Hexbyte Glen Cove Study reports six novel variants for CRISPR-Cas12a in plants, expanding genome engineering thumbnail

Hexbyte Glen Cove Study reports six novel variants for CRISPR-Cas12a in plants, expanding genome engineering

Hexbyte Glen Cove

Associate professor of Plant Science at the University of Maryland Yiping Qi continues to innovate genome editing and engineering in plants, with the ultimate goal of improving the efficiency of food production. His new work contributes six novel variants of CRISPR-Cas12a in plants, testing first in rice as a major global crop. In addition to broadening possible gene editing targets, these tools can edit many different sites at once, or even repress gene expression. Credit: National Institutes of Health, public domain

In a new publication in Nature Communications, associate professor of Plant Science at the University of Maryland Yiping Qi continues to innovate genome editing and engineering in plants, with the ultimate goal of improving the efficiency of food production. His recent work contributes six novel variants of CRISPR-Cas12a that have never before been proven in plants, testing them first in rice as a major global crop. In addition to allowing for a much broader scope of possible gene editing targets, these new tools can edit many different sites in the genome at once, or even repress gene expression to tone down undesirable traits. These patent-pending tools greatly expand the scope of what CRISPR-Cas12a can do in plants, which can help to produce food more effectively to feed a growing global population.

“We are excited about this paper because we’ve contributed two major breakthroughs,” says Qi. “First, we’ve reported multiple Cas12a tools with capabilities in for the first time, and found one [Mb2Cas12a] that hugely broadens the targeting range of Cas12a. Second, we’ve developed a very efficient system that can edit many different sites at once [multiplexed editing], and that allows us to edit 16 different genes in rice in a single generation.”

As Qi explains, Cas12a (like other CRISPR systems) has typically been tied to targeting a specific short sequence of DNA known as a PAM sequence. The PAM sequence is what CRISPR systems typically use to identify where to possibly make their molecular cuts in DNA. However, the new Mb2Cas12a variant introduced by Qi works under relaxed PAM requirements, broadening the scope of what can be targeted for editing the way Qi’s lab recently did for CRISPR-Cas9.

In addition to this discovery, the multiplexed editing system introduced for Cas12a in plants provides specific strategies for efficiently editing multiple sites across the genome all at once. For this proof-of-concept, Qi’s team first targeted six different sites in the genome to enhance rice yield and disease resistance. But when this was successful, the team didn’t stop there.

“I wanted to add more targets to see if there is any limit,” explains Qi. “So we added 10 more and tried to target 16 sites, and we found that across almost all rice chromosomes, we had an amazingly high efficiency with all sites being edited all at once in one generation. And that doesn’t even represent the upper limit necessarily, but it is the most genes in a plant that has ever been recorded as being edited all at once in one generation for Cas12a.”

This system has major implications for precision breeding and the efficiency of food production, says Qi. “For precision breeding, how many genes you can edit at once is really practically important because you can target almost anything and really tailor the product. We targeted disease resistance and yield, but you can add more traits like nitrogen use efficiency, climate resilience traits such as temperature tolerance, and more. It is really a robust system.”

Qi is currently doing work to examine the off-targeting effects of editing more genes at once with more relaxed target site requirements. But in addition to these contributions, this paper also demonstrated Cas12a’s utility as a synthetic repressor of genes in the model plant Arabidopsis as another for genome engineering.

“You can regulate activation or repression of certain genes by using CRISPR not as a cutting tool, but instead as a binding tool to attract activators or repressors to induce or suppress to engineer desirable traits. In this case, Cas12a is acting as glue, not as scissors. You use an inactivated form of Cas12a to inactivate the expression of other . It’s a great new tool for the industry and for future research.”

Future work will expand these tools out of rice and Arabidopsis, and into all kinds of plants and crops. “This type of technology helps increase crop yield and sustainably feed a growing population in a changing world,” says Qi. “I am very pleased to continue to expand the impacts of CRISPR technologies.”

This paper, entitled “Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems,” can be found in Nature Communications.



More information:
“Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems,” Nature Communications, DOI: 10.1038/s41467-021-22330-w

Citation:
Study reports six novel variants for CRISPR-Cas12a in plants, expanding genome engineering (2021, March 29)
retrieved 29 March 2021
from https://phys.org/news/2021-03-variants-crispr-cas12a-genome.html

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part may be reproduced without the written permission. The content is provided for information purposes only.

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Hexbyte Glen Cove 'Sex, lasers and male competition:' fruit flies win genetic race with rivals thumbnail

Hexbyte Glen Cove ‘Sex, lasers and male competition:’ fruit flies win genetic race with rivals

Hexbyte Glen Cove

UC researchers studied the sex combs of the fruit fly Drosophilia bipectinata. Credit: Michal Polak/UC

Scientists have accepted natural selection as a driver of evolution for more than 160 years, thanks to Charles Darwin.

