tanzania and Ghana. |
Cassava breeding materials in Brazil |
Contact, A. Alves, EMBRAPA, Brazil |
|
|
5 |
Drought resistant cassava germplasm lines |
Germplasm |
Seedlings of 109 accessions of selected cassava germplasm (drought and other resistances) certified virus free and ready for distribution/use |
Improvement of cassava breeding lines in West Africa |
Germplasm multiplied in quantity compatible with distribution to selected partners in the range of 10 seedlings per accession per partner. |
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|
6 |
UMCASS33. a disease-resistant, high-yielding cassava variety from Nigeria |
Germplasm |
Released in December 2010, UMCASS33 brings together favorable quality and agronomic characteristics from South American and African cassava. Selected South American cassava provided a higher nutritional content, while African cassava conferred resiliencyand CMD resistantce . CIAT provided the South American cassava, while the local variety resistant to cassava mosaic disease (CMD) was developed from material obtained from the International Institute of Tropical Agriculture (IITA). UMCASS33 has indicated higher yields and tolerance to acid soils conferred from the South American parentage and CMD disease resistance from the African. |
Cultivation by Nigerian farmers and breeding material for elite lines. |
Contact Dr. Emmanuel Okogbenin or Dr. Cheidozie Egesi, National Root Crops Research Institute (NRCRI) at Umudike, Nigeria |
|
|
7 |
Training course materials on phenotyping |
Training Materials |
Training course : phenotyping and water deficit. A ooklet of the course, distributed to participants with copy to GCP; CD rom with all power point presentations, conclusions of the course and spreadsheets for calculating environmental data and soil water balance. Distributed to participants with copy to GCP; six A4 pages presenting techniques (measurements of plant temperature, of evaporative demand, of soil water content, of intercepted radiation, calculation of evapotranspiration); The training course aimed at providing participants with theoretical and practical elements for these choices. Twenty three scientists (level : PhD or master) participated to the course, 6 from Africa, 6 from south Asia, 4 from east Asia, four from Latin America and 3 from Europe. The latter were participants to ongoing GCP projects which received no financial support from the GCP. The course lasted 8 working days (from 3 to 12 July 2006) and the time was split into three parts of similar durations (i) lectures, aimed at providing and discussing the theoretical frameworks, (ii) practical sessions in the greenhouse or in the field aimed at a direct contact with the tools involved in phenotyping, (iii) computer sessions in which each participant could work on practical examples and directly test methods of analysis and reasoning. The course consisted in two sessions : "Characterising the plant environment and the stress" with lecures, a practical experience of measurements in greenhouse and field and computer sessions, and "Assessing phenotypes : trait evaluation" with lectures, a field session and two days of computer sessions. |
General training on phenotyping |
CD rom with all power point presentations, conclusions of the course and spreadsheets for calculating environmental data and soil water balance on demand from GCP (www.generationcp.org) |
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
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 (Risterucci et al., 2000). About 1 miligram of DNA was obtained per accession. The DNA samples are stored and distributed in PCR grade water. |
Since 10 May 2007, DNA has been requested by partners within the GCP (IITA for GCP project on Musa microsatellite marker kit production and composite collection), but also out of GCP (KULeuven, Belgium; CICY, Mexico; Sun Yat-Sen University, Guangzhou, China) |
Contact N. Roux, Bioversity, Rome |
http://www.musa |
|
2 |
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 species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in Musa. |
Diversity studies of Musa collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
|
|
3 |
SSR markers for the BORLI (Musa) map |
Informative Markers |
178 SSR markers and 15 BACs completely sequenced for the BORLI (Musa) map. |
This data set of informative markers consolidates existing publicly available Musa genomic resources and make new resources available (ESTs, BACs, sequence data), Establishing international mapping populations with the view of high precision genetic mapping, Developing publicly available Musa maps anchored with genetic and EST markers with reference to gene and genome sequences from rice and other models, Selective sequencing and immediate publication of A and B genome BAC clones bearing genes potentially involved in important traits; sequencing of random and targeted ESTs, and immediate publication of sequences, Establishment of Musa databases and front-ends to sequence databases; public distribution of clones; training and dissemination of information about Musa genomics and the uses of this information |
Contact Takuji Sasaki, National Institute of Agrobiological Sciences (NIAS), Japan |
Potatoes
|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
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 |
Assessment of diversity in potato collections |
Contact M. Ghislain, International Potato Center (CIP),Lima, Peru |
|
|
2 |
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 the species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in potato. |
Diversity studies of potato collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
|
|
3 |
