In crop research fields, it is now a common sight to see drones or other high-tech sensing tools collecting high-resolution data on a wide range of traits – from simple measurement of canopy temperature to complex 3D reconstruction of photosynthetic canopies.
This technological approach to collecting precise plant trait information, known as phenotyping, is becoming ubiquitous on research fields, but according to experts at the International Maize and Wheat Improvement Center (CIMMYT) and other research institutions, breeders can profit much more from these tools, when used judiciously.
In a new article in the journal Plant Science, CIMMYT Wheat Physiologist Matthew Reynolds and colleagues explain the different ways that phenotyping can assist breeding — from simple to use, “handy” approaches for large scale screening, to detailed physiological characterization of key traits to identify new parental sources — and why this methodology is crucial for crop improvement. The authors make the case for breeders to invest in phenotyping, particularly in light of the imperative to breed crops for warmer and harsher climates.
This work was supported by the International Wheat Yield Partnership (IWYP); the Sustainable Modernization of Traditional Agriculture (MasAgro) Project by the Ministry of Agriculture and Rural Development (SADER) of the Government of Mexico; and the CGIAR Research Program on Wheat (WHEAT).
collaboration and a visionary approach by both researchers and funders are
urgently needed to translate primary plant research results into real impact in
the fields, argue crop improvement experts.
For a number of reasons – including limited
interdisciplinary collaboration and a dearth of funding, revolutionary new
plant research findings are not being used to improve crops.
research” — efforts to convert basic research knowledge about plants into practical
applications in crop improvement – represents a necessary link between the
world of fundamental discovery and farmers’ fields. This kind of research is often seen as more
complicated and time consuming than basic research and less sexy than working
at the “cutting edge” where research is typically divorced from agricultural
realities in order to achieve faster and cleaner results; however, modern tools
— such as genomics, marker-assisted breeding, high throughput phenotyping of
crop traits using drones, and speed breeding techniques – are making it both
faster and cost-effective.
In a new article in Crop Breeding, Genetics, and Genomics, wheat physiologist Matthew Reynolds of the International Maize and Wheat Improvement Center (CIMMYT) and co-authors make the case for increasing not only funding for translational research, but the underlying prerequisites: international and interdisciplinary collaboration towards focused objectives and a visionary approach by funding organizations.
“It’s ironic,” said Reynolds. “Many breeding programs have invested in the exact technologies — such as phenomics, genomics and informatics — that can be powerful tools for translational research to make real improvements in yield and adaptation to climate, disease and pest stresses. But funding to integrate these tools in front-line breeding is quite scarce, so they aren’t reaching their potential value for crop improvement.”
Many research findings are tested for their implications for wheat improvement by the International Wheat Yield Partnership (IWYP) at the IWYP Hub — a centralized technical platform for evaluating innovations and building them into elite wheat varieties, co-managed by CIMMYT at its experimental station in Obregon, Mexico.
IWYP has its roots with the CGIAR Research Program on Wheat (WHEAT), which in 2010 formalized the need to boost both wheat yield potential as well as its adaptation to heat and drought stress. The network specializes in translational research, harnessing scientific findings from around the world to boost genetic gains in wheat, and capitalizing on the research and pre-breeding outputs of WHEAT and the testing networks of the International Wheat Improvement Network (IWIN). These efforts also led to the establishment of the Heat and Drought Wheat Improvement Consortium (HeDWIC).
“We’ve made extraordinary advances in understanding the genetic basis of important traits,“ said IWYP’s Richard Flavell, a co-author of the article. “But if they aren’t translated into crop production, their societal value is lost.”
The authors — all of
whom have proven track records in both science and practical crop improvement
— offer examples where exactly this combination of factors led to the
impactful application of innovative research findings.
Improving the Vitamin A content of maize: A variety of maize with high Vitamin A content has the potential to reduce a deficiency that can cause blindness and a compromised immune system. This development happened as a result of many translational research efforts, including marker-assisted selection for a favorable allele, using DNA extracted from seed of numerous segregating breeding crosses prior to planting, and even findings from gerbil, piglet and chicken models — as well as long-term, community-based, placebo-controlled trials with children — that helped establish that Vitamin A maize is bioavailable and bioefficacious.
