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Publisher’s Platform: Will Whole Genome Sequencing Solve More Outbreaks?

“No illnesses have been reported to date.”

How many times have we read a food recall notice posted on either the FDA or FSIS websites and written by the companies recalling the product who use that self-serving statement?  I would say most of the time.

In the past few months the CDC has reported three outbreaks – one Salmonella outbreak and two Listeria outbreaks that have used whole-genome sequencing to connect ill people to tainted product. Perhaps “No illnesses have been reported to date” is a statement of the past trumped by science.

So, what is the science?

State and CDC public health investigators have used the PulseNet system to identify cases of illness that were part of an outbreak for nearly two decades.  PulseNet, the national subtyping network of public health and food regulatory agency laboratories coordinated by CDC, receives from state laboratories DNA “fingerprints” of bacteria obtained through diagnostic testing using Pulsed-field Gel Electrophoresis (PFGE).

Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) is another technique used by scientists to generate a DNA fingerprint for a bacterial isolate. Scientists usually perform MLVA after PFGE to find out more specific details about the type of bacteria that may be causing an outbreak.

Whole Genome Sequencing, is a newer, more highly discriminatory subtyping method, that has been used to define the following outbreaks:

Oasis Brands Inc., Cheese Recalls and Investigation of Human Listeriosis Cases – One person became ill in September 2013 and two persons became ill in June and August 2014. These three ill persons were reported from three states: New York (1), Tennessee (1), and Texas (1).  All ill persons were hospitalized. One death was reported in Tennessee. One illness was related to a pregnancy and was diagnosed in a newborn.

Wholesome Soy Products, Inc. Sprouts Recall and Investigation of Human Listeriosis Cases - Five people became ill from June through August 2014. These five ill people were reported from two states: Illinois (4) and Michigan (1).  All ill people were hospitalized. Two deaths were reported.

Multistate Outbreak of Salmonella Braenderup Infections Linked to Nut Butter Manufactured by nSpired Natural Foods, Inc. - A total of six persons infected with the outbreak strain of Salmonella Braenderup were reported from five states since January 1, 2014.  The number of ill persons identified in each state was as follows: Connecticut (1), Iowa (1), New Mexico (1), Tennessee (1), and Texas (2).

“No illnesses have been reported to date,” may well be a statement of the past.

Food Safety News

Genome sequencing of the jujube tree completed

BGI Tech and Hebei Agricultural University jointly announced the complete, high quality sequencing of the Jujube genome. Jujube is the most economically important member of the Rhamnaceae family, and the Jujube genome is particularly difficult to sequence due the high level of heterozygosity and other complicating factors. It is the first time that a genome in the Rhamnaceae (Buckthorn) family has been sequenced.

This study has been recently published in Nature Communications.

Jujube is a major commercial fruit with up to 30 million acres under cultivation — close to that of apple and citrus — and China accounts for 99% of the 6 million tons of dried fruit produced annually. Jujube has a much higher vitamin C content than other well-known vitamin C-rich fruits such as orange and kiwi fruit, and also high levels of nucleotides, polysaccharides and other important functional components. Furthermore, the jujube tree is highly resistant to salinity and drought, and grows well in sandy, alkaline and arid areas. Therefor, decoding the genome of the jujube tree will have great implications to exploit those important traits.

The Jujube genome has the highest degree of heterozygosity (1.9%) of plants sequenced to date using next generation sequencing (NGS). In addition, the very high density of simple sequence repeats and low GC content make the Jujube genome particularly challenging for whole genome sequencing and assembly. By using a combination of BAC-to-BAC sequencing and PCR-free whole genome sequencing, the researchers were able to successfully complete the high quality de novo sequencing of 98.6% of the estimated Jujube genome, identifying 32,808 genes.

“This study has accelerated the functional genomics research of the Jujube tree, and will facilitate the genetic improvement and selective breeding of Buckthorn fruit trees,” said Professor Mengjun Liu, head of the research team, for Hebei Agricultural Unviersity. “This research not only shows the expertise of the team and the power of sequencing technology, but we also expect its future applications in bring more value and benefits in healthy food production.”

Story Source:

The above story is based on materials provided by BGI Shenzhen. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Coffee genome sheds light on the evolution of caffeine

The newly sequenced genome of the coffee plant reveals secrets about the evolution of man’s best chemical friend: caffeine.

The scientists who completed the project say the sequences and positions of genes in the coffee plant show that they evolved independently from genes with similar functions in tea and chocolate, which also make caffeine.

In other words, coffee did not inherit caffeine-linked genes from a common ancestor, but instead developed the genes on its own.

The findings will appear on Sept. 5 in the journal Science.

Why Coffee?

With more than 2.25 billion cups consumed daily worldwide, coffee is the principal agricultural product of many tropical countries. According to estimates by the International Coffee Organization, more than 8.7 million tons of coffee were produced in 2013, revenue from exports amounted to $ 15.4 billion in 2009-2010, and the sector employed nearly 26 million people in 52 countries during 2010.

“Coffee is as important to everyday early risers as it is to the global economy. Accordingly, a genome sequence could be a significant step toward improving coffee,” said Philippe Lashermes, a researcher at the French Institute of Research for Development (IRD). “By looking at the coffee genome and genes specific to coffee, we were able to draw some conclusions about what makes coffee special.”

Lashermes, along with Patrick Wincker and France Denoeud, genome scientists at the French National Sequencing Center (CEA-Genoscope), and Victor Albert, professor of biological sciences at the University at Buffalo, are the principal authors of the study.

Scientists from other organizations, particularly the Agricultural Research Center for International Development in France, also contributed, along with researchers from public and private organizations in the U.S., France, Italy, Canada, Germany, China, Spain, Indonesia, Brazil, Australia and India.

The team created a high-quality draft of the genome of Coffea canephora, which accounts for about 30 percent of the world’s coffee production, according to the Manhattan-based National Coffee Association.

