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Drilling down into diversity: DNA fingerprinting for crop plants

May 14, 2012
CIMMYT E-News, vol 4 no. 4, April 2007

apr06The promise of using DNA tools to characterize heterogeneous populations of tropical crops is finally being realized, with help from CIMMYT and partners.

“In the lab where I’m working, we have a number of problems using SSR markers. I’m happy (now) that my problems are solved.” The words are those of Shirangi Imalka Samararatne, researcher in Sri Lanka’s Plant Genetic Resources Centre, after attending the training workshop “Molecular characterization of inbred lines and populations in maize” given in New Delhi, India, by CIMMYT scientists and collaborators during 1-3 April 2007.

Simple sequence repeat (SSR) markers are the tools of choice for molecular studies in many crop species. They require very little DNA to use but can also be misread, if the user does not have the experience to know what to look for, according to CIMMYT molecular geneticist and workshop lecturer Marilyn Warburton. “Moreover, in a population of diverse individuals, you can’t simply choose a single individual for DNA analysis to ‘fingerprint’ the entire population; you need to sample many individuals,” she says. “Participants in this course learned to run SSR markers on individuals and also on bulk samples containing DNA from 15 individuals, saving time and money in fingerprinting the population.”

The workshop was hosted by the Indian Agriculture Research Institute (IARI). It was coordinated by IARI researcher B.M. Prasanna and sponsored by the Generation Challenge Program (GCP) of the Consultative Group on International Agricultural Research (CGIAR), as part of a competitive grant project. The event drew 19 participants from 10 countries in Asia and Africa, with interest in a broad range of crops. Nine resource persons from 5 countries gave lectures, lab presentations, computer training, and hands-on practice.

Presentations covered DNA extraction, detection, and analysis methods, particularly for bulked samples. “The bulked method allows the analysis of relationships between entire plant populations and diversity levels within populations,” says Warburton. “For maize, this means useful DNA characterization of breeding populations, improved open-pollinated varieties, and even traditional maize landraces, in a single polymerase chain reaction (PCR) reaction—something previously not thought possible.” The PCR technique is used to make large numbers of copies of a minute sample of DNA for analysis.

One course participant, John Atoyebi, from Nigeria’s National Centre for Genetic Resources and Biotechnology, hopes to apply the approach to speed the certification and release of new, improved maize varieties for farmers in his country. The process currently involves several years of expensive field testing to prove a new variety is genetically distinct, uniform, and stable. “I’m working on the application of molecular tools, such as DNA fingerprinting, for germplasm identification to avoid duplication and for Nigeria’s variety release program. The course has fulfilled my expectations.”

“This course shows how CIMMYT is helping partners gain access to and master relevant, advanced technology whose applications ultimately benefit farmers,” says Warburton. “The GCP competitive grant project, scheduled to wrap up this year, will show how nearly one thousand maize populations migrated out of Latin America to the rest of the world, providing information about which populations should be used to improve maize breeding material around the world. Course participants who worked on maize will be able to compare their own breeding material to the ones in this study and determine which of the thousand could be incorporated into their program. Further training at CIMMYT is being looked at by some of the course participants through further funding from the GCP”.

For more information: Marilyn Warburton, molecular geneticist (m.warburton@cgiar.org)