News

NEWS

  • Wheat phenotyping workshop

    The International Maize and Wheat Improvement Center (CIMMYT) extends a cordial invitation to participate in the training workshop "Wheat phenotyping for the identification of germplasm with high yield potential and tolerance to drought and heat". This will be held in CIMMYT HQ, Texcoco, State of Mexico, on September 28th, 2018 (from 9:00 – 14:00 hrs) as part of the II Plant Breeding Symposium México 2018 (https://trasmejoragen.wixsite.com/inicio) The objective of this workshop is to train participants in the phenotypic characterization of wheat germplasm. Research themes include: climate change; priority characteristics for wheat for Mexico; phenotyping of genetically diverse materials and in the ...

  • II Plant Breeding Symposium Mexico 2018

    MasAgro Biodiversity announces the II Plant Breeding Symposium Mexico 2018 which will be held on September 6 and 7, 2018 at the CIMMYT HQ, Texcoco. Mexico. This event belongs to the series of DuPont Plant Sciences Symposia. For more information please visit the website:https://trasmejoragen.wixsite.com/inicio

  • New video: Crop biodiversity for healthy, nutritious livelihoods

    Erratic weather, poor soil health, and resource shortages keep millions of maize and wheat farmers in developing countries from growing enough to feed their households and communities or to harvest a surplus to sell.

  • 3rd KDSmart app workshop

    The International Maize and Wheat Improvement Center (CIMMYT) extends a cordial invitation to participate in the training workshop on the use of the KDSmart app. This will be held in Texcoco, State of Mexico, on December 20, 2017 (from 9:00 - 17:00 hrs).

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Catalogue

PRODUCTS CATALOGUE

PRODUCTS CATALOGUE

MasAgro Biodiversity, a component of the Sustainable Modernization of Traditional Agriculture (MasAgro) program, focuses on the utilization and conservation of valuable genetic resources with genetic diversity protected in germplasm banks. This program has the purpose of accelerating the development of Varieties of maize and wheat that can meet the nutrition and nutritional demands of a growing population, facing the challenges of climate change.

By characterizing the genetic configuration of CIMMYT germplasm bank collections, the evaluation of priority characteristics – such as drought tolerance, high temperatures and some diseases – and the development of bioinformatics tools that streamline its analysis, MasAgro Biodiversity has Generated a “platform for the utilization of genetic resources” of maize and wheat.

This platform puts several products at the disposal of the scientific community. MasAgro Biodiversity also offers some services in order to promote equity in access and benefits of the use of maize and wheat diversity.

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  • Tools: Flapjack – high-throughput genotype visualizer

  • ‘Flapjack’ – high-throughput genotype visualizer

    This multi-platform application allows graphing of genotypes and visualization of haplotypes for SNP (single nucleotide polymorphism) data, including those generated by high throughput and comparable genotyping technologies. Its visualizations are rendered in real-time, allowing for rapid navigation and comparisons between lines and markers. Flapjack also performs data analyses including calculating similarity matrices, Principal Coordinates Analysis (PCoA), and the calculating statistics to help with marker assisted backcrossing or F1 pedigree verification. Flapjack was developed by James Hutton Institute, in collaboration with CIMMYT.

    Product details and features

    1. Facilitates visualization of low to high-density genotypic data in mapped, unmapped or combined formats.
    2. Provides interactive visualizations of high-performance genotypic data (i.e. DArTseq), allowing fast navigation and genetic comparisons between lines, molecular markers and chromosomes.
    3. Any map-based information such as Quantitative Trait Locus (QTL) positions can be aligned against graphed genotypes to identify associated haplotypes.
    4. Provides example data and information in file formats ready to import and use.
    5. Phenotypic data can be added to genotypic data to facilitate interpretation.
    6. It is useful for genetic diversity analyses.
    7. It can explore data available in the MasAgro-Biodiversidad project.
    8. Multi-platform application publically available for download.

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  • COMMENTS

    • Flapjack is an excellent tool for visualization of large genotypic data sets. It interfaces well with other software, such as CurlyWhirly, for visualization of PCoA analysis done by Flapjack.

    AVAILABILITY

    Released, with improved versions being periodically released with automatic upgrade https://ics.hutton.ac.uk/flapjack/download-flapjack/

    Primary Users

    Breeders, researchers and students who work with large sets of genotypic data

    For more information

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RESEARCH PORTFOLIO

RESEARCH PORTFOLIO

Genetic resources

Genetic resources

Capacity

Capacity

Data

Data

Pre-breeding Germplasm

Pre-breeding Germplasm

Knowledge

Knowledge

Software

Software

PHILOSOPHY OF OUR APPROACH

PHILOSOPHY OF OUR APPROACH

So many accessions, so few data!

Many genebanks resemble libraries that lack sufficiently informative catalogs. The advent of next-generation DNA-sequencing platforms has made it possible to characterize the genetic diversity conserved in entire genebanks.

Information management

Generating new data by itself is insufficient if it cannot be effectively disseminated, queried, summarized, visualized, and analyzed. Data generation, therefore, has to go hand-in-hand with providing intuitive software and analysis tools to deal with the rapidly expanding datasets describing maize and wheat genetic resources.

Pre-breeding

A ‘reformatting’ of the diversity in genebanks into a more breeder-ready format could lower the barriers to mobilize novel genetic variation into breeding programs, which in good part are due to the dependency of gene effects on genetic backgrounds.

Traits with complex genetic architecture

Some of the most important challenges to agriculture need to be addressed by manipulating genetically complex characters controlled by small-effect alleles (yield potential, heat and drought tolerance, etc.).

Collecting germplasm.

The availability of sufficient numbers of genebank accessions does not appear to be a factor limiting the use of novel genetic variation in breeding programs, and a new initiative will secure the global network of genebanks of humanity’s major food crops for future generations.