Why the past could help unlock grape’s future

Lead author Sean Myles - who until June was undertaking his post-doctorate at the Institute for Genomic Diversity, Cornell University, in New York - says by understanding the domestication and breeding history of a species, we become better informed on how to manage that species in the future.  
Genetic work, such as his, allows scientists and industry to gain an understanding of how much variation there is in breeding programs, whether genetic variation from other wild species can or should be considered and what cultivars to not cross together.  
'We are also beginning to relate specific changes in the DNA to specific traits like berry colour, berry size, cluster density and disease resistance,' Myles said.
'Understanding the structure of the population is essential in making sure that these associations between DNA variants and traits are robust and meaningful.'

The origins

Funded by the US Department of Agriculture (USDA), the grape genetic project's chief aim was to characterise the department's grape germplasm collection, which is one of the most diverse and extensive collections of grapes in the world. It is located in Davis, California.  
'The USDA has a strong interest in characterising all of its germplasm collections on a genetic level because this information is useful in determining what germplasm to keep, what to discard and how to better manage the collection,' he said. 'It is also crucial information for the breeding process: genetic markers can be used to determine which two cultivars should be crossed together and they can also be used to know which offspring from the cross should be kept and which discarded.'  
Myles says in the case of long-lived woody perennials, such as the grape, 'marker-assisted breeding' (MAB) can significantly accelerate the breeding process by saving money and time.  
It means offspring from a cross can be planted in a greenhouse and, if necessary, eliminated at the seedling stage, based on genetic profiles.  
'Sequencing the DNA of the offspring is cheap compared with planting them out in experimental vineyards and evaluating them, so selecting offspring based on DNA markers, rather than measuring traits, is time and cost-effective,' he said.  
However, more work and greater understanding among research institutions is needed to learn how to efficiently and cost-effectively collect lots of genetic data from many samples - which is why the grape genomics project was born. Ultimately, the grape project was a pilot study initiated by the USDA to see how well new technologies work, such as next-generation DNA sequencing and custom genotyping microarrays to assay variation across a large number of cultivars. The added bonus from such research was that Myles and his colleagues demonstrated that the insights gained from doing so are crucial for making decisions about how to move forward with breeding programs and maintaining diversity.

Genetic potential

The research presents one of the most comprehensive studies of genetic variation in the domesticated grape, Vitis vinifera, and its wild ancestor, Vitis sylvestris, completed to date.  
Their results, which are also supported by recent archaeological data, reveal the grape was domesticated in the Near East. From there, the domesticated grape was brought into Western Europe and mixed with local wild grape varieties.
'In this sense, some of the most popular western European cultivars can be considered 'hybrids',' Myles says, but admits more research is needed to test the hypothesis and determine which varieties, such as Merlot or Riesling, may find a cross-parentage with wild Vitis sylvestris.
More surprising, however, was the discovery that many of the current domesticated grape varieties used for wine and table production are closely related.
'The degree of this relatedness is astounding. About 75 per cent of the 600-plus cultivars we examined had at least one first degree relative (i.e. a sibling or parent-offspring relationship) with another cultivar.'  
It means despite thousands of years as a domesticated crop, the genetic make-up of the grape has barely changed.
Myles describes it as 'no strong domestication bottleneck'. It means the domesticated grape has much the same genetic diversity present in it as its wild ancestors.
'So, the result appears to many as a contradiction. The grapes we use today are all highly related to each other, but they are incredibly different and capture much of the diversity that is present in the wild,' he said. 'We believe the widespread use of vegetative propagation explains this apparent contradiction.  
'We have been propagating vines for several hundreds, or likely thousands, of years which means cultivars can remain unchanged over centuries. A few crosses are made here and there over millennia and elite cultivars are kept and further propagated.'
It means the grape has experienced a reduced number of generations since domestication and the genomes of elite cultivars remain virtually unchanged.
Myles says the implications of relying heavily on vegetative propagation instead of making new crosses means grapes' 'genetic space' has been unexplored.
Genetic space, he says, is the unique genetic combinations that can be generated from making large numbers of crosses between diverse cultivars.
This method of vegetative propagation, however, has had - and will continue to have - some very serious side effects.
'It means many of today's most popular cultivars are sitting ducks for pathogens - they have remained essentially unchanged genetically for hundreds of years,' he said.  
'Thus, while pathogens evolve new ways of attacking vines, we treat them with chemicals.
'Instead, what we should be doing is shuffling up the grape genomes by creating new cultivars that may contain desirable characteristics for the wine and tablegrape industries, while also possessing resistance to evolving pathogens.
'The grape is, therefore, hardly domesticated and we've done a poor job of breeding it.'
Myles is confident the real results of the research are that the 'best' is yet to come.
'People think that Pinot or Cabernet are the 'ideal' cultivars at the genetic level, but this is very unlikely,' he said.
'We've explored only a very small fraction of the potential cultivars. The 'best' grape is out there, but it will be a shuffled combination of the genomes of the grapes we are currently using.'
Vegetative propagation has, Myles says, found its supporters in the grape industry because it allows for consistency in viticulture and winemaking.
'They can grow thousands of genetically identical vines for hundreds of years,' he said.
'It eliminates having to deal with genetic variation and allows winemakers to concentrate on optimising methods for making the best possible wine from the grapes that come in each year.'
But, Myles says it's a method that's become a double-edged sword.
'It allowed fantastic wines to be produced, but it also resulted in a limited exploration of the grape's potential.  
'It is costly and time-consuming to breed new grapes. But, if a group of people were to commit to it and make thousands of crosses and evaluate all of the resulting new cultivars, it is possible, if not likely, that we could end up with grapes that are of superior quality and require less chemical input than the top commercial varieties we rely on now.'  
However funding for such a project could be a problem, Myles says, as the wine industry appears convinced that consumers are not interested in new cultivars.  
'We're told consumers want to see the words 'Merlot' or 'Cabernet Sauvignon' on the bottle. That's unfortunate for the grape's future genetic health.'

The next step
Myles believes 'New World' wine regions in the US, Canada and Australia will lead the way in grape breeding developments.
'The wine industries in north-eastern USA and Canada, which rely on hybrid varieties often generated in new breeding programs, are examples of forward-thinking groups of people.  
'There is a tremendous amount of progress to be made in grape breeding and it appears to me that it is these 'marginal' regions that are really leading the way.'
In June, Myles began a new career position as Canada research chairman for Agricultural Genetic Diversity, at the Nova Scotia Agricultural College. He's also swapped research focusses, from grapes to apples. The research project aims to sequence the DNA of a wide range of apple breeds and measure hundreds of traits (i.e. apple size, sweetness, acidity and disease resistance)

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