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Nepalese wheat researchers trained on spot blotch disease in India

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Spot blotch is one of the major diseases in the wheat growing regions of Nepal and the knowledge allowing researchers to identify and understand the disease is thus crucial. A group of 12 wheat technical research staff from Nepal visited Banaras Hindu University (BHU) in Varanasi, India, during 18-21 March 2013 with that purpose exactly: to learn more about the spot blotch disease and participatory varietal selection. The training was coordinated by CIMMYT wheat breeder Arun Joshi under the CRP WHEAT Strategic Initiative 5: durable resistance and management of diseases and insect pests. The main resource persons for the training were Ramesh Chand, Vinod Kumar Mishra, and B. Arun; Naji Eisa (Yemen), Conformt Sankem (Nigeria), Chhavi Tiwari, and Punam Yadav (India), all PhD students from BHU, facilitated the program.

The training covered identification of spot blotch pathogen Bipolaris sorokiniana in the field and the lab; preparation of Bipolaris inoculum using colonized sorghum grain; understanding the spot blotch disease infection process; creating artificial epiphytotic in the polyhouse and the field; screening wheat genotypes under high humidity and temperature in the polyhouse; recording disease severity in field and polyhouse conditions; and increasing data reliability in research on spot blotch of wheat and barley.

Participants first visited the pathology laboratory in the Mycology and Plant Pathology department, where they learned to identify B. sorokiniana under the microscope and to prepare Bipolaris inoculums from colonized sorghum grain. The infection process was explained using different samples available in the lab, as was a new technique for evaluation of spot blotch resistance in barley and wheat using monoconidial culture of the most aggressive isolate of B. sorokiniana developed at BHU. Participants observed the collection of the blotched portions of infected leaves for the production of conidia by associated fungal hyphae. They were also trained in conidia collection for further multiplication and categorization into different classes based on the aggressiveness of isolates.

In-FieldOn the second day, participants visited the polyhouse and research station to learn about screening wheat genotypes
under high humidity and temperature. They recorded the disease severity a number of times and saw that if inoculation is done properly the susceptible genotypes burn. The variation among genotypes for resistance to spot blotch disease was explained with the help of repeated disease notes and developing area under disease progress curve. Participants also observed the CRP project on spot blotch carried out at BHU in collaboration with the Nepal Wheat Research Program. The visiting team fruitfully interacted with the BHU wheat researchers, especially with Chand and Mishra, as well as with master’s and doctoral students working on spot blotch. A planned one-hour question-and-answer session expanded to three hours due to the visitors’ enthusiasm and wide-ranging questions.

On their final day, the team visited three participatory varietal selection sites where Harikirtan Singh, the lead farmer, demonstrated the performance of the most popular and newly developed lines under different seeding conditions (surface seeding, zero tillage, and conventional tillage) and multiplication of a number of agronomically superior zinc-rich wheat lines selected from the HarvestPlus project.

The training also allowed participants to visit other research experiments and trials associated with the Cereal System Initiative South Asia (CSISA) and HarvestPlus projects, and to learn to identify agronomically superior biotic and abiotic resistant varieties.

The Nepalese team regarded the visit highly successful as it provided an excellent opportunity to work with the most recent tools and techniques in spot blotch and other wheat researches and to enrich their experience on proper data recording and conduct of participatory varietal selection trials.

WEMA reaches out to local communities in Kenya

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WEMA13On 02 May 2013, the Water Efficient Maize for Africa (WEMA) project organized a sensitization workshop for local community leaders, provincial administration members, agricultural extension workers, farmers, and representatives of farmer groups. The meeting was held at the Kenya Agricultural Research Institute (KARI) in Kiboko and attracted over 40 participants from the neighboring maize growing areas in the Makueni and Machakos counties in eastern Kenya, along with representatives from CIMMYT, Monsanto, African Biotechnology Stakeholders Forum, and the Ministry of Agriculture. It aimed to explain WEMA’s work on development of drought-tolerant and insect-resistant maize varieties using both conventional and genetic engineering techniques. It was also an opportunity for WEMA to demystify myths, allay fears, and enlighten participants on genetically modified organisms (GMOs) and confined field trials.

In his opening remarks, E.O. Mungabe, KARI-Katumani center deputy director, noted that the use of genetic engineering in crop breeding still triggers panic among some Kenyans. However, the emerging challenges of climate change, diseases such as maize lethal necrosis, and pests like the larger grain borer call for new approaches, as conventional ways of breeding alone might not overcome or solve these problems. “It is necessary that we combine our conventional breeding techniques with genetic engineering to effectively respond to these emerging challenges. Think positively of genetic engineering as a technology that has the potential to address them,” Mungabe explained the situation to the participants. “Africa is a drought-prone continent with approximately 300 million people depending on agriculture for their livelihood,” said Murenga Mwimali, WEMA-Kenya national project coordinator, reminding participants that due to climate change, the incidences and severity of droughts will increase. Combined with insect and pest attacks, this could make maize farming an unrewarding enterprise if these issues are not addressed. Mwimali then briefed the participants on the progress todate in developing drought-tolerant and insect-resistant maize varieties using biotechnology and conventional breeding techniques. “Trials show that these new varieties,” Mwimali added, “will yield 25% more than commercial hybrids.”

Joseph Bii of KARI-Kiboko Rangeland Research Station stressed that 80% of Kenya’s land is classified as arid or semiarid. It is therefore important to develop maize varieties that can tolerate the little and erratic rainfall experienced in these areas to enable farmers to continue the production of Kenya’s main staple crop and an important fodder crop for livestock, maize.

The meeting then focused on the topics of GMOs and confined field trials within the scope of WEMA. The project has so far conducted four confined field trials for genetically modified drought tolerant maize variety MON87460 with promising results; another currently conducted confined field trial with genetically modified maize variety resistant to stem borers (MON810) is progressing well. It might take a few more years before farmers can plant the genetically modified maize varieties, but the drought-tolerant CKH110078 conventional variety developed from the Drought Tolerant Maize for Africa (DTMA) materials is likely to be available this year, according to Mwimali. In addition, 14 water efficient WEMA hybrids are already in national performance trials in Kenya and could, therefore, be released as early as next year.

