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When life gives you sour lemons, use genetics to find out why

Anonymous — Thu, 26 Sep 2019 18:29:14 +0000

When life gives you sour lemons, use genetics to find out why Anonymous (not verified) Thu, 09/26/2019 - 11:29 More News SARAH NIGHTINGALE February 26, 2019

A team of researchers, including two from the University of California, Riverside, has identified the genes responsible for the hallmark sour taste of many citrus fruits. Published Tuesday, Feb. 25 in Nature Communications, the research could help plant breeders develop new, sweeter varieties.

Modern citrus varieties have been bred over thousands of years to generate a broad palette of sour and sweet-tasting fruits. Analyses of their pulp reveals that a single chemical element—hydrogen—is largely responsible for the difference between sour and sweet-tasting varieties, which usually have similar sugar content. The pulp from sour fruits contains more hydrogen ions, giving it a lower pH and a tangy taste that is recognized by acid-sensitive cells in our taste buds. Conversely, pulp from sweeter varieties contains fewer hydrogen ions and tastes less acidic.

Ronald Koes and colleagues at the University of Amsterdam in the Netherlands set out to untangle how some citrus varieties wind up with more acidic juice than others, a process that until now has remained a mystery. Their interest stemmed from a previous study showing that higher acidity in purple petunia flowers resulted in more petal pigmentation.

Intrigued by the Faris variety of lemon tree, which produces branches bearing both sweet and sour fruits, and white and purple-tinged flowers, Koes’ team turned to UCR plant scientists Mikeal Roose and Claire Federici. Using the university’s vast Citrus Variety Collection, which preserves over 1,000 living citrus and related fruit varieties, Roose and Federici selected the Faris lemon and 20 other citrus fruits ranging from wincingly sour to sugary sweet for Koes’ team to analyze.

By studying the expression of genes related to those controlling acidity in petunias, Koes’ team identified two citrus genes, CitPH1 and CitPH5, that are highly expressed in sour varieties and weakly expressed in sweet-tasting varieties. The CitPH1 and CitPH5 genes encode transporter proteins that pump hydrogen ions into the vacuole, a large storage compartment inside juice cells, thus increasing their overall acidity.

Next, the team turned its attention to genes that control the levels of CitPH1 and CitPH5 in juice cells. While down-regulation of CitPH1 and CitPH5 in sweeter tasting varieties arose multiple times independently in different varieties, the researchers found that mutations in genes for a handful of transcription factors (proteins that help turn specific genes on and off) were responsible for reduced expression of CitPH1 and CitPH5, and therefore a sweeter taste.

Roose, a professor of genetics in UCR’s College of Natural and Agricultural Sciences, said the findings could help breeders develop better-tasting citrus fruits. However, he said breeding varieties with severe mutations in the transcription factors such as those studied in the “acidless” citrus would be “overkill,” producing sugary citrus fruits with none of their popular acidic kick. Instead, plant scientists should look to target mutations that have a less dramatic effect on the production and activity of transporter proteins.

“By understanding the mechanism acidification of fruit cells, we can now look for related genes that might reduce the expression of CitPH1 and CitPH5 just enough to engineer or select for new, sweeter varieties,” Roose said.

The title of the paper is “Hyperacidification of Citrus fruits by a vacuolar proton-pumping P-ATPase complex.” In addition to Koes, authors at the University of Amsterdam are Pamela Strazzer, Cornelis Spelt, Shuangjiang Li, Mattijs Bliek, and Francesca Quattrocchio. Roose and Federici’s work was supported by the United States Department of Agriculture (USDA)’s National Institute of Food and Agriculture.

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$3.5 million Givaudan gift will protect citrus collection

Anonymous — Thu, 26 Sep 2019 18:05:29 +0000

$3.5 million Givaudan gift will protect citrus collection Anonymous (not verified) Thu, 09/26/2019 - 11:05 More News UCR NEWS March 14, 2019

The University of California, Riverside announced today a $3.5 million donation from Givaudan to support UCR’s Citrus Variety Collection. The gift will help protect one of world’s most extensive citrus diversity collections from the impending threat of citrus greening disease, also known as Huanglongbing, or HLB.

