Genetic study shows maturity matters in the development of storage disorders

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This illustration shows patterns of genetic activity in Granny Smith apples during an experiment to understand why some fruits develop superficial scald. The circles represent the genes; blue genes generally showed less activity over storage time, while red genes showed increased activity, according to Stephen Ficklin, professor of computational biology at Washington State University who made this graph as part of his research collaboration with molecular biologist Loren Honaas of the US Department of Agriculture. The flat lines connecting the genes indicate a positive relationship and the zigzag lines show a negative relationship. “Together, the picture paints a picture of a large number of genes interacting with each other with groups of genes increasing in activity and others decreasing,” Ficklin said. “Exploring these changes can help identify clusters of genes working together under experimental conditions. ” (Courtesy of Stephen Ficklin / Washington State University)

How does an apple know how old it is?

It may seem like a frivolous question at first glance, but consider this: Fruit maturity is fundamental to decisions about everything from harvest time to window to market. That’s why researchers at the US Department of Agriculture in Wenatchee, Wash., Want to understand the genetic basis for ripening apples and pears.

“All the apples on the tree know when fall is coming,” said Loren Honaas, USDA molecular biologist. “We know they all know when to prepare to mature, but it happens at different times. What distinguishes an early apple from a late apple? Where is this apple during his lifetime?

These are the types of critical scientific questions that Honaas joined the USDA’s Agricultural Research Service in 2016 to tackle, with his background in an area known as functional genomics.

Functional genomics connects a gene to a trait, but on a large scale, because fruit ripening is a complex process controlled by many genes, Honaas said. By comparing huge datasets of genetic activity (including genes that are translated into proteins) at different stages of fruit maturity, computer models can identify patterns of key genes involved throughout the physiological process.

These models can then provide predictive tools to help the industry make better storage or market decisions, or produce fruits resistant to senescence disorders, said Jim Mattheis, postharvest physiologist responsible for research at the Wenatchee laboratory of the ARS.

“The techniques to do it are very complicated, but the goal is really to provide better tools to the industry,” he said.

On the applied science side of the effort, the researchers aim to see if it is possible to develop an index of apple maturity that could apply to all cultivars, based on the signature of gene activity, and are trying to determine why some Anjou pears need ethylene conditioning to trigger ripening. Both projects are supported by industry through the Washington Tree Fruit Research Commission.

“We’re looking for those things that we can measure that will tell us about the future state of the fruit,” Honaas said, comparing it to a panel of medical tests that can predict a patient’s risk of developing heart disease. “Maturity is linked to so many things, so it’s a good place to start. Will this pear ripen? While waiting for the color on the apples, are we throwing the dice ”on the disorders of senescence?

Loren Honaas joined the Postharvest Physiology Laboratory of the United States Department of Agriculture in 2016 to bring his functional genomics experience to priority industry issues regarding fruit maturity, ripening and storage disorders.  (TJ Mullinax / Bon Fruit Grower)
Loren Honaas joined the Postharvest Physiology Laboratory of the United States Department of Agriculture in 2016 to bring his functional genomics experience to priority industry issues regarding fruit maturity, ripening and storage disorders. (TJ Mullinax / Bon Fruit Grower)

New generation post-harvest prescriptions

The field of post-harvest pome fruit science has come a long way over the decades of his career, Mattheis said, reflecting on the innovations of 1-MCP and controlled atmosphere storage and the subsequent refinement of these tools. .

But these advancements are the result of trial and error: put different cultivars under different oxygen levels and see which one works best, for example. The functional genomics approach now allows researchers to research the underlying mechanisms of maturity and develop tools on this basis.

Let us take the complex problem of Angevin refining. By comparing the genetic activity of many fruits at different stages of maturity, they hope to find now invisible indicators of why some fruits are on the way to ripening well while other seemingly identical pears are not. The industry already understands many of the factors that go into ideal maturation – such as crop load, growing season climate, and harvest maturity – but not why they matter, Mattheis said.

“If we know how this fruit is likely to behave, based on its gene expression signature at this level of maturity, we can look to change the results after harvest,” Mattheis said. “Without this recipe, all fruits are in the same CA diet. We’re really trying to move from a subjective management approach to a much more objective approach.

New genomics tools have ushered in an exciting time for the field of postharvest physiology, he said, accelerating new knowledge on previously unanswered questions.

Genomics

The DNA sequencing revolution now gives researchers the opportunity to see a much bigger picture, said Stephen Ficklin, professor of computational biology at Washington State University, who has partnered with the ‘ARS team.

While the first human genome cost $ 2.7 billion and took over a decade, sequencing an organism can now cost thousands of dollars in just a few weeks, he said. New technology allows DNA sequencing to be used to measure gene activity, which means researchers can explore how genes react differently across apple cultivars, weather conditions and pre-harvest treatments and post-harvest. That’s a lot of data to sift through.

Huiting Zhang sorts Bartlett pear samples by color with a laboratory spectrophotometer to analyze maturation responses at the USDA-ARS facility in Wenatchee, Washington.  Data points join millions more as computer models attempt to determine what genetic activity controls the maturation response.  (TJ Mullinax / Bon Fruit Grower)
Huiting Zhang sorts Bartlett pear samples by color with a laboratory spectrophotometer to analyze maturation responses at the USDA-ARS facility in Wenatchee, Washington. Data points join millions more as computer models attempt to determine what genetic activity controls the maturation response. (TJ Mullinax / Bon Fruit Grower)

“What my group is doing is trying to identify patterns in large datasets to find genes that underlie complex traits,” Ficklin said. “We use statistical models and machine learning models to find patterns in the data. “

An apple has 40,000 genes, Honaas said. Two apples of the same cultivar, picked on different dates, could have thousands of differences in their genetic activity. Most of these differences are irrelevant.

“We’re trying to throw out a lot of data on the problem – many varieties, many picking dates – to try to clean up the noise,” he said. “We keep experimenting to find the same genes that are active in the right place at the right time.”

Honaas compared research to finding small puzzle pieces. Previously, using these pieces was like making a puzzle without the picture. Today’s new technologies that can sequence an entire reference genome for each cultivar should provide a framework, helping to link pieces together faster, he said.

“It’s like when you knock over a rock and sometimes there’s a nice bug. We’re finding these interesting things in the genome, ”Honaas said. “We do the experiments and see which genes appear. “

An example: discovering clues as to why warming up a Granny Smith protects her from superficial burns. Other discoveries to date include biomarkers for pear ripening genes – exciting developments, of course, but much more research is needed to determine how to test these biomarkers quickly and cost effectively so that information on the gene activity may continue to inform decisions regarding fruit handling. •

by Kate Prengaman


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