Mutagenized potato seeds |
Germplasm |
2,000 potato seeds mutagenized with EMS at LD20 for development of a saturated mutant population of a wild potato species. |
Potato comparative genomics studies. |
Contact M. Ghislain, International Potato Center, Lima, Peru |
|
|
4 |
A potato germplasm reference set |
Germplasm |
A set of 1027 potato accessions virus free and available for international distribution |
Comparative genomics studies and introduction of diversity and selected traits in potato breeding programs. |
Contact E. Chujoy, International Potato Center (CIP), Lima, Peru |
Sweet potatoes: coming soon
Yams|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
|
1 |
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 species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in Yam. |
Diversity studies of yam collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
Beans
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
A microsatellite kit for the GCP common bean reference germplasm set |
Genomic Resources |
Reference kit of 28 SSRs, with sequence list and protocol, germplasm checks, and allele sizes of microsats for those checks |
Diversity studies in common bean germplasm collections. |
Contact S. Beebe, International Center for Tropical Agriculture(CIAT), Cali, Colombia |
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2 |
Primers for genomics studies of common bean |
Genomic Resources |
Primers for over 1,500 microsatellites were designed based on 417 simple sequence repeat (SSR) loci from non-enriched genomic libraries (Blair et al., 2009b), 248 gene-based microsatellites (Blair et al. 2009c), 85 AT-rich sequences (Blair et al., 2008) and 89,000 BAC-end sequences which were screened to develop BES-SSRs |
Genomics resources for common bean research |
Refer to: |
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3 |
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 subtractive library was created for root tissue under drought versus control treatments. This produced a list of 10 differentially-expressed candidate gene fragments, which were converted into Kaspar molecular markers. A greenhouse trial was conducted to determine the tissue and temporal specificity of these genes' expression under drought versus control treatments |
Genomics resources for common bean research |
Contact S. Beebe,International Center for Tropical Agriculture (CIAT), Cali, Colombia |
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4 |
A common bean reference set of Andean germplasm |
Germplasm |
A Phaseolus reference set of 314 andean accessions genotyped with 36 SSR |
Comparative genomics studies and introduction of diversity and selected traits in common bean breeding programmes. |
Contact S. Beebe, International Center of Tropical Agriculture, Kali, Colombia |
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5 |
Two drought tolerant lines of common bean |
Germplasm |
Inter-genepool crosses were made from five commercial genotypes from southern Africa and ten sources of drought tolerance. Of the latter, half were Andean and half were Mesoamerican. 46 populations were advanced to the F4 generation and more than 1,500 single plant selections from the most promising populations were chosen according to their combining ability, ideotype, and phenotypic performance. • From 22 Andean ´ Andean (AA) and 17 Andean ´ Mesoamerican (AM) populations, advanced to F7 under drought stress, 347 lines were selected in Colombia (DAB series) and Zimbabwe (CBIB series). From this series of crosses two most promising lines were selected for germplasm release. |
Introgression of drought tolerance in common bean |
M. Blair, CIAT, Kali, Colombia at m.blair@cgiar.org to provide names, details. |
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6 |
INTA Fuerte Sequía, a drought tolerant variety of common bean from Nicaragua |
Germplasm |
Inta Fuerte Sequia is recommended for zones with limited water in Nicaragua. Good yields were indicated under seasonal rainfall levels of less than 200 mm. The grain is dark and similar to others currently under cultivation locally and regionally. The variety is resistant to Bean Golden Yellow Mosaic Virus,Common Mosaic Virus, anthracnos, bacteriosis, and angular leaf spot. Physiological maturity is 65 days. Cooking quality is highly acceptable. |
Cultivation by Nicaraguan farmers and breeding material for elite lines. |
Contact,Aurelio Llano. Investigador Nacional, Instituto Nicaragüense de Tecnología Agropecuaria (INTA) |
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7 |
A novel SNP detection technique for common bean |
Protocol |
A new SNP detection technique was developed based on heteroduplex digestion with CelI enzyme that is useful for conversion of resistance markers |
Reference |
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/cropsci2008.07.0413). |
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8 |
A diversity analysis of the GCP reference collection for common bean |
Publication |
A study of genetic diversity, seed size associations and population structure of a core collection of common beans |
Reference |
Blair MW, Díaz 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 Applied Genetics 119: 955-73. DOI: 10.1007/s00122-009-1064-8a |
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
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 |
Assessment of diversity in chickpea collections |
Contact Jean-Francois Rami, CIRAD, Montpellier France |
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2 |
DaRT marker array for chickpea |
Genomic Resources |
An array of 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 diversity of the species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in chickpea. |
