Supermarket tomatoes of the future could be tastier thanks to rare gene

Flavour lost in supermarket tomatoes in a bid to make the fruiting plants bigger and fresher for longer could soon be restored, thanks to the discovery of a new gene.  

Scientists mapped the genomes of 725 cultivated tomatoes and their wild relatives to make the discovery.

They found 4,873 new genes and identified a rare version of a gene called TomLoxC that can make tomatoes tastier.

Dr Clifford Weil, programme director of the National Science Foundation’s Plant Genome Research Program, which supported the work said: ‘How many times do you hear someone say that tomatoes from the store just don’t quite measure up to heirloom varieties?

‘This study gets to why that might be the case and shows that better tasting tomatoes appear to be on their way back.’

Professor Dr Zhangjun Fei from the Boyce Thompson Institute (BRTI) in Ithaca, New York state, said: ‘During the domestication and improvement of the tomato, people mostly focused on traits that would increase production, like fruit size and shelf-life so some genes involved in other important fruit quality traits and stress tolerance were lost during this process.’

TomLoxC is present in 91.2 per cent of wild tomatoes but only 2.2 per cent of older domesticated tomatoes.

Professor James Giovannoni, a BTI faculty member and USDA scientist added: ‘The rare version of TomLoxC now has a frequency of seven per cent in modern tomato varieties, so clearly the breeders have started selecting for it, probably as they have focused more on flavour in the recent decades.’

And the study discovered a new role for the TomLoxC gene.

Professor Giovannoni added: ‘TomLoxC appears, based on its sequence, to be involved in producing compounds from fats

‘We found it also produces flavour compounds from carotenoids, which are the pigments that make a tomato red.

‘So it had an additional function beyond what we expected, and an outcome that is interesting to people who enjoy eating flavourful tomatoes.’

Another trait lost was disease resistance. 

The genes involved in defence responses to different pathogens were the most common group of genes that were missing in the domesticated varieties of tomato.

Professor Giovannoni said: ‘These new genes could enable plant breeders to develop elite varieties of tomatoes that have genetic resistance to diseases that we currently address by treating the plants with pesticides or other cost-intensive and environmentally unfriendly measures.’

The first tomato genome sequence was a large modern variety published in 2012, revealing approximately 35,000 genes and facilitating crop improvement efforts.

Since then, several hundred additional tomato genotypes have been sequenced.

The new study was the first to mine all of these genome sequences – as well as another 166 new sequences generated by the researchers – to hunt for genes that were absent from the reference genome.

The tomato pan-genome has created a new resource for growers to improve tomatoes.

While cultivated tomatoes have a wide range of physical and metabolic variation, there have been several severe bottlenecks during its domestication and breeding meaning they have a narrow genetic base.

The pan-genome helps identify what additional genes beyond the reference might be available for crop breeding and improvement.

Professor Fei added: ‘The pan-genome essentially provides a reservoir of additional genes not present in the reference genome.

‘Breeders can explore the pan-genome for genes of interest, and potentially select for them as they do further breeding to improve their tomatoes.’

The full findings of the study were published in the journal Nature Genetics.

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