Chocolate Farmers Could Benefit From Newly Sequenced Cacao Genome

There should be an image here!A first draft of the cacao genome is complete, a consortium of academic, governmental, and industry scientists announced today. Indiana University Bloomington scientists performed much of the sequencing work, which is described and detailed at the official Web site of the Cacao Genome Database project.

Despite being led and funded by a private company, Mars Inc., Cacao Genome Database scientists say one of their chief concerns has been making sure the Theobroma cacao genome data was published for all to see — especially cacao farmers and breeders in West Africa, Asia and South America, who can use genetic information to improve their planting stocks and protect their often-fragile incomes.

“When you have to wait three or more years for a tree you plant to bear the beans you sell, you want as much information as possible about the seedlings you’re planting,” said Keithanne Mockaitis, IU Center for Genomics and Bioinformatics (CGB) sequencing director and IU project leader. “We expect this information will positively impact some of the poorest regions in the world, where tropical tree crops are grown. Making the genome data public further enables breeders, farmers and researchers around the world to use a common set of tools, and to share information that will help them fight the spread of disease in their crops.”

Mockaitis, a biochemist-turned-genomicist, joined the project in early 2009, and quickly set to work with her collaborators to tackle the challenge of sequencing and accurately pasting together the approximately 400 million base pairs of the tree’s genome. Mockaitis’ Cacao Genome Group partners at the U.S. Department of Agriculture’s Subtropical Horticulture Research Station in Miami sent samples to Bloomington, and these were prepared and sequenced in a redundant manner by her sequencing team in the CGB genomics laboratory. Sequence of some of the same material was generated using additional methods in laboratories of the USDA Agricultural Research Service (USDA-ARS) and at the National Center for Genome Resources in Santa Fe, N.M.

Raw data were then sent to HudsonAlpha Biotechnology Institute, a partner of the U.S. Department of Energy-funded Joint Genome Institute, for assembly. Other important datasets generated by Mockaitis’ group were not the sequences of the DNA itself, but of the RNA, or transcripts produced in different tissues of the tree. Transcript sequences reveal which genes are expressed (turned on).

Finally, IU Bloomington Department of Biology scientist Don Gilbert analyzed both the genome and transcriptome sequences and generated the annotations that point to the locations in which each active gene and its components (exons and introns) reside.

“The final number of genes is still being counted and validated, but we currently estimate the cacao plant has about 35,000 genes,” Mockaitis said.

That’s a typical gene number for flowering plants whose genomes have thus far been sequenced. Humans have approximately 30,000 genes. Rice has about 40,000.

Since its inception about 11 years ago, the CGB has been involved in dozens of different projects that address the workings of different species’ genomes with the use of high-throughput technologies.

“Cacao is something of a first for us,” Mockaitis said. “This is the largest genome the CGB has sequenced to date. As a group we now have more experience and more resources to take on a wider variety of projects.”

Mockaitis says the relative efficiency of the project so far has been due to Mars’ support of the academic and non-profit contributing laboratories.

“We’ve benefited from having a collegial group of researchers, from the USDA-ARS and a variety of genomics-focused laboratories, that each bring different scientific expertise to the table to complete this genome. It’s also been particularly inspiring to see West African cacao researchers come to some of our meetings — they listen to us talk about the esoteric technologies we’re using, and we know that they’ll soon go to work and start benefitting from the data. That’s a rare treat for an academic researcher.”

Mockaitis was first introduced to this project through Roche Diagnostics, based in Indianapolis, which owns the 454 Sequencing technology. Her group had developed improved methods for the sequencing of transcripts (active gene products, above), and was asked to contribute some data to the project. Since then the IU CGB has been able to contribute to the sequence of the genome itself as well.

Unlike some other food products, such as corn or wheat, which are often grown on large, industrial farms, cacao is almost exclusively grown on small farms. There are about 6.5 million chocolate farmers around the world, primarily in West Africa, northern South America, and Southeast Asia. The United States produces virtually no chocolate on its own, instead opting to engage cacao-growing countries with economic policies that support the production and trade of what may be the world’s most popular food.

“Genome sequencing helps eliminate much of the guess-work of traditional crop cultivation,” said Howard-Yana Shapiro, global staff officer of plant science and research at Mars Inc. “Cocoa is what some researchers describe as an ‘orphan crop’ because it has been the subject of little agricultural research compared to corn, wheat and rice. This effort, which will allow fast and accurate traditional breeding, is about applying the best of what science has to offer in taking an under-served crop and under-served population and giving them both the chance to flourish.”