Diversity studies of chickpea collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
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3 |
A validated Chickpea germplasm reference collection |
Genomic Resources |
The Chickpea Reference Set is composed of a core set of accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for prebreeding crosses. |
The Associated Marker kits are a set of markers that has been used to characterize the corresponding reference set collection. Using this same set of markers, any scientist will be able to compare the diversity of his/her own deversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germplasm. |
The International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Germplasm Bank |
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4 |
A SNP dataset for chickpea |
Genomic Resources |
A set of 2,005 SNPs validated and optimzed by KASPar assays |
Genomics resources for chickpea research |
Contact Rajeev Varshney, ICRISAT |
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5 |
SSR markers for chickpea |
Genomic Resources |
A total of 1655 SSR markers (Table 1) were developed from enriched libraries (311; Nayak et al, 2009) and BAC-end sequences (1344, Varshney et al, 2009a). |
Genomics resources for chickpea research |
Contact R. K. Varshney, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India. Refer to: 1) Nayak S, Zhu H, Varghese N, Choi H-K, Datta S, Horres R, Jüngling R, Singh J, PB Kavi Kishor, Kahl G, Winter P, Cook DR, Varshney RK (2010). Integration of novel SSR and gene-based marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical and Applied Genetics 120:1415 |
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6 |
A reference genetic map for chickpea |
Genomic Resources |
A reference genetic map with more than 600 loci including SSRs, DArT and SNPs was built for the interspecific reference mapping population Cicer arietinum ICC 4958 × C. reticulatum PI 489777 |
Genomics resources for chickpea research |
Contact R. K. Varshney, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India 1) Nayak S, Zhu H, Varghese N, Choi H-K, Datta S, Horres R, Jüngling R, Singh J, PB Kavi Kishor, Kahl G, Winter P, Cook DR, Varshney RK (2010). Integration of novel SSR and gene-based marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theoretical and Applied Genetics 120:1415 2) Gujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Prakash AB, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR May GD, Varshney RK (2011) Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). Theor Appl Genetics DOI 10.1007/s00122-011-1556-1 |
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7 |
Drought and salinity reponsive ESTs in the chickpea genome |
Genomic Resources |
A resource of drought-and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). |
Genomics resources for chickpea research |
Varshney RK, Hiremath PJ, Lekha P, Kashiwagi J, Jayashree B, Deokar AA, Vadez V, Xiao Y, Srinivasan R, Gaur PM, Siddique KHM, Town CD and Hoisington DA (2009b). A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.). BMC Genomics (in press). |
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Chefe: A drought tolerant chickpea cultivar for Ethiopia |
Germplasm |
Three cultivars were selected for introgression of drought avoidance root traits through marker-assisted backcrossing: ICCV 92318, ICCV 92311, and ICCV 93954. Crosses were made with the donor parent (ICC 4958), and then backcrossed. "Chefe" was derived from these backcrosses. This cultivar is expected to be released in Tanzania, as well. |
Drought tolerant release for growers and drought tolerance improvement in chickpea breeding lines |
Contact R. K. Varshney, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India |
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9 |
QTL for drought tolerance in chickpea |
Informative Markers |
QTL associated with a ‘hotspot' harbouring several for root-related traits for drought tolerance contributing about 30 percent of phenotypic variation as well as for CID (60 percent of phenotypic variation) including four other minor effect QTL . |
Drought tolerance improvement in chickpea breeding lines |
Markers available from R. K. Varshney,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India Publication pending |
Cowpeas
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
A major gene for Fusarium resistance in cowpea |
Gene |
Two RIL sets were phenotyped for resistance to Fusarium wilt (USA). A major gene for resistance to race 3 of Fusarium was mapped from RIL analysis, and confirmed by analysis of closely related cultivars that differed in resistance |
Breeding for Fusarium resistance in cowpea |
Contact Jeff Ehlers, Unversity of California - Riverside, Riverside, CA USA (jeff.ehlers@ucr.edu) |
To be published |
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2 |
A physical genetic map of cowpea |
Genomic Resources |
The Illumina® 1536 SNP high-throughput GoldenGate assay platform for cowpea was completed and used to genotype 1160 RIL lines (from eight populations). From seven of the RIL populations, 928 SNPs were successfully mapped and used to develop a high-density consensus genetic map having 11 linkage groups and spanning 680 cM (0.69 cM average marker distance). |
Tools for marker-assisted recurrent selection breeding approaches for cowpea improvement |
Also refer to: Muchero W, Diop NN, Bhatt PR, Fenton RD, Wanamaker S, Pottorff M, Hearne S, Cisse N, Fatokun C, Ehlers JD, Roberts PA and Close TJ (2009a). A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0905886106. |
Http://phymap.
http://www.
