Tag Archives: bioinformatics

Banana research in Africa: modern breeding techniques, regulatory and biosafety issues

Registration is now open for an advanced course ‘Banana research in Africa: modern breeding techniques, regulatory and biosafety issues‘ from 19 – 30 September 2016, organized by International Plant Biotechnology Outreach (IPBO–VIB/UGent) in collaboration with KULeuven and NARO, and hosted by NARO-Kawanda in Uganda.

Aimed at Africans engaged in banana improvement programs including scientists, regulators and lawyers, the course will provide training in modern breeding techniques, how to collect relevant and reliable data to perform risk analysis, and how to communicate scientific results and goals.

A researcher checks on the health status of banana seedlings in a screenhouse. Photo by IITA

Supported by the International Institute of Tropical Agriculture, the program will give an overview of the most important banana diseases and how to address them through breeding as well as biotechnological approaches.The program continues with an overview of regulatory and risk assessment principles relevant to the African region. Participants will also obtain insights in to the metabolomics of banana, bioinformatics methods and banana processing.

Finally, a two-day workshop will teach participants how to communicate research findings and goals to a non-scientific audience and the public at large. The sessions will be interactive, including group work, presentations and discussions. The program also includes visits to confined field trials and local farmers.

A number of scholarships with support from VLIR-UOS for accommodation and travel expenses are available. The deadline for scholarship applications is 31 May, 2016.

For more information on the course program, registration, scholarship eligibility criteria and application forms, visit the IPBO-VIB/UGent website or contact: sylvie.debuck@vib-ugent.be

Registration for the course closes 30 June, 2016

The CGIAR Research Program on Roots, Tubers and Bananas (RTB) is working in partnership with NARO, IITA and KULeuven on a number of projects, including a banana drought response study with KULeuven which showed that selection for high transpiration efficiency could be used to identify cultivars with better performance during both well-watered and water-stress conditions, thus projecting good yield during both normal and dry years. With IITA and NARO, the program is also working on accelerating banana breeding and improving knowledge on the banana genome.

Bioinformatics alliance with Boyce Thompson Institute for Plant Research to boost yields in roots, tubers and bananas

Boyce Thompson Institute for Plant Research (BTI) is partnering with CGIAR  and its associate centers to create a shared database and bioinformatics platform to help breeders develop improved root, tuber and banana crops. This platform will enable RTB breeders to access and use massive amounts of genotypic and phenotypic data to develop new varieties with precisely targeted traits for disease resistance, higher yields and consumer acceptability.

Graham Thiele, RTB Program Director, visited Cornell last week, at the invitation of Hale Ann Tufan, project manager for the Next Generation Cassava Breeding project (NEXTGEN Cassava). During the visit he met with BTI project leader Lukas Mueller to learn about Mueller’s experience leading a BTI Bioinformatics group and several large genome sequencing projects. Mueller directs the SOL Genomics Network (SGN), an open-source website for genome data of Solanaceae species such as tomato, potato and pepper, and CassavaBase, a database for cassava breeding information. These databases are always expanding, since users can add genetic annotations, phenotypes, and genetic trait mapping data to the sites.

Graham Thiele, Director of the CGIAR Research Program on Roots, Tubers and Bananas and BTI associate professor Lukas Mueller

RTB Director Graham Thiele (left) and BTI associate professor Lukas Mueller

“I was excited to meet Lukas and see what he’s doing,” said Thiele. “There already is excellent collaboration going on and we want to build on this, giving it more coherence and clarity across the different crops and centers involved.” There are plans to adapt the Cassavabase database for other crops, including bananas, sweetpotatoes and yams, to create a suite of similar tools for these clonally propagated crops and increased scope for collaboration with RTB.

NEXTGEN Cassava is led by Cornell’s International Programs, with BTI providing database development, hosting and management; a similar project for sweetpotato also has recently been funded. Mueller said an expanded partnership with RTB would benefit all parties, since BTI could apply its database knowledge to more a broader array of crops, and environments while helping RTB create better breeding outcomes.

Thiele commented, “A lot of end user traits, especially relevant to quality, are not prioritized by breeding programs, yet these are often gender differentiated. We are exploring ways to capture these with Hale Tufan at NEXTGEN Cassava. We’d like to build synergies and collaborate across crops, creating a space to put the whole lot together.”

Though a formal RTB/BTI/Cornell partnership is still in talks, Thiele said that practical conversations are happening now around using Mueller’s work with SGN and Cassavabase to add value without raising costs and to improve collaboration among the CGIAR research centers: the International Potato Center (CIP) which leads the program, Bioversity International, the International Institute for Tropical Agriculture (IITA) and the International Center for Tropical Agriculture (CIAT).

“Databases are expensive,” said Mueller. “Shared databases reduce cost, but the larger field of application allows for adding features that wouldn’t otherwise be available.”

Post originally published on October 1st, 2014 on the Boyce Thompson Institute website

New online tool allows exchange of knowledge on plant gene families

GreenPhylDB is a comparative genomics platform which has been developed since 2006 by Bioversity International with support from CIRAD and Syngenta. The new version 4, which is now available on line, was promoted during the Biocuration Conference held in Canada last April.

Comparative genomics is a field of biological research in which the genomic features of different organisms can be compared to accelerate gene discovery based on their evolutionary relationship with genes of known function in plants. The information generated can then be used eventually by breeders to produce better performing crops.

