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.