December 27, 2010

Strawberry, Cacao Genomes Could Lead To Tastier Treats

Teams of international scientists have unlocked the genetic code of the wild strawberry and a certain type of cacao used to make fine chocolate, in a breakthrough that could lead to even more scrumptious versions of the treats.

The work should help breeders develop a new generation of "Ëœsuper strawberries' and rich chocolate after identifying the chemicals responsible for their flavorful aroma and nutritional value.

The wild strawberry is closely related to other crops such as peaches, apples, and raspberries, so its genetic map will also help breeders of these plants to produce new varieties, the researchers said.

"This will accelerate research that will lead to improved crops, particularly commercial strawberries," said Oregon State University plant molecular biologist Todd Mockler, one of the lead researchers.

"It could lead to fruit that resists pests, smells better, tolerates heat, requires less fertilizer, has a longer shelf life, tastes better or has an improved appearance," he said.

Dan Sargent of Britain's Biotechnology and Biological Sciences Research Council (BBSRC) Crop Science Initiative, who participated in the project, said working with strawberries helped simplify the process of unlocking the genome.

"Because farmers have been cross-breeding and hybridizing food crops for centuries to improve traits, they tend to have large complicated genomes, but the wild strawberry's is relatively small so we can get access to all of these useful genes comparatively easily."

Sargent, based at East Malling Research (EMR) in Britain, and colleagues sequenced the wild strawberry genome by breaking it up into millions of short segments, which were then sequenced individually and re-assembled.  Researchers at EMR then pieced together the genome using a map based on other strawberry genomes they had previously studied.

"Historically genomes have been sequenced using a combination of longer and shorter sequences. The shorter sequences are quicker and cheaper to sequence but, like with a jigsaw, reassembling the complete picture is harder with lots of little pieces than with fewer big ones," Sargent said.

"For the first time for a plant this genome was sequenced entirely using short sequences. We were able to assimilate all of these small pieces at EMR because previous strawberry genomes we'd worked on were like the picture on the box that told us what the wild strawberry's chromosomes should look like."

Professor Douglas Kell, Chief Executive of BBSRC, said the research would result in other benefits beyond merely better tasting fruit.

"This project relied on the collective expertise of researchers across five continents, but by making their genome sequence freely available to others, they are ensuring that many more talents can put their data to use. This approach will be essential to helping address global food security by providing people with a varied and nutritious diet," he said.

The scientists, which included more than 70 researchers in five continents, found that the wild strawberry genome has roughly 35,000 genes -- about one and a half times the 20,000 to 25,000 genes that humans carry.  Most of these will also be in cultivated varieties, the researchers said.

"This will accelerate research that will lead to improved crops, particularly commercial strawberries," Mockler said.

"It could lead to fruit that resists pests, smells better, tolerates heat, requires less fertilizer, has a longer shelf life, tastes better or has an improved appearance."

Separately, French researchers reported that they had sequences nearly the entire genome for the Criollo variety of the cacao plant, Theobroma cacao, a tropical tree from which chocolate is made.

The researchers said they had identified roughly 29,000 genes covering 76 percent of the estimated full Theobroma cacao genome. 

The team identified a variety of gene families that may improve cacao trees and fruit either by either enhancing their attributes or providing protection from fungal diseases and insects that effect cacao trees.

"Our analysis of the Criollo genome has uncovered the genetic basis of pathways leading to the most important quality traits of chocolate -- oil, flavonoid and terpene biosynthesis," said Siela Maximova, associate professor of horticulture at Penn State University and a member of the research team.

"It has also led to the discovery of hundreds of genes potentially involved in pathogen resistance, all of which can be used to accelerate the development of elite varieties of cacao in the future."

Because the Criollo trees are self-pollinating, they are generally highly homozygous, possessing two identical forms of each gene, making this particular variety a good choice for accurate genome assembly.

The researchers assembled 84 percent of the genome identifying 28,798 genes that code for proteins. They assigned 88 percent or 23,529 of these protein-coding genes to one of the 10 chromosomes in the Criollo cacao tree. They also looked at microRNAs, short noncoding RNAs that regulate genes, and found that microRNAs in Criollo are likely significant regulators of gene expression.

"Interestingly, only 20 percent of the genome was made up of transposable elements, one of the natural pathways through which genetic sequences change," said Guiltinan.

"They do this by moving around the chromosomes, changing the order of the genetic material. Smaller amounts of transposons than found in other plant species could lead to slower evolution of the chocolate plant, which was shown to have a relatively simple evolutionary history in terms of genome structure."

Guiltinan and his colleagues are interested in specific gene families that could link to specific cocoa qualities or disease resistance. They hope that mapping these gene families will lead to a source of genes directly involved in variations in the plant that are useful for acceleration of plant breeding programs.

The researchers identified two types of disease resistance genes in the Criollo genome, and compared these to previously identified regions on the chromosomes that correlate with disease resistance, or QTLs.  They found that there was indeed a correlation between many the resistance genes' QTL locations.

The researchers suggest that a functional genomics approach, one that looks at what the genes do, is needed to confirm potential disease resistant genes in the Criollo genome.

Hidden in the genome the researchers also found genes that code for the production of cocoa butter, a substance highly prized in chocolate making, confectionary, pharmaceuticals and cosmetics.

Most cocoa beans are already about 50 percent fat.  However, these 84 genes control both the amounts and the quality of the cocoa butter.

Other genes were found that influence the production of flavonoids, natural antioxidants and terpenoids, hormones, pigments and aromas.  Altering the genes for these chemicals might produce chocolate with better flavors, aromas and even healthier chocolate, the researchers said.

About 3.7 million tons of cocoa are produced each year. Most cacao farmers earn about $2 per day, although producers of fine cacao earn more.   The trees are sometimes viewed as an environmentally beneficial crop because they grow best under forest shade, allowing for land rehabilitation and enriched biodiversity.

The study involving the strawberry genome was published Sunday in the journal Nature Genetics.  The cocoa genome research was published in a separate study in the same journal.


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