Mockaitis says she hopes the project will have a positive impact on the farmers’ lives and livelihoods.

“It is an export crop that can reduce poverty,” she said. “I believe the work our groups have done will eventually help small farmers stay in business over time, because improved breeding programs based on reliable genome data will give them plants naturally equipped to fight off disease and to thrive in their specific location. This will lead to more sustainable crops and of course a more stable chocolate supply for all of us — pretty important!”

David Bricker @ Indiana University

[awsbullet:endangered species chocolate]

Cloud Computing Method Greatly Increases Gene Analysis

There should be an image here!Researchers at the Johns Hopkins Bloomberg School of Public Health have developed new software that greatly improves the speed at which scientists can analyze RNA sequencing data. RNA sequencing is used to compare differences in gene expression to identify those genes that switched on or off when, for instance, a particular disease is present. However, sequencing instruments can produce billions of sequences per day, which can be time-consuming and costly to analyze. The software, known as Myrna, uses “cloud computing,” an Internet-based method of sharing computer resources. Faster, cost-effective analysis of gene expression could be a valuable tool in understanding the genetic causes of disease. The findings are published in the current edition of the journal Genome Biology. The Myrna software is available for free download here.

Cloud computing bundles together the processing power of the individual computers using the Internet. A number of firms with large computing centers including, Amazon and Microsoft, rent unused computers over the Internet for a fee.

“Cloud computing makes economic sense because cloud vendors are very efficient at running and maintaining huge collections of computers. Researchers struggling to keep pace with their sequencing instruments can use the cloud to scale up their analyses while avoiding the headaches associated with building and running their own computer center,” said lead author, Ben Langmead, a research associate in the Bloomberg School’s Department of Biostatistics. “With Myrna, we tried to make it easy for researchers doing RNA sequencing to reap these benefits.”

To test Myrna, Langmead and colleagues Kasper Hansen, PhD, a postdoctoral fellow, and Jeffrey T. Leek, PhD, senior author of the study and assistant professor in the Department of Biostatistics, used the software to process a large collection of publicly available RNA sequencing data. Processing time and storage space were rented from Amazon Web Services. According to the study, Myrna calculated differential expression from 1.1 billion RNA sequencing reads in less than 2 hours at cost of about $66.

“Biological data in many experiments — from brain images to genomic sequences — can now be generated so quickly that it often takes many computers working simultaneously to perform statistical analyses,” said Leeks. “The cloud computing approach we developed for Myrna is one way that statisticians can quickly build different models to find the relevant patterns in sequencing data and connect them to different diseases. Although Myrna is designed to analyze next-generation sequencing reads, the idea of combining cloud computing with statistical modeling may also be useful for other experiments that generate massive amounts of data.”

The researchers were supported by grants from Amazon Web Services, the National Institutes of Health and the Johns Hopkins Bloomberg School of Public Health.

[Photo above by Bruce Clay, Inc. / CC BY-ND 2.0]

Tim Parsons @ Johns Hopkins University Bloomberg School of Public Health?

[awsbullet:cloud computing dummies]

Genes From Sweet Pepper To Fortify African Banana Against Devastating Wilt Disease

There should be an image here!In a major breakthrough, crop scientists announced today the successful transfer of green pepper genes to bananas, conferring on the popular fruit the means to resist one of the most devastating diseases of bananas in the Great Lakes region of Africa.

The Banana Xanthomonas Wilt (BXW) costs banana farmers about half a billion dollars worth of damage every year across East and Central Africa. The leaves of affected crops turn yellow and then wilt, and the fruit ripens unevenly and before its time. Eventually the entire plant withers and rots.

Dr. Leena Tripathi, a biotechnologist with International Institute of Tropical Agriculture (IITA) and lead author of the paper, said there is still a long way to go before the transgenic bananas find their way onto farmers’ fields, but she called the breakthrough “a significant step in the fight against the deadly banana disease.”

The transformed bananas, newly-infused with one of two proteins from the green pepper, have shown strong resistance to Xanthomonas wilt in the laboratory and in screen houses. The researchers are poised to begin confined field trials in Uganda soon.

Some of the findings on the protective impact of the two proteins — plant ferredoxin-like amphipathic protein (Pflp) and hypersensitive response-assisting protein (Hrap) — were published recently in the journal Molecular Plant Pathology.

