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News Article | April 17, 2017
Site: www.eurekalert.org

Variations in Latin American and Caribbean maize populations may be linked to anthropological events such as migration and agriculture, according to a study published April 12, 2017 in the open-access journal PLOS ONE by Claudia Bedoya from the International Maize and Wheat Improvement Center (CIMMYT) and colleagues. Maize was likely domesticated in Mexico about 9,000 years ago and has provided a nutritional cornerstone in the Americas for many years. As it diffused to different geographic regions, different varieties of maize, known as landraces, arose. While advances in the fields of genetics and archaeology have provided new insights into the diversification and geographic dispersal of maize, the archaeological record on early maize history is incomplete. To further investigate the geographic and genetic variations in maize, the authors of the present study analyzed 194 native Latin American maize populations, representing 131 classified landraces from 23 countries. The authors planted thirty seeds of each population in a greenhouse and harvested and analyzed the DNA of their leaf fragments. The researchers identified three distinct geographic groups of maize in Mexico, and four groups in South America and the Caribbean. Their classifications of maize based on genetic analysis aligned with previous studies examining their molecular and morphological characteristics. While it is difficult to link the dispersal and cultivation of maize with a specific historical timeline, the geographic locations of the different maize populations and their genetic profiles may reflect known human migration patterns from northern Mexico both down toward South America as well as up through the US toward Canada. The authors also suggest that the understanding of maize genetics can be useful in its conservation and in its agricultural application, as this knowledge is essential for breeding and cultivating maize. "The current genetic structure of maize genetic pools in Latin America and the Caribbean, as examined in the current manuscript, can shed light on events and activities in the pre- and post-Columbian Americas," says co-author Marilyn Warburton. "These events include the domestication and migration history of maize, and closely mirror the lifestyles and migrations of indigenous people." In your coverage please use this URL to provide access to the freely available article in PLOS ONE: http://journals. Citation: Bedoya CA, Dreisigacker S, Hearne S, Franco J, Mir C, Prasanna BM, et al. (2017) Genetic diversity and population structure of native maize populations in Latin America and the Caribbean. PLoS ONE 12(4): e0173488. doi:10.1371/journal.pone.0173488 Funding: All work, prior to statistical analysis and publication, was funded by the Generation Challenge Program (grant 3005.14). The GCP has concluded its work and has evolved into the Integrated Breeding Platform . The GCP was funded by the CGIAR. Competing Interests: The authors have declared that no competing interests exist.


