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research: Biometrics and statistics

CIMMYT scientists recognized for significant research impact

Written by Julian Bañuelos-Uribe on . Posted in News.

CIMMYT applies high quality science to develop more resilient agrifood systems. This year three scientists from CIMMYT are included in Clarivate’s 2023 Analysis of the most highly cited academic papers.

Jill Cairns participates at a plenary session. (Photo: Alfonso Cortés/CIMMYT)

While CIMMYT’s mission does explicitly require academic publication from its scientists, “the recognition reflects extensive networking with academia, opening doors for new technologies to benefit resource-poor farmers and consumers as well as lending scientific kudos to CIMMYT and underpinning fundraising efforts,” says Distinguished Scientist and Head of Wheat Physiology, Matthew Reynolds.

Maize Physiologist Jill Cairns and collaborators spearheaded the application of high throughput phenotyping for maize-breeding in sub-Saharan Africa, which she says, “would not have been possible without involving leading academic experts like JL Araus at Barcelona University.”

José Crossa chairs the session: adding value to phenotypic data. (Photo: Alfonso Cortés/CIMMYT)

Biometrician and Distinguished Scientist JosĂ© Crossa has pioneered wheat genetic analysis and use of artificial intelligence to solve crop research questions. “With machine learning tools like Deep Learning, there is a golden opportunity to understand the many complex dimensions of crop adaptation, so data-driven breeding models will have the necessary precision to target complex traits,” he explains. Crossa is widely respected by leading academics in biometrics for his insights on bridging statistical theory to solve real world problems.

Reynolds has built initiatives like the Heat and Drought Wheat Improvement Consortium (HeDWIC) and the International Wheat Yield Partnership (IWYP) that transfer cutting-edge technologies—from many of the best academic institutions in the world—to application in breeding, helping to widen wheat gene pools globally.

Matthew Reynolds speaks at a workshop. (Photo: Alfonso Cortés/CIMMYT)

All three scientists achieved the same recognition last year. As in 2022, Reynolds was awarded for his contribution to scientific literature in plant and animal sciences, while Cairns and Crossa were awarded for their contributions to scientific literature across several fields of research (cross fields).

Since 2001, Clarivate’s Highly Cited Researchers list has identified global research scientists and social scientists who have demonstrated significant and broad influence in their field(s) of research. It recognizes exceptional research performance demonstrated by the production of multiple papers that rank in the top 1% by citations for field and year, according to the Web of Science citation indexing service.

In 2023, the list recognizes 6,849 individuals from more than 1,300 institutions across 67 countries and regions.

CIMMYT scientists rank in top 1% of highly cited papers

Written by Sarah McLaughlin on . Posted in News.

Jill Cairns in front of CIMMYT headquarters. (Photo: Sam Storr/CIMMYT)

Three scientists from the International Maize and Wheat Improvement Center (CIMMYT) are included in Clarivate’s 2022 Analysis of the most highly cited academic papers.

Maize Physiologist Jill Cairns, Distinguished Scientist and Head of Wheat Physiology Matthew Reynolds, and Biometrician José Crossa, all from CIMMYT, were recognized in the 2022 analysis.

Jose Crossa chairing a session on adding value to phenotypic data. (Photo: Alfonso Cortés/CIMMYT)

This year, 7,255 Highly Cited Researcher (HCR) designations were issued to 6,938 individuals globally. The award is given to scientists with papers that rank in the top 1% by citations. Matthew was awarded for his contribution to scientific literature in plant and animal sciences, while José and Jill were awarded for their contributions to scientific literature across several fields of research (cross fields).

Of the world’s population of scientists and social scientists, Highly Cited Researchers are 1 in 1,000.

The analysis highlights disparities in the locations of top cited scientists. For example, 82.9% of recipients are from just ten countries and regions, out of a possible 70, and 71.4% are from the United States of America, China, the United Kingdom, Germany, or Australia. While the recognition is only given to individual scientists, Matthew, JosĂ©, and Jill’s success is related to strong scientific collaborations worldwide.

Matthew Reynolds at IWC9 in Sydney, Australia. (Photo: Julie Mollins)
Godfrey Asea (R) and Daniel Bomet (L) from Uganda’s National Agricultural Research Organization (NARO) admire maize cobs on a farm in Uganda. (Photo: Joshua Masinde/CIMMYT)

Building networks and capacity

Written by Shiela Chikulo on . Posted in News.

The active involvement of partners in the co-design of project and capacity building activities is key to the success of the Accelerating Genetic Gains in Maize and Wheat for Improved Livelihoods (AGG) project, led by the International Maize and Wheat Improvement Center (CIMMYT). To that end, the AGG Regional Collaborative Breeding and Testing Networks launched with virtual meetings on September 14 and 15 for southern African partners, and October 28 and November 2 for eastern African partners.

In addition, the AGG team collaborated with researchers from the Excellence in Breeding (EiB) Platform on a number of capacity development webinars in October and November, on topics including Continuous Improvement for breeding processes, programs and products,  enhancing and measuring genetic gain in crop breeding, and a three-webinar series on statistical analysis for plant breeders with CIMMYT’s Biometrics and Statistics Unit.

