From The University of California-Davis (US) : “Study Challenges Evolutionary Theory That DNA Mutations Are Random”

UC Davis bloc

From The University of California-Davis (US)

January 12, 2022

Media Contacts:

Grey Monroe
Plant Sciences
Cell 530-304-9329
gmonroe@ucdavis.edu

Amy Quinton
UC Davis News and Media Relations
Cell 530-601-8077
amquinton@ucdavis.edu

Emily C. Dooley
College of Agricultural and Environmental Sciences,
Cell 530-650-6807
ecdooley@ucdavis.edu

Findings Could Lead to Advances in Plant Breeding and Human Genetics

1
Studying the genome of thale cress, a small flowering weed, led to a new understanding about DNA mutations. (Pádraic Flood)

-DNA mutations are not random as previously thought
-Findings change our understanding of evolution
-May help researchers breed better crops and fight cancer

A simple roadside weed may hold the key to understanding and predicting DNA mutation, according to new research from The University of California-Davis(US), and The MPG Institute for Developmental Biology [Max-Planck-Institut für Entwicklungsbiologie](DE).

The findings, published today in the journal Nature radically change our understanding of evolution and could one day help researchers breed better crops or even help humans fight cancer.

Mutations occur when DNA is damaged and left unrepaired creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected.

“We always thought of mutation as basically random across the genome,” said Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences who is lead author on the paper. “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.”

Researchers spent three years sequencing the DNA of hundreds of Arabidopsis thaliana, or thale cress, a small, flowering weed considered the “lab rat among plants” because of its relatively small genome comprising around 120 million base pairs. Humans-by comparison-have roughly 3 billion base pairs.

“It’s a model organism for genetics,” Monroe said.

Lab-grown plants yield many variations

Work began at the Max Planck Institute where researchers grew specimens in a protected lab environment, which allowed plants with defects that may not have survived in nature be able to survive in a controlled space.

Sequencing of those hundreds of Arabidopsis thaliana plants revealed more than 1 million mutations. Within those mutations a nonrandom pattern was revealed, counter to what was expected.

“At first glance, what we found seemed to contradict established theory that initial mutations are entirely random and that only natural selection determines which mutations are observed in organisms,” said Detlef Weigel, scientific director at the Max Planck Institute and senior author on the study.

Instead of randomness they found patches of the genome with low mutation rates. In those patches, they were surprised to discover an over-representation of essential genes, such as those involved in cell growth and gene expression.

“These are the really important regions of the genome,” Monroe said. “The areas that are the most biologically important are the ones being protected from mutation.”

The areas are also sensitive to the harmful effects of new mutations. “DNA damage repair seems therefore to be particularly effective in these regions,” Weigel added.

Plant evolved to protect itself

The scientists found that the way DNA was wrapped around different types of proteins was a good predictor of whether a gene would mutate or not. “It means we can predict which genes are more likely to mutate than others and it gives us a good idea of what’s going on,” Weigel said.

The findings add a surprising twist to Charles Darwin’s Theory of Evolution by Natural Selection because it reveals that the plant has evolved to protect its genes from mutation to ensure survival.

“The plant has evolved a way to protect its most important places from mutation,” Weigel said. “This is exciting because we could even use these discoveries to think about how to protect human genes from mutation.”

Future uses

Knowing why some regions of the genome mutate more than others could help breeders who rely on genetic variation to develop better crops. Scientists could also use the information to better predict or develop new treatments for diseases like cancer that are caused by mutation.

“Our discoveries yield a more complete account of the forces driving patterns of natural variation; they should inspire new avenues of theoretical and practical research on the role of mutation in evolution,” the paper concludes.

Co-authors from UC Davis include Daniel Kliebenstein, Mariele Lensink, Marie Klein, from the Department of Plant Sciences. Researchers from The Carnegie Institution for Science (US), Stanford University (US), The Westfield State University (US), The University of Montpellier [Université de Montpellier](FR), Uppsala University[Uppsala universitet](SE), The College of Charleston(US), and The South Dakota State University(US) contributed to the research.

See the full article here .

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UC Davis Campus

The University of California-Davis (US) is a public land-grant research university near Davis, California. Named a Public Ivy, it is the northernmost of the ten campuses of The University of California (US) system. The institution was first founded as an agricultural branch of the system in 1905 and became the seventh campus of the University of California in 1959.