The participants welcomed the opportunity to exchange ideas and get clarifications on many GMO issues: sources of seed and price implications; implications of recycling seed; cross-pollination of GMOs with their local varieties; as well as the reasons why WEMA has not improved local varieties such as Kinyanya. The farmers were also advised on sources of seed and appropriate varieties for their region, particularly the Ministry of Agriculture and the Kenya Plant Health Inspectorate Service through their SMS service, and warned against relying on agro-dealers for information as they are in the business to sell.

The stakeholders toured the MON810 trial and the WEMA confined field trial facility, where they had a chance to observe a genetically modified crop for the first time. It was heartening for the meeting organizers to hear most of the farmers speak positively of the technology and the varieties in the trial, with many expressing their eagerness to try out the genetically modified varieties.

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A new era for Agricultural Innovation in Pakistan

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On 27-28 May, representatives from CIMMYT, USAID, the Pakistan Agricultural Research Council (PARC), ILRI, IRRI, AVRDC, and UC Davis met with colleagues from several Pakistan universities, agricultural secretaries of the provinces, development sector organizations, private sector representatives, and farmer organizations, to discuss and plan the next stage of the USAID-supported Agricultural Innovation Program for Pakistan (AIP).

In his opening address, Randy Chester, USAID’s Deputy Office Chief for Agriculture, stated that “AIP represents a unique and unprecedented collaboration, in that it will bring together the expertise and resources of all of these organizations, including USAID, to increase the income of farmers across Pakistan.” By using the Global Conference on Agricultural Research for Development (GCARD) approach of agricultural research for development (AR4D), AIP “will foster a demand-driven, results-oriented, science research community, and enhance linkages between Pakistan’s agricultural research and innovation communities, the wider global community of agricultural scientists, and the private and civil society sectors,” he concluded.

AIP is a unique program for CIMMYT, aiming to address not only cereals and cereal systems, but also livestock, vegetables, and fruit trees, through a combination of commissioned projects, a competitive grants system, and human resource development. The program will draw on the expertise and resources of the five international partners, but many other Pakistan partners will be brought on as the program develops. PARC Chairman, Iftikhar Ahmad, highlighted the role that Pakistan organizations have to play: “We need a new kind of collaboration,” he said. “It must be a two-way process in that Pakistan must also contribute to international science. Pakistani scientists must play a crucial role in paying back what we get from the outside. Other economies can benefit from Pakistani science as well,” he added.

It would not be the first time that Pakistan has positively impacted worldwide agricultural development. Its national agricultural research system was instrumental in identifying two high-yielding wheat mega-varieties, ‘Mexi-Pak’ and ‘Pak81’, also known as ‘Siete Cerros’ and ‘Seri’, respectively, recalled Hans Braun, Director of CIMMYT’s Global Wheat Program.

During spirited working groups, participants put forward their suggestions for project priorities that will enable AIP to increase the incomes of tens of thousands of farmers, through increased agricultural productivity, in the shortest time frame possible. There will be a strong focus on adapting and up-scaling existing technologies present elsewhere in the region, such as Greenseeker sensors for improved nutrient management.

Closing the meetings, Jonathon Conly, USAID Mission Director, Pakistan, praised the group in their collaboration to revolutionize Pakistan’s agricultural sector. “If we care about driving economic growth, it has to be done by increasing farm productivity, by increasing adoption of technologies, and human capacity,” he said; concluding: “I believe that AIP will lead to the desperately-needed increases in agricultural productivity in this country.”Pakistan35

Giving power to African farmers: learning from the Indian experience

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Bhopal-096From 29 April to 10 May, 16 agricultural engineers, agronomists, machinery importers, and machinery manufacturers from Ethiopia, Kenya, Tanzania, and Zimbabwe took part in a study tour in India organized by CIMMYT, the Indian Council of Agricultural Research (ICAR), the Australian Centre for International Agricultural Research (ACIAR), and the Australian International Food Security Centre (AIFSC). The tour was organized as part of the “Farm Mechanization and Conservation Agriculture for Sustainable Intensification” (FACASI) project to identify opportunities for exchange of technologies and expertise between India and Africa and strengthen South-South collaborations in the area of farm mechanization. The project is funded by AIFSC and managed by ACIAR.

India is the world’s largest producer of pulses, and the second largest producer of wheat, rice, potatoes, and groundnuts. But would India’s agricultural performance be that high if the number of tractors in the country was divided by six and the number of draught animals by three? Such a reduction in farm power would bring Indian agriculture close to the current situation of Kenya and Tanzania. In India, most agricultural operations are mechanized, including planting, harvesting, threshing, shelling, and transportation to the market; in Africa, these are generally accomplished manually. Bringing African agriculture closer to the situation in India is the goal of the FACASI project. This tour was designed as the first step in the construction of an enduring trilateral partnership between Africa, India, and Australia, consolidated by CIMMYT, to facilitate exchange of research and development results in the area of farm mechanization.

During his opening speech, S. Ayyapan, ICAR director general, stressed the importance of farm mechanization for agricultural intensification, pointed at the commonalities between the circumstances of Indian and African smallholders, and invited the group to develop concrete country-specific proposals regarding possible partnerships with India. The participants then spent five days at the Central Institute of Agricultural Engineering (CIAE) in Bhopal, Madhya Pradesh state, where they were exposed to various low-cost gender-friendly technologies for post-harvest operations and weeding; sowing, fertilizing, spraying, and harvesting technologies adapted to animal traction; two-wheel and four-wheel tractors; as well as conservation agriculture based technologies. Through calibration exercises and other field activities, participants gained hands-on experience with these machines. The group also visited the Central Farm Machinery Training and Testing Institute in Budni.

The second part of the study tour took place in the states of Punjab and Haryana, where the group interacted with scientists from the Punjab Agricultural University (PAU) and the Borlaug Institute for South Asia (BISA), and was exposed to various Indian innovations including laser land levelers operated by two-wheel tractors, relay direct seeders, multi-crop planters, crop threshers, and rotary weeders. They also participated in a discussion session organized by a farmer cooperative society at Noorpur-Bet focusing on institutional innovations encouraging farmer access to mechanization, and interacted intensively with Indian agribusinesses such as National Agro-Industry, Dashmesh Mechanical Engineering, Amar Agro Industries, and All India Machinery Manufacturers Association.

