Tag Archives: phenomics

A year in review: Highlights from the RTB Annual Meeting 2015

The Annual Review and Planning Meeting of the CGIAR Research Program on Roots, Tubers and Bananas (RTB) took place last week from 8 – 10 December, 2015 in Lima, Peru.

The event was hosted by the program’s lead center, the International Potato Center (CIP), and brought together over 50 researchers from the five program partner centers – the International Institute of Tropical Agriculture, Bioversity International, the International Center for Tropical Agriculture, CIRAD and CIP – along with colleagues from other partners including Florida State University and Wageningen University. A representative from a key RTB donor, USAID, also attended the event to share in this year’s highlights.

23573958681_4474c2e3e5_o_CROPOver three days, participants reported on highlights and key achievements from the program’s six research themes, which led to enthusiastic and constructive discussion about the results and next steps for the program in 2016. The collegial and dynamic atmosphere set a positive tone for the year ahead as RTB prepares to undergo a significant shift away from research ‘themes’ to ‘flagship projects’ in 2016.

Selected highlights from the Annual Meeting:

Theme 1 – Unlocking the value and use potential of genetic resources

  • Through complementary funding, RTB has enabled the application of next generation sequencing to change our understanding of genetic diversity, genetic resource collections and breeding populations of root, tuber and banana crops.
  • In several crops, including potato and cassava, we are gaining an understanding of the identity of crop varieties, the status of duplication and misidentifications. This is enabling a much higher level of quality control of information on germplasm and breeding populations to assist with more efficient use of RTB resources.

Theme 2 – Accelerating the development and selection of varieties with higher, more stable yield and added value

  • Metabolomics has been successfully applied to banana, potato, and yam to identify differences between genotypes and treatments.
  • DNA sequencing could separate genepools in cassava based on origin. Sequencing data has proven useful to improve the cassava genome. Further gene characterization raises the question of perhaps using genome editing to reduce cyanide levels in cassava.
  • Genome-Wide Association Studies have applied in banana for the first time, and have identified candidate genes for seedlessness.
  • A ‘Trait Observation Network’ to close potato yield gaps in Africa and Asia started this year and involves extensive G x E phenotyping for drought, late blight, virus resistance, and maturity of already genotyped breeding panels.
  • Shovelomics and other root phenotyping methods to analyze root architecture in relation to drought stress shows potential for screening genotypes at early development stages, as root weight and root dry matter weight is correlated with sweetpotato storage root yields.

Theme 3 – Managing priority pests and diseases

  • Results of work on degenerative diseases show that positive selection, which involves visually identifying and selecting only symptomless plants as the seed source for the next generation, can be as effective as the use of clean seed where selection can be done accurately.
  • Pest Risk Analysis along an altitude gradient was used as a proxy for climate change, and revealed that some diseases have higher incidence at lower altitude, and some have higher incidence at lower levels. Hence, climate change is expected to have some positive and negative effects.
  • Crop land connectivity was used to assess risk for invasion and saturation by pathogens and pests, and showed that the Great Lakes region in East Africa has the highest threat for RTB crops combined.
  • An interdisciplinary Banana Bunchy Top Disease Alliance was set up, and practicable models, tools and procedures for containment and recovery were developed.
  • Single Diseased Stem Removal has been found to be a very effective and farmer-friendly method for controlling Banana Xanthomonas Wilt.
  • A successful Private-Public Partnership has been set up to reduce pesticide use to control Potato Tube Moth through the development of a pheromone-based control strategy that attracts and kills the pest.

Theme 4 – Making available low-cost, high quality planting material for farmers

  • A conceptual framework was developed to analyze RTB seed systems, extract lessons and generate recommendations for improving the design and implementation of future interventions.
  • Quality Declared Quality Planting Materials as an alternative to formal certification is a lower cost and more feasible opportunity for seed system with RTB crops where seed is typically bulky and/or perishable.
  • A key message of the research in this theme was that understanding gender roles in seed systems is critical for positive impact.
  • How can positive selection of seed become adopted as more routine practice in improved seed system?
  • A framework for understanding availability, access and use of quality seed  has been developed and specific research questions have been proposed around this linked to a series of case studies.

 At the end of the first day, CIP hosted an Open House afternoon, showcasing the center’s work in areas including a demonstration of remote sensing of a potato field using a drone and in-house software to collect and analyze the data, and an introduction to the Genebank’s collection of in vitro germplasm of potato, sweetpotato and Andean roots and tubers.

Day two of the meeting covered the highlights from Themes 5 and 6:

 Theme 5 – Developing tools for more productive, ecologically robust cropping systems

  • Developing ability to provide targeted recommendations about the next steps for cropping systems improvement, as a function of a farm’s current status (technology limited, resources limited, decision limited).
  • Providing recommendations that can be used by farmers immediately for more robust and profitable cropping systems.
  • Support for farmer soil management through careful analysis of nutrient balances shows promise for smallholder banana production.

Theme 6 – Promoting post-harvest technologies, value chains, and market opportunities

  • Sensory tasting for cassava should be product specific. For example, Gari can be eaten dry, as a paste, in porridge etc. When you want to evaluate the acceptability of Gari you have to decide on one of the products.
  • Much work has gone in to improving drying technologies and there is evidence that some technologies are preferred more than others, such as Cabinet driers in Tanzania.
  • Interlinkages with other projects are building on work that has already been done, e.g. RTB-ENDURE project is testing improved clones in development of value chains in Uganda.
  • Climate change effects: research has shown that the production of bitter alkaloids in the potato tuber increases with temperature making them unacceptable, this has strong implications for  climate change in potato

The meeting concluded with a smaller two-day workshop on 11-12 December to refine the program’s shift away from research ‘themes’ to a new structure based on five ‘flagship projects’ in 2016. More detail about RTB’s new flagship projects will be coming soon.