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3 |
HarvEST:cowpea |
Genomic Resources |
A full-function, online cowpea genomics browser |
Genomics resources for cowpea research |
Contact Jeff Ehlers, Unversity of California - Riverside, Riverside, CA USA (jeff.ehlers@ucr.edu) |
http://www.harvest-web.org/hweb/bin/ |
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4 |
QTL for premature senescence and maturity in cowpea |
Genomic Resources |
A map of QTL for drought stress-induced premature senescence and maturity in cowpea |
Genomics resources for cowpea research |
Muchero W, Ehlers J, Close T and Roberts P (2009). Mapping QTL for drought stress-induced premature senescence and maturity in cowpea [Vigna unguiculata (L.) Walp.]. Theoretical and Applied Genetics 118: 849-863. DOI: 10.1007/s00122-008-0944-7. |
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5 |
A cowpea germplasm reference set |
Germplasm |
A reference set of 374 accessions (cowpea minicore germplasm) |
Comparative genomics studies and introduction of diversity and selected traits in cowpea breeding programs. |
Contact D. Dumet, International Institute of Tropical Agriculture, Ibadan, Nigeria |
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6 |
A microarray chip for expression analysis in cowpea. |
Informative Markers |
41949 EST sequences from drought stressed and non-stressed drought susceptible and tolerant cowpea materials generated, representing 16954 unigenes.T |
he project was developed to generate a unigene set for cowpea and to mine that unigene set with the aim of generating more putative markers.This resource has been mined itself and merged with the newly available GSS data to create a larger unigene set that has been mined to generate 4958 molecular markers and has in addition been utilised to generate a microarray chip for expression analysis. |
Contact S. Hearne, Interantional Institute of Tropical Agriculture (IITA), Lagos, Nigeria |
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7 |
Markers for striga resistance in cowpea |
Informative Markers |
SCARs MahSe 2 marker to SG1 and SG3 resistance, SCARs AGG/CTT 200B to SG5 resistance; Potential parents selected in the field conditions for further Striga resistance breeding; The present project seeks to develop a MAS strategy for cowpea that will allow rapid breeding of Striga resistant varieties in West and Central African countries. Main activities are: Development of molecular markers linked to race specific Striga resistance genes in cowpea, Screening of cowpea genotypes in Striga "hotspots" in West Africa, Testing of markers and development of MAS protocols, Development of user-friendly tool kit for MAS and Diversity analysis of Striga races in Nigeria (SG3) and Senegal (SG6) |
Selection of Striga resistant cowpea in West Africa |
Contact S. Muranaka, International Institute of Tropical Agricultute (IITA), Ibadan, Nigeria |
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8 |
QTLs for resistance to root-know nematodes and Macrophomina phaseolina |
Informative Markers |
Two RIL sets were phenotyped for resistance to root knot nematodes and Macrophomina phaseolina. QTLs for resistance to both diseases were identified from RIL anlaysis and confirmed by analysis of closely relatived cultivars that differed in resistance. |
Breeding for Root Knot Nematode and M. phaseolina resistance in cowpea |
Contact Jeff Ehlers, Unversity of California - Riverside, Riverside, CA USA (jeff.ehlers@ucr.edu) |
To be published |
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
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 of the species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in groundnut. |
Diversity studies of groundnut collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
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2 |
A validated Groundnut germplasm reference collection |
Genomic Resources |
The Groundnut Reference Set is composed of a core set of accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for prebreeding crosses. |
The Associated Marker kits are a set of markers that has been used to characterize the corresponding reference set collection. Using this same set of markers, any scientist will be able to compare the diversity of his/her own deversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germplasm. |
The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Germplasm Bank |
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3 |
A groundnut genetic map |
Genomic Resources |
The first cultivated groundnut (Arachis hypogaea L.) map derived from a RIL population between TAG24 and ICGV86031 |
Genomics resources for groundnut improvement |
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-based genetic linkage map for cultivated groundnut (Arachis hypogaea L.). Theoretical and Applied Genetics 118: 729-739 (DOI: 10.1007/s00122-008-0933 x). |
http://www. |
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4 |
A groundnut BAC library |
Genomic Resources |
A Bacteria Artificial Chromosome (BAC) groundnut library with approximately 80,000 clones |
Genomics resources for groundnut improvement |
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 peanut. BMC Plant Biology 8:14. |
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5 |
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 |