“The Hrap and Pflp genes work by rapidly killing the cells that come into contact with the disease-spreading bacteria, essentially blocking it from spreading any further,” Tripathi said. “Hopefully, this will boost the arsenal available to fight BXW and help save millions of farmers’ livelihoods in the Great Lakes region.”

The novel green pepper proteins that give crops enhanced resistance against deadly pathogens can also provide effective control against other BXW-like bacterial diseases in other parts of the world. Tripathi adds that the mechanism known as Hypersensitivity Response also activates the defenses of surrounding and even distant uninfected banana plants leading to a systemic acquired resistance.

Scientists from the IITA and the National Agricultural Research Organisation (NARO) of Uganda, in partnership with African Agricultural Technology Foundation (AATF), will soon begin evaluating these promising new banana lines under confined field trials. The Ugandan National Biosafety Committee recently approved the tests, which can now move forward.

The genes used in this research were acquired under an agreement from the Academia Sinica in Taiwan.

The highly destructive BXW affects all varieties, including the East African Highland bananas and exotic dessert, roasting, and beer bananas. The crop is also under threat from another deadly disease, the banana bunchy top.

Dr. Tripathi says that there are presently no commercial chemicals, biocontrol agents or resistant varieties that can control the spread of BXW. “Even if a source of resistance is identified today,” Tripathi said, “developing a truly resistant banana through conventional breeding would be extremely difficult and would take years, even decades, given the crop’s sterility and its long gestation period.”

BXW was first reported in Ethiopia 40 years ago on Ensete, a crop relative of banana, before it moved on to bananas. Outside of Ethiopia, it was first reported in Uganda in 2001, then rapidly spread to the Democratic Republic of Congo, Rwanda, Kenya, Tanzania, and Burundi, leaving behind a trail of destruction in Africa’s largest banana producing and consuming region.

BXW can be managed by de-budding the banana plant (removing the male bud as soon as the last hand of the female bunch is revealed) and sterilizing farm implements used. However, the adoption of these practices has been inconsistent at best as farmers believe that de-budding affects the quality of the fruit and sterilizing farm tools is a tedious task.

The research to fortify bananas against BXW using genes from sweet pepper was initiated in 2007.

Jeffrey T. Oliver @ Burness Communications

[Photo above by azrainman / CC BY-ND 2.0]

[awsbullet:Frankenfood]

Scientists Uncover The Genetic Secrets That Allow Tibetans To Thrive In Thin Air

There should be an image here!A new study pinpoints the genetic changes that enable Tibetans to thrive at altitudes where others get sick.

In the online edition of Proceedings of the National Academy of Sciences, an international team has identified a gene that allows Tibetans to live and work more than two miles above sea level without getting altitude sickness.

A previous study published May 13 in Science reported that Tibetans are genetically adapted to high altitude. Now, less than a month later, a second study by scientists from China, England, Ireland, and the United States pinpoints a particular site within the human genome — a genetic variant linked to low hemoglobin in the blood — that helps explain how Tibetans cope with low-oxygen conditions.

The study sheds light on how Tibetans, who have lived at extreme elevation for more than 10,000 years, have evolved to differ from their low-altitude ancestors.

Lower air pressure at altitude means fewer oxygen molecules for every lungful of air. “Altitude affects your thinking, your breathing, and your ability to sleep. But high-altitude natives don’t have these problems,” said co-author Cynthia Beall of Case Western Reserve University. “They’re able to live a healthy life, and they do it completely comfortably,” she said.

People who live or travel at high altitude respond to the lack of oxygen by making more hemoglobin, the oxygen-carrying component of human blood. “That’s why athletes like to train at altitude. They increase their oxygen-carrying capacity,” said Beall.

But too much hemoglobin can be a bad thing. Excessive hemoglobin is the hallmark of chronic mountain sickness, an overreaction to altitude characterized by thick and viscous blood. Tibetans maintain relatively low hemoglobin at high altitude, a trait that makes them less susceptible to the disease than other populations.

“Tibetans can live as high as 13,000 feet without the elevated hemoglobin concentrations we see in other people,” said Beall.

To pinpoint the genetic variants underlying Tibetans’ relatively low hemoglobin levels, the researchers collected blood samples from nearly 200 Tibetan villagers living in three regions high in the Himalayas. When they compared the Tibetans’ DNA with their lowland counterparts in China, their results pointed to the same culprit — a gene on chromosome 2, called EPAS1, involved in red blood cell production and hemoglobin concentration in the blood.