The study tour was concluded by a visit of the Central Soil and Salinity Research Institute (CSSRI) in Karnal to observe the role of conservation agriculture in reclaiming degraded land, and a visit to the Indian Wheat Research Centre in Karnal.

The lessons learnt in India will be put in practice in Ethiopia, Kenya, Tanzania, and Zimbabwe through the FACASI project. The study tour has generated several ideas for the development of new machines by African engineers and created contacts between Indian manufacturers and African machinery importers which may materialize into business opportunities.

High up and hyperspectral

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The aircraft operated near CIMMYT station in Ciudad Obregon ready for hyperspectral imagery collection.
The aircraft operated near CIMMYT station in Ciudad Obregon ready for hyperspectral imagery collection.

Last week CIMMYT obtained a new hyperspectral camera and thus significantly expanded its remote sensing capabilities. Pablo J. Zarco-Tejada, director of QuantaLab remote sensing laboratory, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones CientĂ­ficas (CSIC), CĂłrdoba, Spain, and his team spent 13-17 May 2013 at the Campo Experimental Norman E. Borlaug (CENEB) in Ciudad Obregon, Mexico, installing the new camera on the remote sensing platform they delivered during their last visit in February 2013.

Zarco-Tejada and his team also trained a pilot and CIMMYT staff on the use of the hyperspectral remote sensing equipment, which was obtained through a capacity building project between CIMMYT’s Global Conservation Agriculture Program and QuantaLab-IAS-CSIC, funded by MAIZE and WHEAT CRPs under Strategic Initiative 3.

Hyperspectral flight line acquired near the CIMMYT station at Obregon acquired at 40 cm resolution on 15 May 2013 (left). Areas with dense vegetation and trees orchards shown in red (top inserts). The graph shows the full hyperspectral signatures extracted from the imagery from healthy and stressed vegetation pixels, and from a soil target after radiometric calibration and atmospheric correction methods are conducted in the laboratory at CIMMYT.
Hyperspectral flight line acquired near the CIMMYT station at Obregon acquired at 40 cm resolution on 15 May 2013 (left). Areas with dense vegetation and trees orchards shown in red (top inserts). The graph shows the full hyperspectral signatures extracted from the imagery from healthy and stressed vegetation pixels, and from a soil target after radiometric calibration and atmospheric correction methods are conducted in the laboratory at CIMMYT.

Hyperspectral technology uses the most advanced remote sensing cameras that are sensitive to the visible and near infrared spectral regions. This allows for acquisition of hundreds of images at once, each of them covering a different and narrow spectral region in a continuous mode. While multispectral cameras widely used for crop monitoring through remote sensing methods can acquire only five or six spectral bands at once, the new hyperspectral imager owned and operated by CIMMYT obtains 250 spectral bands at the same time, covering the entire electromagnetic spectrum between the visible and the near infrared regions. This opens up tremendous new and powerful avenues for research on early crop stress detection, physiological assessment, conservation agriculture, plant breeding, disease detection, etc.

The thermal, multispectral, and hyperspectral cameras are installed on the same aircraft which allows researchers to obtain both thermal and multi/hyperspectral images concurrently. With resolutions ranging between 20 and 50 centimeters, it is possible to target single experimental plots as well as within-field spatial variability in commercial fields. The cameras acquire 250 bands of 6.4-nanometer width in the 400-885 nanometer region, scanning swaths of 500 meters at 30-50 centimeter pixel resolution.

This makes it possible to calculate several new spectral indices related to photosynthetic pigments, such as chlorophyll content, carotenoids, xanthophylls, and anthocyanins, as well as measure physiological and structural indicators, which can be used to map nitrogen status and derive nitrogen recommendations to improve wheat quality. Most importantly, the new hyperspectral imager allows for early detection of stress using narrow-band indices related to light-use efficiency, as well as for quantifying chlorophyll fluorescence emissions by the plant, which is the focus of current cutting-edge international research on canopy photosynthesis. This has proved to be a better physiological indicator than other traditional vegetation indices.

The hyperspectral camera was tested over an area near CENEB and is now fully operational for phenotyping and physiological and agronomic research. Image processing methods and hyperspectral analysis procedures were used for signature extraction from the imagery and observation of the spectral differences between healthy and stressed vegetation pixels.

Members of CIMMYT, IAS-CSIC (Spain) and the aircraft crew during the flight tests conducted to test the new hyperspectral camera.
Members of CIMMYT, IAS-CSIC (Spain) and the aircraft crew during the flight tests conducted to test the new hyperspectral camera.

Configuration of the new hyperspectral camera for different operation modes and the identification of successful remote sensing indices will continue through research collaboration between CIMMYT and QuantaLab-IASCSIC. The algorithms and state-of-the-art methods for the processing of the imagery, as well as field instrumentation required for the flights, are now available at CENEB. The same instruments are planned to be used during the upcoming cropping season in El BatĂĄn and Toluca.

Collaborative wheat breeding for durable resistance to stripe rust in China

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Chinese-wheat-growerBreeding of durable resistance to stripe rust —the greatest biotic threat to wheat production in the largest wheat producer and consumer in the world, China— was the major theme of a workshop jointly organized by the CIMMYT-Sichuan office and the Sichuan Academy of Agricultural Sciences (SAAS) at the SAAS Plant Breeding Institute in Chengdu, Sichuan province, China, on 18 May 2013. The workshop aimed to promote the adoption of second-generation parents and slow-rusting breeding strategies in spring wheat-producing areas of China and to facilitate collaborative breeding strategies between SAAS and its sister organizations in neighboring provinces. The workshop consisted of a seminar and a discussion session on germplasm and breeding strategies led by Gary Rosewarne (CIMMYT Global Wheat Program senior scientist) and Bob McIntosh (Emeritus Professor at the University of Sydney), and followed by a field visit to the Southern China Field Station at Xindu.

