Tag Archives: crop wild relatives

Revolutionary mobile app for monitoring crop pests and diseases

Just as the late blight epidemic wiped out potato fields in Ireland in the 19th century, crop pests and diseases still have devastating effects on smallholder farmers today – with scenarios projected to worsen under climate change.

Cassava brown streak disease is spreading westward across the African continent, and together with cassava mosaic disease, threatens the food and income security of over 30 million farmers in East and Central Africa. Likewise, banana is threated by fungal and bacterial diseases and banana bunchy top virus, while sweetpotato is faced with viruses and Alternaria fungi.

Farmers are often unable to properly identify these diseases, while researchers, plant health authorities and extension organizations lack the data to support them.

To overcome these issues, a team under the CGIAR Research Program on Roots, Tubers and Bananas (RTB), are working on a revolutionary app to accurately diagnose diseases in the field, which will be combined with SMS services to send alerts to thousands of rural farmers.

Diagnosing cassava disease in the field. Photo IITA

The team, led by David Hughes of Penn State, and James Legg of IITA – who leads RTB’s flagship project on Resilient Crops – together with scientists from CIAT, CIP and Bioversity International, are presenting their proposal as one of 12 finalists for a $US100,000 grant as part of the CGIAR Platform for Big Data in Agriculture Inspire Challenges at the Big Data in Agriculture Convention 2017 in Cali, Colombia this week.

The concept leverages three critical advances in how knowledge is communicated to the farm level: 1) the democratization of Artificial Intelligence (AI) via open access platforms like Google’s TensorFlow, 2) the miniaturization of technology allowing affordable deployment and 3) the development of massive communication and money exchange platforms like M-Pesa that allow rural extension to scale as a viable economic model enabling last mile delivery in local languages.

Painstaking field work using cameras, spectrophotometers and drones at RTB cassava field sites in coastal Tanzania and on farms in western Kenya has already generated more than 200,000 images of diseased crops to train AI algorithms.

Using many of these images, Hughes, Legg and collaborators were able to develop an AI algorithm with TensorFlow that can automatically classify five cassava diseases, and by collaborating with Google, the team have been able to develop a TensorFlow smartphone app that is currently being field-tested in Tanzania. Penn State has also developed a mobile spectrophotometer through a start-up called CROPTIX. Early results suggest it can accurately diagnose different viral diseases in the field, even if the plant looks healthy.

 “The concept leverages RTB’s global network across multiple crops for testing and scaling with national partners and the private sector in all three continents where we work. This technology will enable small-scale farmers to quickly take action and stop the spread of pests and diseases in their farms, protecting these critical sources of food and income security,” said Graham Thiele, RTB Program Director. “We are really excited about this initiative and delighted to be teaming up with Penn State,” he added.

A Tanzanian farmer examines his cassava plants for the presence of pests and disease. Photo H.Holmes/RTB

The project team has already developed linkages with the Vodafone agriculture SMS platform called DigiFarm, which positions them strategically to link digital diagnostics to large-scale rural text messaging services. The team will deliver farmer tailored SMS alerts on crop diseases and pests to 350,000 Kenyan farmers by July 2018.

Once the diagnostic and SMS systems are up and running, their impact will be determined by assessing how rapid disease diagnosis increases yield in cassava value chains in Kenya involving 28,000 farmers.

An existing platform housed by Penn State (www.plantvillage.org) will enable real time discussions of disease and pest diagnoses across the CGIAR community and with other experts to enhance SMS alerts from the DigiFarm platform.

It’s is envisaged that these innovations, initially piloted in East Africa, will provide a model that can be extended to the range of locations where RTB works, and in so doing impact the farming and livelihoods of hundreds of millions of farmers.

See more in the project flyer. 

Scientists call for action to preserve potato wild relatives

Crop wild relatives are wild plant species that share a common ancestor with cultivated crops. They retain a level of genetic diversity that makes them an invaluable source of raw material for crop improvement. However, their availability for research purposes depends on the coverage and state of the germplasm collections maintained by genebanks.

Large numbers of wild potato species from Peru, the center of potato genetic diversity, are actually absent from these ex situ collections and should be categorized as “high priority” for further collecting, according to a new research published in PLOS ONE journal.

“Crop wild relatives have evolved under natural selection in their native range coming to be adapted to specific conditions such as high temperatures, salinity, and assorted pests and diseases,” explains Nora Castañeda-Álvarez, the lead author and scientist at CIAT’s Crop Wild Relatives (CWR) research team. “Such traits can be bred into crop plants, greatly benefiting agricultural production, but only if these germplasm resources are made available to breeders,” she adds.

The potato’s CWR are already widely used in global breeding programs, and their contribution to agriculture should only increase as breeders search for tolerance to biotic and abiotic stresses and as the development of molecular tools and biotechnology makes the identification and utilization of diverse genetic materials more efficient. As agriculture faces climate change, their potential for utilization is such that the Global Crop Diversity Trust and the Millennium Seed Bank of the Royal Botanic Gardens at Kew in the UK are currently leading a project entitled “Adapting agriculture to climate change: collecting, protecting and preparing crop wild relatives.”