Next, the scientists looked at how coffee’s genetic make-up is distinct from other species.

Compared to several other plant species including the grape and tomato, coffee harbors larger families of genes that relate to the production of alkaloid and flavonoid compounds, which contribute to qualities such as coffee aroma and the bitterness of beans.

Coffee also has an expanded collection of N-methyltransferases, enzymes that are involved in making caffeine.

Upon taking a closer look, the researchers found that coffee’s caffeine enzymes are more closely related to other genes within the coffee plant than to caffeine enzymes in tea and chocolate.

This finding suggests that caffeine production developed independently in coffee. If this trait had been inherited from a common ancestor, the enzymes would have been more similar between species.

“The coffee genome helps us understand what’s exciting about coffee — other than that it wakes me up in the morning,” Albert said. “By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffee’s independent pathway in evolution, including — excitingly — the story of caffeine.”

Why caffeine is so important in nature is another question. Scientists theorize that the chemical may help plants repel insects or stunt competitors’ growth. One recent paper showed that pollinators — like humans — may develop caffeine habits. Insects that visited caffeine-producing plants often returned to get another taste.

The new Science study doesn’t offer new ideas about the evolutionary role of caffeine, but it does reinforce the idea that the compound is a valuable asset. It also provides the opportunity to better understand the evolution of coffee’s genome structure.

“It turns out that, over evolutionary time, the coffee genome wasn’t triplicated as in its relatives: the tomato and chile pepper,” Wincker said. “Instead it maintained a structure similar to the grape’s. As such, evolutionary diversification of the coffee genome was likely more driven by duplications in particular gene families as opposed to en masse, when all genes in the genome duplicate.”

This stands in contrast to what’s been suggested for several other large plant families, where other investigators have noted correlations between high species diversity in a group and the presence of whole genome doublings or triplings.

“Coffee lies in the plant family Rubiaceae, which has about 13,000 species and is the world’s fourth largest; thus, with no genome duplication at its root, it appears to break the mold of a genome duplication link to high biodiversity,” Denoeud said.

Agriculture and Food News — ScienceDaily

Canola genome sequence reveals evolutionary ‘love triangle’

An international team of scientists including researchers from the University of Georgia recently published the genome of Brassica napus-commonly known as canola — in the journal Science. Their discovery paves the way for improved versions of the plant, which is used widely in farming and industry.

Canola is grown across much of Canada and its native Europe, but the winter crop is increasingly cultivated in Georgia. Canola oil used for cooking is prized for its naturally low levels of saturated fat and rich supply of omega-3 fatty acids, but the plant is also used to produce feed for farm animals and as an efficient source for biodiesel.

“This genome sequence opens new doors to accelerating the improvement of canola,” said Andrew Paterson, Regents Professor, director of UGA’s Plant Genome Mapping Laboratory and co-corresponding author for the study. “We can use this knowledge to tailor the plant’s flowering time, make it more resistant to disease and improve a myriad of other traits that will make it more profitable for production in Georgia and across the country.”

Canola has one of the most complex genomes among flowering plants, forming thousands of years ago during the Neolithic Era when two plant species-Brassica rapa and Brassica oleracea-combined in the wild. Plants in the B. rapa family include turnips and cabbages, while B. oleracea encompasses cauliflower, cabbage, collards, broccoli, kale and other common vegetables.

The Plant Genome Mapping Laboratory played prominent roles in the sequencing both B. rapa and B. oleracea in 2011 and 2014, respectively.

“Understanding the genomes of B. rapa and B. oleracea was key to piecing together the canola genome,” Paterson said. “It’s like a genetic love triangle between the three species, with canola sometimes favoring genes from B. rapa or B. oleracea or sometimes both.”

While much the world’s canola is used to make cooking oil and protein-rich animal feed, it is also used in the production of lipstick, lip gloss, soap, lotion, printing ink and de-icing agents.

The growing interest in carbon reduction and more environmentally friendly fuel alternatives is also good news for canola growers, as this genome sequence may ultimately help researchers develop feedstocks that are suited to more sustainable biofuel production.

Global canola production has grown rapidly over the past 40 years, rising from the sixth largest oil crop to the second largest, according to the U.S. Department of Agriculture.

Much of the production in America is concentrated along the northern plains, but the recent construction of a canola processing plant near the South Carolina-Georgia border has spurred interest for growers in the Southeast.

Additional UGA researchers for the project include Xiyin Wang, assistant research scientist and co-first author for the paper; Tae-ho Lee and Yupeng Wang, former postdoctoral researchers; and current and former graduate students Hui Guo, Huizhe Jin, Jingping Li, Xu Tan, Haibao Tang, and Yupeng Wang.

Story Source:

The above story is based on materials provided by University of Georgia. The original article was written by James Hataway. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Genome analysis helps in breeding more robust cows

Genome analysis of 234 bulls has put researchers, including several from Wageningen Livestock Research, on the trail of DNA variants which influence particular characteristics in breeding bulls. For example, two variants have proven responsible for disruptions to the development of embryos and for curly hair, which is disadvantageous because more ticks and parasites occur in curly hair than in short, straight hair. These are the first results of the large 1000 Bull Genomes project on which some 30 international researchers are collaborating. They report on their research in the most recent edition of the science journal Nature Genetics.

Most breeding characteristics are influenced by not one but a multiplicity of variants. It is therefore important to be able to use all the variants in breeding, say the Wageningen researchers. In order to make this possible, Rianne van Binsbergen, PhD researcher at the Animal Breeding and Genomics Centre of Wageningen UR, investigated whether the genomes of all the common bulls in the Netherlands can be filled with the help of these 234 bulls. Currently, these bulls have been genotyped with markers of 50,000 or 700,000 DNA variants. The positive results indicate the direction for further research into the practical use of genome information in breeding.