China has the largest area prone to stripe rust epidemics in the world. Traditionally, the disease has been controlled through genetic strategies focused on incorporating major seedling resistance genes to provide immunity. However, this method places strong pressure on the fungus to evolve and overcome these genes. Since the 1950s, the development of virulent pathotypes to widely used resistance genes has caused numerous serious stripe rust epidemics, with the major ones in 1990 and 2002 resulting in the loss of 2.65 and 1 million tons of grain, respectively. Given China’s importance in the world’s wheat production and consumption, any threat to the country’s wheat production has implications for global food security.

CIMMYT has pioneered breeding of durable resistance to stripe rust through the incorporation of multiple, slow-rusting loci, a breeding strategy well established at SAAS but largely ignored by most other wheat breeders in China who still focus on major seedling resistance. At the beginning of this century, SAAS and CIMMYT established a shuttle breeding system to introduce slowrusting loci into Sichuan germplasm. Five high-yielding but susceptible Sichuan lines were sent to Mexico each year for three years; Ravi Singh, CIMMYT distinguished scientist and head of Bread Wheat Improvement, then made single backcrosses with several CIMMYT donor lines. The resulting lines were advanced in Toluca and Obregón, Mexico, and large populations of early generation materials were sent back to Sichuan for further advancement and final selection. Fixed lines from these first generation crosses have shown good levels of resistance in China, along with yields comparable to those of the check varieties. There is currently a range of second generation parental lines with slow-rusting loci in Chinese backgrounds; it is expected that with these as donors, researchers should be able to raise yield potential further while maintaining resistance.

The workshop resulted in a proposed collaborative strategy which would allow breeders representing different regions of China to receive several lines of second generation Chinese slow-rusting donors and to conduct single backcrosses with some of their elite germplasm that has become susceptible. Chinese scientists involved in the process will be invited to help select early generation materials using the bulk selection methodology. After selection, large early generation populations will be sent back to the regions for further selection and advancement under local conditions. “We anticipate that through this mentoring process, breeders will feel comfortable adopting new breeding strategies that can increase their efficiencies and ensure that durable stripe rust resistant lines are released throughout China,” explained Rosewarne.

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Swiss Ambassador visits CIMMYT-Harare

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Physiologist Jill Cairns talks about climate change with the Swiss Ambassador.
Physiologist Jill Cairns talks about climate
change with the Swiss Ambassador.

The Ambassador of Switzerland to Angola, Malawi, Zambia, and Zimbabwe, Luciano Lavizzari, accompanied by the Swiss Agency for Development and Cooperation (SDC) Food Security program officer for Zimbabwe Mkhululi Ngwenya, visited the CIMMYT Regional office for Southern Africa in Harare, Zimbabwe, on 23 April 2013. The CIMMYT-Harare staff provided a tour around the facilities and briefed them on CIMMYT’s work on food security geared towards finding solutions to challenges faced by farmers.

In the beginning of the visit, CIMMYT physiologist Jill Cairns discussed the issue of climate change. “As a result of climate change, the seasons are going to be much shorter,” explained Cairns, adding that in a region with the lowest maize yields globally, a lot more effort is required to deploy germplasm and farming systems adapted to respond to constraints in the region. Cairns discussed the work done by CIMMYT scientists in countering stresses such as low nitrogen, drought, and heat stress along the maize breeding pipeline from population development, pedigree breeding, to regional and on-farm trials in over 100 diverse locations. She also covered the phenotyping tools used in the research work and highlighted research gains in maize yields, many of which result from highly drought-tolerant maize lines and improved efficiencies of maize breeding pipeline in Eastern and Southern Africa.

John MacRobert, seed systems specialist, highlighted the importance of harmonizing seed systems in the region. “Some countries, like Zimbabwe, have very well developed seed sectors, while others are largely informal,” MacRobert said, stressing the negative consequences this may have on farmers. He then explained the importance of on-farm trials in incorporating farmer preferences such as grain texture in breeding work, using the example of SDC-funded New Seed Initiative for Maize in Southern Africa (NSIMA), a project whose acronym is fashioned after a popular maize staple dish in Zambia and Malawi known as nsima: “NSIMA targets a subset of smallholder farmers who consume the maize that they grow.” MacRobert also highlighted collaboration with other SDC projects whose seed systems encourage community-based seed companies targeting smallholder farmers.

Next on the agenda was conservation agriculture covered by agronomist Christian Thierfelder. “It is crucial to link improved varieties with the best management practices to ensure the sustainability of the cropping system,” stressed Thierfelder who then went on to demonstrate a range of sowing equipment from a stick to animal traction planters used in conservation agriculture.

Seed systems specialist Peter Setimela explains the importance of regional on-farm trials to the Swiss Ambassador Luciano Lavizzari (middle) and SDC Food Security program officer for Zimbabwe Mkhululi Ngwenya.
Seed systems specialist Peter Setimela explains the importance of regional on-farm trials to the Swiss Ambassador Luciano Lavizzari (middle) and SDC Food Security program officer for Zimbabwe Mkhululi Ngwenya.

Socioeconomist Girma T. Kassie turned attention to the consequences of lack of funding for smallholder farmers. For example, lack of funding programs to help the smallholder farmers acquire equipment limits uptake of improved planting practices. “Research on the impact of improved technologies aimed at improving livelihoods of smallholder farmers can help identify the gaps in technology transfer,” he added. Afterwards, the visitors toured CIMMYT trials where they observed the discussed technologies in the field.

CIMMYT has had a long-standing relationship with Switzerland through SDC, which currently funds several CIMMYT projects geared towards improving food security of smallholder farmers in East and Southern Africa. The projects, focusing on post-harvest losses reduction, conservation agriculture, and improved seed systems, include the Effective Grain Storage Project (EGSP), Seeds and Markets Project (SAMP), Harmonized Seed Security Project (HaSSP), and NSIMA. In addition, the SDC funds the ‘SDC-Junior Professional Officer’ supporting agronomist Stephanie Cheesman at the Global Conservation Agriculture Program team. CIMMYT highly appreciates the continued support from the Swiss government through SDC.

