World Congress on Root and Tuber crops
Plenary Session Friday January 22, 2016
Special RTB Session Graham Thiele
90mn
RTB: Progress, Priorities and Planning for Climate Resilience
Graham Thiele1* and Tahirou Abdoulaye2*
1) CRP on Root, Tubers and Bananas for Food Security and Income (RTB), Lima,
Peru, 2) IITA, Ibadan,
* g.thiele@cgiar.org, t.abdoulaye@cgiar.org
More than 300 million people below the poverty line in developing countries depend on root, tuber
and banana crops for food and income, particularly in Africa, Asia and the Americas. The CGIAR
Research Program on Roots, Tubers and Bananas (RTB) is working globally to harness the untapped
potential of those crops in order to improve food security, nutrition, income and climate change
resilience of smallholders.
RTB is changing the way the research centers work and collaborate, creating a more cohesive and
multidisciplinary approach to common challenges and goals through knowledge sharing,
multidirectional communications, communities of practice and crosscutting initiatives. Participating
centers work with an array of national and international institutions, nongovernmental
organizations and stakeholders’ groups, and RTB aims to promote greater cooperation among them
while strengthening their capacities as key players. Because the impact of RTB research is highly
dependent on its adoption by next users and end users, the program’s research options are
developed together with stakeholders and are informed by their needs and preferences. Because
women and youth are widely involved in the growing and marketing of RTB crops, face a different
set of constraints than men, and have traditionally been the last to benefit from agricultural
research and extension, RTB is working to improve gender responsiveness and youth employment
with its partners.
RTB conducted a strategic ex ante assessment of research priorities for its five crops (Cassava, Yam,
Banana, Potatoes and Sweet Potatoes) following a rigorous six step approach. This global exercise
used the same approach across crops and Centers to provide estimates of potential impact to each
research option per crop. Using opinions of nearly 1,700 experts (online and direct interviews)
across the globe, research options have been identified and ranked for each crop. Research options
were also ranked by region and gender of experts involved in the surveys.
A total of 31 research options were then selected to be evaluated using an economic surplus
method. This provided estimates of impact using a set of economic indicators that included adoption
potential, Net Present Value (NPV), internal rates of return (IRR) on the research investments, total
number of beneficiaries and number of people potentially lifted out of poverty. Economic surplus
estimates indicate that returns are positive and above the social cost of capital and that the
estimated number of beneficiaries ranges from 2 million to 600,000 in the high adoption scenarios
for the technologies with largest impact. Overall, evaluation results indicate that RTB crops have
huge potential in poverty reduction due to the number of people in all regions who depend on those
crops. Also the positive returns to investments in RTB crops are indicative of value for money if
partners support research on those crops. RTB is planning to use the results to inform program
planning for the second phase.
RTB is building on this priority assessment and reorganizing around five new flagship projects
spanning the breadth of research from discovery to improving livelihoods at scale. Adaptation to
climate change will feature as one of the most important grand challenges to be addressed.
Participants will be invited to contribute to on-line priority setting for building climate change
resilience, the most pressing challenge of our generation for agricultural research.
Speaker 13
PS13
Joe Tohme
20mn
An Overview of Root and Tuber Crops Genomics
Joe Tohme
j.tohme@cgiar.org
Agrobiodiversity Research Director, CIAT, Colombia
The roots and tubers research communities have advanced quickly in the use of genomics and
metabolomics since the last GCP-21 Congress in Uganda. Whole genome sequences from African
and Latin American cassava accessions were obtained. Using RADSeq, at least 1000 accessions from
Latin America and Africa were sequenced. The sequenced data provided insights into the genetic
structure of African cassava germplasm as well as the relationships between Latin American and
African germplasm. Sequencing of major roots and tubers pathogens has also progressed. The
construction of a Cassava pan-genome its closest wild relatives was initiated in 2015. A similar
potato initiative was also launched. Several roots and tubers and associated pathogens databases
were established. The wealth of sequence data will allow the roots and tubers communities to
embark on major initiatives of genome editing using CRISPR technology. Already successes in using
CRISPR-CAS 9 technology in potato were reported in 2015. The roots and tubers research
communities still needs to address the challenges of setting up: 1) a rapid global diagnostics alert
system to monitor and predict the threat of cassava diseases and 2) the establishment of high
throughput phenomics platforms. Digital Genebank, roots phenotyping and uses of Big Data will be
discussed.