Originally working separately, the authors of the study first put their findings together at a March 2009 meeting at the National Evolutionary Synthesis Center in Durham, NC. “Some of us had been working on the whole of Tibetan DNA. Others were looking at small groups of genes. When we shared our findings we suddenly realized that both sets of studies pointed to the same gene — EPAS1,” said Robbins, who co-organized the meeting with Beall.

While all humans have the EPAS1 gene, Tibetans carry a special version of the gene. Over evolutionary time individuals who inherited this variant were better able to survive and passed it on to their children, until eventually it became more common in the population as a whole.

“This is the first human gene locus for which there is hard evidence for genetic selection in Tibetans,” said co-author Peter Robbins of Oxford University.

Researchers are still trying to understand how Tibetans get enough oxygen to their tissues despite low levels of oxygen in the air and bloodstream. Until then, the genetic clues uncovered so far are unlikely to be the end of the story. “There are probably many more signals to be characterized and described,” said co-author Gianpiero Cavalleri of the Royal College of Surgeons in Ireland.

For those who live closer to sea level, the findings may one day help predict who is at greatest risk for altitude sickness. “Once we find these versions, tests can be developed to tell if an individual is sensitive to low-oxygen,” said co-author Changqing Zeng of the Beijing Institute of Genomics.

“Many patients, young and old, are affected by low oxygen levels in their blood — perhaps from lung disease, or heart problems. Some cope much better than others,” said co-author Hugh Montgomery, of University College London. “Studies like this are the start in helping us to understand why, and to develop new treatments.”

Robin Ann Smith @ National Evolutionary Synthesis Center (NESCent)

[Photo above by reurinkjan / CC BY-ND 2.0]

[awsbullet:Peter Kelder]

New Genes Involved In Human Eye Color Identified

There should be an image here!Three new genetic loci have been identified with involvement in subtle and quantitative variation of human eye colour. The study, led by Manfred Kayser of the Erasmus University Medical Center Rotterdam, The Netherlands, is published May 6 in the open-access journal PLoS Genetics.

Previous studies on the genetics of human eye colour used broadly-categorized trait information such as ‘blue’, ‘green’, and ‘brown’; however, variation in eye colour exists in a continuous grading from the lightest blue to the darkest brown. In this genome-wide association study, the eye colour of about 6000 Dutch Europeans from the Rotterdam Study was digitally quantified using high-resolution full-eye photographs. This quantitative approach, which is cost-effective, portable, and time efficient, revealed that human eye colour varies along more dimensions than are represented by the colour categories used previously.

The researchers identified three new loci significantly associated with quantitative eye colour. One of these, the LYST gene, was previously considered a pigmentation gene in mice and cattle, whereas the other two had no previous association with pigmentation.

These three genes, together with previously identified ones, explained over 50% of eye colour variance, representing the highest accuracy achieved so far in genomic prediction of complex and quantitative human traits.

“These findings are also of relevance for future forensic applications”, said Kayser, “where appearance prediction from biological material found at crime scenes may provide investigative leads to trace unknown persons”.

Tamsin Milewicz @ Public Library of Science

[Photo above by Tywak / CC BY-ND 2.0]

[awsbullet:Contact Lens Travel Kit]

Genetic Basis For Health Benefits Of Mediterranean Diet

There should be an image here!Eating a diet rich in the phenolic components of virgin olive oil represses several pro-inflammatory genes. Researchers writing in the open access journal BMC Genomics suggest that this partly explains the reduced risk of cardiovascular disease seen in people who eat a ‘Mediterranean diet’.

Francisco Perez-Jimenez from the University of Cordoba, Spain, led a team of researchers who studied the effects of eating a breakfast rich in phenol compounds on gene expression in 20 patients with metabolic syndrome, a common condition associated with increased risk of cardiovascular disease and type 2 diabetes. The study participants ate controlled breakfasts, and for six weeks before the study they had to avoid all drugs, vitamin tablets and other supplements. Perez-Jimenez said, “We identified 98 differentially expressed genes when comparing the intake of phenol-rich olive oil with low-phenol olive oil. Several of the repressed genes are known to be involved in pro-inflammatory processes, suggesting that the diet can switch the activity of immune system cells to a less deleterious inflammatory profile, as seen in metabolic syndrome.”

Phenols are micronutrients of olive oil; the extra-virgin varieties have a particularly large phenol fraction. According to Perez-Jimenez, “These findings strengthen the relationship between inflammation, obesity and diet and provide evidence at the most basic level of healthy effects derived from virgin olive oil consumption in humans. It will be interesting to evaluate whether particular phenolic compounds carry these effects, or if they are the consequence of a synergic effect of the total phenolic fraction.”

