Genomic project discovers new tomato genes

Previously unknown genes, including some for flavour, were missing from the original genome map done in 2012

If you think that store-bought tomatoes lack flavor and sweetness, you’re not alone. It’s been a complaint of consumers for years.

But now, scientists at the U.S. Department of Agriculture’s Agricultural Research Service may have found the solution by developing the tomato pan-genome.

A genome is the reference map for an organism’s genes and what those genes do. A genome profiles a single variety of a plant or a single species of animal. However, the tomato pan-genome includes all the genes from 725 different cultivated and closely related wild tomatoes.

The study revealed 4,873 unknown genes — including genes for flavour — that were absent from the original genome reference.

Tomatoes originated in the Andean region of South America. They have undergone hundreds of years of domestication and the breeding of so many cultivars with physical and metabolic variations has enhanced yield, shelf life, disease resistance, and stress tolerance. But it has resulted in severe genetic bottlenecks with today’s tomatoes having a narrow genetic base.

“The pan-genome effort was driven by a desire to capture what was missed in sequencing a single reference genome,” said molecular biologist James Giovannoni with the ARS Plant, Soil and Nutrition Research Laboratory in Ithaca, New York.

The tomato genome was sequenced in 2012 by an international consortium. That identified a large number of genes, but it led to the loss of some of the genes’ underlying important variations. Pan-genome, however, is a composite genome from sequencing more than 700 tomato varieties, including wild relatives, early domesticates, heirloom types and modern varieties.

“We are interested in fruit ripening; how it is controlled genetically and how it brings about desirable flavour and nutrient characteristics of the fruit,” said Giovannoni. “Tomato is considered a ‘model’ system for fruit biology due to a number of features that make it easy to work with. We assumed that important genes associated with ripening and quality would be found as these characteristics vary so much among varieties and gene variation must underlie some of this. We did not specifically expect to identify flavour genes nor those that influence flavour via aroma, as was the case, but we did hope to find interesting fruit quality associated genes.”

Giovannoni said the reference tomato genome revealed 35,000 genes. The tomato is highly inbred, so they anticipated finding less novelty. In addition, the domesticated tomato is somewhat narrow in terms of what germplasm has been used in breeding. Much of what has been bred until recently reflected the relatively small number of varieties brought back to Europe by the Spanish in the 1500s.

“We did not know what to expect but an increase of 15 percent (some 5,000 new genes for a 35,000 gene reference) was not surprising,” he said.

He said the classes of genes that emerged would be valuable to breeders.

“The most prevalent class of novel genes are potentially related to disease resistance,” he said.

More research is necessary to be sure but this group of genes could become very helpful in reducing crop loss, cost of pesticides and other disease issues, he said.

He said at least 12 wild tomato species are interfertile and the modern tomato (Solanum lycopersicum) resulted from the domestication of one of them (Solanum pimpinellifolium), which was the only red-fruited wild species. They served as the basis for much tomato breeding until, in the mid 1900s, breeders revisited the wild species in search of genetic resistance to tomato diseases.

“(Now) breeders can use the pan-genome as a resource in determining what additional varieties to test for certain traits and the genes that underlie them, which could be easily selected using modern molecular breeding,” he said.

The researchers focused on finding genes absent from the reference genome but prevalent in the additional genes analyzed. One that is relatively rare in modern tomatoes is a variant version of TomLOXc. This gene breaks down fats into compounds that are volatile (gaseous) with aromas influencing flavours.

“We showed that the presence of this gene variant also results in the conversion of carotenoids into aroma compounds that influence flavour,” he said. “The enzyme encoded by this gene likely does not metabolize carotenoids directly. Rather, we suspect the intermediates of lipid (fat) metabolism act on the carotenoids to convert them to the volatile apocarotenoids. Interestingly, this gene is prevalent in wild tomatoes but nearly absent in older varieties and likely unintentionally lost during breeding when focusing on other traits like yield, disease resistance and shelf life. But it seems to be making a resurgence in more modern varieties roughly in parallel with the timing of more interest in flavour by consumers.”

He said that knowing the gene that underlies a trait makes it easier to breed for because breeders can use molecular diagnostics to select for the gene.

Why the desired qualities of sweetness and flavour were lost in the first place was more by accident than design in breeders’ pursuit of shelf life and firmness to meet supply chain demands. In addition, that desirable gene may have been linked to others with undesirable effects related to plant performance, yield or characteristics.

The pan-genome research led by Giovannoni and co-researcher bioinformatics scientist Zhangjun Fei with the Boyce Thompson Institute was published in Nature Genetics.

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