“Every year, hundreds of gene families are characterized through peer-review publications but their structure and classification is hardly captured by dedicated databases”, explains Valentin Guignon, a Bioinformatics specialist who has been working on GreenPhylDB. “To address this situation, we developed a user-friendly interface allowing customize to either pre-computed protein sequence clusters or to create new ones based on prior knowledge of a given gene family”.

The information can be then shared with collaborators and/or reviewers with a unique URL on the GreenPhyl comparative genomics website. Users can easily register through a registration form or by using an external Open ID account such as GMail or Yahoo!.

Valentin Guignon and fellow Bioversity scientists Alberto Cenci and Mathieu Rouard received a prize for the 3rd best poster when presenting GreenPhylDB at Toronto’s Biocuration Conference last April.

See more on SlideSharehttp://www.slideshare.net/BioversityInternational/exchange-your-knowledge-on-plant-gene-families

Reference:  Guignon V, Cenci A, Rouard M, Exchange your knowledge on plant gene families, Biocuration 2014 (ISB2014), the Seventh International Biocuration Conference, University of Toronto in Toronto, Canada, April 6-9, 2014, poster session.

greenphyl2

 

 

By Véronique Durroux-Malpartida

 

Bioinformatics key to using genetic and metabolite data for breeding

As scientists collaborate on a global effort to map RTB genes and metabolites and link that information to traits, they are increasingly reliant on bioinformatics – the use of computers to organize, analyze and share biological data. The effort requires the creation of web platforms that will allow researchers in different countries to upload, access, and analyze data, and facilitate the use of that information for crop improvement.

The field of bioinformatics is relatively young and rapidly evolving, driven largely by advances in genomics (the use of DNA sequencing to map a species’ genome and document genetic variation). Gene sequencing produces vast amounts of data, which researchers need significant computer power to manage, clean, and assemble before they can even begin to associate it with traits. They then need interactive platforms to share the information with other scientists.

The bioinformatics component of the current RTB genomic research is especially challenging because the genomics are being complimented by metabolomics (the study of the metabolites involved in cellular processes), and data from both areas will be used for phenomics (the study of how genes, the metabolic processes they control and the environment determine phenotype, or traits).

The effort involves vast amounts of data – for example, there are approximately 31,000 genes in cassava, 37,000 in banana and 39,000 in potato, whereas each of those crops may contain as many as 20,000 metabolites. Genetic sequences and metabolite profiles will be completed for between 1,000 and 2,000 different accessions by the end of 2004, data that will then be associated with phenotype information from greenhouses and different field environments.

“Having large amounts of data will allow us to link as much of the genomic and metabolomic information as possible to phenotype,” said Luis Augusto Becerra Lopez-Lavalle, a molecular geneticist at the International Center for Tropical Agriculture (CIAT) and the theme leader for RTB’s theme two (development of improved varieties). “The challenge is that we are generating all this data, but we need to manage it. We need to convert big data into smart data, so that we can translate them into breeding gain. To do that, we need many brains working together.”

One of the principal brains focused on RTB genomic data management is that of Manuel Ruiz, a researcher at the French Agricultural Research Centre for International Development (CIRAD) who is a visiting scientist at CIAT. His team was involved in the first complete sequencing of the banana genome at CIRAD and is supporting the data management side of ongoing gene sequencing and metabolite profiling of different banana varieties.

Manuel RuizOne of Ruiz’s missions at CIAT is to transfer some of the lessons learned from banana to the other RTB crops. He explained that one of his first projects is to develop bioinformatics tools for correlating the metabolite and genetic data being generated for banana.

“The idea is to develop something generic while working on banana that can be used for cassava and other crops,” said Ruiz, adding that for cassava, he will need to collaborate with the Next Generation Cassava Breeding Project, based at Cornell University.

“One of our ideas is to develop platforms to facilitate association studies using information from genes and metabolites. There currently aren’t many tools to do that, so we need to develop some,” he said.

Ruiz helped to develop, and serves as the scientific manager of the South Green bioinformatics platform – a clearinghouse of tools and databases for genomic research in Mediterranean and Southern Hemisphere crops that was created by CIRAD, Bioversity International, The French National Institute for Agricultural Research (INRA), Montpellier SupAgro university and the Institute of Research for Development (IRD).

“We didn’t try to reinvent the wheel, or develop everything ourselves,” Ruiz said of South Green, explaining that they usually tried to adapt existing software. He said that even though metabolic association studies are relatively new, significant progress has been made on crops such as rice. He and Becerra identified advanced research institutions working on rice as potential strategic partners for RTB’s genomic and metabolomic work.

SouthGreen

Ruiz observed that the initial challenges are managing all the data and helping scientists in different parts of the world to access and analyze it. He noted that one big issue is disk storage capacity, since the ongoing genetic sequencing and metabolite profiling are producing terabytes of data. He added that cloud technology could be one solution for helping researchers access data.

“We need high-power capacity for data storage and analysis. We need to use multiple servers with nodes in order to perform many tasks in parallel. We are now more focused on the genetic information, but we have to prepare for the metabolic information that is being generated,” he said.

Once the initial data management issues are resolved, and researchers begin to link genes and metabolites to crop traits, Ruiz will be involved in the development of web platforms to help breeders use that information for crop improvement.

Ruiz observed that the way to deal with all these challenges is to collaborate with scientists at other institutions involved in similar research. He hopes that such collaboration will not only help RTB meet the current bioinformatic challenges, but that the different genomic platforms will eventually all become connected and that the tools developed for one will be shared with the others.

“For bioinformaticians to survive, we need to collaborate,” he said. “We can’t work alone. It’s impossible.”

See also: Bioversity International and CIRAD organized a crash course in banana bioinformatics in November 2013