Flood-tolerant rice: Weather variability due to climate change effects is predicted to include both droughts and floods. Developing rice varieties that can withstand submergence in water due to flooding is an important outcome of translational research which has resulted in important gains for rice agriculture. In this case, the genetic trait for flood tolerance was recognized, but it took a long time to incorporate the trait into elite germplasm breeding programs. In fact, the development of flooding tolerant rice based on a specific SUB 1A allele took over 50 years at the International Rice Research Institute in the Philippines (1960–2010), together with expert molecular analyses by others. The translation program to achieve efficient incorporation into elite high yielding cultivars also required detailed research using molecular marker technologies that were not available at the time when trait introgression started.
include new approaches for improving the yield potential of spring wheat and the
discovery of traits that increase the climate resilience of maize and sorghum.
One way researchers apply academic research to field impact
is through phenotyping. Involving the use of cutting edge technologies and
tools to measure detailed and hard to recognize plant traits, this area of
research has undergone a revolution in the past decade, thanks to more
affordable digital measuring tools such as cameras and
sensors and more powerful and accessible computing power and accessibility.
Scientists are now able to identify at a detailed scale
plant traits that show how efficiently a plant is using the sun’s radiation for
growth, how deep its roots are growing to collect water, and more — helping
breeders select the best lines to cross and develop.
Phenotyping is key to understanding the physiological and
genetic bases of plant growth and adaptation and has wide application in crop
improvement programs. Recording trait
data through sophisticated non-invasive imaging, spectroscopy, image analysis,
robotics, high-performance computing facilities and phenomics databases allows
scientists to collect information about traits such as plant development,
architecture, plant photosynthesis, growth or biomass productivity from
hundreds to thousands of plants in a single day. This revolution was the
subject of discussion at a 2016 gathering of more than 200
participants at the International Plant Phenotyping Symposium hosted
by CIMMYT in Mexico and documented in a
special issue of Plant Science.
There is currently an explosion in plant science. Scientists
have uncovered the genetic basis of many traits, identified genetic markers to
track them and developed ways to measure them in breeding programs. But most of
these new findings and ideas have yet to be tested and used in breeding
programs – wasting their potentially enormous societal value.
Establishing systems for generating and testing new
hypotheses in agriculturally relevant systems must become a priority, Reynolds
states in the article. However, for success, this will require
interdisciplinary, and often international, collaboration to enable established
breeding programs to retool. Most
importantly, scientists and funding organizations alike must factor in the long-term
benefits as well as the risks of not taking timely action. Translating a
research finding into an improved crop that can save lives takes time and
commitment. With these two prerequisites, basic plant research can and should positively
impact food security.
Authors would like to acknowledge the following funding organizations for their commitment to translational research.
The International Wheat Yield Partnership (IWYP) is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) in the UK; the U. S. Agency for International Development (USAID) in the USA; and the Syngenta Foundation for Sustainable Agriculture (SFSA) in Switzerland.
The Heat and
Drought Wheat Improvement Consortium (HeDWIC) is supported by the Sustainable
Modernization of Traditional Agriculture (MasAgro) Project by the Ministry of
Agriculture and Rural Development (SADER) of the Government of Mexico; previous
projects that underpinned HeDWIC were supported by Australia’s Grains Research
and Development Corporation (GRDC).
Queensland Government’s Department of Agriculture and Fisheries in
collaboration with The Grains Research and Development Corporation (GRDC) have
provided long-term investment for the public sector sorghum pre-breeding
program in Australia, including research on the stay-green trait. More
recently, this translational research has been led by the Queensland Alliance
for Agriculture and Food Innovation (QAAFI) within The University of
validation work and ASI translation and extension components with support from
the United Nations Development Programme (UNDP) and the Bill and Melinda Gates
Financial support for the maize proVA work was partially provided by HarvestPlus (www.HarvestPlus.org), a global alliance of agriculture and nutrition research institutions working to increase the micronutrient density of staple food crops through biofortification. The CGIAR Research Program MAIZE (CRP-MAIZE) also supported this research.