Regional Statistics Course – module 2

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One-week course on genetic analysis and plant breeding

Drs. Jiankang Wang and Huihui Li, Genetic Resources Program, CIMMYT

Objectives of the workshop

Through lectures, practices and discussions, you will learn:

  • Plant breeding methodology
  • Applied quantitative genetics
  • Estimation of recombination between two linked loci
  • Construction of genetic linkage maps
  • Principles of QTL mapping and statistical comparison of diff erent mapping methods
  • Identifi cation of quantitative trait genes with additive (and dominance) effects
  • Identification of quantitative trait genes with epistasis eff ects
  • QTL by environment analysis
  • Modeling of plant breeding
  • Comparison and optimization of plant breeding strategies
  • Integration of known gene information into conventional plant breeding

Who should attend?

CIMMYT’s partners who are interested in applied quantitative genetics, linkage analysis, linkage map construction, QTL mapping, simulation and optimization of breeding strategies will benefi t from this course. Participants should be familiar with basic methods in plant genetics, plant breeding and statistics.

Computers: Each participant must bring a laptop computer that can run Microsoft Windows applications. A USB memory stick will be distributed to all participants at the beginning of the course. This contains the lecture presentations, the QTL IciMapping integrated software V3.3, QU-GENE simulation tools, exercises and answers, etc.

Tentative program

Day 1: Introduction of quantitative genetics

Genetic population and population structure, additive and dominance genetic model, mating designs and estimation of genetic variance and heritability, prediction of genetic gain, correlated selection and index selection etc.

Tentative program

Day 2: Genetic linkage analysis

in biparental genetic populations, genetic interference and mapping function, linkage map construction, handling redundant markers, integration of multiple linkage maps to generate a consensus map.

Day 3: Mapping additive (and dominance) QTL

Principle of QTL mapping, conventional Interval Mapping, Inclusive Composite Interval Mapping (ICIM) of QTLs, QTL by Environmental Interactions

Day 4: Mapping epistatic QTL and segregation distortion Loci (SDL)

Two-dimensional scanning for additive by additive interactions, two-dimensional scanning for additive by additive, additive by dominance, dominance by additive, and dominance by dominance interactions, segregation distortion loci mapping, QTL mapping with chromosome segment substitution (CSS) lines, other QTL mapping methods, QTL mapping in nested association mapping (NAM) populations, and frequently asked questions in QTL mapping studies

Day 5: Modeling and simulation of plant breeding programs

Principles of breeding simulation, defi ning genetic models in QU-GENE, defi ning breeding methods in QuLine, comparing breeding methods through simulation, and use of know genes in plant breeding

Regional Statistics Course – module 1

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Generation, analysis and interpretation of experimental and genetic designs applied to plant breeding

General objectives of the course

Through lectures, practicals and discussion, you will learn:

  • Basic experimental designs theory
  • Randomized complete blocks, incomplete blocks, augmented and partially-replicated designs
  • Analysis of variance, fi xed and mixed models
  • Design and analysis of multi-environment trials, including modeling genotype-by-environment interaction
  • Spatial analysis of individual and combined experiments
  • Genetic designs, selection indices and genomic breeding values (GEBVs)
  • Use of statistical software including SAS, GenStat, R, and ASReml

Primary lecturers

Dr. Mateo Vargas, Genetic Resources Program, CIMMYT;
E-mail: vargas_mateo@hotmail.com
Dr. Gregorio Alvarado, Genetic Resources Program, CIMMYT;
E-mail: G.Alvarado@cgiar.org

Program

I. Randomized complete blocks designs (RCBD) and multiple comparison procedures

Objectives:

  1. Identify the basic components of variation in a randomized complete blocks design.
  2. Analyze information generated from fi eld experiments using RCBD and interpret the results of analysis

Contents:

  1. Advantages and disadvantages, fixed effect models
  2. Generation of designs using SAS
  3. Statistical model and Analysis of Variance
  4. Example of analysis and interpretation using SAS, GENSTAT, R
  5. Multiple Comparison Tests: Least Signifi cant Diff erence(LSD), Honest Signifi cant Diff erence (Tukey), Scheffé

II. Incomplete blocks designs or lattices

Objectives:

  • Identify the basic components of variation in an incomplete blocks design (IBD), recovery of intrablock and interblock information
  • Increase the precision of experiments using covariance structures with the purpose of extract correlation sources between experimental plots
  • Analyze information generated from experiments in agree with the former designs and interpret the results

Contents:

  1. Incomplete Block Designs (BIBDs) or Lattices
  2. Advantages of Linear Mixed Models
  3. Alpha Lattice Designs: Generation using AlphaWin, DiGGer
  4. Statistical modeling with and without covariate(s)
  5. Example of analysis and interpretation using SAS, GENSTAT, R
  6. Best Linear Unbiased Estimators (BLUEs), LSD, Grand Mean and Coeffi cient of Variation using the Standard Errors of Diff erences (SED)
  7. Best Linear Unbiased Predictors (BLUPs), Heritability in Broad Sense (H2) and Genetic Correlations

III. Augmented designs and spatial analysis

Objectives:

  1. Identify the basic characteristics and evaluate the advantages of the Augmented Designs and the Spatial Analysis
  2. Analyze information generated from experiments based on Augmented Designs and Spatial Analysis, interpretation of the results

Contents:

  1. Basic concepts and properties of augmented designs
  2. Basic concepts and properties of spatial analysis
  3. Generation of augmented designs using DiGGer, GENSTAT and ASREML
  4. Analysis and Interpretation of augmented designs and spatial analysis using SAS, GENSTAT and ASREML
  5. Analysis and Interpretation of augmented designs and spatial analysis using SAS, GENSTAT and ASREML

IV. Multi Environment trials

Objectives:

  1. Increase validation space of conclusions by mean of evaluating trials among various locations, years or combinations between them and make a best selection of genotypes
  2. Estimate and interpret the genetic parameters of evaluated populations at multi-environment trials
  3. Model and interpret the Genotype by Environment interaction using diff erent strategies
  4. Introduce external information of environmental and/ or genotypic covariates for assist in the interpretation of genotype by environment interaction
  5. Analyze information generated from multienvironment trials using diff erent software and make the interpetation of analysis outputs