These training events and regional meetings provided opportunities for well over 100 breeders from CIMMYT, national agricultural research systems (NARS) and seed companies to refresh their capacities to improve genetic gains, and to collectively review and discuss upcoming project activities, current issues of interest, and broader project objectives within their current regional context.

Several themes of importance to partners emerged during the network virtual meetings, for attention in future AGG activities and capacity development work.

Gender inclusion and the impact of COVID-19

Ugandan partners, including Godfrey Asea, director of the National Crops Resources Research Institute at Uganda’s National Agricultural Research Organization, and Josephine Okot, founder and managing director of Victoria Seeds, applauded the project’s emphasis on inclusion of women’s knowledge and preferences in breeding programs.

“We notice that this time there is a lot of focus on gender-inclusiveness,” remarked Asea. “I can tell you there is need for enhanced capacity building for both the private sector and research in proper gender inclusion.”

They also noted the importance of building local capacity, not just for food security but also for other value chain items like raw materials. “COVID-19 has demonstrated to all policy-makers that we cannot depend on the global supply chains,” said Okot. “How can we leverage this project if, for instance, some private sector actors want to [know] the appropriate protein-content maize for, say, animal feed?”

Godfrey Asea (R) and Daniel Bomet (L) from Uganda’s National Agricultural Research Organization (NARO) admire maize cobs on a farm in Uganda. (Photo: Joshua Masinde/CIMMYT)
Godfrey Asea (R), director of the National Crops Resources Research Institute (NaCRRI) at Uganda’s National Agricultural Research Organization (NARO), and Daniel Bomet (L), a maize breeder at NARO, admire maize cobs on a farm in Uganda. (Photo: Joshua Masinde/CIMMYT)

Demand for knowledge

NARS members in Tanzania requested increased support on how to measure or assess genetic gains, especially at the national level, to allow them to establish a baseline upon which genetic gains would be pegged for the project lifecycle.

With statistics an essential element to plant breeding — from analyzing yield trials to ranking varieties — the webinar series in Statistical Analysis for Plant Breeders was a first step towards meeting these capacity development needs.

“The idea of this webinar series was to share insights on how we can improve the breeding plans using statistical methods in an effective way,” said Juan Burgueño, the head of CIMMYT’s Biometrics and Statistics Unit. “The training offered both theory and hands-on experience using open-access software.”

Reaching farmers

Looking beyond breeding, meeting participants also discussed how to improve access and adoption of improved varieties among farmers.

“For a large country such as Tanzania, it is at times very hard to reach the farmers,” said Zabron Mbwaga, managing director of the Tanzania-based Beula Seed Company and Consultancy Limited. “We may have a lot of seed in the store, but how to get the farmers to adopt the newer varieties is quite difficult. This is more so when farmers tend to stick to varieties which they know well and are always reluctant to adopt the new varieties,” he explained.

“We need to put in a lot of effort to set up demonstration farms and enhance other awareness-raising activities such as radio programs so that farmers can know about the new varieties.”

This interest in working with smallholder farmers along the entire value chain was echoed by partners in southern Africa.

“Through this project, we would like to explore ways of collaborating along the whole value chain — as the Agriculture Research Council, other partners and small to medium enterprises — to make it an effective chain,” said Kingstone Mashingaidze, senior research manager at the South Africa Agricultural Research Council. “By planning together, we can identify best-fits for all activities in the value chain and ultimately benefit the smallholder farmers.”

About the AGG Regional Collaborative Breeding and Testing Networks

The AGG Regional Collaborative Breeding and Testing Networks aim to improve breeding efficiencies among partners by enabling the use of modern tools and approaches and enriching the existing network of research organizations, public and private seed companies, farmers’ organizations, non-governmental organizations and community-based organizations. It is expected that these networks will lead to increased efficiency and communications across the partnership network and within countries, improved sharing of best practices and protocols, and increased collective ownership of products for accelerated variety development and turnover.

The virtual meetings for the Regional Collaborative Breeding and Testing Network for southern Africa convened participants from Malawi, Mozambique, South Africa, Zambia and Zimbabwe, while meetings for eastern Africa had participants from Ethiopia, Kenya, Tanzania and Uganda.

AGG communications staff Joshua Masinde and Shiela Chikulo contributed to this story.

Ángela Pacheco Gil

Written by Rodrigo Ordóñez on . Posted in Uncategorized.

Ángela Pacheco is a Fellow in Applied Agricultural Statistics/Biometrics, working with the Genetic Resources program.

She investigates and applies statistical techniques to collaborate with technicians and scientists in multiple projects. In addition, she develops statistical software to facilitate the analysis of data as well as statistics training.

CIMMYT Principal Scientist Sarah Hearne presents her research at the PAG conference. (Photo: CIMMYT)

CIMMYT scientists join fellow experts in San Diego for world’s largest plant and animal genomics conference

Written by Alison Doody on . Posted in Features.