Groundnut disease improvement in the Bill and Melinda Gates Foundation funded project, Improving Groundnut Productivitiy for Marginal Environments in Sub-Saharan Africa |
H. Upadaya, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India |
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6 |
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, ICG 6022/(FDRS)4/ICG4440/ICG6222 |
Groundnut disease improvement in the Bill and Melinda Gates Foundation funded project, Improving Groundnut Productivitiy for Marginal Environments in Sub-Saharan Africa |
H. Upadaya, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India |
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7 |
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 |
Groundnut disease improvement in the Bill and Melinda Gates Foundation funded project, Improving Groundnut Productivitiy for Marginal Environments in Sub-Saharan Africa |
H. Upadaya, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India |
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8 |
Sources of drought tolerance in Groundnut |
Germplasm |
Highly contrasting drought tolerant germplasm identified from 300 genotypes screened for the GCP reference collection |
Groundnut drought tolerance improvement in the Bill and Melinda Gates Foundation funded project, Improving Groundnut Productivitiy for Marginal Environments in Sub-Saharan Africa |
H. Upadaya, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India |
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9 |
Drought-tolerant groundnut synthetics |
Germplasm |
(A. batizocoi K9484 x A. stenosperma V10309)4x and (A. gregoryii V6389 x A. stenosperma V10309)4x |
Breeding for improved drought tolerance in groundnut |
David Bertioli at davidbertioli@unb.br |
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10 |
Gene markers for peanut |
Informative Markers |
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. |
Identification of amphiploids used by CERAAS Senegal and ICRISAT-India |
http://www.biomedcentral.com/ |
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11 |
QTLs for disease resistance in groundnut |
Informative Markers |
34 sequence-confirmed candidate disease resistance genes and five QTL mapped on the reference AA-genome population. |
Breeding for disease resistant groundnut |
Leal-Bertioli, SCM, José, ACFV; Alves-Freitas, DMT, Moretzsohn, MC, Guimarães, PM, Nielen, S, Vidigal, B, Pereira, RW, Pike, J, Fávero, AP, Parniske, M, Varshney, R, Bertioli, DJ. (2009) Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biology, 9:112. |
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Lentils - coming soon
Pigeonpeas|
# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
DaRT marker array for pigeon pea |
Genomic Resources |
An array of DArT markers for pigeon pea 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 species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in pigeon pea. |
Diversity studies of pigeon pea collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
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2 |
A validated Pigeon Pea germplasm reference collection |
Genomic Resources |
The Pigeon Pea Reference Set is composed of a core set of accessions representing the genetic diversity of the entirety of the ICRISAT germplasm bank collection. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for prebreeding crosses. |
The Associated Marker kits are a set of markers that has been used to characterize the corresponding reference set collection. Using this same set of markers, any scientist will be able to compare the diversity of his/her own deversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germplasm. |
The International Crops Research Institute for the Semi-Arid Tropics(ICRISAT) Germplasm Bank |
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Coconut
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# |
Product |
Type |
Description |
Current Use |
Access |
Access URL |
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1 |
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 the species. The use of the microarray platform make s this tool very efficient because all markers on a particular DArT array are scored simultaneously. This genomic resource will facilitate genetic studies in coconut. |
Diversity studies of coconut collections |
Available through Diversity Arrays Technology Pty Ltd (DArT P/L) |
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2 |
A validated Coconut germplasm reference collection |
Genomic Resources |
The Coconut Reference Set is composed of a core set of accessions representing the entirety of the genetic diversity of coconut. The reference set represents a critical resource for plant scientists to study new adaptative traits, discover new favorable alleles and also new parental lines for prebreeding crosses. |
The Associated Marker kits are a set of markers that has been used to characterize the corresponding reference set collection. Using this same set of markers, any scientist will be able to compare the diversity of his/her own deversity panel with the reference set, and request appropriate accessions from the reference set to introduce new diversity in his/her germplasm. |
Bioversity International |
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