WSU, international researchers, publish apple genome

by Brian Charles Clark, College of Agricultural, Human, and Natural Resource Sciences

PULLMAN – An international team of scientists from Italy, France, New Zealand, Belgium and the USA have published a draft sequence of the domestic apple genome in the current issue of Nature Genetics.

The availability of a genome sequence for the apple will allow scientists to more rapidly identify which genes provide desirable characteristics to the fruit and which genes and gene variants provide disease or drought resistance to the plant. This information can be used to rapidly improve the plants through more informed selective breeding.

An organism’s genome is the total of all its genetic information, including genes. Genes carry information that determines, among other things, a plant’s appearance, health, productivity and color and taste of the fruit.

All in the family

The domestic apple is the main fruit crop of the world’s temperate regions. It is a member of the plant family Rosaceae that includes many other economically important species, including cherry, pear, peach, apricot, strawberry, and rose, to name just a few.

Washington state accounts for approximately 60 percent of total apple production in the U.S. and Rosaceae fruit production is a multibillion dollar industry in the state. Washington state scientists played an important role in the project.

WSU and golden delicious

Led by WSU horticultural genomicist Amit Dhingra, the Washington-based team sequenced and analyzed a unique version of the genome of the golden delicious apple in which all duplicated chromosomes are genetically identical. This information was used to validate the sequence of the more complicated “heterozygous” golden delicious apple (in which duplicated chromosomes are not identical).

Getting specific

“Before genome sequencing, the best we could do was correlate traits with genes. Now we can point to a specific gene and say, ‘This is the one; this gene is responsible for this trait’. That trait of interest might be, for instance, a disease, which is why sequencing the human genome was such an important milestone. Or the trait might be for something desirable, like flavor in a piece of fruit. We are already working on finding physiological solutions to issues like bitter pit in current apple varieties with the gene-based information available to us and lay a foundation for improved varieties in the future through generation of sports (mutations) and breeding,” Dhingra said.

WSU-UW, medical and horticultural

The Washington state contribution to the sequencing work was a unique collaboration between the cross-state Apple Cup rivals of WSU and the University of Washington.

Microbiologist Roger Bumgarner’s lab at the University of Washington provided the initial sequencing expertise and capability to the project, which was later complemented and replaced by sequencing expertise in the Dhingra genomics lab, who obtained the same DNA sequencing instrument used in Bumgarner’s lab.

“UW is a world leader in medical research and WSU is a world leader in agricultural research,” said Bumgarner. “Technological advancements and techniques initially used to study medically important genomes and problems can be rapidly applied to genomes and problems of agricultural importance. We both had something to contribute and to learn from one another. I think there are many more opportunities for such collaborations to develop in the coming years.”

Comparing fruit genomes

After the sequencing was completed, WSU computational biologist Ananth Kalyanaraman contributed to the analysis by comparing the apple genome with that of pear, peach and grape to identify the differences and commonalities that exist between these fruit crops.

Origin question settled

While the apple genome provides a valuable resource for future research, one pressing question answered by the international team’s paper in Nature Genetics was one of origin.

Scientists have long wanted to know—and have for years argued vehemently about—the ancestor of the modern domesticated apple. The question is now settled: Malus sieversii, native to the mountains of southern Kazakhstan, is the apple’s wild ancestor. Now that that question is settled, scientists will begin using the apple genome to help breed apples with desirable new traits, including disease resistance and, potentially, increased health-benefitting qualities.

Dan Bernardo, dean of the WSU College of Agricultural, Human, and Natural Resource Sciences, said, “The Washington apple is an icon of quality around the globe. This is a natural home for the advanced science necessary to map the tree fruit genome and actively study how it functions.”

Defining differences

“Having the apple genome sequence will greatly accelerate our ability to define the differences between apple cultivars at the genetic level,” said Kate Evans, an apple breeder based at the WSU Tree Fruit Research and Extension Center. “This will allow us to exploit these differences and target areas of diversity to incorporate into the breeding program, resulting in improved cultivars for the consumers that are also better suited for long-term, sustainable production.”

Desireable traits

“The sequencing of the apple genome and its publication provides a tool for researchers worldwide to better understand the relationship between apple genes and their expression. This is a first step in helping the WSU genetics, genomics and breeding team to identify desirable traits that could be incorporated into new varieties, including fruit quality desired by consumer and insect and disease resistance that would reduce dependence on pesticides,” said Jay Brunner, director of the WSU Tree Fruit Research and Extension Center in Wenatchee.

Vertical team strength

Horticultural geneticist Cameron Peace, based at WSU’s Pullman campus in the department of horticulture and landscape architecture, pointed out that “Our strength at WSU is a vertically integrated team,” which includes:

  • generation and analysis of this vital sequence (Dhingra)
  • translation into accessible data (Main)
  • utile breeding tools (Peace)
  • crop improvement by breeding (Evans and Oraguzie)
  • production of improved trees and apples (Washington apple industry)

“Our pipeline of genomics, genetics and breeding at WSU is revolutionizing the efficiency and speed at which genetically superior cultivars are developed and adopted by industry,” Peace said.