Scientists from the International Maize and Wheat Improvement Center (CIMMYT) presented last week at the International Plant and Animal Genome Conference (PAG) in San Diego, USA.

PAG is the largest agricultural genomics meeting in the world, bringing together over 3,000 leading genetic scientists and researchers from around the world to present their research and share the latest developments in plant and animal genome projects. It provides an important opportunity for CIMMYT scientists to highlight their work translating the latest molecular research developments into wheat and maize breeding solutions for better varieties.

To meet global food demand by 2050, agricultural production must increase by 60% — while at the same time minimizing harm to the environment. This is the process of sustainable intensification, recommended by organizations like the United Nations and the EAT Lancet Commission as a key strategy for transforming our struggling global food systems.

Genomics is crucial to sustainable intensification. By studying a plant or animal’s genetic architecture, researchers can better understand what drives crop or livestock productivity, quality, climate resilience, and resistance to pests and diseases. With this information scientists can speed up efforts to develop better varieties and stay ahead of climate- and disease-related threats.

Philomin Juliana stands next to the logo of the PAG conference. (Photo: CIMMYT)
Philomin Juliana stands next to the logo of the PAG conference. (Photo: CIMMYT)

At the conference, wheat scientist Philomin Juliana shared her findings on successfully identifying significant new chromosomal regions for wheat yield and disease resistance using the full wheat genome map. Juliana and her colleagues have created a freely-available collection of genetic information and markers for more than 40,000 wheat lines which will accelerate efforts to breed superior wheat varieties. She also discussed the value of genomic and high-throughput phenotyping tools for current breeding strategies adopted by CIMMYT to develop climate-resilient wheat.

Principal scientist Sarah Hearne discussed the smarter use of genebank exploration for breeding. Germplasm banks are reserves of native plant variation representing the evolutionary history of the crops we eat. They are a vital source of genetic information, which can accelerate the development of better, more resilient crops. However, it is not easy for breeders and scientists to identify or access the genetic information they need. Using the whole genebank genotypic data, long-term climate data from the origins of the genebank seeds and novel analysis methods, Hearne and her colleagues were able to identify elite genetic breeding material for improved, climate resilient maize varieties. They are now extending this approach to test the value of these data to improve breeding programs and accelerate the development of improved crops.

Distinguished scientist Jose Crossa discussed the latest models and methods for combining phenomic and genomic information to accelerate the development of climate-resilient crop varieties. He highlighted the use of the Artificial Neural Network — a model inspired by the human brain — to model the relationship between input signals and output signals in crops. He also discussed a phenotypic and genomic selection index which can improve response to selection and expected genetic gains for all of an individual plant’s genetic traits simultaneously.

Sarah Hearne presents on the smart use of germplasm banks to accelerate the development of better wheat and maize varieties. (Photo: Francisco Gomez)
Sarah Hearne presents on the smart use of germplasm banks to accelerate the development of better wheat and maize varieties. (Photo: Francisco Gomez)

Principal scientist Kanwarpal Dhugga gave a presentation on approaches to improve resistance against maize lethal necrosis (MLN) in Africa. MLN is an aggressive disease that first appeared in Kenya in 2011, devastating maize production. It has since spread to neighboring countries. Under a grant from the Bill & Melinda Gates Foundation, Dhugga and his colleagues at CIMMYT and Corteva Agriscience have identified a small genomic region explaining more than 50% of variation in MLN resistance. They are currently validating a few candidate genes in this region. Once done, they will use gene editing directly in elite lines from eastern Africa to accelerate the development of improved, disease resistant maize hybrids.

Genomic breeder Umesh Rosyara demonstrated the genomic selection pipeline and other tools at a workshop using the online Galaxy software. Galaxy is an open-source software that allows users to access powerful computational analysis tools. The CGIAR Excellence in Breeding Platform (EiB) has set up an instance of Galaxy that contains a suite of bioinformatics analysis tools, R-packages — a free software environment for statistical computing and graphics — and visualization tools to manage routine genomic selection (GS) and genome wide association studies (GWAS) analysis. This allows crop breeders and genomic scientists without a programming background to conduct these analyses and create crop-specific workflows.

“PAG is currently the main international meeting touching both crop and livestock genomics, so it’s an invaluable chance to connect and share insights with research and breeding colleagues around the world,” said Hearne. “It’s also an important forum to highlight how we are linking upstream and field, and help others do the same.”

Kanwarpal Dhugga (left) takes a selfie with his colleagues in the background during the PAG conference. (Photo: Kanwarpal Dhugga/CIMMYT)
Kanwarpal Dhugga (left) takes a selfie with his colleagues in the background during the PAG conference. (Photo: Kanwarpal Dhugga/CIMMYT)
CIMMYT's multi-crop, multi-use zero-tillage seeder at work on a long-term conservation agriculture trial plot at the center's global headquarters in Mexico. Maize crop residues are visible in the foreground. (Photo: CIMMYT)

New publications: Durum wheat selection under zero tillage increases early vigor and is neutral to yield

Written by Alison Doody on . Posted in Publications.