Graeme Baldwin @ BioMed Central

[Photo above by Andreas Levers / CC BY-ND 2.0]

[awsbullet:Mediterranean diet]

Gene That Ties Stress To Obesity And Diabetes Discovered

There should be an image here!The constant stress that many are exposed to in our modern society may be taking a heavy toll: Anxiety disorders and depression, as well as metabolic (substance exchange) disorders, including obesity, type 2 diabetes and arteriosclerosis, have all been linked to stress. These problems are reaching epidemic proportions: Diabetes, alone, is expected to affect some 360 million people worldwide by the year 2030. While anyone who has ever gorged on chocolate before an important exam understands, instinctively, the tie between stress, changes in appetite and anxiety-related behavior, the connection has lately been borne out by science, though the exact reasons for this haven’t been crystal clear. Dr. Alon Chen of the Weizmann Institute’s Neurobiology Department and his research team have now discovered that changes in the activity of a single gene in the brain not only cause mice to exhibit anxious behavior, but also lead to metabolic changes that cause the mice to develop symptoms associated with type 2 diabetes. These findings were published online this week in the Proceedings of the National Academy of Sciences (PNAS).

All of the body’s systems are involved in the stress response, which evolved to deal with threats and danger. Behavioral changes tied to stress include heightened anxiety and concentration, while other changes in the body include heat-generation, changes the metabolism of various substances and even changes in food preferences. What ties all of these things together? The Weizmann team suspected that a protein known as Urocortin-3 (Ucn3) was involved. This protein is produced in certain brain cells — especially in times of stress — and it’s known to play a role in regulating the body’s stress response. These nerve cells have extensions that act as ‘highways’ that speed Ucn3 on to two other sites in the brain: One, in the hypothalamus — the brain’s center for hormonal regulation of basic bodily functions — oversees, among other things, substance exchange and feelings of hunger and satiety; the other is involved in regulating behavior, including levels of anxiety. Nerve cells in both these areas have special receptors for Ucn3 on their surfaces, and the protein binds to these receptors to initiate the stress response.

The researchers developed a new, finely-tuned method for influencing the activity of a single gene in one area in the brain, using it to increase the amounts of Ucn3 produced in just that location. They found that heightened levels of the protein produced two different effects: The mice’s anxiety-related behavior increased, and their bodies underwent metabolic changes, as well. With excess Ucn3, their bodies burned more sugar and fewer fatty acids, and their metabolic rate sped up. These mice began to show signs of the first stages of type 2 diabetes: A drop in muscle sensitivity to insulin delayed sugar uptake by the cells, resulting in raised sugar levels in the blood. Their pancreas then produced extra insulin to make up for the perceived ‘deficit.’

‘We showed that the actions of single gene in just one part of the brain can have profound effects on the metabolism of the whole body,’ says Chen. This mechanism, which appears to be a ‘smoking gun’ tying stress levels to metabolic disease, might, in the future, point the way toward the treatment or prevention of a number of stress-related diseases.

Yivsam Azgad @ Weizmann Institute of Science

[Photo above by David Friel / CC BY-ND 2.0]

[awsbullet:stress obesity diabetes]

Traces Of Early Native Americans – In Sunflower Genes

There should be an image here!New information about early Native Americans’ horticultural practices comes not from hieroglyphs or other artifacts, but from a suite of four gene duplicates found in wild and domesticated sunflowers.

In an upcoming issue of Current Biology, Indiana University Bloomington biologists present the first concrete evidence for how gene duplications can lead to functional diversity in organisms. In this case, the scientists learned how duplications of a gene called FLOWERING LOCUS T, or FT, could have evolved and interacted to prolong a flower’s time to grow. A longer flower growth period means a bigger sunflower — presumably an attribute of great value to the plant’s first breeders.

“Our paper shows how gene duplication creates potential for evolutionary innovation not just through creating new gene content but also through new interactions among duplicates,” said Ben Blackman, the report’s lead author.

Blackman conducted the research as an IU Bloomington Ph.D. student. He is now a postdoctoral fellow at Duke University.

Biologists have long thought the accidental duplication of genetic material provides important fodder for evolution. Less risky than modifying an existing, possibly important gene, duplicates offer an out — one copy can continue its normal activities while the other copy acquires new functions. That’s a hypothesis, anyway. The Current Biology paper suggests reality may be a little more complex.