Dairy and beef cattle The project demonstrates how useful large-scale DNA analyses can be, says Professor Roel Veerkamp, Professor of Numerical Genetics at Wageningen University and board member of the 1000 Bull Genomes project. He emphasises that the requirements for dairy and beef cattle are becoming ever more exacting: “Until the mid nineties, a cow primarily had to produce a lot of milk. But since then, expectations have gone up. Farmers are looking for more robust cows. In practice, that means good fertility, longer life, udders that give good protection against infections, improved claws and more efficient feed utilisation. That adds up to a lot of characteristics, which are governed by all kinds of genes. In order to bring them together in a cow in the best and fastest way possible, genomic selection is important for breeding organisations such as CRV, and by means of genome analysis we want to improve this further,” says Veerkamp.

Bull genome The genome of a bull consists of 3 billion ‘letters’. In the 234 bulls studied, the researchers found a total of over 28 million positions on the DNA which displayed variation, in other words where the animals have different letters. Currently, CRV uses approximately 50,000 variants, the so-called single nucleotide polymorphisms (SNP) for genomic selection, by linking SNP patterns of a very large number of animals to characteristics which are important for robustness. Together with CRV and the other partners in the Breed4Food programme, the researchers are investigating whether the new genome information can help to predict even better which characteristics the offspring will have.

The bull analysis presented at this time is the first phase of the 1,000 Bull Genomes project, a database which is planned to incorporate the genomes of a thousand bulls from all over the world. The bulls analysed to date are primarily from Australia, the Netherlands, Germany and France. “However, there are now many more countries involved and we have already exceeded 1000 bulls,” says Professor Veerkamp.

Story Source:

The above story is based on materials provided by Wageningen University and Research Centre. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Chromosome-based draft of the wheat genome completed

Several Kansas State University researchers were essential in helping scientists assemble a draft of a genetic blueprint of bread wheat, also known as common wheat. The food plant is grown on more than 531 million acres around the world and produces nearly 700 million tons of food each year.

The International Wheat Genome Sequencing Consortium, which also includes faculty at Kansas State University, recently published a chromosome-based draft sequence of wheat’s genetic code, which is called a genome. “A chromosome-based draft sequence of the hexaploid bread wheat genome” is one of four papers about the wheat genome that appear in the journal Science.

The genetic blueprint is an invaluable resource to plant science researchers and breeders, said Eduard Akhunov, associate professor of plant pathology and a collaborator with the International Wheat Genome Sequencing Consortium.

“For the first time, they have at their disposal a set of tools enabling them to rapidly locate specific genes on individual wheat chromosomes throughout the genome,” Akhunov said. “This resource is invaluable for identifying those genes that control complex traits, such as yield, grain quality, disease, pest resistance and abiotic stress tolerance. They will be able to produce a new generation of wheat varieties with higher yields and improved sustainability to meet the demands of a growing world population in a changing environment.”

Although a draft, the sequence provides new insight into the plant’s structure, organization, evolution and genetic complexity.

“This is a very significant advancement for wheat genetics and breeding community,” Akhunov said. “The wheat genome sequence provides a foundation for studying genetic variation and understanding how changes in the genetic code can impact important agronomic traits. In our lab we use this sequence to create a catalog of single base changes in DNA sequence of a worldwide sample of wheat lines to get insights into the evolution and origin of wheat genetic diversity.”

Akhunov, Shichen Wang, a programmer and bioinformatics scientist in plant pathology, and Jesse Poland, assistant professor of plant pathology, collaborated with the International Wheat Genome Sequencing Consortium to order genes along the wheat chromosomes.

Other Kansas State University researchers in the department of plant pathology involved include Bikram Gill, university distinguished professor and director of the Wheat Genetics Resource Center, and Bernd Friebe, research professor, who developed genetic material that was essential for obtaining the chromosome-based sequence of the wheat genome.

A second paper in Science details the first reference sequence of chromosome 3B, the largest chromosome in common wheat.

“The wheat genome only has 21 chromosomes, but each chromosome is very big and therefore quite complicated,” Akhunov said. “The largest chromosome, 3B, has nearly 800 million letters in its genetic code. This is nearly three times more information than is in the entire rice genome. So trying to sequence this chromosome — and this genome — end-to-end is an extremely complicated task.”

In order to analyze the vast amount of genetic information, researchers used a technique called shotgun sequencing. This divided the wheat genome into chromosomes and then split each chromosome into smaller segments. Chromosomal segments were analyzed by short gene sequences and overlapping sequences were stitched together with computer software.

The chromosome-based daft sequence the critical step before the full wheat genome is sequenced, Akhunov said. The sequencing approach developed for the 3B chromosome can now be applied for sequencing the remaining chromosomes in wheat. The consortium estimates the full genome sequence will be available in three years.

The research is funded by the U.S. Department of Agriculture’s National Institute of Food and Agriculture.

“Wheat is a staple source of food for the majority of the world. As the global population continues to rapidly increase, we will need all the tools available to continue producing enough food for all people in light of a changing climate, diminishing land and water resources and changing diets and health expectations,” said Sonny Ramaswamy, director of USDA’s National Institute of Food and Agriculture and a former Kansas State University faculty member. “This work will give a boost to researchers looking to identify ways to increase wheat yields.”

Story Source:

The above story is based on materials provided by Kansas State University. The original article was written by Greg Tammen. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

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The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

A-maize-ing double life of a genome

Early maize farmers selected for genes that improved the harvesting of sunlight, a new detailed study of how plants use ‘doubles’ of their genomes reveals. The findings could help current efforts to improve existing crop varieties.

Oxford University researchers captured a ‘genetic snapshot’ of maize as it existed 10 million years ago when the plant made a double of its genome — a ‘whole genome duplication’ event. They then traced how maize evolved to use these ‘copied’ genes to cope with the pressures of domestication, which began around 12,000 years ago. They discovered that these copied genes were vital to optimizing photosynthesis in maize leaves and that early farmers selecting for them ‘fuelled’ the transformation of maize into a high-yield crop.

A report of the research is published this week in the journal Genome Research.

