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Author: Sarah Fernandes

Managing seeds and agricultural losses in the wake of extreme climate events: Lessons from Nepal

A women farmer picking up lodged paddy field after the untimely flash floods in Nepal (Photo: Sravan Shrestha/ICIMOD)
A women farmer picking up lodged paddy field after the untimely flash floods in Nepal (Photo: Sravan Shrestha/ICIMOD)

As climate change-induced disasters surge around the world, it is the people of the least developed countries paying the bulk of the costs.  According to the International Disaster Database, the number of disasters across the globe has risen by 74.5% — comparing data from 1980–1999 with 2000–2019 — and these numbers are expected to increase due to the most recent climate change scenarios. The major climate change impacts identified by the Intergovernmental Panel on Climate Change relevant for Nepal include an increase in economic losses from weather and climate-related events, with a significant contribution related to agricultural losses.

In Nepal, for example, an unexpected and untimely excessive rainfall and flood in October of 2021 caused massive damage to the ready-to-harvest crop across all major rice-producing areas of Nepal – threatening the food security and livelihood of the country’s smallholder rice farmers.

A rice damage assessment was essential to gather insights on the seed production losses and propose anticipatory measures for seed management and distribution to farmers for the next season. Thanks to a collaboration between scientists from the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Integrated Mountain Development (ICIMOD), a rapid loss assessment through a survey of rice-growing farmers was conducted to quickly assess the damage and recommend critical operational decisions to the Nepali government to mitigate the impact. With the help of an operational mobile app, Geofairy, the USAID-supported Nepal Seed and Fertilizer project (NSAF), implemented by CIMMYT, surveyed 253 farmers in six districts of the mid and far western region with a particular focus on the potential seed production losses for next year’s cultivation.

Unforeseen disaster

The 2021 disaster in Nepal came as a shock to farmers: the 2021 monsoon was proceeding as forecasted in the seasonal outlook, and by the end of the season, farmers were generally expecting bumper rice crops. The withdrawal of southwest monsoon system was declared in early October. However, from 18-20 October 2021, instead of dry spell, the country experienced a three-day excessive rainfall and accompanying flooding that caused massive damage to the ready-to-harvest crop across all major rice-producing areas in the southern lowland Terai region of Nepal.

The partially harvested and standing crop suffered three kinds of damage. First, farmers near the riverbanks lost their ready-to-harvest paddy as it was swept away by flash floods. The second category was in the low-lying southern plains, where rainwater inundated the harvested, but not collected, paddy fields for more than two days, causing seeds or grains on the panicles to sprout. Sprouted seeds on the mother plant have reduced germination capacity and vigor, and cannot be stored for a long period while maintaining the germination capacity. The third damage was stem and root lodging (falling over) due to powerful winds.

Digital technologies for rapid damage assessment

With conventional approaches, on-ground damage assessments after a disaster can take weeks, sometimes months, limiting critical operational decisions in the first few hours and days. However, Nepal’s Ministry of Agriculture and Livestock Development (MoALD) was already prepared: since 2019, the Ministry has been using satellite remote sensing for in-season rice area estimation through the USAID-supported SERVIR HKH program.

Thanks to the platform, experts from ICIMOD were able to share a satellite image-based assessment as early as 22 October 2021: two days after the flood.

This existing digital crop monitoring platform was used to produce a rapid-damage assessment to provide an analytical basis for initial decisions. In the rapid damage assessment, GMP IMERGE satellite data was used to measure the rainfall intensity across Nepal (Figure 1) and Selntinel-1 SAR satellite data was used to map flood water extent in the Terai district of Nepal on 21 October 2022. The assessment also served as a planning tool for in-depth damage evaluation for farmer compensations.

Widespread flooding

Figure 1. Rainfall distribution during 18-20 October 2021 based on the GPM IMERGE satellite precipitation data

Satellite precipitation data showed the occurrence of hefty rainfall in Morang, Sunsari, Saptari, Siraha and Jhapa districts in the Eastern region. In the Western region, Kailali and Kanchanpur experienced intense rainfall, while most of the central districts of the Terai region remained below heavy rain.

Based on satellite images acquired, the flood extent assessment showed major flood spread in the western parts, including Kanchanpur, Kailali, Bardiya and Banke districts (Figure 2). The flood water extent remained lower in the Eastern districts compared to the West. The causes of severe damage were from direct rain pour and winds in the Eastern region, and flood swept from riverbanks in the Western parts.