CIMMYT's multi-crop, multi-use zero-tillage seeder at work on a long-term conservation agriculture trial plot at the center's global headquarters in Mexico. Maize crop residues are visible in the foreground. (Photo: CIMMYT)
CIMMYT’s multi-crop, multi-use zero-tillage seeder at work on a long-term conservation agriculture trial plot at the center’s global headquarters in Mexico. Maize crop residues are visible in the foreground. (Photo: CIMMYT)

New research published in Field Crops Research by scientists at the International Maize and Wheat Improvement Center (CIMMYT) responds to the question of whether wheat varieties need to be adapted to zero tillage conditions.

With 33% of global soils already degraded, agricultural techniques like zero tillage — growing crops without disturbing the soil with activities like plowing — in combination with crop residue retention, are being considered to help protect soils and prevent further degradation. Research has shown that zero tillage with crop residue retention can reduce soil erosion and improve soil structure and water retention, leading to increased water use efficiency of the system. Zero tillage has also been shown to be the most environmentally friendly among different tillage techniques.

While CIMMYT promotes conservation agriculture, of which zero tillage is a component, many farmers who use CIMMYT wheat varieties still use some form of tillage. As farmers adopt conservation agriculture principles in their production systems, we need to be sure that the improved varieties breeders develop and release to farmers can perform equally well in zero tillage as in conventional tillage environments.

The aim of the study was to find out whether breeding wheat lines in a conservation agriculture environment had an effect on their adaptability to one tillage system or another, and whether separate breading streams would be required for each tillage system.

The scientists conducted parallel early generation selection in sixteen populations from the breeding program. The best plants were selected in parallel under conventional and zero-till conditions, until 234 and 250 fixed lines were obtained. They then grew all 484 wheat lines over the course of three seasons near Ciudad Obregon, Sonora, Mexico, under three different environments — zero tillage, conventional tillage, and conventional tillage with reduced irrigation — and tested them for yield and growth traits.

The authors found that yields were better under zero tillage than conventional tillage for all wheat lines, regardless of how they had been bred and selected, as this condition provided longer water availability between irrigations and mitigated inter-irrigation water stress.

The main result was that selection environment, zero-till versus conventional till, did not produce lines with specific adaptation to either conditions, nor did it negatively impact the results of the breeding program for traits such as plant height, tolerance to lodging and earliness.

One trait which was slightly affected by selection under zero-till was early vigor — the speed at which crops grow during the earliest stage of growth. Early vigor is a useful adaptive trait in conservation agriculture because it allows the crop to cope with high crop residue loads — materials left on the ground such as leaves, stems and seed pods — and can improve yield through rapid development of maximum leaf area in dry environments. Results showed that varieties selected under zero tillage showed slightly increased early vigor which means that selection under zero tillage may drive a breeding program towards the generalization of this useful attribute.

The findings demonstrate that CIMMYT’s durum wheat lines, traditionally bred for wide adaptation, can be grown, bred, and selected under either tillage conditions without negatively affecting yield performance. This is yet another clear demonstration that breeding for wide adaptation, a decades-long tradition within CIMMYT’s wheat improvement effort, is a suitable strategy to produce varieties that are competitive in a wide range of production systems. The findings represent a major result for wheat breeders at CIMMYT and beyond, with the authors concluding that it is not necessary to have separate breeding programs to address the varietal needs of either tillage systems.

This work was implemented by CIMMYT as part of the CGIAR Research Program on Wheat (WHEAT).

Read the full study:
Durum wheat selection under zero tillage increases early vigor and is neutral to yield.

Four CIMMYT scientists among world’s most influential scholars, based on citations

Written by Mary Donovan on . Posted in News.

Four scientists from the CIMMYT community have been included in the Highly Cited Researchers list for 2019, Published by the Web of Science Group, a Clarivate Analytics company.

The list identifies scientists and social scientists who have demonstrated significant influence through publication of multiple papers, highly cited by their peers, during the last decade. For the 2019 list, analysts surveyed papers published and cited during 2008-2018 which ranked in the top 1% by citations for their ESI field and year.

Researchers are selected for their exceptional research performance in one of 21 fields, or across several fields.

This year’s recipients affiliated with CIMMYT include:

  • JosĂ© Crossa: Cross-field category. CIMMYT Distinguished Scientist at the Biometrics and Statistics Unit with the Genetic Resources Program.
  • Julio Huerta: Cross-field category. CIMMYT-seconded INIFAP wheat breeder and rust geneticist.
  • Matthew Reynolds: Cross-field category. CIMMYT Distinguished Scientist, wheat physiologist and Mexican Academy of Sciences member.
  • Ravi Prakash Singh: Agricultural Sciences category. CIMMYT Distinguished Scientist and Head of Bread Wheat Improvement.

It is a significant honor to be part of this list, as it indicates that their peers have consistently acknowledged the influence of their research contributions in their publications and citations.

“Congratulations and thanks to these colleagues for effectively communicating their excellent science, multiplying CIMMYT’s impact by influencing thousands of readers in the international research community,” said CIMMYT Genetic Resources Program Director Kevin Pixley.