Contents:

  1. Combined analysis across multi trials:
    • Statistical models
    • Estimation of BLUEs and BLUPs with and without covariate(s)
    • LSD, Grand Mean and Coeffi cient of Variation using the Standard Errors of diff erences (SED)
    • Heritability in Broad Sense (H2 ) and Genetic Correlations among locations
    • Dendrogram and PCA Biplot of genetic correlations matrix among locations
  2. Demo of the META: Suite of SAS programs which performs everyone of the all before trials under diff erent conditions: Randomized Complete Blocks Designs, Incomplete Block Designs with and without covariate(s), Individual and Combined Analyses
  3. Statistical models for the interpretation of the genotype by environment interaction: AMMI, SREG, GREG, SHMM
  4. Statistical models incorporating environmental and/ or genotypic covariates
    • Partial least Squares regression (PLS)
    • Factorial regression (FR)
    • Modelling with structural equations
  5. Practical using SAS, GENSTAT, R

V. Genetic designs, selection indices and genomic breeding values (GEBVs)

A. Genetic designs

Objectives:

  1. Increase the knowledge of basic issues of genetic plant breeding using statistical software
  2. Strategies for comprehension of genetic plant breeding using genetic designs

Contents:

  1. Importance of genetic plant breeding
  2. A genetic plant breeding defi nition
  3. Challenges and needs of the plant breeders
  4. Genetic designs
  5. How to design a genetic mating scheme, commonly mating designs
    • Single-Pair mating
    • North Carolina I
    • North Carolina II
    • Line by Tester
    • Diallel designs
    • Use of statistical software for analysis of genetic designs
    • Recent advances in genetic designs

B. Phenotypic selection indices: Smith, ESIM, Kempthorne and Nordskog, RESIM

C. Genomic selection indices: Lande and Thompson, Lange and Whitaker

D. Genomic breeding values (GEBVs)

US Ambassador to Pakistan visits National Agricultural Research Center in Islamabad

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Pakistan-(1)
US ambassador hands Wintersteiger keys to the chairman of PARC.

On 8 May 2013, US ambassador Richard Olson reaffirmed the United States government’s long-term support to farming communities in Pakistan during his visit to the National Agricultural Research Center (NARC) in Islamabad. The visit, organized by CIMMYT in collaboration with US embassy in Pakistan and Pakistan Agricultural research Council (PARC)/NARC, was to recognize the success of the Wheat Productivity Enhancement Project (WPEP), a USDA program implemented by CIMMYT in collaboration with national and provincial research partners, and to inaugurate the harvesting ceremony for the Ug99 resistant wheat variety called NARC 2011. “Since the 1950s, the United States has been working to support agriculture in Pakistan,” stated Olson. “Wheat accounts for approximately 60% of the daily caloric intake of the average Pakistani, so our joint efforts to combat this disease are critical.”

Muhammad Imtiaz, CIMMYT country liaison officer and wheat breeder, briefed the ambassador on CIMMYT’s mission to sustainably increase productivity of wheat and maize systems to ensure global food security and reduce poverty. “CIMMYT collaboration on sustainable agricultural research with national and provincial research institutes in Pakistan began when Dr. Manzoor Bajwa and Dr. Norman Borlaug worked together to develop ‘Mexi-Pak,’ the wheat variety that started the Green Revolution in Pakistan and helped to double Pakistan’s wheat production between 1965 and 1970,” Imtiaz commented on the long-lasting importance of the partnership for Pakistani farmers. The work is not over as the need for disease resistant wheat varieties continues: experts estimate that Pakistan’s annual wheat harvest could be reduced by as much as 50% if and when Ug99 arrives. “Agriculture contributes 21% to the GDP of Pakistan and employs 45% of the labor force, making it one of the most significant economic drivers of Pakistan,” Imtiaz explained the importance of the sector. Pakistani farmers grew about 24 million tons of wheat on 8 million hectares last year, accounting for about 2.4% of the GDP.

Abdul Basit Khan, Additional Secretary at the Ministry of National Food Security and Research, and Iftikar Ahmed, PARC Chairman, appreciated CIMMYT’s effective role in wheat improvement through technical support and implementation of international funded projects, and reiterated its importance for enhancement of the research efficiency and capacity of Handing over of Wintersteiger key to Chairman PARC Pakistani national institutes.

Nutritious Maize for Ethiopia and gender

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8212177139_56b53c6eea_n The Nutritious Maize for Ethiopia (NuME) aims to develop and promote quality protein maize (QPM) in the major maize growing areas of Ethiopia, including the highlands and the dry lands, to improve nutritional status of children. The project has a strong gender component, ensuring women’s full participation in all activities and equal share of benefits, which was discussed during a Gender Analysis and Strategy workshop at the ILRI campus in Addis Ababa, Ethiopia, on 16 April 2013. The purpose of the event was to present gender analysis and gender strategy developed by Kidist Gebreselasie, NuME gender consultant, to implementation partners, receive partners’ input, agree on strategy, and discuss future developments. The workshop was attended by representatives from the Ethiopian Institute of Agricultural Research (EIAR), ministries of health and agriculture, the Ethiopian Health and Nutrition Research Institute (EHNRI), SG2000, FRI, the Ethiopian Seed Enterprise, other seed companies, Hawassa University, Harvard Institute of Public Health, and CIDA (the project’s funder). CIMMYT was represented by Dagne Wegary (interim project coordinator), Dennis Friesen (project advisor/consultant), Vongai Kandiwa (gender specialist), and Hugo De Groote (agricultural economist).