News Article | February 15, 2017
Site: www.nature.com

An infection that struck wheat crops in Sicily last year is a new and unusually devastating strain of fungus, researchers say — and its spores may spread to infect this year’s harvests in Europe, the world’s largest wheat-producing region. “We have to be careful of shouting wolf too loudly. But this could be the largest outbreak that we have had in Europe for many, many years,” says Chris Gilligan, an epidemiologist at the University of Cambridge, UK, who leads a team that has modelled the probable spread of the fungus’s spores. In alerts released on 2 February, researchers revealed the existence of TTTTF, a kind of stem rust — named for the characteristic brownish stain it lays down as it destroys wheat leaves and stems. The alarm was raised by researchers at the Global Rust Reference Center (GRRC), which is part of Aarhus University in Denmark, and the International Maize and Wheat Improvement Center (CIMMYT), headquartered in Texcoco, Mexico. Last year, the stem rust destroyed tens of thousands of hectares of crops in Sicily. What’s particularly troubling, the researchers say, is that GRRC tests suggest the pathogen can infect dozens of laboratory-grown strains of wheat, including hardy varieties that are usually highly resistant to disease. The team is now studying whether commercial crops are just as susceptible. Adding further concern, the centres say that two new strains of another wheat disease, yellow rust, have been spotted over large areas for the first time — one in Europe and North Africa, and the other in East Africa and Central Asia. The potential effects of the yellow-rust fungi aren’t yet clear, but the pathogens seem to be closely related to virulent strains that have previously caused epidemics in North America and Afghanistan. The Food and Agriculture Organization of the United Nations (FAO) in Rome issued similar alerts about the three diseases on 3 February. Severe wheat damage in Europe could affect food prices, inflation and the region’s economic stability, says James Brown, a plant pathologist at the John Innes Centre in Norwich, UK. But researchers hope that by putting out alerts before European wheat crops have started to grow this year, they will give farmers enough warning to monitor fields and apply fungicides, halting the disease’s spread. Plant breeders can also start to ramp up efforts to produce resistant varieties. “Timely action is crucial,” says Fazil Dusunceli, a plant pathologist at the FAO. In the mid-twentieth century, devastation caused by stem rust spurred efforts to breed wheat strains that could resist the fungi. That research — led by agronomist Norman Borlaug — famously led to the Green Revolution in agriculture, increasing crop yields around the world. But stem rust returned in the late 1990s and 2000s, with a variety called Ug99 that spread through Africa and parts of the Middle East. It ruined harvests and caused international concern because, says Dusunceli, more than 90% of wheat crops were susceptible to it. So far, however, it hasn’t hit large wheat-producing regions such as Europe, China and North America. Researchers are developing resistant crops. Stem rust epidemics haven't been seen in Europe since the 1950s, says Mogens Hovmøller, who leads the GRRC’s testing team. “It’s not a challenge plant breeders have faced for many years,” agrees Brown. But the outbreak that hit Sicily in 2016 suggests that the disease has now returned. Unusually, even the hardy durum wheat, used to make pasta, is susceptible to it, says Hovmøller. But it’s too early to say whether the new infection could be as devastating as Ug99. Models based on wind and weather patterns, conducted by Gilligan's team at Cambridge University together with CIMMYT and the UK's Met Office in Exeter, suggest that stem-rust spores released during the Sicilian outbreak may well have been deposited throughout the Mediterranean region. That doesn’t mean the infection will spread — the spores may not have survived the winter, for example — but it is worrying enough for researchers to raise the alarm. The yellow-rust strains are also a concern, says Hovmøller. For Europe, perhaps the most alarming is one provisionally called Pst(new), which was spotted in Sicily, Morocco, Italy and northern Europe in 2016. The fungus is related to a virulent strain that hit North America in the 2000s, but it is not clear how aggressive it is. Researchers are accustomed to finding one or two new wheat-rust strains each year in Europe; these must be guarded against but are not usually dangerously virulent. But since 2010, the region has experienced a greater influx of wheat pathogens, says Hovmøller. He doesn’t know why, but speculates that it could be down to warmer autumns and milder winters attributable to climate change, combined with changes in farming practices, such as sowing wheat earlier in the season. Increases in international travel — potentially spreading spores on clothing — could also be a factor, speculates Brown. Hovmøller and others will in the next few weeks ask the European Research Council for funds to establish an early-warning system. That will help partners including breeders, scientists and agrochemical companies in Europe to share diagnostic facilities and information about potential outbreaks. Dusunceli thinks that such a network might have helped to mitigate the Sicily outbreak, which in turn would have meant that fewer spores could spread to other parts of the continent. “I wouldn’t question the necessity for an early-warning system,” he says.


Erenstein O.,International Maize and Wheat Improvement Center
Agricultural Systems | Year: 2011

Conservation agriculture practices are being advocated to help sustain crop productivity gains and secure environmental sustainability in the Trans-Gangetic Plains, India's Green Revolution heartland. The paper illustrates the use of village surveys as a quasi-quantitative system analysis tool to derive implications for agricultural research and development. Drawing from village surveys in 170 communities, the paper assesses current crop residue management practices in Punjab and Haryana's rice-wheat, basmati-wheat and non-rice-wheat cropping systems. The prevalence of wheat as the winter crop implies an intensive collection, trading and use of wheat straw as basal feed for dairy livestock; which contrasts with the diverse crop residue management of the monsoon crops. The increased use of combine harvesters has spurred the rapid advent of mechanical wheat straw reapers whereas the bulk of combine harvested rice straw is burned in situ. Present crop residue management practices are largely incompatible with year-round mulch retention despite significant biomass production. The research and development community faces the challenge of evening out straw use and management over seasons to ensure at least partial residue retention if its calls for conservation agriculture in this important sub-region are to succeed. The paper also reiterates the worrying decline of groundwater tables associated with the rice-wheat system. © 2010 Elsevier Ltd.


Prasanna B.M.,International Maize and Wheat Improvement Center
Journal of Biosciences | Year: 2012

Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. 'Seeds of Discovery' (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is expected to aid in effective identification and use of novel alleles and haplotypes for maize improvement. Multi-institutional efforts are required at the global level to systematically explore the maize germplasm to diversify the genetic base of elite breeding materials, create novel varieties and counter the effects of global climate changes. © Indian Academy of Sciences.


Bellon M.R.,Diversity for Livelihoods Programme | Hodson D.,Food and Agriculture Organization of the United Nations | Hellin J.,International Maize and Wheat Improvement Center
Proceedings of the National Academy of Sciences of the United States of America | Year: 2011