For more information, you can view the full Highly Cited Researchers 2019 list and information on the methodology.

Jose Crossa

Written by Emma Orchardson on . Posted in Uncategorized.

Jose Crossa works at the Biometrics and Statistics Unit conducting research on genomic models and models for genomic x environment interaction to help CIMMYT researchers achieve their goals. He also teaches courses on statistical genetics.

Breaking Ground: Fernando H. Toledo researches new models of analysis under simulated scenarios

Written by Leslie DomĂ­nguez on . Posted in Features.

Postcard_Fernando Toledo

Genomics is a wide theme of interest for geneticists. As part of the efforts to advance on this subject, Fernando H. Toledo, associated scientist in agricultural statistics at the International Maize and Wheat Improvement Center (CIMMYT), is working on the research of genomic selection models to increase accuracy. His research considers several complex traits and environmental conditions under climate change scenarios.

The research in which Toledo works is multidisciplinary — it involves genetics and breeding knowledge, as well as statistics and computer science. “This work is fundamental for the breeding and farming community. Our aim is to allow breeders to pursue precise selection of new genetic materials with good performance and ensuring food security in the field under varying environmental conditions.”

Fernando H. Toledo was born in SĂŁo Paulo, Brazil, but grew up in Curitiba, ParanĂĄ, one of the biggest agricultural states in the country. He obtained his engineering degree, with a major in crop science, at ParanĂĄ Federal University.

He got his master’s degree in genetics and plant breeding at Lavras Federal University, under the supervision of Magno Ramalho, one of the most prestigious breeders in Brazil. During his Ph.D. in quantitative genetics at the Agricultural College of the University of São Paulo, Fernando was advised by Roland Vencovsky, known as the father of quantitative genetics in the country. “The main lesson I took from both of them was that biometrics science must try to answer the breeders’ questions.”

Toledo got a scholarship from the Brazilian National Council for Scientific and Technological Development (CNPq) to spend a season at CIMMYT in 2013, where he developed part of his thesis about the use of selection indices under the supervision of José Crossa.

CIMMYT’s work is highly relevant to breeding activities in Brazil. It dates back to the 1950s when Brazilian breeders and geneticists took maize populations and varieties to be important resources of their current germplasm. “The public and private sectors in Brazil recognize the importance of CIMMYT, which awoke my interest in working in a relevant institute for agriculture in developing countries.”

In 2015, Toledo applied for a postdoctoral position at the Biometrics and Statistics Unit of the Genetic Recourses Program at CIMMYT. He started working as an associate scientist in 2017.

As part of this unit, Toledo is currently involved in the planning and analysis of field trials comprising phenotypic and genomic data. He is developing new models and methods for these analysis as well as plant breeding simulations. “Genomic selection has been used over CIMMYT’s breeding programs before but there are still a lot of improvements to implement, so new models of analysis can be tested under simulated scenarios, which results in better recommendations for breeders.”

On top of that, he is implementing new open-source high-performance software products to facilitate the use of cutting-edge methods for data analysis. “I really like the connection we can build at CIMMYT in terms of practical work for breeders and the development of new statistical methods, models, tools and software we release to attend their requirements, with the main aim of improving precision during the selection of the best genetic materials.”

Led by Juan Burgueño, senior biometrician and head of the Biometrics and Statistics Unit, Toledo is training students, scientists and partners regarding statistical concepts and data analysis. “These trainings courses are a great opportunity to share our work with others and to learn the scientists’ needs in order to improve our capabilities.”

Toledo’s main inspiration to continue his work at CIMMYT is having the opportunity to generate knowledge for others in developing countries. “Our work is driven by the breeders’ needs and that usually helps them to improve their understanding by using what we developed for them and making it a forward-backward relation, which is fascinating.”

New publications: Role of Modelling in International Crop Research

Written by Emma Orchardson on . Posted in Publications.

“Crop modelling has the potential to significantly contribute to global food and nutrition security,” claim the authors of a recently published paper on the role of modelling in international crop research.  “Millions of farmers, and the societies that depend on their production, are relying on us to step up to the plate.”

Among other uses, crop modelling allows for foresight analysis of agricultural systems under global change scenarios and the prediction of potential consequences of food system shocks. New technologies and conceptual breakthroughs have also allowed modelling to contribute to a better understanding of crop performance and yield gaps, improved predictions of pest outbreaks, more efficient irrigation systems and the optimization of planting dates.

While renewed interest in the topic has led in recent years to the development of collaborative initiatives such as the Agricultural Model Intercomparison and Improvement Project (AgMIP) and the CGIAR Platform for Big Data in Agriculture, further investment is needed in order to improve the collection of open access, easy-to-use data available for crop modelling purposes. Strong impact on a global scale will require a wide range of stakeholders – from academia to the private sector – to contribute to the development of large, multi-location datasets.