FT genes play a role in sensitizing flowering plants to seasons, and their expression is usually triggered by changes in day length. Some flowering plants express FT genes early in the growing season as days get longer. Sunflower FT genes are expressed toward the end of the growing season when days are getting shorter. As far as biologists know, all flowering plants have at least one FT gene.

Blackman and his colleagues identified four FT genes in sunflower, Helianthus annuus, which are known as HaFT paralogs. Each of the paralogs, HaFT1 through HaFT4, has a unique genetic sequence, but is similar enough to the others to conclude three of them were the result of DNA duplication events in sunflower’s distant past.

“Based on the level of divergence between the various HaFTs and the presence of a single FT copy in lettuce, we inferred that one copy became two during a whole genome doubling event that occurred roughly 30 million years ago,” Blackman said. “One of those copies proliferated further through two small-scale duplications that we infer occurred much more recently.”

The scientists examined each paralog’s expression patterns within sunflower, and by strategically cloning variants of the HaFT genes into the model plant Arabidopsis thaliana, discerned the paralogs’ physiological properties in one another’s presence.

One of the paralogs, HaFT3, has lost function and is no longer expressed. Countless genome surveys show “non-functionalization” is a common fate for gene duplicates in plants and other eukaryotes, possibly because the extra dose of genetic expression can be wasteful or overtly harmful to the organism.

Two of the paralogs, HaFT2 and HaFT4, are structurally similar to each other and have retained normal function. The proteins they encode are produced in leaves in response to day length. It is believed the HaFT2 and HaFT4 proteins travel down to the stem and up to the shoot tip, where they compel meristem cells to develop into flower buds, but this has yet to be shown conclusively for Helianthus annuus.

HaFT1 isn’t produced in the leaves but at the site of HaFT2 and HaFT4’s target — the shoot tip and the green bracts that will radiate out from the flower itself. There are two basic versions of the HaFT1 called alleles. The domesticated HaFT1 allele is distinguished from the wild allele by the omission of a single nucleotide. But what a difference that nucleotide makes. The protein produced from the domesticated HaFT1 is larger than its wild cousin and has a novel domain.

Only two of the 23 wild populations surveyed possess both types of the HaFT1 allele.

That is not the case for domesticated sunflower populations, for which the domestic version of HaFT1 completely (or almost completely) dominates. Modern domesticated sunflowers used in farming are homogeneous for domesticated HaFT1. The scientists also examined “landraces,” Native Americans’ own domesticated cultivars, some of which are quite old. These too are dominated by domesticated HaFT1.

By comparing the activity of domesticated and wild HaFT1, the scientists learned it is the domesticated version of HaFT1 that lengthens the time period during which flowers grow and mature. This can have a wide variety of effects, from increasing the size of the sunflowers’ seed disk to increasing the flowers’ total seed mass.

Despite its name, domestic HaFT1 isn’t the result of domestication — its origin likely precedes human cultivation. It is called domestic, because it is the version of HaFT1 that caused traits early Native Americans seem to have preferred as they bred the plants for horticulture. Genetic evidence the scientists collected from a broad survey of domesticated and wild HaFT1 genes suggests domesticated HaFT1 experienced a “selective sweep” around the time early Native Americans would have begun cultivating sunflower.

“Our study is the first to provide both strong functional evidence and strong evolutionary evidence that a particular nucleotide variant in this one gene — HaFT1 — was critical for early sunflower domestication,” Blackman said.

How HaFT1 was exerting its flower-delaying effects was not clear until the scientists cloned HaFT1, HaFT2 and HaFT4 into Arabidopsis thaliana in different combinations. A. thaliana’s own FT gene had been removed. Cloning genes in this way can eliminate complicating factors when scientists are interested in knowing how a few genes (and the proteins they encode) interact.

Domesticated HaFT1 had no impact on flowering in the presence of HaFT2. But HaFT1 did delay A. thaliana flowering in the presence of HaFT4. The scientists concluded the newer HaFT1 and older HaFT4 are interacting, possibly directly, in such a way to interfere with HaFT4’s function, thereby delaying flowering.

“In the sunflower story, what is most interesting in my view is how evolution has exploited both recent and ancient gene duplicates in the same gene family to achieve shifts in flowering time and photoperiod sensitivity,” said IU Bloomington plant evolutionary biologist Loren Rieseberg, the study’s principal investigator.

David Bricker @ Indiana University

[Photo above by Philipp Daun / CC BY-ND 2.0]

[awsbullet:Native American history]