Climate change is predicted to have major impacts on small-scale farmers in Mexico whose livelihoods depend on rain-fed maize. We examined the capacity of traditional maize seed systems to provide these farmers with appropriate genetic material under predicted agro-ecological conditions associated with climate change. We studied the structure and spatial scope of seed systems of 20 communities in four transects across an altitudinal gradient from 10-2,980 m above sea level in five states of eastern Mexico. Results indicate that 90% of all of the seed lots are obtained within 10 km of a community and 87% within an altitudinal range of ±50 m but with variation across four agro-climate environments: wet lowland, dry lowland, wet upper midlatitude, and highlands. Climate models suggest a drying and warming trend for the entire study area during the main maize season, leading to substantial shifts in the spatial distribution patterns of agro-climate environments. For all communities except those in the highlands, predicted future maize environments already are represented within the 10-km radial zones, indicating that in the future farmers will have easy access to adapted planting material. Farmers in the highlands are the most vulnerable and probably will need to acquire seed fromoutside their traditional geographical ranges. This change in seed sources probably will entail important information costs and the development of new seed and associated social networks, including improved linkages between traditional and formal seed systems and more effective and efficient seed-supply chains. The study has implications for analogous areas elsewhere in Mexico and around the world.


Semagn K.,International Maize and Wheat Improvement Center
Methods in Molecular Biology | Year: 2014

Taxonomists must be familiar with a number of issues in collecting and transporting samples using freezing methods (liquid nitrogen and dry ice), desiccants (silica gel and blotter paper), and preservatives (CTAB, ethanol, and isopropanol), with each method having its own merits and limitations. For most molecular studies, a reasonably good quality and quantity of DNA is required, which can only be obtained using standard DNA extraction protocols. There are many DNA extraction protocols that vary from simple and quick ones that yield low-quality DNA but good enough for routine analyses to the laborious and time-consuming standard methods that usually produce high quality and quantities of DNA. The protocol to be chosen will depend on the quality and quantity of DNA needed, the nature of samples, and the presence of natural substances that may interfere with the extraction and subsequent analysis. The protocol described in this chapter has been tested for extracting DNA from eight species and provided very good quality and quantity of DNA for different applications, including those genotyping methods that use restriction enzymes. © 2014 Springer Science+Business Media New York.


Lobell D.B.,Stanford University | Sibley A.,Stanford University | Ivan Ortiz-Monasterio J.,International Maize and Wheat Improvement Center
Nature Climate Change | Year: 2012

An important source of uncertainty in anticipating the effects of climate change on agriculture is limited understanding of crop responses to extremely high temperatures. This uncertainty partly reflects the relative lack of observations of crop behaviour in farmers' fields under extreme heat. We used nine years of satellite measurements of wheat growth in northern India to monitor rates of wheat senescence following exposure to temperatures greater than 34 °C. We detect a statistically significant acceleration of senescence from extreme heat, above and beyond the effects of increased average temperatures. Simulations with two commonly used process-based crop models indicate that existing models underestimate the effects of heat on senescence. As the onset of senescence is an important limit to grain filling, and therefore grain yields, crop models probably underestimate yield losses for +2 °C by as much as 50% for some sowing dates. These results imply that warming presents an even greater challenge to wheat than implied by previous modelling studies, and that the effectiveness of adaptations will depend on how well they reduce crop sensitivity to very hot days. © 2012 Macmillan Publishers Limited. All rights reserved.


News Article | February 18, 2017
Site: www.eurekalert.org

Over many thousands of years, farmers have bred maize varieties so the crops are optimally adapted to local environments. A new study, published Feb. 6 in Nature Genetics, analyzed close to 4,500 maize varieties - called landraces - bred and grown by farmers from 35 countries in the Americas to identify more than 1,000 genes driving large-scale adaptation to the environment. "The study provided a powerful catalog of the genes necessary for corn to adapt to different latitudes and elevations across the world," said senior author Edward Buckler, a research geneticist at the USDA-Agricultural Research Service and adjunct professor of plant breeding and genetics at the Institute for Genomic Diversity at Cornell. "It takes a thousand genes to attune a plant for a particular latitude and the elevation where it is grown. That's what we are mapping here," Buckler said. The researchers also identified genes associated with flowering time - the period between planting and the emergence of flowers, which is a measure of the rate of development. Flowering time is a basic mechanism through which plants integrate environmental information to balance when to make seeds instead of more leaves. "Flowering time is the trait that is most correlated with every other trait," Buckler said. The study found that more than half of single nucleotide polymorphisms (the most basic form of genetic variation) associated with altitude were also associated with flowering time, revealing these traits are highly linked. Current technology, including a new rapid experimental design called F-One Association Mapping (FOAM), allowed the researchers to use the collection of diverse maize varieties to figure out which genes were important for adaptation. "With global climate change over the next century, we can directly use this information to figure out what genes are important" to greatly speed up breeding efforts of maize, Buckler said. "We're tapping the wisdom of farmers over the last 10,000 years to make the next century's corn." Sarah Hearne, a molecular geneticist at the International Maize and Wheat Improvement Center (CIMMYT) and a maize research lead scientist with Seeds of Discovery, is also a senior author of the paper. J. Alberto Romero Navarro, a doctoral student in plant breeding and genetics, is the paper's first author. Hearne and colleagues at CIMMYT envisioned the project, led the logistical efforts and conducted field trials, while Romero, Buckler and Cornell colleagues led the genomic analysis of the data. The study was supported by Mexico's Ministry of Agriculture, Livestock, Rural Development, Fisheries and Food through the Sustainable Modernization of Traditional Agriculture initiative. Additional support from the USDA-Agricultural Research Service, Cornell University and the National Science Foundation facilitated the completion of the data analysis.