Resource-poor farmers worldwide stand to gain from developments in the field of crop modelling. Photo: H. De Groote/CIMMYT.
Resource-poor farmers worldwide stand to gain from developments in the field of crop modelling. (Photo: H. De Groote/CIMMYT)

In “Role of Modelling in International Crop Research: Overview and Some Case Studies,” CGIAR researchers outline the history and basic principles of crop modelling, and describe major theoretical advances and their practical applications by international crop research centers. They also highlight the importance of agri-food systems, which they view as key to meeting global development challenges. “The renewed focus on the systems-level has created significant opportunities for modelers to participant in enhancing the impact of science on developments. However, a coherent approach based on principles of transparency, cooperation and innovation is essential to achieving this.”

The authors call for closer interdisciplinary collaboration to better serve the crop research and development communities through the provision of model-based recommendations which could range from government-level policy development to direct crop management support for resource-poor farmers.

Read the full article in Agronomy 2018, Volume 8 (12).

Check out other recent publications by CIMMYT researchers below:

  1. A framework for priority-setting in climate smart agriculture research. 2018. Thornton, P.K., Whitbread, A., Baedeker, T., Cairns, J.E., Claessens, L., Baethgen, W., Bunn, C., Friedmann, M., Giller, K.E., Herrero, M., Howden, M., Kilcline, K., Nangia, V., Ramirez Villegas, J., Shalander Kumar, West, P.C., Keating, B. In: Agricultural Systems v. 167, p. 161-175.
  2. Cereal consumption and marketing responses by rural smallholders under rising cereal prices. 2018. Mottaleb, K.A., Rahut, D.B. In: Journal of Agribusiness in Developing and Emerging Economies v. 8, no. 3, p. 461-479.
  3. Community typology framed by normative climate for agricultural innovation, empowerment, and poverty reduction. 2018. Petesch, P., Feldman, S., Elias, M., Badstue, L.B., Dina Najjar, Rietveld, A., Bullock, R., Kawarazuka, N., Luis, J. In: Journal of Gender, Agriculture and Food Security v. 3, no. 1, p. 131-157.
  4. Fit for purpose? A review of guides for gender-equitable value chain development. 2018. Stoian, D., Donovan, J.A., Elias, M., Blare, T. In: Development in Practice v. 28, no. 4, p. 494-509.
  5. Gendered aspirations and occupations among rural youth, in agriculture and beyond: a cross-regional perspective. 2018. Elias, M., Netsayi Mudege, Lopez, D.E., Dina Najjar, Kandiwa, V., Luis, J., Jummai Yila, Amare Tegbaru, Gaya Ibrahim, Badstue, L.B., Njuguna-Mungai, E., Abderahim Bentaibi. In: Journal of Gender, Agriculture and Food Security v. 3, no. 1, p. 82-107.
  6. Genome-wide association study reveals novel genomic regions for grain yield and yield-related traits in drought-stressed synthetic hexaploid wheat. 2018. Bhatta, M.R., Morgounov, A.I., Belamkar, V., Baenziger, P.S. In: International Journal of Molecular Sciences v. 19, no. 10, art. 3011.
  7. Identificacion de areas potenciales en Mexico para la intervencion con maiz biofortificado con zinc = Identification of potential areas in Mexico for intervention with biofortified high-zinc maize. 2018. Ramirez-Jaspeado, R., Palacios-Rojas, N., Salomon, P., Donnet, M.L. In: Revista Fitotecnia Mexicana v. 4, no. 3, p. 327 – 337.
  8. Impact of climate-change risk-coping strategies on livestock productivity and household welfare: empirical evidence from Pakistan. 2018. Rahut, D.B., Ali, A. In: Heliyon v. 4, no. 10, art. e00797.
  9. Impact of conservation agriculture on soil physical properties in rice-wheat system of eastern indo-gangetic plains. 2018. Kumar, V., Kumar, M., Singh, S.K., Jat, R.K. In: Journal of Animal and Plant Sciences v. 28, no. 5, p. 1432-1440.
  10. Impact of ridge-furrow planting in Pakistan: empirical evidence from the farmer’s field. 2018. Hussain, I., Ali, A., Ansaar Ahmed, Hafiz Nasrullah, Badar ud Din Khokhar, Shahid Iqbal, Azhar Mahmood Aulakh, Atta ullah Khan, Jamil Akhter, Gulzar Ahmed. In: International Journal of Agronomy v. 2018, art. 3798037.
  11. Introduction to special issue: smallholder value chains as complex adaptive systems. 2018. Orr, A., Donovan, J.A. In: Journal of Agribusiness in Developing and Emerging Economies v. 8, no. 1, p. 2-13.
  12. Local dynamics of native maize value chains in a peri-urban zone in Mexico: the case of San Juan Atzacualoya in the state of Mexico. 2018. Boue, C., Lopez-Ridaura, S., Rodriguez Sanchez, L.M., Hellin, J. J., Fuentes Ponce, M. In: Journal of Rural Studies v. 64, p. 28-38.
  13. Local normative climate shaping agency and agricultural livelihoods in sub-Saharan Africa. 2018. Petesch, P., Bullock, R., Feldman, S., Badstue, L.B., Rietveld, A., Bauchspies, W., Kamanzi, A., Amare Tegbaru, Jummai Yila. In: Journal of Gender, Agriculture and Food Security v. 3, no. 1, p. 108-130.
  14. Maize seed systems in different agro-ecosystems; what works and what does not work for smallholder farmers. 2018. Hoogendoorn, C., Audet-BĂ©langer, G., Boeber, C., Donnet, M.L., Lweya, K.B., Malik, R., Gildemacher, P. In: Food security v. 10, no. 4, p. 1089–1103.
  15. Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79. 2018. Case, A.J., Bhavani, S., Macharia, G., Pretorius, Z.A., Coetzee, V., Kloppers, F.J., Tyagi, P., Brown-Guedira, G., Steffenson, B.J. In: Theoretical and Applied Genetics v. 131, no. 10, p. 2245–2266.
  16. Potential for re-emergence of wheat stem rust in the United Kingdom. 2018. Lewis, C.M., Persoons, A., Bebber, D.P., Kigathi, R.N., Maintz, J., Findlay, K., Bueno-Sancho, V., Corredor-Moreno, P., Harrington, S.A., Ngonidzashe Kangara, Berlin, A., Garcia, R., German, S.E., Hanzalova, A., Hodson, D.P., Hovmoller, M.S., Huerta-Espino, J., Imtiaz, M., Mirza, J.I., Justesen, A.F., Niks, R.E., Ali Omrani., Patpour, M., Pretorius, Z.A., Ramin Roohparvar, Hanan Sela, Singh, R.P., Steffenson, B.J., Visser, B., Fenwick, P., Thomas, J., Wulff, B.B.H.,  Saunders, D.G.O. In: Communications Biology v. 1, art. 13.
  17. Qualitative, comparative, and collaborative research at large scale: an introduction to GENNOVATE. 2018. Badstue, L.B., Petesch, P., Feldman, S., Prain, G., Elias, M., Kantor, P. In: Journal of Gender, Agriculture and Food Security v. 3, no. 1, p. 1-27.
  18. Qualitative, comparative, and collaborative research at large scale: the GENNOVATE field methodology. 2018. Petesch, P., Badstue, L.B., Camfield, L., Feldman, S., Prain, G., Kantor, P. In: Journal of Gender, Agriculture and Food Security v. 3, no. 1, p. 28-53.
  19. Transaction costs, land rental markets, and their impact on youth access to agriculture in Tanzania. 2018. Ricker-Gilbert, J., Chamberlin, J. In: Land Economics v. 94, no. 4, p. 541-555.
  20. What drives capacity to innovate? Insights from women and men small-scale farmers in Africa, Asia, and Latin America. 2018. Badstue, L.B., Lopez, D.E., Umantseva, A., Williams, G.J., Elias, M., Farnworth, C.R., Rietveld, A., Njuguna-Mungai, E., Luis, J., Dina Najjar., Kandiwa, V. In: Journal of Gender, Agriculture and Food Security v. 3, no. 1, p. 54-81.