‘Although whole genome duplication events are widespread in plants finding evidence of exactly how plants use this new ‘toolbox’ of copied genes is very difficult,’ said Dr Steve Kelly of Oxford University’s Department of Plant Sciences, lead author of the report. ‘With crops like wheat it’s not yet possible for us to unravel the ‘before and after’ of the associated genetic changes, but with maize we can chart how these gene copies were first acquired, then put to work, and finally ‘whittled down’ to create the modern maize plant farmed today.’

It is particularly useful for such genetic detective work that close relatives of maize did not duplicate their genomes 10 million years ago: those that retained a single copy went on to become the plant we now know as sorghum. This enabled the researchers to compare genetic data from these ‘duplicated’ and ‘non-duplicated’ descendants of ancient maize, something that is not yet possible with other duplicated crops like wheat.

In the wild plants have to overcome the challenges posed by pathogens and predators in order to survive. However, once domestication by humans began plants grown as crops had to cope with a new set of artificial selection pressures, such as delivering a high yield and greater stress tolerance.

‘Whole genome duplication events are key in allowing plants to evolve new abilities,’ said Dr Kelly. ‘Understanding the complete trajectory of duplication and how copied genes can transform a plant is relevant for current efforts to increase the photosynthetic efficiency of crops, such as the C4 Rice Project [c4rice.irri.org/]. Our study is great evidence that optimizing photosynthesis is really important for creating high-yield crops and shows how human selection has ‘sculpted’ copies of genes to create one of the world’s staple food sources.’

Story Source:

The above story is based on materials provided by University of Oxford. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Sequenced salmon genome: Scientific breakthrough from international collaboration

The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG) announced completion of a fully mapped and openly accessible salmon genome. This reference genome will provide crucial information to fish managers to improve the production and sustainability of aquaculture operations, and address challenges around conservation of wild stocks, preservation of at-risk fish populations and environmental sustainability. This breakthrough was announced at the International Conference on Integrative Salmonid Biology (ICISB) being held in Vancouver.

Salmonids are an important piece of the economic and social fabric of communities on BC’s coastline and many other countries including Norway and Chile. The fisheries and aquaculture sector is one of the economic engines of BC: seafood is the province’s largest agri-food export, contributing $ 870 million of the province’s total agri-food exports of $ 2.5 billion. High value species such as salmon make a significant economic contribution to the economy. Canada’s Atlantic salmon related aquaculture revenues exceed $ 600 million annually and BC is the only province with a commercial salmon fishery.

Salmonids are also a key species for research and while some salmon genetic information is known, many fundamental questions have remained: a fully assembled reference sequence available for researchers worldwide will have a major impact on revealing information about salmon and other salmonids, such as rainbow trout and Pacific salmon.

Viruses and pathogens are a challenging hazard to livelihoods and economies dependent on salmon and this sequence provides real support to improve the production of salmonids in a sustainable way. Other benefits of the salmon sequence include applications for food security and traceability and broodstock selection for commercially important traits. Healthier food, more environmentally sound fish farming and better interactions with wild salmon are all positive outcomes from this research.

“Knowledge of the whole genome makes it possible to see how genes interact with each other, and examine the exact gene that governs a certain trait such as resistance against a particular disease,” says Dr. Steinar Bergseth, Chair of the International Steering Committee for the ICSASG. “The development of vaccines and targeted treatment is much closer.”

The international collaboration involves researchers, funding bodies and industry from Canada, Chile and Norway. The successful completion of the salmon genome provides a basis for continued partnerships between these and other countries involved in research and industrial development of salmonids.

“A better scientific understanding of this species and its genome is a critical step towards improving the growth and management of global fisheries and aquaculture,” says Dr. Alan Winter, President & CEO of Genome BC. “Additionally, the level of international collaboration seen in this project is a testament to the importance of global coordination to address challenges too big for any one country individually.”

The aquaculture industries need to produce healthy food in a sustainable and efficient manner to be in line with the consumer demands. “The knowledge of the sequence will certainly give us a long awaited tool to achieve this” says Petter Arnesen, Breeding Director of Marine Harvest, Norway.

Story Source:

The above story is based on materials provided by Genome BC. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Milestone in salmon research: Genome fully sequenced

Fully sequencing the Atlantic salmon genome is a landmark achievement — and provides a wellspring of new opportunities for scientists and the aquaculture industry worldwide.

The detailed overview of the salmon’s genetic material provides the framework for new research and development that may solve many longstanding riddles.

“We now have the complete sequence of the Atlantic salmon genome, every letter and code.

This is a powerful tool for understanding the connection between the salmon’s genetic codes and its biology,” says Steinar Bergseth, Special Adviser at the Research Council of Norway.

As chair of the international project, Dr Bergseth made the genetic code public at a scientific conference in Vancouver, Canada, on 10 June 2014.

Help streamline the industry

The new knowledge will be useful in efforts to develop new vaccines, improve feeding and understand more about what happens when escaped farmed fish mix with their wild counterparts. Selective breeding of salmon will be more targeted and efficient.

In the longer term, the genomic knowledge will help to streamline the aquaculture industry while providing consumers with healthier farmed salmon, produced with as little environmental impact as possible.

Petter Arnesen, Breeding Director at the fish farming company Marine Harvest, agrees that 10 June is a milestone for anyone involved in aquaculture. Marine Harvest is one of the industrial partners in the genome project and has contributed to its funding.

Better breeding tools

“The sequence will make it possible to develop new, more effective selective breeding tools that will make us even better at choosing parent fish with desired traits for the next generation of salmon,” says Mr Arnesen.

“Enhanced knowledge about the genetic material allows us to utilise more of the genetic variation from within the stocks that farmed salmon are produced from. Furthermore, the sequence opens up new prospects for studying biological and physiological processes.”

Healthier fish

Mr Arnesen emphasises that selective breeding practices in no way involve gene modification, but rather are a means to finding the right individuals to select as parent fish — individuals that naturally have desired traits that producers want to pass on to coming generations of production salmon.