News Article | February 15, 2017
Site: phys.org

A new study, published Feb. 6 in Nature Genetics, analyzed close to 4,500 maize varieties – called landraces – bred and grown by farmers from 35 countries in the Americas to identify more than 1,000 genes driving large-scale adaptation to the environment. "The study provided a powerful catalog of the genes necessary for corn to adapt to different latitudes and elevations across the world," said senior author Edward Buckler, a research geneticist at the USDA-Agricultural Research Service and adjunct professor of plant breeding and genetics at the Institute for Genomic Diversity at Cornell. "It takes a thousand genes to attune a plant for a particular latitude and the elevation where it is grown. That's what we are mapping here," Buckler said. The researchers also identified genes associated with flowering time – the period between planting and the emergence of flowers, which is a measure of the rate of development. Flowering time is a basic mechanism through which plants integrate environmental information to balance when to make seeds instead of more leaves. "Flowering time is the trait that is most correlated with every other trait," Buckler said. The study found that more than half of single nucleotide polymorphisms (the most basic form of genetic variation) associated with altitude were also associated with flowering time, revealing these traits are highly linked. Current technology, including a new rapid experimental design called F-One Association Mapping (FOAM), allowed the researchers to use the collection of diverse maize varieties to figure out which genes were important for adaptation. "With global climate change over the next century, we can directly use this information to figure out what genes are important" to greatly speed up breeding efforts of maize, Buckler said. "We're tapping the wisdom of farmers over the last 10,000 years to make the next century's corn." Sarah Hearne, a molecular geneticist at the International Maize and Wheat Improvement Center (CIMMYT) and a maize research lead scientist with Seeds of Discovery, is also a senior author of the paper. J. Alberto Romero Navarro, a doctoral student in plant breeding and genetics, is the paper's first author. Hearne and colleagues at CIMMYT envisioned the project, led the logistical efforts and conducted field trials,while Romero, Buckler and Cornell colleagues led the genomic analysis of the data. Explore further: Genomic tools can help researchers develop crops quickly


News Article | December 2, 2016
Site: phys.org

The collaboration works with breeding centers around the world to identify unmet needs and has developed tools to make the process of adding a trait into an existing, high-yield crop variety more efficient. Researchers at the International Maize and Wheat Improvement Center (CIMMYT) are using the tools to develop corn varieties with greater resistance to viruses. Researchers at GOBII, the Genomic and Open-source Breeding Informatics Initiative, worked with developers from the Hutton Institute to build upon the existing data visualization application, Flapjack. Its new tools enable breeders to select the best possible parental lines and help users to perform marker-assisted backcrossing (MABC)—a process that involves repeated breeding with the high-yield parent to ensure that only the desired genes are transferred. Researchers estimate that they can cut a year or two from the four or five years required to develop a new variety. "We have been delighted with this early success of our joint work with the GOBII team at Cornell and anticipate it will form the foundation of a mutually valuable partnership," said David Marshall of the Hutton Institute. Previously, these types of molecular breeding tools only existed within biotech companies. But GOBII, a Cornell-led project funded by the Bill & Melinda Gates Foundation, is tailoring these free tools for breeders in developing countries. They are building data management software in collaboration with the international crops research centers ICRISAT in India, CIMMYT in Mexico and IRRI in the Philippines. "Having the right data management systems and analysis tools can have a huge impact on crop improvement. Breeders can manage their programs more efficiently, make better selection decisions, and potentially reduce labor and land costs," said Elizabeth Jones, project manager of GOBII. Michael Olsen, a molecular geneticist at CIMMYT, is test-driving the tools in his work to develop lines of corn that are resistant to maize lethal necrosis, a disease that has devastated corn crops in Kenya. Olsen's research involves 43 separate breeding crosses, bred over five generations.The new tools help him to visualize the relevant genes and identify donor strains that are most likely to successfully interbreed. "The recently released MABC tool developed by JHI with input from the GOBII project was a tremendous time saver this past cycle," said Olsen. "The tool is very well designed for an applied breeding program conducting MABC projects." Next, GOBII will conduct training sessions for the tools at breeding centers in India, Africa, Mexico, the Philippines and at Cornell. The tools can be used to improve any trait in any crop plant. Explore further: Plant breeders take cues from consumers to improve kale

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