Figure 2. Flood extent on 21 October 2021 in Kanchanpur district based on the Sentinel-1 satellite data

Assessment results: Reduced seed quality and shortage of rice seed supply for the next planting season

According to a field-based assessment, the two most popular varieties, Radha-4 and Sarju-52, are the most affected by the flood, especially in Banke, Bardiya, Kailali and Kanchanpur districts. Accordingly, 89% of Radha-4 and 42% of Sarju-52 seed production field has faced partial or complete loss in the surveyed districts. As per the district-wise loss assessment, 80% of Sirju-52 grown in Kailali and 61% in Kanchanpur suffered 50-100% damage. Similarly, nearly 60% of Radha-4 grown in Banke and Bardiya districts has suffered a crop loss ranging from 50-100%. This clearly indicates a huge shortage of these varieties for the next rice season which calls for immediate action to mitigate the seed deficit.

The survey found that farmers in Bardiya, Banke and Kailali had severe or complete crop loss, while those in Kanchanpur, Kapilvastu and Rupendehi had partial crop failure (Figure. 3)

Figure 3. Level of rice loss (%) due to flood, based on a rapid crop loss assessment in six districts of Nepal

Losses and the limits of early warning systems

According to the government’s final estimates, about 1,10,000 ha of rice crop area was damaged across the country. Respondents from the western districts reported that 80% of the farmers could only manage 50% or less than the expected harvest. The farmers reported an average input cost of $526 per hectare (NPR 63,162 per ha) and gross expected income of $972 per hectare (NPR 116,674 per ha) – leaving a very narrow margin of profit. To compensate for this economic blow, the government distributed  $43 million (NPR 5.52 billion) among the farmers. However, with a total loss of $0.1 billion (NPR 12 billion), farmers still suffered a great loss.

Figure 4. Percentage of safe harvest in four western districts (Kapilvastu, Rupandehi, Kanchanpur and Bardiya) of Nepal

Although early warning systems were in place in the surveyed districts, some respondents expressed low trust and reliability in the early warnings and only 20% of respondents were aware of the heavy rainfall forecast issued three days before the extreme event. Earlier studies in the Ganges basin have suggested that a 10–20-day lead-time forecast is needed to avoid agriculture losses. However, predicting a high magnitude of low-frequency extreme events with sufficient advance notice is still a significant challenge in climate science.

How to mitigate and weather such challenges?

Nepal’s rice seed replacement rate is around 20%, which means that about 80% of farmers are not accessing good quality seeds every season. The addition of this untimely flash flood and the subsequent seed loss will further worsen seed availability, in turn contributing to food insecurity at the national level. The assessment findings have several implications for actions needed to mitigate future climate shocks.

  • Among other mitigation approaches, stakeholders need to assess in-country level quality rice seed availability and design a plan to mobilize preferred varieties from the surplus districts — less affected by the flood — to those in need.
  • During challenging times, maintaining seed quality standards might be difficult. Hence, stakeholders need to consider adopting a flexible quality standard such as “quality declared seeds” in similar emergency scenarios. The “quality declared seed” standard helps as an important intervention when normal seed production is greatly affected by drought and/or flood. It offers alternative seed quality standards for seed producers to provide seeds and ensure continuity of crop production.
  • Promoting climate-resilient varieties, especially lodging- or submergence-tolerant rice varieties, will better withstand flooding as compared to the susceptible ones.
  • Furthermore, farmers need access to a suitable crop insurance scheme to offset seed losses during extreme weather events. For instance, seed growers can purchase a group insurance scheme where customized premiums could be available to the members.

Some of the above mitigation approaches can be applied when extreme weather events are well forecasted and less severe. However, in the wake of an emerging climate crisis and limited mitigation options, there is a need to balance efforts on all aspects of adaptation, including the adoption of crop management practices including accelerated varietal turnover to modify threats and prevent adverse impacts, strengthen early warning systems with a focus on last-mile connection to minimize damages, and develop innovative mechanisms to address risk transfer and loss and damage compensations for sharing losses.