He is convinced that the salmon genome sequence will help to promote a healthier aquaculture industry.

“We are seeking to produce fish that are as healthy as possible,” continues Mr Arnesen, “and among other traits that entails better disease resistance. Salmon lice are currently our biggest challenge, along with other parasites and viruses.”

Solving environmental challenges

Using the salmon genome as a tool, salmon producers hope to raise fish that grow faster, which means less time spent at sea.

The sequence, he asserts, “is also going to play a major role in solving our environmental challenges, if we can for instance select for individuals that are more resistant to disease and parasites and that can adapt well to new feed types. For many consumers, environmental soundness is an integral part of product quality. The conscientious consumer will not buy salmon if its production is harmful to the environment.”

Fighting disease

Improved vaccines have eliminated most of the bacterial diseases that were causing substantial losses at fish farms into the 1990s. These vaccines, however, are not effective against viruses — so one solution is selecting parent fish with virus-resistant traits to use as broodstock for salmon egg production.

AquaGen is another industrial partner in the genome project that is looking forward to utilising the sequenced genome. A major supplier of salmon eggs, the company invests heavily in research and development.

One project that AquaGen started up in 2005 was a collaboration with the Centre for Integrative Genetics (CIGENE), at the Norwegian University of Life Sciences, and the Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima) to make a precise map of the genetic markers that make certain salmon individuals resistant to the IPN (infectious pancreatic necrosis) virus.

Success

Over the years this virus has been the cause of major disease outbreaks at fish farms around the world, leading to significant economic losses. The research project has paid off.

“The IPN project has been a huge success,” says Nina Santi, head of R&D at AquaGen. “Since we started using eggs from fish with the desired traits, the number of IPN outbreaks in Norway has dropped from 200 per year to 50.”

Could have saved years of work

The project also illustrates the progress to be gained from knowing the complete salmon genome.

First step

“After the IPN markers were identified in 2007,” continues Dr Santi, “we have been working for seven years on mapping the mechanism for resistance to the IPN virus. Had we had access to the genome sequence now being made public, it would have saved us several years.”

She stresses that the sequence is only the first step.

“Now we know the genome of one individual, which the scientists named Sally, but we are more interested in understanding the variations between individuals. Our next step is to sequence different generations in order to find out, for example, which of them is most resistant to disease and exhibits good growth and red fillet colour.”

Extraordinary potential to create value

Survival rates just a few per cent higher translate into major earnings for the Norwegian aquaculture industry, where the annual turnover is NOK 45 billion (approximately 5,6 billion Euro/7,6 billion Dollars), according to Odd Magne Rødseth, Chairman of the Board at AquaGen.

“In the past 15 to 20 years,” Dr Rødseth explains, “viruses have been the primary cause of mortality. What we are seeing now is the result of better selective breeding programmes focused on disease resistance. Mortality has dropped four to five per cent for the latest year-class of salmon. This is due to what is in effect the elimination of IPN, thanks to practical application of new knowledge about the salmon genome. This increase in survival means an additional profit of NOK 2.6 billion (approximately 320 million Euro/440 million Dollars) .”

Now that the entire salmon genome has been sequenced and made available, Dr Rødseth is certain that it will become cheaper and faster to find other significant genes in the future.

“In the next three to five years,” he predicts, “we will probably be hearing more success stories like the IPN achievement.”

Complex genetic material

The international genome project has revealed the salmon’s genetic material as very complex.

Whereas most species (including humans) have two copies of each chromosome, salmon have four, which posed special challenges during the already painstaking work of sequencing.

The five-year project is the largest research collaboration ever carried out between the salmon-producing countries of Canada, Chile and Norway. The sequence is now being made available to the global research community and industry alike.

“This will strengthen salmon-related research in many fields, from physiology and genetics to nutrition and reproduction,” says Kjell Maroni of the Norwegian Seafood Research Fund (FHF). “It will also open up more possibilities for international cooperation, which will benefit the entire aquaculture industry.”

Researchers and industry involved with other salmonids such as rainbow trout, char and Pacific salmon will also find useful applications for this new tool.

Continued international work

Participants at the 10 June conference in Canada will be discussing possibilities for continued international collaboration based on the reference sequence.

Countries other than Norway, Canada and Chile are also invited to take part.

“These efforts, if successful, will yield great returns in the form of future understanding of salmonids and their environment,” says Dr Bergseth, emphasising how crucial it is to use the sequence now that it has been obtained:

“Now we have a new textbook at our disposal, but it won’t help if we don’t consult it. Salmon is Norway’s most important production animal, and we have invested a great deal in the genome project. Now we need to continue to invest in R&D to translate that knowledge into products of value.

Agriculture and Food News — ScienceDaily

Milestone in salmon research: Genome fully sequenced

Fully sequencing the Atlantic salmon genome is a landmark achievement — and provides a wellspring of new opportunities for scientists and the aquaculture industry worldwide.

The detailed overview of the salmon’s genetic material provides the framework for new research and development that may solve many longstanding riddles.

“We now have the complete sequence of the Atlantic salmon genome, every letter and code.

This is a powerful tool for understanding the connection between the salmon’s genetic codes and its biology,” says Steinar Bergseth, Special Adviser at the Research Council of Norway.

As chair of the international project, Dr Bergseth made the genetic code public at a scientific conference in Vancouver, Canada, on 10 June 2014.

Help streamline the industry

The new knowledge will be useful in efforts to develop new vaccines, improve feeding and understand more about what happens when escaped farmed fish mix with their wild counterparts. Selective breeding of salmon will be more targeted and efficient.

In the longer term, the genomic knowledge will help to streamline the aquaculture industry while providing consumers with healthier farmed salmon, produced with as little environmental impact as possible.

Petter Arnesen, Breeding Director at the fish farming company Marine Harvest, agrees that 10 June is a milestone for anyone involved in aquaculture. Marine Harvest is one of the industrial partners in the genome project and has contributed to its funding.

