Genomics are key to improving fruit varieties
Genetic sequencing of peach, which has a relatively small number of genes, is a national research priority.
Genetics and genomics have been buzz words in the tree fruit industry since the Tree Fruit Technology Roadmap named them top priorities five years ago, and they were prominent during the International Fruit Tree Association’s annual conference this year.
Genetics is the study of genes, while genomics refers to the complete genetic makeup of an organism (all its genes). As scientists identify the various genes in an organism and where they’re located, tantalizing possibilities arise in the area of plant breeding. Breeders are talking about developing new fruit varieties or products with the kinds of traits that consumers want and, more critically, that have the potential to return higher profits to producers.
Dr. Amy Iezzoni, cherry breeder at Michigan State University, likens the genes in an organism to names in a city phone book, and the genome to a street map. Sequencing is equivalent to the process of locating names from the phone book on the map. The functions of genes are comparable to the activities of individuals in the city, and functional circuits, which involve many genes, are somewhat like a bus system, she said.
“All these genes are working together in functional circuits, and the power of genomics is it allows us to look at the expression of many genes at one time,” she said. “What we want to do is optimize the circuits that result in the best fruit growth and development.”
Dr. Abahaya Dandekar of the University of California, Davis, said DNA was discovered 50 years ago. DNA is a nucleic acid that contains the genetic instructions for an organism. Genetics and genomics are reverse engineering in that they deconvolute the system to understand the parts, so that this knowledge can be used in breeding. Functional genomics tells how the genome works, what each part does, and how the parts work together.
It took 15 years for scientists from around the world to identify and map all the 30,000 genes in human DNA, a feat that was completed in 2000. The genes of more than 150 organisms, including rice, have been sequenced during the past decade. Some plants have even greater numbers of genes than humans, while some have fewer.
Scientists are hoping to sequence the genome of peach, which has a relatively small genome and probably half as many genes as apple. Pilot projects to begin sequencing peach are under way. Preliminary work suggests that it is technically feasible, but funding to sequence the full genome has not yet been secured.
Peach and apple are in the Rosaceae family of plants, which also includes pears, plums, cherries, strawberries, roses, and almonds. A $4 million national research initiative for rosaceous crops is helping to jump-start research across the country to understand the complex biological processes underlying the traits in those plants.
Dr. Jay Norelli, biotechnologist with the U.S. Department of Agriculture’s research lab at Kearneysville, West Virginia, is developing fireblight-resistant rootstocks through genetic modification. Norelli said fireblight resistance is a complex trait that results from many genes working together.
“Genomics is allowing us to get a much more complete picture of what’s going on,” he said. “It’s more of a systems approach to biology.”
Genomics allows scientists to take more of a global approach and look at all of the genes instead of just one. The technology is getting faster and cheaper. High-power computing allows scientists to look at as many as 150,000 genes at a time and has created a new field of biology called bioinformatics, which is the management and analysis of data, using advanced computer techniques. It is an important part of genomics research because of the vast amount of complex data involved.
Dr. Dorrie Main, bioinformaticist at Washington State University, heads the Web-based Genome Database for Rosaceae, which is an international repository for all genetic information available about the family, including data from peach genetics research from around the world. It’s designed to promote rapid collaboration between researchers, allowing them to compare and contrast various types of data to discover new information.
“Basically, we take the raw data generated by researchers worldwide and try to make sense of it,” Main said.
It’s going to take big money to fund genomics research, Norelli noted, which means that scientists can no longer work independently. “One of the challenges for the research community is learning to work together and pool resources.”
Researchers in apple used to compete for resources with others working in peach or strawberry, for example, he said. “Now, we’re learning to share them. That’s going to be the key to getting the money.”
In March this year, scientists released a white paper, or strategic planning document, called the U.S. Rosaceae Genomics, Genetics, and Breeding Initiative. Key issues are how to improve the quality, shelf life, and safety of fruit, reduce chemical use, reduce production costs, and develop stress-tolerant plants. Addressing those challenges will require an expansion of the genomics, genetics, and germplasm knowledge base for those crops. Sequencing peach is seen as a high priority, and one of the building blocks to reaching other goals, Iezzoni said.
Knowledge about the genetic makeup of rosaceous crops will help scientists develop genetic markers that can be used for marker-assisted selection in traditional breeding programs. Such markers show if potential selections have desirable traits, such as color, size, or crispness or disease-resistance in apples, and speed up the breeding process. The knowledge could also be used to genetically modify plants, though it’s not known how well consumers would accept modified fruits.
Dr. Jim McFerson, manager of the Washington Tree Fruit Research Commission, who was among more than 40 scientists who contributed to the white paper, said this is the first time that scientists working with rosaceous crops have come together to discuss and articulate their research priorities in genomics, genetics, and breeding. He sees it as a continuation of the process that began with the National Tree Fruit Technology Roadmap five years ago.
“It documents our priorities and documents how we intend to achieve them,” he said. “It puts us in the position of working as a community, rather than individual researchers.”