CIMMYT and CGIAR senior leaders share vision ahead

(Left to right) Bram Govaerts, Claudia Sadoff, Joaquín Lozano and Kevin Pixley stand for a group photo next to the Norman Borlaug sculpture at CIMMYT’s global headquarters in Texcoco, Mexico. (Photo: Alfonso Cortés/CIMMYT)
(Left to right) Bram Govaerts, Claudia Sadoff, Joaquín Lozano and Kevin Pixley stand for a group photo next to the Norman Borlaug sculpture at CIMMYT’s global headquarters in Texcoco, Mexico. (Photo: Alfonso Cortés/CIMMYT)

Senior leadership from CGIAR had the opportunity to strengthen ties with senior leaders and researchers from the International Maize and Wheat Improvement Center (CIMMYT) during a visit on April 25–26, 2022. Claudia Sadoff, Executive Management Team Convener and Managing Director for Research Delivery and Impact, visited CIMMYT’s global headquarters in Texcoco, Mexico, and the experimental station in Toluca, west of Mexico City. Joining her was Joaquín Lozano, CGIAR’s Regional Director for Latin America and the Caribbean.

On April 25, 2022, scientists provided an overview of CIMMYT’s research in Africa and Asia and discussed with Sadoff how CIMMYT’s science and operations contribute to the One CGIAR 2030 Strategy. Examples included sustainable agri-food systems research in South Asia and maize research in Africa, with emphasis on work that aligns with CGIAR’s Action Areas and impact. These sessions underlined CIMMYT’s involvement in multiple CGIAR Initiatives, its influence on policy, and evidence of translating science into impact on the ground.

Lozano and Sadoff toured the facilities, including the CIMMYT Museum, the Wellhausen-Anderson Plant Genetic Resources Center, and the Applied Biotechnology laboratory. Along the way, scientists explained their latest research and answered questions about conservation agriculture, innovation hubs, climate-smart technologies, and scale-appropriate mechanization.

In the afternoon, CIMMYT and CGIAR representatives had targeted discussions on poverty reduction, gender equity and social inclusion, climate adaptation, environmental health and biodiversity,

The remainder of the first day was spent at the Bioscience complex, with visits to the wheat molecular breeding lab, the greenhouse, the wheat quality laboratory, and the maize quality laboratory, which hosted a discussion on nutrition and health.

(Left to right) Joaquín Lozano, Claudia Sadoff, Carolina Sansaloni, Bram Govaerts and Alberto Chassaigne stand for a group photo inside the germplasm bank at CIMMYT’s global headquarters in Texcoco, Mexico. (Photo: Alfonso Cortés/CIMMYT)
(Left to right) Joaquín Lozano, Claudia Sadoff, Carolina Sansaloni, Bram Govaerts and Alberto Chassaigne stand for a group photo inside the germplasm bank at CIMMYT’s global headquarters in Texcoco, Mexico. (Photo: Alfonso Cortés/CIMMYT)

Honoring our roots, growing into the future

On April 26, 2022, Lozano and Sadoff joined representatives from the Mexican and Indian governments, CIMMYT colleagues, and other partners at CIMMYT’s experimental station in Toluca for a dedication event for the late Sanjaya Rajaram.

In Sadoff’s speech, she praised CIMMYT’s highly committed staff and shared her honor at being invited to such an event. “Dr. Norman Borlaug, Dr. Sanjaya Rajaram, Dr. Ravi Singh, and many more talented researchers who have worked and continue to work at CIMMYT have built an outstanding international research organization that has been a role model for other CGIAR centers,” she said. “In view of this impressive history, it is very important that we all contribute to continue CIMMYT’s legacy and to multiply its impact worldwide, but also to honor those great colleagues who have truly inspired us with their impressive achievements.”

After the event, Lozano and Sadoff toured the station and praised the engaging program produced by CIMMYT.

For Lozano, it was his second visit to CIMMYT. “It was an honor to be back at CIMMYT HQ in Mexico this week with Claudia,” he said. “It’s evident that CIMMYT’s science, staff and partners support and proactively contribute to our global research strategy for a food-secure future. A big thanks to Bram Govaerts and the CIMMYT team for such a constructive dialogue and hospitality.”

Two approaches better than one: identifying spot blotch resistance in wheat varieties

Spot blotch, a major biotic stress challenging bread wheat production is caused by the fungus Bipolaris sorokiniana. In a new study, scientists from the International Maize and Wheat Improvement Center (CIMMYT) evaluate genomic and index-based selection to select for spot blotch resistance quickly and accurately in wheat lines. The former approach facilitates selecting for spot blotch resistance, and the latter for spot blotch resistance, heading and plant height.

Genomic selection

The authors leveraged genotyping data and extensive spot blotch phenotyping data from Mexico and collaborating partners in Bangladesh and India to evaluate genomic selection, which is a promising genomic breeding strategy for spot blotch resistance. Using genomic selection for selecting lines that have not been phenotyped can reduce the breeding cycle time and cost, increase the selection intensity, and subsequently increase the rate of genetic gain.