Better breeding tools

“The sequence will make it possible to develop new, more effective selective breeding tools that will make us even better at choosing parent fish with desired traits for the next generation of salmon,” says Mr Arnesen.

“Enhanced knowledge about the genetic material allows us to utilise more of the genetic variation from within the stocks that farmed salmon are produced from. Furthermore, the sequence opens up new prospects for studying biological and physiological processes.”

Healthier fish

Mr Arnesen emphasises that selective breeding practices in no way involve gene modification, but rather are a means to finding the right individuals to select as parent fish — individuals that naturally have desired traits that producers want to pass on to coming generations of production salmon.

He is convinced that the salmon genome sequence will help to promote a healthier aquaculture industry.

“We are seeking to produce fish that are as healthy as possible,” continues Mr Arnesen, “and among other traits that entails better disease resistance. Salmon lice are currently our biggest challenge, along with other parasites and viruses.”

Solving environmental challenges

Using the salmon genome as a tool, salmon producers hope to raise fish that grow faster, which means less time spent at sea.

The sequence, he asserts, “is also going to play a major role in solving our environmental challenges, if we can for instance select for individuals that are more resistant to disease and parasites and that can adapt well to new feed types. For many consumers, environmental soundness is an integral part of product quality. The conscientious consumer will not buy salmon if its production is harmful to the environment.”

Fighting disease

Improved vaccines have eliminated most of the bacterial diseases that were causing substantial losses at fish farms into the 1990s. These vaccines, however, are not effective against viruses — so one solution is selecting parent fish with virus-resistant traits to use as broodstock for salmon egg production.

AquaGen is another industrial partner in the genome project that is looking forward to utilising the sequenced genome. A major supplier of salmon eggs, the company invests heavily in research and development.

One project that AquaGen started up in 2005 was a collaboration with the Centre for Integrative Genetics (CIGENE), at the Norwegian University of Life Sciences, and the Norwegian Institute of Food, Fisheries and Aquaculture Research (Nofima) to make a precise map of the genetic markers that make certain salmon individuals resistant to the IPN (infectious pancreatic necrosis) virus.

Success

Over the years this virus has been the cause of major disease outbreaks at fish farms around the world, leading to significant economic losses. The research project has paid off.

“The IPN project has been a huge success,” says Nina Santi, head of R&D at AquaGen. “Since we started using eggs from fish with the desired traits, the number of IPN outbreaks in Norway has dropped from 200 per year to 50.”

Could have saved years of work

The project also illustrates the progress to be gained from knowing the complete salmon genome.

First step

“After the IPN markers were identified in 2007,” continues Dr Santi, “we have been working for seven years on mapping the mechanism for resistance to the IPN virus. Had we had access to the genome sequence now being made public, it would have saved us several years.”

She stresses that the sequence is only the first step.

“Now we know the genome of one individual, which the scientists named Sally, but we are more interested in understanding the variations between individuals. Our next step is to sequence different generations in order to find out, for example, which of them is most resistant to disease and exhibits good growth and red fillet colour.”

Extraordinary potential to create value

Survival rates just a few per cent higher translate into major earnings for the Norwegian aquaculture industry, where the annual turnover is NOK 45 billion (approximately 5,6 billion Euro/7,6 billion Dollars), according to Odd Magne Rødseth, Chairman of the Board at AquaGen.

“In the past 15 to 20 years,” Dr Rødseth explains, “viruses have been the primary cause of mortality. What we are seeing now is the result of better selective breeding programmes focused on disease resistance. Mortality has dropped four to five per cent for the latest year-class of salmon. This is due to what is in effect the elimination of IPN, thanks to practical application of new knowledge about the salmon genome. This increase in survival means an additional profit of NOK 2.6 billion (approximately 320 million Euro/440 million Dollars) .”

Now that the entire salmon genome has been sequenced and made available, Dr Rødseth is certain that it will become cheaper and faster to find other significant genes in the future.

“In the next three to five years,” he predicts, “we will probably be hearing more success stories like the IPN achievement.”

Complex genetic material

The international genome project has revealed the salmon’s genetic material as very complex.

Whereas most species (including humans) have two copies of each chromosome, salmon have four, which posed special challenges during the already painstaking work of sequencing.

The five-year project is the largest research collaboration ever carried out between the salmon-producing countries of Canada, Chile and Norway. The sequence is now being made available to the global research community and industry alike.

“This will strengthen salmon-related research in many fields, from physiology and genetics to nutrition and reproduction,” says Kjell Maroni of the Norwegian Seafood Research Fund (FHF). “It will also open up more possibilities for international cooperation, which will benefit the entire aquaculture industry.”

Researchers and industry involved with other salmonids such as rainbow trout, char and Pacific salmon will also find useful applications for this new tool.

Continued international work

Participants at the 10 June conference in Canada will be discussing possibilities for continued international collaboration based on the reference sequence.

Countries other than Norway, Canada and Chile are also invited to take part.

“These efforts, if successful, will yield great returns in the form of future understanding of salmonids and their environment,” says Dr Bergseth, emphasising how crucial it is to use the sequence now that it has been obtained:

“Now we have a new textbook at our disposal, but it won’t help if we don’t consult it. Salmon is Norway’s most important production animal, and we have invested a great deal in the genome project. Now we need to continue to invest in R&D to translate that knowledge into products of value.

Agriculture and Food News — ScienceDaily

Genome of another diploid cotton Gossypium arboreum cracked

Chinese scientists from Chinese Academy of Agricultural Sciences and BGI successfully deciphered the genome sequence of another diploid cotton– Gossypium arboreum (AA) after the completed sequencing of G. raimondii (DD) in 2012. G. arboreum, a cultivated cotton, is a putative contributor for the A subgenome of cotton. Its completed genome will play a vital contribution to the future molecular breeding and genetic improvement of cotton and its close relatives. The latest study today was published online in Nature Genetics.