The gift will pay for a 2.8-acre protective screened structure for new trees and back-up collections of the UCR Citrus Variety Collection, established more than 100 years ago. The collection includes two trees of about 1,000 types of citrus, and occupies 22.3 acres on the UCR campus, as well as two smaller, remote sites.

Tracy Kahn holds up a Valentine pummelo, a grapefruit-like citrus hybrid developed at UC Riverside. Photos/ Stan Lim

The collection will be known as the Givaudan Citrus Variety Collection at the University of California, Riverside, for a 10-year period. Givaudan is the world’s leading flavour and fragrance company.

“As global leaders in citrus, protecting citrus biodiversity and creating a sustainable future is a primary focus for Givaudan,” said Louis D’Amico, president of Givaudan’s Flavour Division. “Our long and ongoing partnership with UCR is one of the ways that Givaudan champions biodiversity and sustainability. We are pleased to make this gift and to continue the strong collaboration we have with this outstanding university.”

Announcing the gift in the Variety Collection’s groves on March 14, Givaudan Global Citrus Product Manager Dawn Streich alluded to the urgency posed by HLB.

“A significant part of our latest gift to UCR will protect the collection from greening– today’s main challenge to citrus,” Streich said.

Citrus Greening disease, also known as Huanglongbing, is caused by a bacterium that is transmitted by the Asian Citrus Psyllid. The bacterium affects the way in which nutrients are transferred from root to tree, and once infected, the tree yield will be lower, fruit appearance and flavor affected, with the disease ultimately killing the tree.

Prevalent in Florida, Brazil, and Mexico, the disease is a global issue and has been detected in every major citrus growing region.

Citrus Variety Collection curator Tracy Kahn said the recent discovery of HLB in Riverside, 2.25 miles from

Kathryn Uhrich, dean of the College of Natural and Agricultural Sciences, was among speakers at the March 14 gift announcement.

UCR’s Citrus Variety Collection “crystalized the need for further protection.”

“Working with partners like Givaudan enables us to protect our collection while working on solutions which can help commercial citrus growers,” Kahn said. “This announcement further cements our long-term collaboration with Givaudan, focusing attention on the preservation of the citrus variety collection. This latest gift will help ensure that the collection is well protected.”

Givaudan’s officials say its partnership with UCR, which began in 2006, has led to discovery of new citrus ingredients and flavours.

“This partnership gives us access to rare varietals, which combined with our creative approach to citrus, delivers unique insight for our customers– inspiring consumer preferred products around the globe,” Streich said.

In 2011, A Givaudan gift created the Givaudan Citrus Variety Collection Endowed Chair to support and maintain UCR’s Citrus Variety Collection. In addition to building the screenhouse, the gift announced today will add to the endowment, assuring support of the collection in perpetuity.

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It’s not easy being green

Anonymous — Thu, 26 Sep 2019 17:54:01 +0000

It’s not easy being green Anonymous (not verified) Thu, 09/26/2019 - 10:54 More News JULES BERNSTEIN June 14, 2019

Despite how essential plants are for life on Earth, little is known about how parts of plant cells orchestrate growth and greening. By creating mutant plants, UC Riverside researchers have uncovered a cellular communication pathway sought by scientists for decades.

Chan Yul Yoo, UCR molecular biologist and first author on both greening studies.

Both plants and humans have specialized light-sensitive proteins. In humans these proteins reside in the retina, allowing us to see. In plants, they are called phytochromes and are housed mainly in the nucleus, which serves as master control for the cell’s activities.

The process of photosynthesis, which converts carbon dioxide into sugar and fuels plant growth, begins when light hits the phytochromes in the nucleus. The nucleus then has to send a command to a sub-organ called a plastid to transform itself into a chloroplast, which manufactures the green pigment chlorophyll.

“The nucleus is like the federal government of the cell, while a sub-organ called the plastid functions more like the state,” said UCR’s Meng Chen, an associate professor of cell biology whose lab is one of few in the world focused on phytochrome communications. “Until now, we did not know how the nucleus sent the ‘turn green’ command to the plastids, telling them to activate their photosynthesis genes.”

The way Chen’s team arrived at the answer is detailed in two new papers published today in the journal Nature Communications.

