Breakthrough method revolutionizes agricultural crop improvement for enhanced properties
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Since the agricultural revolution, mankind has strived to enhance plant varieties through genetic diversity. However, until recently, our understanding was limited to the functions of individual genes, which account for just 20% of the genome. The remaining 80%, comprised of genes grouped in families, remained a mystery on a large genomic scale.
In a groundbreaking achievement, Tel Aviv University researchers have harnessed the power of CRISPR technology to develop an innovative and scalable genetic modification method. This breakthrough allows us to uncover the roles and characteristics of duplicated genes in plants. As a result, the team has successfully identified numerous overlooked features, paving the way for a revolutionary approach to crop improvement. This remarkable development has the potential to revolutionize agricultural practices across a wide range of crops and traits, including increased yields and enhanced resistance to drought and pests.
Overcoming Genetic Redundancy
This groundbreaking research was led by postdoctoral student Dr. Yangjie Hu, under the guidance of Prof. Eilon Shani and Prof. Itay Mayrose from the School of Plant Sciences and Food Security at TAU's The George S. Wise Faculty of Life Sciences. Collaborating with scientists from France, Denmark, and Switzerland, the team utilized the CRISPR gene editing technology along with bioinformatics and molecular genetics methods to develop this novel gene-location method. The research was published in the prestigious journal Nature Plants.
"We wanted to apply this technique to improve the control of creating mutations in plants for the purposes of agricultural improvement, and specifically to overcome the common limitation posed by genetic redundancy." – Prof. Itay Mayrose
Genetic redundancy, caused by gene families, has long posed a challenge in plant research. Previous methods of genetic intervention were limited by the inability to precisely identify genes responsible for specific traits. The accepted method to address this challenge is to produce mutations, that is, to modify genes in different ways, and then to examine changes in the plant’s traits as a result of the mutation in the DNA and to learn from this about the function of the gene.
Thus, for example, if a plant with sweeter fruit develops, it can be concluded that the altered gene determines the sweetness of the fruit. This strategy has been used for decades, and has been very successful, but it also has a fundamental problem: an average plant such as tomato or rice has about 30,000 genes, but about 80% of them do not work alone but are grouped in families of similar genes. Therefore, if a single gene from a certain gene family is mutated, there is a high probability that another gene from the same family (actually a copy very similar to the mutated gene) will mask the phenotypes in place of the mutated gene. Due to this phenomenon, called genetic redundancy, it is difficult to create a change in the plant itself, and to determine the function of the gene and its link to a specific trait.
The research team
The team addressed this challenge by using CRISPR and designing sgRNA sequences that guide an enzyme called Cas9 found naturally in bacteria to cut specific genetic sequences associated with entire gene families. Prof. Mayrose explains that "this genetic editing method allows us to design different sgRNA sequences to allow Cas9 to cut almost any gene that we want to change. We wanted to apply this technique to improve the control of creating mutations in plants for the purposes of agricultural improvement, and specifically to overcome the common limitation posed by genetic redundancy."
In the first stage, a bioinformatics study was carried out on a computer, which, unlike most studies in the field, initially covered the entire genome. The researchers chose to focus on the Arabidopsis plant, which is used as a model in many studies and has about 30,000 genes. First, they identified and isolated about 8,000 individual genes, which have no family members, and therefore no copies in the genome. The remaining 22,000 genes were divided into families, and for each family appropriate sgRNA sequences were computationally designed. Each sgRNA sequence was designed to guide the Cas9 cutting enzyme to a specific genetic sequence that characterizes the entire family, with the aim of creating mutations in all family members so that these genes can no longer overlap each other. In this way, a library was built that totaled approximately 59,000 sgRNA sequences, where each sgRNA by itself can simultaneously modify 2-10 genes at once from each gene family, thereby effectively neutralizing the phenomenon of genetic redundancy.
In addition, the sgRNA sequences were divided into ten sub libraries of approximately 6,000 sgRNA sequences each, according to the presumed role of the genes – such as coding for enzymes, receptors, transcription factors, etc. According to the researchers, establishing the libraries allowed them to focus and optimize the search for genes responsible for desired traits, a search that until now has been largely random.
"We believe that this is the future of agriculture: controlled and targeted crop improvement on a large scale. Today, we are applying the method we developed to rice and tomato plants with great success, and we intend to apply it to other crops as well." – Prof. Eilon Shani
In the next step, the researchers moved from the computer to the laboratory. Here they generated all 59,000 sgRNA sequences designed by the computational method and engineered them into new plasmid libraries (i.e., circular DNA segments) in combination with the cutting enzyme. The researchers then generated thousands of new plants containing the libraries - where each plant was implanted with a single sgRNA sequence directed against a specific gene family.
The researchers observed the traits that were manifested in the plants following the genome modifications, and when an interesting phenotype was observed in a particular plant, it was easy to know which genes were responsible for the change based on the sgRNA sequence that was inserted into it. Also, through DNA sequencing of the identified genes, it was possible to determine the nature of the mutation that caused the change and its contribution to the plant's new properties.