Speaker 14
PS14
Prof. Ming Peng
25mn
Genomics approaches to unlock the high yield potential of cassava, a
tropical model plant
Ming Peng*1,2, Wenquan Wang*1,2, Shengkui Zhang1,2, Ping’an Ma1,
Haiyan Wang1, Cheng Lu1, Xin Chen1, Zhiqiang Xia1, Meiling Zou1, and
Xincheng Zhou1,2
1. Institute of Tropical Biosciences & Biotechnology, Chinese Academy of Tropical
Agriculture Sciences, Haikou 571101, China
2. Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou 571101,
China
Corresponding to Wenquan Wang (Wangwenquan@itbb.org.cn) and Ming Peng (Pengming@itbb.org.cn )
Cassava, a typical tropical food, feed and bio-fuel crop, has huge potential for biomass and starch
accumulation, and the subtle responsibility to solar light, temperature, water and mineral elements
which makes it to be an ideal model plant for tropical crops. However, the understanding of the high
interesting metabolism and genomics involved in the crop is limited. Here, we reported the recent
breakthroughs in the genomics of cassava, including the comparative sequencing and annotation of
a wild ancestor and a cultivar, a pioneering simplified re-sequencing tool and transcriptomic analysis
in diverse population level, as well as the findings based on these works. A set of genes unique in
cultivars or wild ancestor, and highly selected in evolution and domestication have been unwrapped,
they are ascribed into nine important biological processes, include of cell and cell parts,
developmental process, metabolic process, biological regulation, response to stimulus, etc. We
launched a carbon flux diversification and starch accumulation model, and the loading and
unloading models of carbohydrates up to in leave and in storage root of cassava. We design a
universal protocol to test the adaptation to high and low temperature, solar light and drought,
Finally, the current challenges and future potential of cassava as a model plant are discussed.
Keywords cassava, tropical model genomics, yield potential, adaptability
Speaker 15
PS15
Xin Liu
25mn
Analysis of the Potato Genome Sequence
Xin Liu
Email: liuxin@genomics.cn
BGI Shenzhen
Main Building, Beishan Industrial Zone, Beishan Road, Yantian District,
Shenzhen, Guangdong, P. R. China
The potato (Solanum tuberosum L.) genome was the first high-quality draft genome sequence of a
Solanaceae species. The complete sequence of the potato genome has been recognized as a new
start both for research and industry. As the most important worldwide non-grain crop, especially in
the developing countries, this genomic resources released by PGSC (Potato Genome Sequencing
Consortium) provided vital insights into the genetic mechanisms of tuberization, thus it is facilitating
the genetic improvement and breeding of potato. For the genome assembly, we encountered
challenges in applying the shotgun sequencing method to assemble the heterozygous diploid clone
(RH) at first, as the majority of the potato cultivars are highly heterozygous or even autotetraploid.
We then resolved this by selecting a homozygous doubled-monoploid potato clone (DM). After
assembling the DM genome, we analyzed the RH data to elucidate the genetic/haplotype diversity
and likely causes of inbreeding depression. Through extensive comparative intra-genomic and intergenomic analyses, we identified two ancient whole genome duplication events (WGDs) in the potato
genome, one of which is the Solanaceae-specific and the other is the palaeopolyploid event shared
within all eudicots. Orthologous and paralogous gene cluster analysis showed thousands of genes
were expanded in the Solanaceae or asteroid clade, and many were specifically recruited for the
tuber development and disease resistance. Meanwhile, we identified differential gene expression in
32 DM and 16 RH RNA-seq data of varied tuber developmental stages, and those genomes might be
related to responses to abiotic and biotic stresses. The potato genome sequence together with the
analysis of the genome, provided important resource for the community.