In the opening session of the workshop, Gebreselasie presented her synthesis developed in collaboration with CIMMYT scientists and based on literature review, analysis of a baseline survey (both men and women were interviewed), and an indepth study of two target areas (including focus group discussions and key informant interviews). Gebreselasie found that while men are responsible for plowing and purchase of inputs, including seed, women are responsible for household chores such as cooking and child care. However, both men and women contribute to harvesting and weeding. Planting is either a shared activity, or one done by men. Children are also involved in agricultural activities as they play an important role in herding animals and providing feed and water. Dairy and poultry production management is largely a women’s responsibility; although women receive a substantial part of the income resulting from these activities, their access to resources, as compared to men’s, is largely limited, particularly when it comes to extension services. The agricultural extension system focuses on men and female-headed households; wives are expected to learn from their husbands. Women are also rarely invited to agricultural trainings, especially when they take place outside of their own farm. It is much easier for women to access health extension than agricultural extension workers.

Gebreselasie then outlined a gender strategy to address the above listed constraints and to improve women’s participation in project activities. This involves increasing women’s attendance at QPM demonstrations by inviting them directly and by organizing separate sessions for women during field days, ensuring that the time and place is convenient for them. Gebreselasie suggested involvement of health extension workers in QPM promotion and higher level of women’s involvement in farm radio activities (targeting women). Furthermore, partners should be given incentives to involve women more, and they should also be provided gender training at all levels.

After the presentation, the workshop participants reviewed their organizations’ experiences in gender activities and their responses to the analysis, and discussed ways to incorporate the strategy in their activities.

The NuME gender strategy was later presented and discussed during a meeting of the Project Steering Committee on 23 May at ILRI. CIDA representative Stefna Pacquette emphasized that the strategy needs to involve women in a meaningful way beyond simple participation in project activities. “While focusing on nutrition, NuME can provide a vehicle for strengthening women’s role in the household,” Pacquette noted. “It can also get men to feel more comfortable with women’s presence and participation in traditional male roles.” The next necessary step for NuME is the recruitment of a gender specialist to aid implementation of the strategy.

Generating drought tolerant maize varieties in Latin America

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S03TLWN-ears-ColombiaOn 26-27 April 2013, the FONTAGRO “Generation and validation
of drought tolerant maize varieties to stabilize and reduce mycotoxin damage resulting from climate change” project held its end-of-project meeting in La Ceiba, Honduras, along with the Central American Cooperative Program for the Improvement of Crops and Animals (PCCMCA) meeting (21-26 April). The event highlighted the advances to date, the project’s products, and recommendations for follow-up to ensure that the products reach farmers.

Since 2009, the project generated 5,000 doubled haploid (DH) lines which are currently being evaluated by CIMMYT. The populations were developed from inbred lines identified for drought tolerance, ear rot resistance, and reduced mycotoxin accumulation. The project also identified a set of inbred lines with high levels of ear rot and mycotoxin resistance. The information has been shared with project partners and other breeders for wide use, and CIMMYT will distribute these lines to interested parties. CIMMYT maize breeder Luis Narro commented on the research on diseases, ear rots in particular. “Ear rot is increasing in incidence and severity in South America. Evaluation of 18 commercial hybrids in Peru revealed ear rot incidences as high as 42% on susceptible hybrids in some locations,” he said. “Ear rot tolerant hybrids identified in this project will play an important role in mitigating the detrimental effects posed by ear rots and mycotoxin contamination. These need to be promoted to reach farmers rapidly.” As far as mycotoxins are concerned, the team also identified promising hybrids from validation trials documenting the natural incidence of mycotoxins in Peru, Colombia, and Mexico. This study showed that fumonisins are the most prevalent mycotoxin in South America (compared to aflatoxin and deoxynivalenol).

“The project has generated many products and validated some that are now being released in several countries,” said the project leader George Mahuku. Among those are four varieties released in Honduras (three white and one yellow); one white variety in Colombia; two varieties (one yellow, one white) and a yellow hybrid in Nicaragua, and three varieties (two yellow and one white) in Panama. Three hybrids outperforming the local commercial checks are under validation in Peru. Furthermore, two varieties showing the stability and rustic nature of CIMMYT-generated varieties were released in Colombia, Honduras, and Nicaragua. All the released cultivars are moderately tolerant to the tar spot complex disease which is becoming more common in Latin America.
CIMMYT maize breeder Felix San Vicente presented on the advances that have been made in breeding for drought tolerance and ear rot resistance. “We need to establish and maintain a regional network to test our products in marginal areas,” he noted. “We hope that we will be able to leverage funding from the CRP [MAIZE] to continue the validation and dissemination of these important and promising products in the region.” During the meeting, scientists presented 29 papers, 5 of which contained results from the FONTAGRO project. The papers of CIMMYT colleagues Román Gordon and Oscar Cruz were awarded for their contributions to the maize section of the project: Gordon received the first prize for his paper “Selection of maize varieties for tolerance to water stress in Panama 2010-2012,” and Cruz received the second prize for his paper on “Participatory validation of white and yellow maize varieties in two regions of Honduras.”

Fontagro-Laceiba-Honduras-019The project has generally been considered very successful. “We now know which mycotoxins are important in the region and we have the products to potentially minimize the risk,” commented Mahuku. “What we need is to widely test and disseminate the products so that they reach as many farmers as possible. With a little infusion of resources, the dedication demonstrated by this group, and support from policy makers, I have no doubt that we will get there.”

During 23-25 July, FONTAGRO will hold its annual meeting (VIII Taller de Seguimiento TĂ©cnico de Proyectos FONTAGRO) in Uruguay. The “Generation and validation of drought tolerant maize varieties to stabilize and reduce mycotoxin damage resulting from climate change” is one of five projects finishing this year; its representatives were invited to present their results and compete for a financial award given to the best project. If the project wins, the financial resources could help with continued and wider validation of products generated by this project.

Honoring Dr. Evangelina Villegas Moreno, celebrating science and humanity

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DSC_0420“I am so excited to be here,” said Dr. Evangelina Villegas as she received her Outstanding Alumni Award from the Department of Grain Science and Industry at the Kansas State University (KSU) at CIMMYT-El Batán on 07 May 2013. “This award is not just for me,” she added, “it is for everyone who worked with me, and everyone I worked with. I have such fond memories of my time both at CIMMYT and Kansas State, and I am very appreciative of the awards I am receiving today.” Awards? Yes, besides the KSU Award honoring Dr. Villegas and her achievements in helping to alleviate hunger and malnutrition, she also received the CIMMYT-Borlaug Award for her contributions to the Green Revolution. “Eva is an incredible woman who helped to achieve incredible progress in the improvement of maize and wheat,” said Thomas Lumpkin, CIMMYT director general, during the ceremony.