 

Linear Selection Indices in Modern Plant Breeding

New publications: Book on linear selection indices, first on the subject in thirty years

Written by Courtney Brantley on . Posted in Publications.

Linear Selection Indices in Modern Plant BreedingAfter two years of meticulous work, the book Linear Selection Indices in Modern Plant Breeding has been released by Springer International Publishing for use by plant and animal breeders worldwide. The authors of the book, J. Jesus Céron-Rojas and José Crossa, are scientists with the Biometrics and Statistics Unit of the Genetic Resources Program at the International Maize and Wheat Improvement Center (CIMMYT). The authors saw a window of opportunity to better explain how various types of linear selection indices can be constructed, interpreted, optimized and applied in breeding through the research presented in this book.

As the first book released on the subject in over thirty years, the publisher describes it as “essential reading for plant quantitative geneticists” and “a valuable resource for animal breeders.” Its high-profile scientific contributions are expected to generate an extensive impact in the international community of theoretical and practical plant and animal breeders.

To examine classification more closely, breeders use indices to categorize traits of interest to make complete representations of desired qualities in plants and animals. Focused on the linear selection index theory and its statistical properties, breeders will be able to use phenotypic and genotypic information to assess the genetic merits of the candidates to selection.

The book is published as open access and available online.

This book is the result of financial support from the Bill & Melinda Gates Foundation, the United States Agency for International Development (USAID), the International Maize and Wheat Improvement Center (CIMMYT), the CGIAR Research Program on Maize (MAIZE)and the CGIAR Research Program on Wheat (WHEAT).