Historically, part of the challenge has been identifying which of the 25,000 nuclear genes is responsible for regulating the cell’s greening process. To find the regulators, Chen and his team reasoned that the same genes must control not only plant greening, but other processes as well, such as height.

“The regulator we were looking for would control both qualities, height and color,” Chen said.

Seedlings (a) grown in dark, (b) in light, (c) blind phytochrome mutant, and (d) albino rcb-10 mutant found by Chen's lab.

They took a small flowering plant and chemically created versions of it unable to manufacture chloroplasts, even when exposed to light. Next, they looked for mutants that are both albino and tall. As luck would have it, Chen’s team found they’d created some mutants with both qualities.

Comparing the wild plant DNA with the mutated plant DNA allowed the team to identify two genes responsible for regulating greening.

“Plants without either of these genes fail to respond to light, becoming tall and albino seedlings,” said study co-author Chan Yul Yoo, a UCR molecular biologist and first author of both papers.

Understanding the master control of chloroplast development could have profound implications for new technologies to improve crop yields and help plants cope with climate change. But the benefits of this discovery are not limited to plants. Chen’s laboratory is funded by the National Institutes of Health because of the implications of this work on cancer research.

Mitochondria, the power generators of plant and animal cells, play a role in cancer because they are involved in programmed cell death. Communications between a cell’s nucleus and mitochondria are analogous to communications between a plant cell nucleus and chloroplasts.

“Uncovering the nucleus-chloroplast communication pathway in plants could yield new insights into mitochondrial gene expression in human cells and its misregulation in cancers,” Chen said.

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Scientists decode DNA secrets of world’s toughest bean

Anonymous — Thu, 26 Sep 2019 17:31:09 +0000

Scientists decode DNA secrets of world’s toughest bean Anonymous (not verified) Thu, 09/26/2019 - 10:31 More News JULES BERNSTEIN July 09, 2019

UC Riverside scientists have decoded the genome of black-eyed peas, offering hope for feeding Earth’s expanding population, especially as the climate changes.

Understanding the genes responsible for the peas’ drought and heat tolerance eventually could help make other crops tougher too. Black-eyed peas are small beans with dark midsections. They’ve been a global dietary staple for centuries due to their environmental toughness and exceptional nutritional qualities, such as high protein and low fat. In sub-Saharan Africa they remain the number one source of protein in the human diet.

A genome is the full collection of genetic codes that determine characteristics like color, height, and predisposition to diseases. All genomes contain highly repetitive sequences of DNA that UCR Professor of Computer Science and project co-leader Stefano Lonardi likens to “hundreds of thousands of identical jigsaw puzzle pieces.”

Lonardi described the process of figuring out how the jigsaw puzzle sequences fit together as “computationally challenging.” In order to do so, Lonardi’s team assembled the genome many times with different software tools and parameters. Then they created new software capable of merging these various genome solutions into a single, complete picture.

With the success of this project, the black-eyed pea joins only a handful of other major crops whose genomes have been fully sequenced. The team’s work on the project was published in the June issue of The Plant Journal, where it was featured as the cover story, and Lonardi’s free software can be downloaded online.

Research on black-eyed peas, a legume also known as cowpea, started at UC Riverside more than 40 years ago. But cowpeas’ presence in Riverside predates the university by about 200 years.

“The cowpea has been here supporting people since early colonial times,” said project co-leader Timothy Close, a UCR professor of botany and plant sciences. ‘It’s nice that we’ve brought this plant with so much local history up to state of the art for scientific research.”

This is the first high-quality reference genome for the cowpea. Work on it began three years ago, made possible mainly by a $1.6 million grant from the National Science Foundation, or NSF. An additional $500,000 NSF grant also supported the computational efforts.

A clue to the complexity of the project is the size of the research team. In addition to Close and Lonardi, the many other UCR scientists on the team included María Muñoz-Amatrían, Qihua Liang, Steve Wanamaker, Sassoum Lo, Hind Alhakami, Rachid Ounit, Philip Roberts, Jansen Santos, Arsenio Ndeve, and Abid Md. Hasan. Additional team members inside the U.S. came from UC Davis, the Department of Energy’s Joint Genome Institute in California, the National Center for Genome Resources in New Mexico, and the U.S. Department of Agriculture in Iowa. International team members came from Finland, France, Brazil, and the Czech Republic.