In this way, many new traits were mapped that until now were blocked due to genetic redundancy. Specifically, the researchers identified specific proteins that comprise a mechanism related to the transport of the hormone cytokinin, which is essential for optimal plant development.
Commercialization and Future Impact
Prof. Shani concludes: "The new method we developed is expected to be of great help to basic research in understanding processes in plants, but beyond that, it has enormous significance for agriculture: it makes it possible to efficiently and accurately reveal the pool of genes responsible for traits we seek to improve - such as resistance to drought, pests, and diseases, or increasing yields. We believe that this is the future of agriculture: controlled and targeted crop improvement on a large scale. Today we are applying the method we developed to rice and tomato plants with great success, and we intend to apply it to other crops as well."
Recognizing the transformative potential of this breakthrough, Tel Aviv University's technology commercialization company, Ramot, partnered with the AgChimedes group to establish DisTree, a company dedicated to applying this technology to different crops. This collaboration, along with financial investment and professional support, aims to revolutionize agricultural genetics and ensure nutritional security in the face of climate crises.
Deadly epidemic killed all the black sea urchins in the Gulf of Eilat, placing coral reefs at risk
- Life Sciences
Recent, unsettling studies conducted by Tel Aviv University have unveiled a deadly epidemic responsible for the widespread decimation of black sea urchins in the Mediterranean Sea and the Gulf of Eilat. Over the span of just a few months, the entire population of black sea urchins in Eilat was eradicated. For instance, within a few weeks, thousands of sea urchins inhabiting a site near the northern shore of the Gulf of Eilat perished. The severity of the epidemic is such that only skeletal remains of black urchins now occupy the site. Disturbingly, similar occurrences have been observed at various other locations in the Gulf of Eilat, as well as in neighboring countries including Jordan, Egypt, Saudi Arabia, Greece, and Turkey.
"At first we thought it was some kind of pollution or poisoning, or a local chemical spill (…) but when we examined additional sites in Eilat, Jordan, and Sinai, we quickly realized that this was not a local incident. All findings pointed to a rapidly spreading epidemic." - Dr. Omri Bronstein.
Unveiling Deadly Epidemic
The studies were led by Dr. Omri Bronstein and PhD students Rotem Zirler, Lisa-Maria Schmidt, Gal Eviatar, and Lachan Roth from the School of Zoology, at The George S. Wise Faculty of Life Sciences, and The Steinhardt Museum of Natural History at Tel Aviv University. The papers were published in Frontiers in Marine science and Royal Society Open Science.
The researchers underscore the vital importance of sea urchins, particularly the long-spined Diadema setosum, as keystone species essential for the thriving equilibrium of coral reefs. They express a pressing concern, stating, "It must be understood that the threat to coral reefs is already at an all-time peak, and now a previously unknown variable has been added. This situation is unprecedented in the documented history of the Gulf of Eilat."
According to the researchers' hypothesis, the cause of the deadly epidemic can be attributed to a pathogenic ciliate parasite that has spread from the Mediterranean to the Red Sea. In response to the gravity of the situation, an urgent report outlining the current state has been submitted to the Israel Nature and Parks Authority, instigating deliberation on emergency measures to safeguard Israel's coral reefs.
"Sea urchins in general, and Diadema setosum in particular, are considered key species essential for the healthy functioning of coral reefs. The sea urchins are the reef's 'gardeners' – they feed on the algae and prevent them from taking over and suffocating the corals that compete with them for sunlight." – Dr. Omri Bronstein
Dr. Omri Bronstein and a dying sea urchin
"At first we thought it was some kind of pollution or poisoning, or a local chemical spill, from the industry and hotels in the north of the Gulf of Eilat, but when we examined additional sites in Eilat, Jordan, and Sinai, we quickly realized that this was not a local incident," explains Dr. Bronstein. "All findings pointed to a rapidly spreading epidemic. Similar reports are coming in from colleagues in Saudi Arabia. Even sea urchins that we grow for research purposes in our aquariums at the Interuniversity Institute, and sea urchins at the Underwater Observatory Marine Park in Eilat, contracted the disease and died, probably because the pathogen got in through the pumping systems."
Dr. Bronstein describes it as a fast and violent death: "Within just two days a healthy sea urchin becomes a skeleton with massive tissue loss. While some corpses are washed ashore, most sea urchins are devoured while they are dying and unable to defend themselves, which could speed up contagion by the fish who prey on them."
Invasion and Vanishing Species
In recent years, Dr. Bronstein's research group has dedicated their efforts to the investigation of marine invasions, with a specific focus on the long-spined Diadema setosum. "Until recently, the black sea urchins with long spines, familiar to many of us, was one of the dominant species in Eilat's coral reef," reflects Dr. Bronstein. "Sea urchins in general, and Diadema setosum in particular, are considered key species essential for the healthy functioning of coral reefs. The sea urchins are the reef's 'gardeners' – they feed on the algae and prevent them from taking over and suffocating the corals that compete with them for sunlight. Regrettably, these once-thriving sea urchins have vanished from the Gulf of Eilat and are quickly disappearing from constantly expanding parts of the Red Sea further to the south," shares Dr. Bronstein with a sense of lament.