As one of the most important economic crops in the world, cotton also serves as an excellent model system for studying polyploidization, cell elongation and cell wall biosynthesis. However, breeders and geneticists have had little knowledge of the genetic mechanisms underlying the complex allotetraploid nature of the cotton genome (AADD). It has been proposed that all of today’s diploid cotton species may have evolved from a common ancestor, and all tetraploid cotton species came from interspecific hybridization between the cultivated species G. arboreum and the non-cultivated species G. raimondii.

After the completed sequencing of G. raimondii in 2012, researchers started the work on decoding the genome of G. arboreum. In this study, they sequenced and assembled the G. arboreum genome using whole-genome shotgun approach, yielding a draft cotton genome with the size of 1,694 Mb. About 90.4% of the G. arboretum assembled scaffolds were anchored and oriented on 13 pseudochromosomes.

Furthermore, researchers found the long terminal repeat (LTR) retrotransposons insertions and expansions of LTR families contributed significantly to forming the double-sized G. arboreum genome relative to that of G. raimondii. Further molecular phylogenetic analyses suggested that G. arboreum and G. raimondii diverged about 5 million years ago, and the protein-coding capacities of these two species remained largely unchanged.

To investigate the plant morphology mechanisms of cotton species, a series of comparative transcriptome studies were performed. Results suggested that NBS-encoding subfamilies played an essential role on the immune to Verticillium dahliae. The resistance of G. raimondii on Verticillium dahliae was caused by expansion and contraction in the numbers of NBS-encoding genes, accordingly the loss in the genome of G. arboreum was responsible to their susceptible.

Another interesting finding of this study is the cotton fiber cell growth, and they found the 1-aminocyclo-propane-1-carboxylic acid oxidase (ACO) gene was a key modulator. Researchers suggest the overproduction of ACO maybe the reason why G. raimondii have a poor production of spinnable fiber, while the inactivation of ACO in G. arboreum might benefit its fiber development.

The G. arboreum genome will be an essential reference for the assembly of tetraploid cotton genomes and for evolutionary studies of Gossypium species. It also provides an essential tool for the identification, isolation and manipulation of important cotton genes conferring agronomic traits for molecular breeding and genetic improvement.

Story Source:

The above story is based on materials provided by BGI Shenzhen. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

First peanut genome sequenced

The International Peanut Genome Initiative — a group of multinational crop geneticists who have been working in tandem for the last several years — has successfully sequenced the peanut’s genome.

Scott Jackson, director of the University of Georgia Center for Applied Genetic Technologies in the College of Agricultural and Environmental Sciences, serves as chair of the International Peanut Genome Initiative, or IPGI.

The new peanut genome sequence will be available to researchers and plant breeders across the globe to aid in the breeding of more productive and more resilient peanut varieties.

Peanut, known scientifically as Arachis hypogaea and also called groundnut, is important both commercially and nutritionally. While the oil- and protein-rich legume is seen as a cash crop in the developed world, it remains a valuable sustenance crop in developing nations.

“The peanut crop is important in the United States, but it’s very important for developing nations as well,” Jackson said. “In many areas, it is a primary calorie source for families and a cash crop for farmers.”

Globally, farmers tend about 24 million hectares of peanuts each year and produce about 40 million metric tons.

“Improving peanut varieties to be more drought-, insect- and disease-resistant can help farmers in developed nations produce more peanuts with fewer pesticides and other chemicals and help farmers in developing nations feed their families and build more secure livelihoods,” said plant geneticist Rajeev Varshney of the International Crops Research Institute for Semi-Arid Tropics in India, who serves on the IPGI.

The effort to sequence the peanut genome has been underway for several years. While peanuts were successfully bred for intensive cultivation for thousands of years, relatively little was known about the legume’s genetic structure because of its complexity, according to Peggy Ozias-Akins, a plant geneticist on the UGA Tifton campus who also works with the IPGI and is director of the UGA Institute of Plant Breeding, Genetics and Genomics.

“Until now, we’ve bred peanuts relatively blindly, as compared to other crops,” said IPGI plant geneticist David Bertioli of the Universidade de Brasília. “We’ve had less information to work with than we do with many crops, which have been more thoroughly researched and understood.”

The peanut in fields today is the result of a natural cross between two wild species, Arachis duranensis and Arachis ipaensis, which occurred in north Argentina between 4,000 and 6,000 years ago. Because its ancestors were two different species, today’s peanut is a polyploid, meaning the species can carry two separate genomes, designated A and B subgenomes.

To map the peanut’s structure, researchers sequenced the genomes of the two ancestral parents because together they represent the cultivated peanut. The sequences provide researchers access to 96 percent of all peanut genes in their genomic context, providing the molecular map needed to more quickly breed drought- and disease-resistant, lower-input and higher-yielding varieties of peanuts.

The two ancestor wild species had been collected in nature, conserved in germplasm banks and then used by the IPGI to better understand the peanut genome. The genomes of the two ancestor species provide excellent models for the genome of the cultivated peanut. A. duranenis serves as a model for the A subgenome of the cultivated peanut while A. ipaensis represents the B subgenome.

Knowing the genome sequences of the two parent species will allow researchers to recognize the cultivated peanut’s genomic structure by differentiating between the two subgenomes present in the plants. Being able to see the two separate structural elements also will aid future gene marker development-the determination of links between a gene’s presence and a physical characteristic of the plant. Understanding the structure of the peanut’s genome will lay the groundwork for new varieties with traits like added disease resistance and drought tolerance.

In addition, these genome sequences will serve as a guide for the assembly of the cultivated peanut genome that will help to decipher genomic changes that led to peanut domestication, which was marked by increases in seed number and size. The genome sequence assemblies and additional information are available at http://peanutbase.org/files/genomes/.

The International Peanut Genome Initiative brings together scientists from the U.S., China, Brazil, India and Israel to delineate peanut genome sequences, characterize the genetic and phenotypic variation in cultivated and wild peanuts and develop genomic tools for peanut breeding. The initial sequencing was carried out by the BGI, Shenzhen, China, known previously as the Beijing Genomics Institute.