Harnessing the power of the “omics” to improve RTB varieties

RTB researchers are collaborating with a growing network of scientists at institutions around the world in an ambitious effort to unlock the genetic and metabolic secrets of root, tuber and banana crops, and help breeders use that information to develop better varieties more quickly.

This cutting-edge initiative incorporates the latest advances in gene sequencing, metabolite profiling and bioinformatics to better understand the genes and cellular processes responsible for traits such as drought tolerance, nutritional content and resistance to pests and diseases. It combines research in the three “omics” – genomics (the use of DNA sequencing to map a species’ genome and document genetic variation), metabolomics (the study of the metabolites involved in cellular processes) and phenomics (the study of how genes, the metabolic processes they control and environmental influences determine phenotype, or traits).

The primary goal is to complete genome-wide association studies (GWAS) of the main RTB crops. GWAS involve genetic sequencing of many accessions of a crop and comparing those sequences with field data to identify which genes are responsible for specific traits. It forms the bases of genomic breeding, which is increasingly being used in Europe and North America, but has yet to be applied to crops such has banana, cassava, sweetpotato and yam. RTB is complementing GWAS with metabolomic research to identify some of the metabolites in the metabolic pathways that connect genes with traits of interest.

Undertaking GWAS for RTB crops has only become possible in recent years, since the first genome sequences for potato and banana were completed and published in 2011 and 2012 respectively. A draft of the cassava genome was published in 2009, but that genome is currently the focus of a more comprehensive mapping by the Next Generation Cassava Breeding Project, based at Cornell University. Genome sequences for sweetpotato and yam have yet to be completed, but RTB plans to coordinate gene sequencing and GWAS of those crops in the coming years.

Collecting, organizing, and analyzing the data for such research is a mammoth undertaking. There are approximately 31,000 genes in cassava, 37,000 in banana and 39,000 in potato, whereas scientists don’t yet know how many genes sweetpotato and yam have. Each crop may also contain as many as 20,000 metabolites. Researchers are concentrating on a tiny portion of those genes and metabolites, yet the task of managing the data sets produced by gene sequencing and metabolite studies and associating them with traits requires new software and significant data management capabilities. The project will consequently require input from a wide range of experts and institutions.

Luis Augusto Becerra

Luis Augusto Becerra Lopez-Lavalle, CIAT

“This year, I have approached every person that I think can help with this,” said Luis Augusto Becerra Lopez-Lavalle, a molecular geneticist at the International Center for Tropical Agriculture (CIAT) and the leader for RTB’s theme two (development of improved varieties). “I hope to settle the last strategic partnerships in 2014, then we’ll concentrate on the data sets.”

The five RTB partners were involved in the initial genome sequences of their respective crops – the French Agricultural Research Centre for International Development (CIRAD) spearheaded the banana genome sequence – and the International Institute of Tropical Agriculture (IITA) is one of Cornell’s partners in the Next-Gen Cassava project.

Becerra explained that while the Next-Gen Cassava project is concentrating on cassava accessions from Africa, CIAT, in collaboration with the Beijing Genomics Institute (BGI), is working with accessions from across South America as well as Africa. He said the goal is to sequence 1,200 cassava accessions by the end of 2014.

The first set of genetic sequences and metabolite profiles are being completed using plants grown in controlled environments, but those accessions have also been planted in the field, so that subsequent data can be compiled for samples from normal field and stress environments. By comparing data from the control plants with samples from field tests, researchers can identify genes linked to stress tolerance or resistance.

By complementing this genomic research with metabolite studies, RTB scientists will gain a better understanding of the crops’ systems biology. Becerra observed that as powerful as genome wide association studies are, they ignore the metabolic pathways through which genetic information results in phenotype.

“We have all this potential, but we don’t know how these genes interact with one another and what biological networks they feed into,” he said.

To map those pathways and identify the metabolites associated with traits of interest, RTB has partnered with Royal Holloway, University of London, which has been involved in metabolomic research on tomato and other crops. Paul Fraser, a professor of Biochemistry at Royal Holloway who is coordinating the metabolite profiles of RTB crops, explained that they complement genomic information in various ways. They can result in identification of metabolic markers linked to traits of interest and can provide insight into the history of RTB crop domestication, which will give breeders a better understanding of the pedigrees of accessions and help them choose which parental stock to use.

Paul Fraser

Paul Fraser, Royal Holloway, University of London

“Breeders will be able to move much more quickly to integrate the traits that they want, and they will get higher genetic gain,” Fraser said.

He explained that he hopes to begin training breeders in the application of the metabolomic and genomic information the project generates in the second half of 2015, though he expects to have metabolite information that can be incorporated into breeding programs by late 2014.

Fraser noted that metabolomic data have uses beyond breeding, such as quality assessment and food safety. For example, metabolites associated with flavor, texture or appearance can be used to test for characteristics that consumers want, or compare improved varieties with varieties that are already popular on the market.

Becerra explained that while RTB is initially concentrating on banana, cassava and potato, the lessons learned and platforms developed for those crops will be applied to sweetpotato and yam as soon as possible.