A dying urchin in the Mediterranean Sea (photo: Dr. Omri Bronstein)
Several months ago, Dr. Bronstein was alerted to the initial reports of widespread mortality by colleagues in Greece and Turkey, where the sea urchins had invaded, likely via the Suez Canal. "In 2006, the first sighting of this species of sea urchin occurred in the southern regions of Turkey," Dr. Bronstein adds. This phenomenon, known as biological invasion, carries far-reaching ecological implications, pervasively affecting the eastern Mediterranean, particularly along Israel's coastline. "We have been monitoring the dynamics of this species' invasion in the Mediterranean since its first emergence," he shares.
In 2016, they discovered the first Diadema setosum sea urchin along Israel’s Mediterranean coastline – a lone urchin sighted at Gordon Beach in Tel Aviv. For over a decade since the first discovery in Turkey, the Mediterranean populations of these sea urchins remained small and usually hidden. However, since 2018 the sea urchin population in the Mediterranean has been growing exponentially, reaching a state of population explosion – with giant populations of thousands and even tens of thousands found in Greece and Turkey.
"The window of opportunity for preserving a thriving population of this species in Eilat has regrettably closed. To establish a safeguard population, we must act without delay, by preserving healthy individuals from the Israeli Mediterranean before the encroaching disease from the north reaches this region." Dr. Omri Bronstein
"However, during the course of our research, while scrutinizing the invasion of sea urchins in the Mediterranean, we began to receive reports on sudden extensive mortality," says Dr. Bronstein. "While the extinction of an invasive species is supposedly not a bad thing, we must be aware of two major risks: Firstly, we don't yet know how this mortality and its causes might impact local species in the Mediterranean. Secondly, and of far greater significance, the geographic proximity shared by the eastern Mediterranean and the Red Sea provides a potential conduit for the swift transmission of the pathogen into the Red Sea. As we feared and predicted, this is what appears to have happened."
Dr. Bronstein and his research team (photo: courtesy of Dr. Omri Bronstein)
A Reminiscent Crisis
The massive loss of sea urchins reminded the TAU researchers of one of the most devastating events in marine ecology: the disappearance of the sea urchins in the Caribbean. Until 1983, the Caribbean coral reef thrived as a vibrant tropical ecosystem, much like the one in the Gulf of Eilat. But as the sea urchins vanished, the uncontrollable growth of algae took over, blocking sunlight from reaching the corals and forever altering the reef into a sea of algae.
Dr. Bronstein reveals, "Just last year, the Caribbean experienced another outbreak of the disease, resulting in the demise of the remaining urchin populations. However, unlike previous incidents, we now possess advanced scientific and technological resources to analyze the forensic evidence. Researchers from Cornell University successfully pinpointed the cause of mortality in the Caribbean: a pathogenic ciliate parasite. The identical pathology observed in the dying sea urchins of Greece, Turkey, and the Red Sea corroborates this finding."
Dr. Bronstein's pioneering research not only identified the unprecedented mass mortality of an invasive species in the Mediterranean but also shed light on the alarming decline of the widely prevalent sea urchin species, Diadema setosum. In a groundbreaking study, Dr. Bronstein issued a a warning that the epidemic plaguing the Mediterranean could extend its reach to the nearby Red Sea. Sadly, this cautionary prediction has become a disheartening reality.
Urgent Measures and Closing Window
"The gravity of the situation cannot be understated: the Red Sea is witnessing an alarming surge in mortality, surpassing the extent observed in the Mediterranean. Looming in the background is an ominous uncertainty: What is the exact cause of the sea urchin die-offs? Is it the same Caribbean pathogen or an entirely new and unfamiliar factor? Regardless, it is evident that this pathogen spreads through water, and we anticipate a rapid escalation of sickness and demise among the entire population of these sea urchins in both the Mediterranean and the Red Sea."
"In my view, it is imperative that we swiftly establish a safeguard population for these sea urchins, ensuring the potential for their reintroduction into the wild. Similar to the approach taken with COVID-19, the trajectory of this epidemic remains uncertain. Will it eventually subside on its own, or persist for years, radically transforming coral reefs? However, unlike the COVID-19 pandemic, there are no available vaccines or treatments for the afflicted sea urchins. Hence, our efforts must be steadfastly directed towards prevention. The window of opportunity for preserving a thriving population of this species in Eilat has regrettably closed. To establish a safeguard population, we must act without delay, by preserving healthy individuals from the Israeli Mediterranean before the encroaching disease from the north reaches this region. While this is a complex undertaking, it is imperative if we aspire to secure the future of this unique species, which plays a critical role in the destiny of coral reefs," concludes Dr. Bronstein.
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