Studying metabolites for faster, better plant breeding

Studying metabolites for faster, better plant breeding

Metabolites are the small molecules produced by living cells. Identifying the unique metabolic signature of plant tissues can help plant breeders quickly identify the desired traits in crop varieties. An exciting partnership with Royal Holloway University of London (RHUL) is conducting groundbreaking studies of the metabolites of cassava, potato, yams, sweetpotato, and bananas.

Plants produce thousands of small chemical compounds known as metabolites. Like a DNA fingerprint, which offers a portrait of a plant’s genes and thus what it is capable of doing, a survey of the metabolites in a specific tissue, such as the leaves, can tell us what that tissue is doing, how it is responding to its changing environment and what might be happening in the roots or elsewhere in the plant.

Metabolites are the end result of genes switching on and off and directing all the complex workings of the cell. As a result, metabolomics (the study of the metabolites) offers insights into important genetic questions, fast-tracking through the layers of cellular regulation to deliver a functional printout of the genome. That is why RTB has invested in metabolomics, across all our major crops, working closely with RHUL. This long-term partnership that began in 2012 is now attracting significant international funding, and developing technologies that will soon be transferred to partners in other RTB flagship programs.

RHUL and RTB established protocols to extract and analyze plant metabolites, especially in young plants, to see if they would be good proxies for products in the mature plants – the roots, tubers and bananas. This remarkable progress has been documented in six publications, customized metabolite libraries and a database of the metabolomes of key crops produced over the last two years.

The analysis of the metabolites in leaves and tubers in different yam species highlighted the potential for predicting tuber composition from leaf profiles. In cassava, higher amylose (starch) content in the roots is indicated by particular leaf metabolites.

Leaf metabolites that are associated with high amylose are one example of a biomarker, something relatively easy to detect or measure that predicts the level of an important trait that may be more difficult to assay. Identifying these metabolites can help breeders to rapidly select improved crop varieties.

Michael Friedmann, science officer with RTB, sees great potential. Breeders can use metabolomics to enhance the selection of parental lines and offspring that have unique chemical features, which make them resilient to climate change, or more resistant to pests and diseases, or make them more nutritious.

A study of potatoes revealed nine metabolites that seem to be linked to plant responses to drought, suggesting probable pathways involved. Previous studies have shown these metabolites interfere with the ability of drought-tolerant plants to retain water from the soil or antioxidant mechanisms to protect from damage. In addition, these metabolites can be monitored by high-throughput techniques such as near-infrared spectroscopy (NIRS), thus allowing for many genotypes to be screened to study the metabolites’ functional role in large genetic studies and to identify linked molecular markers. Therefore, future studies will enhance the discovery of drought-tolerant potato lines.

In cassava, research identified the metabolomes of one line that were resistant to thrips and another resistant to whitefly pests. For example, the cassava line susceptible to thrips had higher levels of the metabolites free catechin/epicatechin, which could indicate lower condensed tannin levels, thought to provide resistance to the pest. Likewise, disease-resistant banana lines also had specific metabolomes, with the line Calcutta 4, a parent usually used in crosses to confer resistance to various diseases, showing higher levels of  the metabolites rutin, chlorogenic acid and caffeoyl-malate, which could be related to its resistance traits. The metabolomics study on the mechanisms associated with whitefly resistance in cassava suggested a strategy based on reinforcement of cell walls, with more lignification in the resistant line. Identifying such metabolites will make it easier for breeders to search through many more young plants to spot potential winners.

Farmers weeding their cassava fields in Uganda. S. Fernandes (RTB)
The RTB scientific community strategically invested to build and integrate metabolomics. Today metabolomics is allowing researchers to look at natural variation while opening the possibility of faster trait discovery. Current work at the International Center for Tropical Agriculture (CIAT) elucidating the mechanism of whitefly resistance is a clear example of its potential, said Luis Augusto Becerra RTB, FP1 leader.

An important goal for breeders is to select for more nutritious crops, while ensuring that people will like and adopt the new varieties. Many metabolites are involved in the taste and smell of foods. A metabolomics study was linked to a sensory study in potato, that addressed various quality parameters such as potato flavor intensity, sweetness, savoriness, sourness, bitterness and mealiness, comparing breeding lines, landraces and wild potatoes. The metabolomic profiling identified 77 metabolites and showed differences between the different potato types. For example, breeding lines showed less starch degradation, thus sugars were released during cooking -- an important trait in breeding programs. The associations between metabolites and sensory properties are still being analyzed. Consequently, this work will provide guidelines for which metabolites to screen for after harvest, cold storage and cooking for product quality. Likewise, another study in sweetpotato showed that breeders can select even more nutritious sweetpotatoes by looking beyond the orange color, which is associated with pro-vitamin A content. Some carotenoids, such as mutachrome, supply less pro-vitamin A, while still producing an orange sweetpotato. Metabolomics gives sweetpotato  breeders a robust way to decide which varieties will deliver the most vitamin A.

Metabolomics as a technology will be key in quality trait assessment, said Paul Fraser of Royal Holloway - University of London. In combination with similar, cutting edge technologies and breeding populations it gives us a way to identify and validate alleles of interest.

For now, metabolomics work requires expensive laboratory equipment and trained staff, which means that the partnership with RHUL will continue to be important to breeders. However, equipment is becoming cheaper and RHUL is already training staff in partner countries; the hope is that in-country metabolomics centers will soon be available to local breeding programs.

This phase of RTB’s research into metabolomics has already produced important results and points to promising new avenues to explore. It also established a strategic partnership between RTB and the metabolomics research group at RHUL, building on our complementarities. RTB teams have learned to design trials and prepare material for metabolite extractions, and RHUL gained experience working under the constraints of developing countries where some equipment may be lacking. This bodes well for extending and deepening this important partnership.