Two scenarios were tested for predicting spot blotch: fixed effects model (less than 100 molecular markers associated with spot blotch) and genomic prediction (over 7,000 markers across the wheat genome). The clear winner was genomic prediction which was on average 177.6% more accurate than the fixed effects model, as spot blotch resistance in advanced CIMMYT wheat breeding lines is controlled by many genes of small effects.

“This finding applies to other spot blotch resistant loci too, as very few of them have shown big effects, and the advantage of genomic prediction over the fixed effects model is tremendous”, confirmed Xinyao He, Wheat Pathologist and Geneticist at CIMMYT.

The authors have also evaluated genomic prediction in different populations, including breeding lines and sister lines that share one or two parents.

Spot blotch susceptible wheat lines (left) and resistant lines. (Photo: Xinyao He and Pawan Singh/CIMMYT)
Spot blotch susceptible wheat lines (left) and resistant lines. (Photo: Xinyao He and Pawan Singh/CIMMYT)

Index selection

One of the key problems faced by wheat breeders in selecting for spot blotch resistance is identifying lines that are genetically resistant to spot blotch versus those that escape and exhibit less disease by being late and tall. “The latter, unfortunately, is often the case in South Asia”, explained Pawan Singh, Head of Wheat Pathology at CIMMYT.

A potential solution to this problem is the use of selection indices that can make it easier for breeders to select individuals based on their ranking or predicted net genetic merit for multiple traits. Hence, this study reports the first successful evaluation of the linear phenotypic selection index and Eigen selection index method to simultaneously select for spot blotch resistance using the phenotype and genomic-estimated breeding values, heading and height.

This study demonstrates the prospects of integrating genomic selection and index-based selection with field based phenotypic selection for resistance in spot blotch in breeding programs.

Read the full study:
Genomic selection for spot blotch in bread wheat breeding panels, full-sibs and half-sibs and index-based selection for spot blotch, heading and plant height

Cover photo: Bipolaris sorokiniana, the fungus causing spot blotch in wheat. (Photo: Xinyao He and Pawan Singh/CIMMYT)

CIMMYT scientists identify novel genomic regions associated with spot blotch resistance

Spot blotch, caused by the fungus Biopolaris sorokiniana poses a serious threat to bread wheat production in warm and humid wheat-growing regions globally, affecting more than 25 million hectares and resulting in huge yield losses.

Chemical control approaches, including seed treatment and fungicides, have provided acceptable spot blotch control. However, their use is unaffordable to resource-poor farmers and poses a hazard to health and the environment. In addition, “abiotic stresses like heat and drought that are widely prevalent in South Asia compound the problem, making varietal genetic resistance the last resort of farmers to combat this disease,” according to Pawan Singh, Head of Wheat Pathology at the International Maize and Wheat Improvement Center (CIMMYT). Therefore, one of CIMMYT’s wheat research focus areas is developing wheat varieties that carry genetic resistance to the disease.

Signs of spot blotch on wheat. (Photo: Philomin Juliana/CIMMYT)
Signs of spot blotch on wheat. (Photo: Philomin Juliana/CIMMYT)

Previously, only four spot blotch resistance genes in bread wheat had been identified. Through a new study, CIMMYT scientists have identified novel genomic regions associated with spot blotch resistance using the genome-wide association mapping approach with 6,736 advanced breeding lines from different years (2013 to 2020), evaluated at CIMMYT’s spot blotch screening platform in Agua Fría, in Mexico’s state of Morelos.

The study’s results are positive and confirmed that:

  • Many advanced CIMMYT breeding lines have moderate to high resistance to spot blotch.
  • Resistance to the disease is conferred quantitatively by several minor genomic regions that act together in an additive manner to confer resistance.
  • There is an association of the 2NS translocation from the wild species Aegilops ventricosa with spot blotch resistance.
  • There is also an association of the spot blotch favorable alleles at the 2NS translocation, and two markers on the telomeric end of chromosome 3BS with grain yield evaluated in multiple environments, implying that selection for favorable alleles at these markers could help obtain higher grain yield and spot blotch resistance.

“Considering the persistent threat of spot blotch to resource-poor farmers in South Asia, further research and breeding efforts to improve genetic resistance to the disease, identify novel sources of resistance by screening different germplasm, and selecting for genomic regions with minor effects using selection tools like genomic selection is essential,” explained Philomin Juliana, Molecular Breeder and Quantitative Geneticist at CIMMYT.