But University of Cincinnati biologist Michal Polak says Darwin’s book “The Descent of Man” only tells part of the story. Sometimes when the victor vanquishes his sexual rival, the quest to pass genes to the next generation is just beginning.

According to a new UC study published in the journal Current Biology, male flies with the most impressive sexual ornamentation also have super sperm that can outcompete that of rivals in the post-mating fertilization game.

UC studied Drosophila bipectinata, a tiny red-eyed fruit fly from the South Pacific. The male’s forelegs have a distinctive “sex comb,” dark bristles that female fruit flies find appealing—like the colorful train of a male peacock. Scientists previously found that female flies prefer males with more robust sex combs, which the males use to grasp the female’s abdomen before mating.

UC researchers found a strong link between the most impressive sex combs and that male’s competitive success at passing on his genes even after a female fly has mated with other flies. And this competitive edge persisted even after the male’s sex comb was surgically removed with a high-precision laser in UC experiments.

“This is the first robust demonstration of a genetic link between a traditionally Darwinian trait and success in postcopulatory sexual competition,” Polak said. “That’s the surprising link: precopulatory and postcopulatory fitness.”

In his groundbreaking 1859 book “On the Origin of Species,” Darwin framed the idea of by describing how the “fittest” animals pass on their genes to the next generation. This fitness is manifested in having the largest antlers, the most vibrant colors or the vigor to defend a territory.

But Darwin’s theory was incomplete, Polak said, because it failed to recognize that sexual selection continues during and after mating. Female fruit flies are promiscuous, often choosing multiple mates. Fruit flies are hardly alone in that regard, Polak said.

“Promiscuity is much more common across animal species than once was thought,” Polak said.

UC biologist Michal Polak studies the competitive race to pass on genes that takes place after multiple males mate with a female. Credit: Andrew Higley/UC Creative

Scientists living in prim and proper Victorian England did not give enough consideration to the microscopic race to fertilize that begins after mating among multiple successful suitors.

“You have to consider the social context in which Darwin was living,” Polak said.

What females gain from mating with multiple suitors is not always clear, Polak said. But when they do, postcopulatory sexual selection provides a competitive edge.

“It’s evident even in primates. Female chimpanzees and bonobos are promiscuous, so the males have large testes that produce big volumes of sperm,” Polak said.

“And you have species like gorillas where females are not promiscuous. Silverback males enforce monogamy. And lo and be hold, their testes are much smaller relative to body size compared to chimps.”

And if you’re wondering, the relative size of human testes falls somewhere between gorillas and chimps, Polak said.

Polak, a professor of biology in UC’s College of Arts and Sciences, decided to study this species of fruit fly after encountering it while conducting fieldwork in Queensland, Australia.

“I was watching these flies mate on a fruit and looked under the microscope and saw these beautiful sex combs. I thought it would make a good model system to study,” Polak said.

“Sexual selection picks up on these traits and they become really exaggerated,” he said.

UC researchers found a link between a fruit fly’s sexual ornamentation and its success over rivals in fertilizing eggs. Pictured are UC graduate Kassie Hooker, left, and UC biologists Joshua Benoit and Michal Polak. Credit: Andrew Higley/UC Creative

For their study, UC biologists artificially selected males with the largest and smallest sex combs in 11 successive generations of fruit flies to create high and low genetic lines.

Kassie Hooker from 2012 to 2015 worked in Polak’s lab as an undergraduate biology student, undertaking the arduous task of categorizing generations of male fruit flies based on the size of the sex combs on their legs. By counting the teeth in each comb, she separated the males with the largest and smallest sex combs to create distinct genetic lines.

To show that the male fruit fly’s sex comb doesn’t provide any reproductive benefit in mating, researchers used ultraprecise lasers to trim the sex in the high line males to mimic those found in the low line males. But these postsurgical males continued to fertilize more eggs even when females mated with lower-line males first.

The research was supported by the National Science Foundation.

UC assistant professor Joshua Benoit, a study co-author, analyzed the RNA of the flies and identified seminal fluid genes that may be responsible for giving high-line a fertilization advantage.

“There aren’t many studies more interesting than this one,” Benoit said. “Sex, lasers, and male competition, which could describe most 1980s action movies.”

Darwin proposed the theory of sexual selection to account for the evolution of male weaponry and extravagant ornamental displays, Polak said. But UC’s study found a far more complex and interesting battle among the sexes.

“We established a link between Darwinian traits and the postcopulatory arena, which Darwin didn’t recognize was important in evolution at all,” Polak said.



More information:
Michal Polak et al, Positive genetic covariance between male sexual ornamentation and fertilizing capacity, Current Biology (2021). DOI: 10.1016/j.cub.2021.01.046

Citation:
‘Sex, lasers and male competition:’ fruit flies win genetic race with rivals (2021, February 12)
retrieved 12 February 2021
from https://phys.org/news/2021-02-sex-lasers-male-competition-fruit.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
part may be reproduced without the written permission. The content is provided for information purposes only.

Read More Hexbyte Glen Cove Educational Blog Repost With Backlinks —