Check out other recent publications by CIMMYT researchers below:

1. Soil organic matter underlies crop nutritional quality and productivity in smallholder agriculture. Wood, S.A., Baudron, F. In: Agriculture, Ecosystems and Environment v. 266, p. 100-108.
2. Wheat−the cereal abandoned by GM: genetic modification of wheat for disease resistance could help stabilize food production. Wulff, B.B.H., Dhugga, K. In: Science v. 361, no. 6401, p. 451-452.
3. Breeding for provitamin A biofortification of maize (Zea mays L.). Maqbool, M. A., Aslam, M., Issa, A.B., Khan, M. S. In: Plant Breeding v. 137, no. 4, p. 451-469.
4. Occurrence of the root-knot nematode species in vegetable crops in Souss region of Morocco. Janati, S., Abdellah Houari, Ahmed Wifaya, Adil Essarioui, Abdelaziz Mimouni, Abderrahim Hormatallah, Mohamed Sbaghi, Dababat, A.A., Mokrini, F. In: Plant Pathology Journal v. 34, no. 4, p. 308-315.
5. High N fertilizer application to irrigated wheat in Northern Mexico for conventionally tilled and permanent raised beds : effects on N balance and short term N dynamics. Grahmann, K., Verhulst, N., Dittert, K., Govaerts, B., Buerkert, A. In: Journal of Plant Nutrition and Soil Science vol. 181, no. 4, p. 606-620.
6. Correction to: bayesian functional regression as an alternative statistical analysis of high-throughput phenotyping data of modern agriculture. Montesinos-López, A., Montesinos-Lopez, O.A., De los Campos, G., Crossa, J., Burgueño, J., Luna-Vazquez, F.J. In: Plant Methods v. 14, art. 57.
7. ÎČ-cryptoxanthin–biofortified hen eggs enhance vitamin a status when fed to male Mongolian gerbils. Heying, E.K., Leary Ziemer, K., Tanumihardjo, J.P., Palacios-Rojas, N., Tanumihardjo, S. A. In: The Journal of Nutrition v.148, no. 8, p. 1236-1243.
8. Urgent action to combat climate change and its impacts (SDG 13) : transforming agriculture and food systems. Campbell, B.M., Hansen, J.W., Rioux, J., Stirling, C., Twomlow, S., Wollenberg, E. In: Current Opinion in Environmental Sustainability v. 34, p. 13-20.
9. Factors affecting the adoption of multiple climate-smart agricultural practices in the Indo-Gangetic plains of India. Aryal, J.P., Rahut, D.B., Maharjan, S., Erenstein, O. In: Natural Resources Forum v. 42, no. 3, p. 141-158.

Juan Burgueño

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Juan Burgueño is a senior scientist and head of CIMMYT’s biometrics and statistics unit. He and his team are committed to developing new mathematical and statistical methodologies, and applying them to solve the problems CIMMYT and partner researchers face.

Burgueño and his team mainly focus on research, consultancy and training on a broad range of topics like experimental design, multi-environment cultivar trials, agronomy, pathology and entomology experiments, genetic resources conservation, mapping quantitative trait loci, genome selection and genetic diversity.

As head of the unit, he coordinates the team’s efforts in these areas and strengthens CIMMYT’s team of biometricians in order to effectively collaborate and help CIMMYT’s staff and partners. Burgueño mainly contributes to experimental design, statistical modeling, genome selection and analysis of high-throughput phenotyping data.

Field trial design workshop for smallholder farmers who grow maize landraces

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As part of the efforts of the Sustainable Modernization of Traditional Agriculture (MasAgro) program aimed at improving food security based on maize landraces in marginal areas of the state of Oaxaca, Mexico, a workshop on trial design was held from 19-21 February to improve the precision of data on improved maize landraces in smallholder farmers’ fields. Attending the workshop were partners from the National Forestry, Agriculture and Livestock Research Institute (INIFAP) and the Southern Regional University Center of the Autonomous University of Chapingo (UACh).

The objective was to continue to have positive impacts on the marginalized communities of Oaxaca, by adapting to the hillside conditions and poor, uneven and broken up soils that often characterize the plots of farmers who grow maize landraces. The very varied trial designs in farmers’ fields, plus the varied population structure of maize landraces make it difficult for scientists to create efficient designs.

The training workshop was led by Dr. Martha Willcox, CIMMYT Maize Landrace program, and designed by Dr. Juan Burgueño and Mr. Claudio Ayala, who sought to facilitate breeding research in smallholder farmers’ fields and to continue to work for the benefit of more than 400 Oaxacan farmers. The project’s multi-disciplinary base includes genetic improvement, agronomic management and biostatistics in order to generate greater value and scientifically confirm the benefits that are being achieved in the fields of the country’s poorest farmers.

It should be noted that during the four years that MasAgro has worked on participatory breeding (2014-2017), INIFAP, UACh and CIMMYT have found that in marginalized communities, maize landraces with the characteristics mentioned above not only yield more, but also generate higher returns on investments, which benefits farmers. Smallholder farmers grow maize in many ecological niches outside the areas most favorable for intensive commercial agriculture and in areas where hybrid improvement programs have not been introduced or worked due to the extreme conditions, including fog, drought and disease. Maize landraces are better adapted to those areas and have the culinary qualities needed to make every-day and festive local dishes.

In addition, not only has maize production for home consumption improved, but farmers are now linked to gastronomic markets. During project years and with its help, maize began to be exported, with 10,000 kilograms exported in 2014 and more than 900,000 kg exported in 2017.