Read the full study:
Genome-Wide Association Mapping Indicates Quantitative Genetic Control of Spot Blotch Resistance in Bread Wheat and the Favorable Effects of Some Spot Blotch Loci on Grain Yield

Cover photo: Researchers evaluate wheat for spot blotch at CIMMYT’s experimental station in Agua Fría, Jiutepec, Morelos state, Mexico. (Photo: Xinyao He and Pawan Singh/CIMMYT)

CGIAR Initiative to increase resilience, sustainability and competitiveness in Latin America and the Caribbean

(Photo: CIMMYT)
(Photo: CIMMYT)

Este artículo también está disponible en español.

With the participation of more than 30 researchers from four CGIAR Centers located in the Americas, a planning workshop for a new CGIAR Research Initiative, AgriLAC Resiliente, was held on April 4–6, 2022. Its purpose was to define the implementation of activities to improve the livelihoods of producers in Latin America, with the support of national governments, the private sector, civil society, and CGIAR’s regional and global funders, and partners.

“This workshop is the first face-to-face planning meeting aimed at defining, in a joined-up manner and map in hand, how the teams across Centers in the region will complement each other, taking advantage of the path that each Center has taken in Latin America, but this time based on the advantage of reaching the territories not as four independent Centers, but as one CGIAR team,” says Deissy Martínez Barón, leader of the Initiative from the Alliance of Bioversity International and CIAT.

AgriLAC Resiliente is an Initiative co-designed to transform food systems in Latin America and the Caribbean. It aims to increase resilience, ecosystem services and the competitiveness of agrifood innovation systems in the region. Through this Initiative, CGIAR is committed to providing a regional structure that enhances its effectiveness and responds better to national and regional priorities, needs and demands.

This Initiative is one of a number that the CGIAR has in Latin America and the Caribbean and consists of five research components:

  1. Climate and nutrition that seeks to use collaborative innovations for climate-resilient and nutritious agrifood systems;
  2. Digital agriculture through the use of digital and inclusive tools for the creation of actionable knowledge;
  3. Competitiveness with low emissions, focused on agroecosystems, landscapes and value chains, low in sustainable emissions;
  4. Innovation and scaling with the Innova-Hubs network for agrifood innovations and their scaling up;
  5. Science for timely decision making and the establishment of policies, institutions and investments in resilient, competitive and low-emission agrifood systems.

The regional character of these CGIAR Initiatives and of the teams of researchers who make them a reality in the territories with the producers, was prominent in the minds of the leadership that also participated in this workshop. Martin Kropff, Global Director, Resilient Agrifood Systems, CGIAR; Joaquín Lozano, Regional Director, Latin America and the Caribbean, CGIAR; Óscar Ortiz, Acting Director General of the International Potato Center; Jesús Quintana, Manager for the Americas of the Alliance of Bioversity International and CIAT; and Bram Govaerts, Director General of the International Maize and Wheat Improvement Center (CIMMYT), all stated the importance of CGIAR being central to every discussion in which the teams are co-constructing a greater consensus on what AgriLAC Resliente is, what it wants to achieve, the approach it will use, and the goals it aims to achieve through synergies among its five components.

Acting as an integrated organization is also an opportunity for CGIAR to leverage co-developed solutions and solve local challenges in the global South related to climate change and agrifood systems transformation. “Building the new CGIAR involves tons of collaboration and coordination. In this AgriLAC Resiliente workshop, we have had a dialogue full of energy focused on achieving real impact” highlighted Bram Govaerts. He continued, “this is an occasion to strengthen teamwork around this CGIAR Initiative in which the Integrated Agrifood System Initiative approach will be applied in the Latin American region, which is a very interconnected region” he pointed out.

One of the main results of this workshop is an opportunity to carry out the integration of the CGIAR teams in the implementation of the AgriLAC Resiliente Initiative, with applied science and the decisive role of the partners at each point of the region, as mechanisms for change.

In 2022, the research teams will begin to lay the groundwork for implementing the Initiative’s integrative approach to strengthen the innovations to be co-developed with partners and collaborators in the Latin American region, that encompass the interconnected nature of the global South.

Learn more about the Initiative:
AgriLAC Resiliente: Resilient Agrifood Innovation Systems in Latin America and the Caribbean

This article, authored by the AgriLAC Resiliente team, was originally published on CGIAR.org.