The university is classified among “R1: Doctoral Universities – Very high research activity”. The University of California-Davis faculty includes 23 members of The National Academy of Sciences, 30 members of The American Academy of Arts and Sciences (US), 17 members of the American Law Institute, 14 members of the Institute of Medicine, and 14 members of the National Academy of Engineering. Among other honors that university faculty, alumni, and researchers have won are two Nobel Prizes, a Presidential Medal of Freedom, three Pulitzer Prizes, three MacArthur Fellowships, and a National Medal of Science.

Founded as a primarily agricultural campus, the university has expanded over the past century to include graduate and professional programs in medicine (which includes the University of California-Davis Medical Center), law, veterinary medicine, education, nursing, and business management, in addition to 90 research programs offered by University of California-Davis Graduate Studies. The University of California-Davis School of Veterinary Medicine is the largest veterinary school in the United States and has been ranked first in the world for five consecutive years (2015–19). University of California-Davis also offers certificates and courses, including online classes, for adults and non-traditional learners through its Division of Continuing and Professional Education.

The UC Davis Aggies athletic teams compete in NCAA Division I, primarily as members of the Big West Conference with additional sports in the Big Sky Conference (football only) and the Mountain Pacific Sports Federation.

Seventh UC campus

In 1959, the campus was designated by the Regents of the University of California as the seventh general campus in the University of California system.

University of California-Davis’s Graduate Division was established in 1961, followed by the creation of the College of Engineering in 1962. The law school opened for classes in fall 1966, and the School of Medicine began instruction in fall 1968. In a period of increasing activism, a Native American studies program was started in 1969, one of the first at a major university; it was later developed into a full department within the university.

Graduate Studies

The University of California-Davis Graduate Programs of Study consist of over 90 post-graduate programs, offering masters and doctoral degrees and post-doctoral courses. The programs educate over 4,000 students from around the world.

UC Davis has the following graduate and professional schools, the most in the entire University of California system:

UC Davis Graduate Studies
Graduate School of Management
School of Education
School of Law
School of Medicine
School of Veterinary Medicine
Betty Irene Moore School of Nursing

Research

University of California-Davis is one of 62 members in The Association of American Universities (US), an organization of leading research universities devoted to maintaining a strong system of academic research and education.

Research centers and laboratories

The campus supports a number of research centers and laboratories including:

Advanced Highway Maintenance Construction Technology Research Laboratory
BGI at UC Davis Joint Genome Center (in planning process)
Bodega Marine Reserve
C-STEM Center
CalEPR Center
California Animal Health and Food Safety Laboratory System
California International Law Center
California National Primate Research Center
California Raptor Center
Center for Health and the Environment
Center for Mind and Brain
Center for Poverty Research
Center for Regional Change
Center for the Study of Human Rights in the Americas
Center for Visual Sciences
Contained Research Facility
Crocker Nuclear Laboratory
Davis Millimeter Wave Research Center (A joint effort of Agilent Technologies Inc. and UC Davis) (in planning process)
Information Center for the Environment
John Muir Institute of the Environment (the largest research unit at UC Davis, spanning all Colleges and Professional Schools)
McLaughlin Natural Reserve
MIND Institute
Plug-in Hybrid Electric Vehicle Research Center
Quail Ridge Reserve
Stebbins Cold Canyon Reserve
Tahoe Environmental Research Center (TERC) (a collaborative effort with Sierra Nevada University)
UC Center Sacramento
UC Davis Nuclear Magnetic Resonance Facility
University of California Pavement Research Center
University of California Solar Energy Center (UC Solar)
Energy Efficiency Center (the very first university run energy efficiency center in the Nation).
Western Institute for Food Safety and Security

The Crocker Nuclear Laboratory on campus has had a nuclear accelerator since 1966. The laboratory is used by scientists and engineers from private industry, universities and government to research topics including nuclear physics, applied solid state physics, radiation effects, air quality, planetary geology and cosmogenics. University of California-Davis is the only University of California campus, besides The University of California-Berkeley (US), that has a nuclear laboratory.

Agilent Technologies will also work with the university in establishing a Davis Millimeter Wave Research Center to conduct research into millimeter wave and THz systems.