Dr. Villegas spent more than 20 years working for CIMMYT as a cereal chemist in charge of the cereal protein quality laboratory. “It was in this laboratory,” noted Lumpkin in his opening speech, “that Dr. Villegas worked with Dr. Surinder K. Vasal to develop quality protein maize, or QPM.” By the year 2000, QPM was grown on more than 1 million hectares worldwide, dramatically reversing the effects of malnutrition and increasing child health. This work earned the two researchers the 2000 World Food Prize. Dr. Villegas was the first female ever awarded this accolade, and she became a role model for women worldwide. But her “contributions to society did not end with science,” Lumpkin reminded the audience. Dr. Villegas was also responsible for overseeing an education fund for the young ‘bird boys’ of CIMMYT, who were hired to protect the experimental crops from being eaten by birds. Her efforts helped many of them pay for schooling.

After Lumpkin’s introductory speech, the microphone went to Dirk Maier, head of the Department of Grain Sciences and Industry at KSU, where Dr. Villegas received her Master’s degree in 1962. “I was reading Noel Vietmeyer’s ‘Our Daily Bread, The Essential Norman Borlaug’ and it was not until I got to about page 176 when I learned about Dr. Villegas,” said Maier. “We feel very sorry that it took us so many years to realize what a distinguished alumna we have in Dr. Villegas. We use her story to inspire our students; it helps them to understand the importance of food production and food security.” JesĂșs Moncada de la Fuente, director general of Colegio de Postgraduados and long-time friend of Dr. Villegas, then lauded her friendly personality and incredible flexibility in her work: “Usually, people work only on wheat, or only on maize, but Evangelina worked on both. She was a hybrid in that sense.”

“We are honored to call Dr. Evangelina Villegas a member of the CIMMYT family, and are delighted that she has chosen to receive her most recent accolade, from Kansas State University, here at CIMMYT Headquarters,” concluded Lumpkin before taking Dr. Villegas and the guests on a tour around CIMMYT, including the new Biosciences Complex.

CIMMYT promotes China-Australia collaboration on wheat improvement

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PM-Visit-China-Apr2013The Chinese Academy of Agricultural Sciences (CAAS)
and Murdoch University, Australia, with financial support from the Chinese Ministry of Science and Technology and the Australian government, officially opened the Australia-China Joint Center for Wheat Improvement in Beijing, China, on 9 April 2013. The center is one of six approved jointly by the two governments. It was opened in the presence of the Prime Minister of Australia Honorable Julia Gillard, CAAS President Jiayang Li, CIMMYT distinguished scientist and liaison officer for China Zhonghu He, and Rudi Appels from Murdoch University. The establishment of the center builds upon more than 10 years of successful wheat quality improvement collaboration between the CAAS-CIMMYT wheat program and Murdoch University.

During 15-17 April, over 50 participants from Murdoch and 8 Chinese institutes attended a workshop for the Australia-China Joint Center for Wheat Improvement held in Beijing. They focused on discovery of new genes, development of elite germplasm, and development of gene specific markers by genomic approach for important traits such as yield, drought resistance, and quality. Ten scholarships, each for 12 months, are available for Chinese postgraduate students to work on thesis research at Murdoch University.

Conservation agriculture in Central Asia: A bumpy road to food security?

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ACConservation agriculture methods enable producers to sustainably intensify production, improve soil health, and minimize or avoid negative externalities. However, these practices have not yet taken off in most Central Asian countries. The FAO Sub-Regional Office for Central Asia, in cooperation with CIMMYT, ICARDA, and the national counterparts, conducted a study on the status of conservation agriculture in Central Asia to develop policy recommendations for its promotion. The document titled “Conservation Agriculture in Central Asia: Status, Policy, Institutional Support, and Strategic Framework for its Promotion” presents the existing opportunities for adoption and uptake of conservation agriculture techniques, as well as the conditions that need to be taken into account in designing and promoting policy and institutional support strategies for its up-scaling.

The challenges facing the dissemination and adoption of conservation agriculture practices in the region include development of enabling government policies and institutional environment to mainstream conservation agriculture, changing the farmers’ tillage mind-set, training to operate conservation agriculture equipment, and availability and accessibility of suitable implements. However, the authors believe that there is a great potential to revitalize the withered economies of Central Asian countries via improved productivity and higher total output through conservation agriculture based agricultural development. Kazakhstan, the only country that has actively embraced conservation agriculture, provides great evidence for such claims. With the support of CIMMYT, FAO, ICARDA, the World Bank, the Ministry of Agriculture of Kazakhstan, and other international organizations and donors, Kazakhstan began adoption of conservation agriculture practices in 2000; by 2012 there were 2 million hectares —13% of the country’s wheat growing area— under conservation agriculture. According to the FAO Investment Center mission to Kazakhstan, the adoption of zero tillage and conservation agriculture had raised domestic wheat production by almost 2 million tons, which equals some US$ 0.58 billion more income over 2010-12, enough grain to satisfy the annual cereal requirements of almost 5 million people, and the sequestering of about 1.8 million additional tons of CO2 per year. CIMMYT’s work in Kazakhstan demonstrates that the challenges facing Central Asia regarding conservation agriculture can be overcome. “The main achievement of CIMMYT in Kazakhstan has been the changing of the minds of farmers and scientists,” observes Bayan Alimgazinova, head of the Crop Production Department of KazAgroInnovation. Auyezkhan K. Darinov, president-chairman of the Republic Public Union of Farmers of Kazakhstan adds: “Kazakhstan is now the most experienced in conservation agriculture in Central Asia.” Hopefully, the practices and experience will spread to other Central Asian countries seeking to ensure food security.

For the full FAO report: Conservation Agriculture in Central Asia: Status, Policy, Institutional Support, and Strategic Framework for its Promotion.

For more information on conservation agriculture in Kazakhstan: Water-saving techniques salvage wheat in drought-stricken Kazakhstan.