As with humans, there are differences between individual cowpeas. Knowing which genes are responsible for qualities in individuals such as color, size, or pathogen resistance will help breeders develop new varieties even better able to withstand external challenges.

“Having the genome sequence helps scientists make decisions about the choice of parent plants to crossbreed in order to produce their desired progeny,” Close said.

One of the cowpea traits that scientists are now trying to understand is its remarkable ability to recover from drought stress.

“We’re trying to figure out why cowpeas are so resilient to harsh conditions,” said Close. “As we move into a world with less water available to agriculture, it will be important to capitalize on this ability and expand on it, taking the lead from cowpeas to guide improvements in other crops that are vulnerable to climate change.”

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Grains in the rain

Anonymous — Wed, 25 Sep 2019 22:18:20 +0000

Grains in the rain Anonymous (not verified) Wed, 09/25/2019 - 15:18 More News Jules Bernstein September 18, 2019

Of the major food crops, only rice is currently able to survive flooding. Thanks to new research, that could soon change -- good news for a world in which rains are increasing in both frequency and intensity.

The research, published today in Science, studied how other crops compare to rice when submerged in water. It found that the plants – a wild-growing tomato, a tomato used for farming and a plant similar to alfalfa – all share at least 68 families of genes in common that are activated in response to flooding.

UCR student Sean Cabanlit collecting tissue samples from rice roots submerged underwater. (Julia Bailey-Serres / UCR)

Rice was domesticated from wild species that grew in tropical regions, where it adapted to endure monsoons and waterlogging. Some of the genes involved in that adaptation exist in the other plants but have not evolved to switch on when the roots are being flooded.

“We hope to take advantage of what we learned about rice in order to help activate the genes in other plants that could help them survive waterlogging,” said study lead Julia Bailey-Serres, a UC Riverside professor of genetics.

In the study, the team examined cells that reside at the tips of roots of the plant, as roots are the first responders to a flood. Root tips and shoot buds are also where a plant’s prime growing potential resides. These regions contain cells that can help a plant become more resilient to flooding.

Drilling down even further, the team looked at the genes in these root tip cells, to understand whether and how their genes were activated when covered with water and deprived of oxygen.

“We looked at the way that DNA instructs a cell to create particular stress response in a level of unprecedented detail,” said one of the lead researchers, UC Riverside’s Mauricio Reynoso.

“This is the first time that a flooding response has been looked at in a way that was this comprehensive, across evolutionarily different species,” added study co-author Siobhan Brady, an associate professor of plant biology at UC Davis.

The genes involved in flooding adaptations are called submergence up-regulated families (SURFs). “Since evolution separated the ancestors of rice and these other species as many as 180 million years ago, we did not expect to find 68 SURFs in common,” said co-author Neelima Sinha, professor of plant biology at UC Davis.

The study was an international collaboration funded by the National Science Foundation’s Plant Genome Research Program. Researchers from UC Davis, as well as Emory, Argentina’s National University of La Plata and Netherland’s Utrecht University participated.

While UC Riverside researchers conducted flooding experiments and analysis of rice plant genomes, scientists at Davis did the same with the tomato species while the alfalfa-type plant work was done at Emory.

Though the SURFs were activated in all the plants during the flooding experiments, their genetic responses weren’t as effective as in rice. The wild tomato species that grows in desert soil withered and died when flooded.

Climate change also produces periods of excessive drought, and separate efforts are under way to examine crop resilience to those conditions as well. However, Bailey-Serres said flooding responses are understudied compared to drought, making this work all the more important.

The group is now planning additional studies to improve the survival rates of the plants that currently die and rot from excess water.

This year is not the first in which excessive rains have kept farmers from being able to plant crops like corn, soybeans and alfalfa. Floods have also damaged the quality of the crops they were able to grow. As the climate continues to change, this trend is likely to continue. Without efforts to ensure our crops adapt, the security of the world’s food supply is at risk.

“Imagine a world where kids do not have enough calories and nutrients to develop,” said Bailey-Serres. “We as scientists have an urgency to help plants withstand floods, to ensure food security for the future.”

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