The CGIAR Research Program on Wheat (WHEAT) is led by the International Maize and Wheat Improvement Center (CIMMYT), with the International Center for Agricultural Research in the Dry Areas (ICARDA) as a primary research partner. Funding comes from CGIAR, national governments, foundations, development banks and other agencies, including the Australian Centre for International Agricultural Research (ACIAR), the UK Department for International Development (DFID) and the United States Agency for International Development (USAID).
International gathering highlights cutting edge efforts to improve yields, nutrition, and climate change resilience of a globally vital staple food
by Julie Mollins
As many regions worldwide baked under some of the most persistent
heatwaves on record, scientists at a major conference in Canada shared data on
the impact of spiraling temperatures on wheat.
In the Sonora desert in northwestern Mexico, nighttime temperatures varied 4.4 degrees Celsius between 1981 and 2018, research from the International Maize and Wheat Improvement Center (CIMMYT) shows. Across the world in Siberia, nighttime temperatures rose 2 degrees Celsius between 1988 and 2015, according to Vladimir Shamanin, a professor at Russia’s Omsk State Agrarian University who conducts research with the Kazakhstan-Siberia Network on Spring Wheat Improvement.
“Although field trials across some of the hottest wheat growing environments worldwide have demonstrated that yield losses are in general associated with an increase in average temperatures, minimum temperatures at night – not maximum daytime temperatures –are actually determining the yield loss,” said Gemma Molero, the wheat physiologist at CIMMYT who conducted the research in Sonora, in collaboration with colleague Ivan Ortiz-Monasterio.
“Of the water taken up by the roots, 95% is lost from leaves via transpiration and from this, an average of 12% of the water is lost during the night. One focus of genetic improvement for yield and water-use efficiency for the plant should be to identify traits for adaptation to higher night temperatures,” Molero said, adding that nocturnal transpiration may lead to reductions of up to 50% of available soil moisture in some regions.
The Intergovernmental Panel on Climate Change (IPCC) reported in October that temperatures may become an average of 1.5 degrees Celsius warmer in the next 11 years. A new IPCC analysis on climate change and land use due for release this week, urges a shift toward reducing meat in diets to help reduce agriculture-related emissions from livestock. Diets could be built around coarse grains, pulses, nuts and seeds instead.
Scientists attending the International Wheat Congress in Saskatoon, the city at the heart of Canada’s western wheat growing province of Saskatchewan, agreed that a major challenge is to develop more nutritious wheat varieties that can produce bigger yields in hotter temperatures.
As a staple crop, wheat provides 20% of all human calories consumed worldwide. It is the main source of protein for 2.5 billion people in the Global South. Crop system modeler Senthold Asseng, a professor at the University of Florida and a member of the International Wheat Yield Partnership, was involved in an extensive study in China, India, France, Russia and the United States, which demonstrated that for each degree Celsius in temperature increase, yields decline by 6%, putting food security at risk.
Wheat yields in South Asia could be cut in half due to chronically high temperatures, Molero said. Research conducted by the University of New South Wales, published in Environmental Research Letters also demonstrates that changes in climate accounted for 20 to 49% of yield fluctuations in various crops, including spring wheat. Hot and cold temperature extremes, drought and heavy precipitation accounted for 18 to 4% of the variations.
At CIMMYT, wheat breeders advocate a comprehensive
approach that combines conventional, physiological and molecular breeding
techniques, as well as good crop management practices that can ameliorate heat
shocks. New breeding technologies are making use of wheat landraces and wild
grass relatives to add stress adaptive traits into modern wheat – innovative approaches that have led to new
heat tolerant varieties being grown by farmers in warmer regions of Pakistan,
“HeDWIC is a pre-breeding program that aims to deliver genetically diverse advanced
lines through use of shared germplasm and other technologies,” Reynolds said in
Saskatoon. “It’s a knowledge-sharing and training mechanism, and a platform to deliver proofs
of concept related to new technologies for adapting wheat to a range of heat
and drought stress profiles.”