Speaker 16
PS16
Motoaki Seki
25mn
Integrated Omic Analysis Towards Advancement of
Cassava Molecular Breeding
Yoshinori Utsumi1, Tetsuya Sakurai1, Chikako Utsumi1,2, Vu The Ha1,
Yoshio Takei1,3, Tomonari Hirano4,5, Tomoko Abe5, Manabu Ishitani6, Joe
Tohme6, Dong Van Nguyen7, Vu Anh Nguyen7, Kanokporn Triwitayakorn8,
Punchapat Sojikul9, Jarunya Narangajavana9, Ham Huy Le7, Motoaki
Seki1,2,3*
1. RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
2. Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho,
Kawaguchi, Saitama 332-0012, Japan.
3. Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama,
Kanagawa 244-0813, Japan.
4. Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-nishi, Miyazaki 889-2192, Japan.
5. Nishina Center for Accelerator-Based Science, RIKEN, Wako, Saitama 351-0198, Japan.
6. Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali,
Colombia.
7. National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute (AGI), Hanoi, Vietnam.
8. Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom 73170, Thailand.
9. Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
Cassava is an important tropical crop that provides food security and income generation in tropical
and subtropical countries. The RIKEN group has developed an integrative, functional-genomics
platform for cassava towards advancing cassava molecular breeding and understanding various
physiological processes. The construction of this platform has been performed in collaboration with
the Agricultural Genetics Institute (AGI), Mahidol University (MU), and the International Center for
Tropical Agriculture (CIAT). The platform provides: a) Full-length cassava cDNA resources based on
these cultivars (KU 50, MECU72 and MPer417-003)1),2), b) ESTs using next generation sequencing
(NGS) (MECU72, MPer417-003, Huay Bong 60 and Hanatee)3), c) an integrative cassava database4), d)
a cassava microarray containing more than 30,000 genes3), e) a cassava transformation system5), and
f) a cassava breeding system that utilizes heavy-ion beam irradiation. Our groups have optimized the
system for induction of friable embryonic calli in model cassava5). Using the improved protocol, we
have produced several transgenic cassava plants, such as overexpression of fructose-bisphosphate
aldolase for improving the photosynthesis and cassava biomass, and analyzed them. Furthermore,
we have analyzed the molecular mechanisms of various biological phenomenon in cassava, such as
tuberization process6),7), disease resistance3), drought8) and high-salinity stress9) response by
integrative Omic (Transcriptome, Metabolome and Hormonome) analyses. We hope that our
approach using the platform will advance the molecular breeding of useful cassava, such as highyield, increased stress tolerance and beneficial modifications of starch quality.
References: 1) Sakurai et al. (2007) BMC Plant Biol.; 2) Fernando et al. (in prep.); 3) Utsumi et al. (revised); 4)
Sakurai et al. (2013) PLOS ONE; 5) Ha and Utsumi et al. (in prep.); 6) Utsumi et al. (in prep.); 7) Sojikul et al.
(2015) Plant Mol. Biol.; 8)Utsumi et al. (2012) DNA Res.; 9) Patanun et al. (in prep.)
Speaker 16
PS16
Herve Vanderschuren
25mn
Large-scale Quantitative Proteomics of Cassava:
Achievements, Current Limitations and Strategic
Advances
Vanderschuren Hervé1,2*
1) Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liège, Belgium, 2)
Plant Biotechnology Lab, Swiss Federal Institute of Technology (ETH),
Switzerland
* herve.vanderschuren@ulg.ac.be
Proteomics studies have gained increasing importance in crop research over the last decade. The
development of proteomics techniques allowing increased proteome coverage and quantitative
measurements of proteins have been particularly instrumental to characterize proteomes and their
modulation during plant development, biotic and abiotic stresses. Label-free quantitative shotgun
approaches are emerging as superior to label-based approaches, such as 2-D gel or isobaric tags for
relative and absolute quantification (iTRAQ), for rapid and cost-effective proteome characterization.
We previously showed that over 2600 unique proteins can be detected and quantitated in cassava
root, which is the largest cassava root proteome coverage reported to date. Our recent studies
suggest that over 5500 unique proteins can be detected and quantitated in cassava leaves. Despite
those achievements, a number of challenges remain ahead. In order to fully exploit the potential of
cassava proteomics, we need to improve detection of low-abundant proteins and post-translational
modifications, to better integrate proteomics datasets with other existing databases and to bring
the benefits of proteomics studies to the field by identifying proteome signatures associated with
improved traits.