In the case of potato, one of the world’s most important food crops grown in over 125 countries, some wild species are sources of valuable traits offering resistance to frost and late blight, one of the most devastating potato diseases worldwide. The tuber crop has proven to be vulnerable to climate change, with growing areas moving upwards in the Andes, and a potential increase of pests and diseases due to rising temperatures. Habitat destruction is a main threat for continued in situ conservation of the potato’s CWR, particularly given the fact that many of them are highly endemic.

Under the umbrella of the CGIAR Research Program on Roots, Tubers and Bananas (RTB), scientists of the International Potato Center (CIP) and the International Center for Tropical Agriculture (CIAT) have collaborated and analyzed the state of ex situ conservation of 73 of the closest wild relatives of potato (Solanum section Petota): a “gap analysis” aimed to critically analyze the present-day representativeness of public genebank collections globally, determine high priority geographic areas for collecting CWR in order to fill the gaps in genebanks, and also to identify species that need attention for in situ conservation monitoring. Significant gaps were found in global ex situ collections: in order to address them, a total of 32 species (43.8%) were consequently assigned high priority for further collecting.

Wild potatoes (A. Salas/CIP)

Wild potatoes (A. Salas/CIP)

“In remote areas of the Andean highlands, access to species was very limited,” explains Alberto Salas, an agronomist at the International Potato Center (CIP) who spent decades studying potato varieties and distribution in the Americas, collecting a wide array of wild potato germplasm.  CIP has identified more than 4,300 different varieties of edible potatoes, along with numerous wild potatoes species (it is host to the largest potato collection in the world, with more than 7000 potato accessions safeguarded in its genebank). “Now road construction itself, along with climate change, can also represent a threat to these species as their habitat is changing,” Salas adds, before informing that:  “The S. aymarasense can’t be found in Chalhuanca, Apurímac anymore since they built a road. Fortunately the species is in the CIP’s genebank. In Huancayo, department of Junín, the construction of the Pahual village has led to the disappearance of S. rhomboideilanceolatum.

Also as a result of the analysis, a total of 20 and 18 wild potato species were assessed as medium and low priority for further collecting, respectively. Priorities for further collecting include:

  • Species completely lacking representation in germplasm collections, specifically ayacuchense, S. olmosense and S. salasianum in Peru and S. neovavilovii in Bolivia.
  • Other high priority species, with geographic emphasis on the center of species diversity, specifically 28 species that are currently present yet severely underrepresented in genebanks.
  • Medium priority species that are needed for increasing the representativeness of the complete genepool in ex situ

According to the authors of the study, such collecting efforts are key steps in ensuring the long-term availability of the wild potato genetic resources. They should also be combined with increased efforts to improve ex situ conservation technologies and methods, perform genotypic and phenotypic characterization of wild relative diversity, monitor wild populations in situ, and make conserved wild relatives and their associated data accessible to the global research community.

“In times when new collection expeditions are difficult to conduct, climate change is a reality and habitat destruction is widespread, it is essential that in situ reserves are established,” says second author Stef de Haan. “In situ conservation is complementary to genebanks and can support ongoing evolution and adaptive shifts in population genetics,” he asserts.

Castañeda-Álvarez NP, de Haan S, Juárez H, Khoury CK, Achicanoy HA, Sosa CC, Bernau V, Salas A, Heider B, Simon R, Maxted N, Spooner DM (2015). Ex situ conservation priorities for the wild relatives of potato (Solanum L. section Petota). PLOS ONE

 See also:

Poster with main highlights of this research: http://www.slideshare.net/CWRdiversity/gap-analysis-potato

Crop Wild Relatives and Climate Change website

 By Véronique Durroux-Malpartida

 Solanum incamayoense - A potato wild relative growing in a greenhouse of the INTA Balcarce research station for regeneration (Credit: Ariana Digilio/INTA, Balcarce)

Solanum incamayoense – A potato wild relative growing in a greenhouse of the INTA Balcarce research station for regeneration (Credit: Ariana Digilio/INTA, Balcarce)

Conservation of crop wild relatives of sweetpotato is key to crop improvement

Grown in more than 114 countries worldwide, sweetpotatoes are an important staple crop particularly in Sub-Saharan Africa and East and Southeast Asia. They have increasingly been the focus of attention of crop breeding efforts to enhance food security in food-insecure regions of Africa. Orange-fleshed sweetpotatoes, in particular, show promise as a solution to vitamin A-deficiency, thanks to their high beta-carotene content. The crop can be cultivated from humid to semi-arid conditions, and has proven to be resilient to natural disasters. Scientists, however, believe that its potential is still largely untapped and that crop wild relatives of sweetpotato, in particular, urgently deserve attention for their promising contribution to crop improvement.