Publication appreciated

Jim McFerson, manager of the Washington Tree Fruit Research Commission, said of the publication of the genome sequence, “We love it! We think it’s great. We’re investing in the future: that’s been the intent of the Research Commission and its collaboration with WSU all along. With the team at WSU and their collaborators, we are now able to take this basic information and develop what we really want: cultivars specific to growing conditions in Washington, and fruit that delights consumers.

“This publication is yet another indication of the leadership shown by Dr. Dhingra, WSU faculty, and the administration of the WSU College of Agricultural, Human, and Natural Resource Sciences in identifying and achieving high-priority research objectives,” McFerson said.

Ralph Cavalieri, associate dean and director of the WSU Agricultural Research Center, agreed. “This publication is an appropriate recognition of the vision that led to the apple genome project. I am very pleased that WSU is part of the world-leading team that made this happen. I am confident that the results will lead to improved varieties for our producers and enhanced scientific understanding of many aspects of the apple from production through postharvest.”

Cherry breeder Nnadozie Oraguzie, based at the WSU Irrigated Agriculture Research and Extension Center in Prosser, Wash., said, “The publication of the apple genome sequence is a welcome development and speaks to the rapid research advancements in tree-fruit crops. The genome sequence data provides the blueprint for genes that underlie many horticultural traits. Research efforts can now be directed towards mining the sequence data to identify genes relevant to traits that breeders are interested in and characterizing them to understand their function and then identify variants that are linked to traits of interest. This will facilitate marker-assisted breeding, or DNA-informed breeding, to improve breeding efficiency and cost effectiveness. The quicker delivery of new high quality cultivars with consumer appeal would boost the profitability of the tree fruit industry.”

In collaboration with Nnadozie Oraguzie, Kate Evans and several other international collaborators from Italy, Chile and France, Dhingra and his colleagues are also leading the sequencing of the sweet cherry and pear genomes to directly benefit breeding efforts in these crops.

“This sort of DNA information can be used to inform breeding,” McFerson said. “We don’t expect a quick fix, but our long-term research investment strategy has been to invest in knowledge products.”

Cameron Peace agreed, but pointed out that, “Wonderful opportunities also exist in more immediate applications. We will use the blueprint to understand the genetic basis of existing and new cultivar performance – such as why some cultivars taste great out of storage and others are an embarrassment. This knowledge would allow management systems to be tailored to genetic performance categories rather than being painstakingly determined for each cultivar individually. We are vigorously pursuing this avenue also.”

Genome available online

The apple genome is available digitally on Dhingra’s Genomics Lab website as well as the Tree Fruit Genome Database Resources website, the online Rosaceae family genomic database accessed by scientists millions of times per year. Housed on WSU servers, the Tree Fruit Genome Database is managed by Doreen Main, a bioinformaticist based in Pullman in the department of horticulture and landscape architecture. Main recently finished a decade-long collaboration that resulted in the sequencing of the genome of peach.

“The integration of this apple genome sequence data with other peach and strawberry genome sequence data will maximize the utility of this data to the world-wide plant research community and further enhance WSU’s reputation as a leader in plant science,” said Main.

“Bioinformatic prediction of the function of the genes deciphered from this sequence will speed up development of functional markers that we can use for innovative crop improvement through apple and other tree-fruit breeding programs,” said Main. “Pear, sweet cherry and raspberry are some other Washington fruit crops closely related to apples, so the benefits of this work will also accrue to improvement in those commodities.”

Platform for interdisciplinary training

The sequencing project has also created a platform for interdisciplinary training of graduate and undergraduate students. “The genome discovery project is serving as an excellent platform to expose computer science students to new frontiers in biology, provide interdisciplinary training, and eventually help in the development and application of novel computational tools for an important problem in biology,” said assistant professor of computer science and project collaborator Ananth Kalyanaraman.

“The sequencing project continues, as it’s an iterative process that results in ever-greater resolution,” said Dhingra. “And that means we can continue to train the next generation of scientists using cutting-edge technology. We’re fortunate in that we’ve received funding for graduate students to train in this area through the National Institutes of Health Biotechnology Training Program, as well as scholarship funding through the Achievement Rewards for College Scientists Foundation. So far, we’ve graduated two students trained in this area while five more are continuing work in my lab.”

The work is the result of collaboration between 18 research institutions. The apple genome project is supported by funding from the Autonomous Province of Trento, Italy and the New Zealand Foundation for Research Science and Technology. In the Dhingra lab, it was supported by a National Research Initiative competitive grant from the USDA National Institute of Food and Agriculture, the WSU department of horticulture and landscape architecture, the Agriculture Research Center at WSU, the Washington Tree Fruit Research Commission.