Speaker 17
PS17
Songbi Chen
30mn
Proteomic Application in Cassava Breeding
Songbi Chen1, Feifei An1, Wenli Zhu1, Jingjing Xue1, Astride SM
Djabou1, Priscila G Figueiredo1, Luiz JCB Carvalho2, Qing X Li3,
Kaimian Li4
1. Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical
Agricultural Sciences, Danzhou, China; 2. Genetic Resources and Biotechnology,
Embrapa, Brazil; 3. Department of Molecular Biosciences and Bioengineering,
University of Hawaii at Manoa, Honolulu, USA; 4. Institute of Tropical Biosciences
and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou,
China
Proteomics, studying global proteins relevant to expression, structures, functions and activities in
living organisms, is an essential tool to analyze the expression and function of genome. Recently
proteomics has provided important means and new clues for cassava breeding. The present study
simply introduced the proteomics research platform and summarized the application of proteomics
in cassava breeding of varieties with the high photosynthesis efficiency, high starch accumulation,
high content of proteins and carotenoids, and high tolerance to extreme environments. Cassava
postharvest physiological deterioration (PPD) involved in calcium signaling, reactive oxygen species
and programmed cell death would be described in the present study, indicating cassava PPD is a
complex physiological and biochemical process. In addition, proteomics was also used to detect the
effects of RNAi silencing of GBSSI gene on cassava storage roots. Furthermore, the post-translational
modification of proteins and the interaction of protein to protein in combination with cassava whole
genome and transcriptome would be used to determine the biological functions of key protein
groups in differential pathways in cassava growing and development in response to extreme
environments.
Key words: Cassava, Proteomics, Breeding, Variety improvement
Speaker 18
PS18
Leena Tripathi
30mn
Genetic Transformation of Root and Tuber Crops and
Banana
Leena Tripathi1*, Tripathi1, J.N., Manoharan1, R., Kiburiba2, J.,
Tushemereirwe2, W.K., Roderick3, H. and Atkinson3, H. J.
1. International Institute of Tropical Agriculture (IITA), Nairobi, Kenya, 2. National
Agriculture Research Laboratories (NARL), Kampala, Uganda, 3. Centre for Plant
Sciences, University of Leeds, Leeds LS2 9JT, UK
Email: *L.Tripathi@cgiar.org
Food production needs to be increased by 70% in order to feed growing population by 2050. The
future food needs can only be met through harnessing scientific innovations and technologies in
agriculture. Roots, tubers, and bananas (RTB) contribute currently to 14% of global food supply but
are still highly vulnerable to pests, diseases, and drought. It's critical to meet the global challenges of
producing more staple food with less land and water, minimizing losses due to pests and diseases,
improving nutrition, and helping farmers adapt to climate change. Improved variety development
should be at the heart of the new solutions needed to tackle these challenges. RTB crop
improvement is particularly slow and complex due to clonal-propagation that maintains both high
heterozygosity and negative alleles. New pests and diseases are emerging — for example, banana
xanthomonas wilt, fusarium wilt, banana bunchy top disease, cassava brown streak disease - and
rapidly spreading. Genetic engineering along with other conventional technologies can be used to
increase the production of main RTB crops, improve the efficiency of production, reduce the
environmental impact of agriculture, and provide access to food and income for small-scale
farmers. Genetic engineering has proven to be a useful alternative method for the introduction of
new desirable traits and offer numerous advantages to circumvent the natural bottlenecks for
traditional breeding, bypassing the long crossing cycles required in breeding programs. With the
advent of plant biotechnology and the rapid development of gene transfer techniques, the potential
to introduce desirable character traits is no longer restricted to those occurring in close relatives.
However, these applications require efficient plant transformation protocols. “Genetic
Transformation Platform” has been established at International Institute of Tropical Agriculture
(IITA) and transgenic technologies are being used in collaboration with different national and
international partners for the improvement of banana and plantain (Musa sp.), cassava (Manihot
esculenta) and yam (Dioscorea sp.). There are various GM products for RTB crops under
development such as banana varieties resistance to xanthomonas wilt disease and nematodes.
Products can be available to farmers in 5-8 years. Such resistant varieties would boost the available
arsenal to fight disease epidemic and save livelihoods in Africa. This paper will present transgenic
research for improvement of RTB crops for disease and pest resistance.