Assembly was done at the BGI, the USDA-ARS in Ames, Iowa, and at the University of California, Davis. The project was funded by the peanut industry through the Peanut Foundation and by MARS Inc. and three Chinese academies (Henan Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences and Shandong Academy of Agricultural Sciences).

A complete list of the institutions involved with the project and the other funding sources is available at www.peanutbioscience.com.

In the U.S. peanuts are a major row crop throughout the South and Southeast. While they are a major economic driver for the U.S. economy, the legume is also crucial to the diets and livelihoods of millions of small farmers in Asia and Africa, many of whom are women.

Apart from being a rich source of oil (44 percent to 55 percent), protein (20 percent to 50 percent) and carbohydrates (10 percent to 20 percent), peanut seeds are an important nutritional source of niacin, folate, calcium, phosphorus, magnesium, zinc, iron, riboflavin, thiamine and vitamin E.

“While the sequencing of the peanut can be seen as a great leap forward in plant genetics and genomics, it also has the potential to be a large step forward for stabilizing agriculture in developing countries,” said Dave Hoisington, program director for the U.S. Agency for International Development Feed the Future Peanut and Mycotoxin Innovation Lab, which is hosted at UGA.

“With the release of the peanut genome sequence, researchers will now have much better tools available to accelerate the development of new peanut varieties with improved yields and better nutrition,” he said.

Agriculture and Food News — ScienceDaily

Sugar beet genome sequenced and analyzed

Dec. 18, 2013 — A new study, published in Nature today, describes the sugar beet reference genome sequence generated by researchers both from the Centre for Genomic Regulation (CRG), the Max Planck Institute for Molecular Genetics and the University of Bielefeld, in cooperation with other centres and plant breeders.

Sugar beet accounts for nearly 30% of the world’s annual sugar production, according to FAO, and provides a source for bioethanol and animal feed.

The sugar beet genome sequence provides insights into how the genome has been shaped by artificial selection along time.

What do foodstuff like muffins, bread or tomato sauce have in common? They all contain different amounts of white refined sugar. But, what perhaps may result amazing is that this sugar is probably sourced from a plant very similar to spinach or chard, but much sweeter: the sugar beet. In fact, this plant accounts for nearly 30% of the world’s annual sugar production, according to the Food and Agriculture Organization for the United Nations (FAO). Not in vain for the last 200 years, has it been a crop plant in cultivation all around the world because of its powerful sweetener property.

Now, a team of researchers from the Centre for Genomic Regulation (CRG) and the Max Planck Institute for Molecular Genetics (Berlin, Germany), lead by Heinz Himmelbauer, head of the Genomics Unit at the CRG in Barcelona, together with researchers from Bielefeld and further partners from academia and the private sector, have been able to sequence and analyse for the first time the sweet genes of beetroot. The results of the study, that will be published today in Nature, shed also light on how the genome has been shaped by artificial selection.

“Information held in the genome sequence will be useful for further characterization of genes involved in sugar production and identification of targets for breeding efforts. These data are key to improvements of the sugar beet crop with respect to yield and quality and towards its application as a sustainable energy crop,” the authors suggest.

Sugar beet is the first representative of a group of flowering plants called Caryophyllales, comprising 11,500 species, which has its genome sequenced. This group encompasses other plants of economic importance, like spinach or quinoa, as well as plants with an interesting biology, for instance carnivorous plants or desert plants.

27,421 protein-coding genes were discovered within the genome of the beet, more than are encoded within the human genome. “Sugar beet has a lower number of genes encoding transcription factors than any flowering plant with already known genome,” adds Bernd Weisshaar, a principle investigator from Bielefeld University who was involved in the study. The researchers speculate that beets may harbor so far unknown genes involved in transcriptional control, and gene interaction networks may have evolved differently in sugar beet compared to other species. The researchers also studied disease resistance genes (the equivalent to the immune system in animals) which can be identified based on protein-domains. These genes turned out as particularly plastic, with beet-specific gene family expansions and gene losses.

Many sequencing projects nowadays targeted at the analysis of novel genomes also address the description of genetic variation within the species of interest. Commonly, “this is achieved by generating sequencing reads obtained from high-throughput sequencing technologies, followed by alignment of these reads against the reference genome to identify differences,” explains Heinz Himmelbauer, a principle investigator of this study.

The current work, nevertheless, went one step further and generated genome assemblies from four additional sugar beet lines. This allowed the researchers to obtain a much better picture of intraspecific variation in sugar beet than would have been possible otherwise. In summary, 7 million variants were discovered throughout the genome. However, variation was not uniformly distributed: The authors found regions of high, but also of very low variation, “reflecting both the small population size from which the crop was established, as well as the human selection, which has shaped the plants’ genomes. Additionally, gene numbers varied between different sugar beet cultivars, which contained up to 271 genes not shared with any of the other lines,” as Juliane Dohm and André Minoche, two scientists involved in the study commented.

The researchers also performed an evolutionary analysis of each sugar beet gene in order to put them into context with already known genes of other plants. This analysis allowed them to identify gene families that are expanded in sugar beet compared to other plants, but also families that are absent. Notably such gene families were most commonly associated with stress response or with disease resistance, added Toni Gabaldon, group leader in the CRG Bioinformatics and Genomics programme and ICREA research professor.

Finally, the work also provides a first genome sequence of spinach, which is a close relative of sugar beet.

Thanks to the sugar beet genome sequence made by the researchers and the associated resources generated, future studies on the molecular dissection of natural and artificial selection, gene regulation and gene-environment interaction, as well as biotechnological approaches to customize the crop to different uses in the production of sugar and other natural products, are expected to be held.

“Sugar beet will be an important cornerstone of future genomic studies involving plants, due to its taxonomic position,” the authors claim.

ScienceDaily: Agriculture and Food News