Aims include reaching agreement
across borders and institutions on the most promising research areas to achieve
climate resilience, arranging trait research into a rational framework, facilitating
and developing a bioinformatics cyber-infrastructure, he said, adding that
attracting multi-year funding for international collaborations remains a
area of climate research at CIMMYT involves the development of an affordable
alternative to the use of nitrogen fertilizers to reduce planet-warming
greenhouse gas emissions. In certain plants, a trait known as biological
nitrification inhibition (BNI) allows them to suppress the loss of nitrogen
from the soil, improving the efficiency of nitrogen uptake and use by
themselves and other plants.
“Every year, nearly a fifth of the world’s fertilizer is used to grow wheat, yet the crop only uses about 30% of the nitrogen applied, in terms of biomass and harvested grains,” said Victor Kommerell, program manager for the multi-partner CGIAR Research Programs (CRP) on Wheat and Maize led by the International Maize and Wheat Improvement Center.
has the potential to turn wheat into a highly nitrogen-efficient crop: farmers
could save money on fertilizers, and nitrous oxide emissions from wheat farming
could be reduced by 30%.”
Excluding changes in land use such as deforestation, annual greenhouse gas emissions from agriculture each year are equivalent to 11% of all emissions from human activities. About 70% of nitrogen applied to crops in fertilizers is either washed away or becomes nitrous oxide, a greenhouse gas 300 times more potent than carbon dioxide, according to Guntur Subbarao, a principal scientist with JIRCAS.
To exploit this roots-based characteristic,
breeders would have to breed this trait into plants, said Searchinger, who
presented key findings of the report in Saskatoon, adding that governments and
research agencies should increase research funding.
Other climate change mitigation efforts must
include revitalizing degraded soils, which affect about a quarter of the
planet’s cropland, to help boost crop yields. Conservation agriculture
techniques involve retaining crop residues on fields instead of burning and
clearing. Direct seeding into soil-with-residue and agroforestry also can play
a key role.
Based on a rigorous large-scale study spanning five decades
of wheat breeding progress under cropping systems with low, medium and high
fertilizer and chemical plant protection usage, the authors conclude that
modern wheat breeding practices aimed at high-input farming systems have
promoted genetic gains and yield stability across a wide range of environments
and management conditions.
In other words, wheat breeding benefits not only large-scale
and high-input farmers but also resource-poor, smallholder farmers who do not
use large amounts of fertilizer, fungicide, and other inputs.
This finding underscores the efficiency of a centralized
breeding effort to improve livelihoods across the globe – the philosophy behind
the breeding programs of the International Maize and Wheat Improvement Center
(CIMMYT) over the past 50 years.
It also contradicts a commonly held belief that breeding for
intensive systems is detrimental to performance under more marginal growing
environments, and refutes an argument by Green Revolution critics that breeding
should be targeted to resource-poor farmers.
“Given that wheat is the most widely grown crop in the
world, sown annually on around 220 million ha and providing approximately 20%
of human calories and protein, the social and economic implications are large,“
Among other implications,
The study found that modern breeding has reduced
groups of genes (haplotypes) with negative or neutral effects – a finding which
will help breeders combine positive haplotypes in the future, including for
The study demonstrates the benefits of breeding
for overall yield potential, which — given that wheat is grown over a wider
range of environments, altitudes and latitudes than any other crop, with widely
ranging agronomic inputs – has significant cost-saving implications.
Braun and Reynolds acknowledge that the longstanding beliefs
challenged by this study have a range of influences, from concern about rural
livelihoods, to the role of corporate agribusiness and the capacity of Earth’s
natural resources to sustain 10 billion people.
While they welcome the conclusions as a validation of their
work, they warn against seeing the study as “a rubber stamp for all things
‘high-input’” and encourage openness to new ideas as the need arises.
“If the climate worsens, as it seems destined to, we must
certainly be open to new ways of doing business in crop improvement, while
having the common sense to embrace proven technologies, ” they conclude.
This new publication summary was originally posted on the CIMMYT blog.
Resource-poor farmers worldwide stand to gain from developments in the field of crop modelling. Photo: H. De Groote/CIMMYT.
“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.
In “Role of Modelling in International Crop Research: Overview and Some Case Studies,” CGIAR researchers, including CIMMYT wheat physiologist Matthew Reynolds, 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.