Speaker 19
PS19
Luis Becerra
30mn
Applying “omics” tools to RTB germplasm, unravels
new avenues for its nutritional and environmental
resilience improvement and understanding of
its dissemination patterns
Becerra Lopez-Lavalle, Luis Augusto
International Center for Tropical Agriculture, Cali, Colombia
Email: L.A.Becerra@CGIAR.ORG
Strategic investment in omics research for banana/plantain, cassava, potato, sweet-potato and yams
is advancing rapidly in many fronts. The various omics approaches in RTBs hold much promise, but
await further refinement before they ready to deliver on robust solutions to accelerate the pace RTB
varieties, with improved productivity, nutrition, disease and pest resistance, are deployed in
environments suffering extreme climatic shifts. There is no questions that omics can provide
extremely useful information, some of which cannot be obtained by undertaking traditional
germplasm evaluation either for conservation or breeding.
A step forward in this direction has been the genome-wide association studies (GWAS) undertaken
by banana and cassava to elucidate the genetic architectures of complex domestication syndromes
such as seedless fruits or roots with high cyanide content, respectively. This push to augment
existing observational studies with additional layers of molecular information has resulted in highdimensional data matrices leading to the emergence of research in integrative systems biology for
these crops. Using SNP genetic markers and principles of genomic breeding values, genomic
selection (GS) was successfully implemented with some hands-on experience using an important
cassava disease for Africa (i.e. cassava mosaic disease).
Similarly, metabolomics profiling on all RTBs is allowing to characterize biological networks, as well
as, explore the corresponding conceptual and analytical challenges behind them. Metabolomics
should prompt a re-examination of conventional phenotypic measures where heterogeneous or
correlated phenotypes can be fine-mapped. The metabolomics approach has allowed unravel the
gene networks responsible of drought tolerance in potato, and the potential mechanisms for insect
resistance in cassava. Equally important is the potential of using metabolite profiling for early
selection of high quality banana fruits using biomarkers on the leaves. For crops like yams a game
changer traits are to be exploited as a potential cash crop initiative (i.e. steroids).
Speaker 20
PS20
Jean-Luc Janninck
30mn
Next Generation Cassava Breeding: Initial Estimates of
Response to Genomic Selection for Clonally Propagated
Crops
Jean-Luc Jannink jeanluc.work@gmail.com,
USDA-ARS and Cornell University, New-York, USA
Jean-Luc Jannink1,2, Marnin D. Wolfe1, Ismail Y. Rabbi3, Chiedozie Egesi4,
Robert Kawuki5, Peter Kulakow3, NEXTGEN cassava project6
1. Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell Univ., Ithaca, NY, USA
2. USDA-ARS, R.W. Holley Center for Agriculture and Health, Ithaca, NY, USA
3. International Institute for Tropical Agriculture (IITA), Ibadan, Oyo, Nigeria
4. National Root Crops Research Institute (NRCRI), Umudike, Umuahia, Nigeria
5. National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
6. Hale Tufan, Project Manager, International Programs, College of Agriculture and Life Sciences, Cornell
University, Ithaca, NY, USA, www.nextgencassava.org
Genomic selection (GS) seeks to increase gain from selection by accelerating the breeding cycle
using predictions of performance rather than extensive evaluation. The GS methods were primarily
developed for livestock that, like many clonally propagated crops, are outcrossed. An important
difference, however, is clonal propagation, which increases the per generation mutation rate and
therefore may increase non-additive components of genetic variation. For the past three years, the
NEXTGEN Cassava project has been implementing genomic selection by collaboration between IITA,
NRCRI, NaCRRI, and Cornell University. The IITA breeding program has initially adopted a one-year
breeding cycle for cassava that has enabled us to complete three cycles of selection. The progeny of
two cycles have been clonally evaluated in breeding trials, and data presented here is from those
trials rather than from rigorous evaluation trials that are not yet complete. We will pay particular
attention to whether genomic data improve performance prediction accuracy over what would be
possible using pedigree data. Two aspects can be considered, estimation of relationships among
families, and prediction within families. These analyses will be discussed from the perspective of a
framework for cassava improvement that seeks incremental population improvement.