01 December 2010

What’s on and what's next on the genome mapping forefront?

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Fruits’ and vegetables’ genome maps accelerate the work of connecting agricultural important traits with genes. This may lead to reduced fertilizer use, increased crop disease resistance and higher agricultural yields. New technologies promise cheaper and faster genome map production

Researchers have made great strides towards developing fruit and vegetable breeding tools, but they still have a long way to go, according to Dr. Daniel Sargent at East Malling Research in the UK. He focuses on disease resistance and fruit quality in Rosaceae crops.

“The possibilities are endless,” he said. “You could use a genome sequence to identify genes associated with any trait. We know the genes’ location in, for example, apple, grape and peach. We now have to look at traits within the plants and associate those traits with the available gene sequences. But the sequence of one cultivar, pinot or Golden Delicious, for example, doesn’t tell us the mutations responsible for all traits in all available varieties. We will always have a need for continuing cultivar re-sequencing, for associating traits with genes in mapping populations and for developing molecular markers useable for the breeders,” Daniel Sargent said.

As an example of genome mapping on the forefront Dr. Yves Lespinasse at INRA-INH-University of Angers Joint Research Unit for Genetics and Horticulture in France commented on the apple genome sequence. “This is the first publication for the Rosaceae which includes a lot of fruit species. For now, the peach sequence is already public but not yet formally published. Work is in progress on the strawberry.” He and colleagues are studying vegetables and fruits such as carrot, apple and pear.

It is obviously difficult to say when all known fruits’ and vegetables’ genomes have been mapped, but new technologies may accelerate the process substantially. “With third generation technologies coming to market soon, we may soon be able to sequence our target genome in a short period of time for a small amount of money. The machine will cost less than a hundred thousand dollars. This means genome sequencing will become accessible to almost every lab working on molecular genetics and genomics. If these technologies deliver what they promise we could have genome sequences for great numbers of crop plants within the next five years,” Sargent said.

Mapping projects will offer many possibilities to breeders and consumers. Lespinasse highlighted some of those. “The biggest benefits of mapping fruit genomes are to speed up the process of selecting new varieties, especially for disease and pest resistance, or healthier and tastier fruits. For example, the publication of the apple genome identifies 992 genes, analogs of resistance genes to bioaggressors. This is a very useful reservoir for genetic improvement and breeding.”

Sargent and colleagues can use markers for strawberries to select specific traits. He wishes that genome sequencing will change marker accessibility. “Private breeding programmes have identified specific markers but they will often keep those markers for their own benefit rather than sharing with the community because of marker development cost,” he said. “The genome sequence availability will hopefully reduce the marker development cost and make those markers accessible to more people.”

A drastic decrease in sequencing equipment cost will definitely escalate breeding. Within a few years the work of connecting disease resistance traits with genes will show results through essential agrochemical reduction.
 

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