“Sweetpotato can grow in marginal soils and some varieties thrive even in difficult conditions like heat and drought. The crop requires little attention and can grow profusely. However we observe large yield gaps due to vulnerability to pests and diseases as well as climate change,” says Bettina Heider, a genetic resources specialist at the International Potato Center (CIP) and co-author of a recently-published scientific paper on crop wild relatives (CWR) of sweetpotato.

To develop improved varieties, plant breeders require a diverse pool of genetic resources, which is not entirely available in the case of sweetpotato. Crop wild relatives, the undomesticated “cousins” of cultivated crops, grow well in difficult conditions, and can be used to introduce greater tolerance to heat and other stresses to the crop.

For Colin Khoury, a researcher at the International Center for Tropical Agriculture (CIAT) and lead author of the study, it is surprising to see how underutilized the sweetpotato CWR are, given their potential. “This is due to the lack of basic scientific data for the crop, including an underdeveloped taxonomy and an insufficient understanding of their geographical distributions,” he explains.

Knowledge of CWR is indeed limited. “The fourteen species that constitute the crop wild relatives of sweetpotato (the Batatas complex) are a complicated group of flowering plants: they hybridize and this makes understanding their biology more challenging,” explains Rick Miller, a co-author and a professor of biological sciences at Southeastern Louisiana University, USA. “The genetics of the CWR also is complicated. Some of the species have double the chromosome numbers due to something called polyploidy and sweetpotato itself has chromosomes that have doubled twice. Together this makes even knowing what to call each of the different kinds of morning glories in the Batatas complex difficult,” he adds.


Sweetpotato crop wild relative I. cynanchifolia (R. Scotland/U. Oxford)

Heider, Khoury, Miller and colleagues from CIP, CIAT, USDA and research universities, revised taxonomic and geographic information on sweetpotato CWR, modeled their distributions, determined their availability to crop breeders, and explored their adaptations to various climatic and soil conditions.

Through a gap analysis the researchers identified further collecting needs for each wild species, and classified them by order of priority. A total of 78.6% of the wild relatives of sweetpotato considered in the study were assigned high priority for further collecting due to insufficient accessions in genebanks.

The scientists identified a total of 50 countries as targets for further collecting.  Regions of particular importance are central and southern Mexico and the southeastern USA, where many wild species can be found growing together. “Unfortunately it is in these ‘hotspots’ of great genetic diversity that the risk of losing it is particularly high. The research on CWR has confirmed that not only do we have few sweetpotato genetic resources in genebanks and herbariums, but the formal conservation of in situ resources is also very limited,” indicates Heider, who hopes to see more interest develop for a crop whose potential for food security is great.

The research also offered an opportunity to explore geographic, climatic, and soil data to identify species that may be useful in terms of breeding. “We specifically looked for drought- and heat-tolerance, which are major issues in Sub-Saharan Africa and also increase vulnerability to major pest incidence in the region,” Khoury explains: “We found that a number of these species, such as Ipomoea littoralis, I. trifida, I. splendor-sylvae, I. leucantha, I. triloba, and wild I. batatas were potentially distributed in regions with low precipitation and high heat, well beyond the comfortable range of cultivated sweetpotato. Such species could be good candidates for exploration for these traits.” This work represents some of the major advances that were made within the CWR project team, since the publication of the initial gap analysis method in 2010.


Drought experiment with sweetpotato crop wild relatives in the greenhouse at Southeastern Louisiana University. The research is being carried out by two undergraduate researchers, Tyler Gardner and Nicholas O’Quin, with Dr. Rick Miller (R. Miller/SELU)

Another remarkable aspect of the research is that it brought together taxonomic, genetic resource, and breeder experts working on the crop. “Perhaps the biggest impact of the paper will be the further collaborative efforts generated through this first collaboration. Much still needs to be done to understand which these species are, and what diversity they possess. A network of researchers across the world is anxious to work on answering these questions,” says Khoury.

The research, supported by the CGIAR Research Program on Roots, Tubers and Bananas (RTB), falls under “Adapting agriculture to climate change: collecting, protecting and preparing crop wild relatives,” an initiative managed by the Global Crop Diversity Trust and the Millennium Seed Bank of the Royal Botanic Gardens at Kew, England.

 Reference: Khoury CK, Heider B, Castañeda-Alvarez NP, Achicanoy HA, Sosa CC, Miller RE, Scotland RW, Wood JR, Rossel G, Eserman LA, Jarret RL, Yencho G, Bernau V, Juarez H, Sotelo S, de Haan S and Struik PC (2015). Distributions, ex situ conservation priorities, and genetic resource potential of crop wild relatives of sweetpotato [Ipomoea batatas (L.) Lam., I. series Batatas]. Front. Plant Sci. 6:251. doi: 10.3389/fpls.2015.00251


By Véronique Durroux-Malpartida