Showing posts with label Plant Breeding. Show all posts
Showing posts with label Plant Breeding. Show all posts

Tuesday, September 19, 2017

Plant geneticists develop a new application of CRISPR to break yield barriers in crops

Mutating regulatory regions varies yield traits 'the way a dimmer switch controls a light bulb'

Scientists at Cold Spring Harbor Laboratory (CSHL) have harnessed the still untapped power of genome editing to improve agricultural crops. Using tomato as an example, they have mobilized CRISPR/Cas9 technology to rapidly generate variants of the plant that display a broad continuum of three separate, agriculturally important traits: fruit size, branching architecture and overall plant shape. All are major components in determining how much a plant will yield. The method is designed to work in all food, feed, and fuel crops, including the staples rice, maize, sorghum and wheat.

"Current rates of crop yield increases won't meet the planet's future agricultural demands as the human population grows," says CSHL Professor Zachary Lippman, who led the research. "One of the most severe limitations is that nature hasn't provided enough genetic variation for breeders to work with, especially for the major yield traits that can involve dozens of genes. Our lab has now used CRISPR technology to generate novel genetic variation that can accelerate crop improvement while making its outcomes more predictable."

The team's experiments, published today in Cell, involve using CRISPR "scissors" to make multiple cuts within three tomato genome sequences known as a promoters -- areas of DNA near associated genes which help regulate when, where, and at what level these "yield" genes are active during growth. In this way generating multiple sets of mutations within each of these regulatory regions, the scientists were able to induce a wide range of changes in each of the three targeted traits.

"What we demonstrated with each of the traits," explains Lippman, "was the ability to use CRISPR to generate new genetic and trait variation that breeders can use to tailor a plant to suit conditions. Each trait can now be controlled in the way a dimmer switch controls a light bulb."

By using CRISPR to mutate regulatory sequences -- the promoters of relevant "yield" genes rather than the genes themselves -- the CSHL team finds that they can achieve a much subtler impact on quantitative traits. Fine-tuning gene expression rather than deleting or inactivating the proteins they encode is most likely to benefit commercial agriculture because of the flexibility such genetic variation provides for improving yield traits.

"Traditional breeding involves great time and effort to adapt beneficial variants of relevant genes to the best varieties, which must continuously be improved every year," says Lippman. "Our approach can help bypass this constraint by directly generating and selecting for the most desirable variants controlling gene activity in the context of other natural mutations that benefit breeding. We can now work with the native DNA and enhance what nature has provided, which we believe can help break yield barriers."

Each of the mutated areas creates what are known as quantitative trait loci (QTL). In any given plant, QTL have arisen naturally over thousands of years, the result of spontaneous mutations that caused subtle changes in yield traits. Searching for and exploiting QTL from nature has been an objective of plant breeders for centuries, but the most valuable QTL -- those that cause subtle changes in traits -- are rare. Lippman and his team have now shown that CRISPR-generated QTL can be combined with existing QTL to create "toolkits" of genetic variation that exceed what is found in nature.

Story Source: https://www.sciencedaily.com 

Sunday, May 21, 2017

Phenological growth stages of quinoa (Chenopodium quinoa) based on the BBCH scale

Quinoa (Chenopodium quinoa) is a pseudocereal native from the Andean region of South America that has increased in importance worldwide. Quinoa is now considered an alternative to traditional crops in a climate change scenario, considering its ability to adapt to marginal soils, droughts and frosts. Despite the interesting agronomic and nutritional features of this crop, research into quinoa is characterised by individual attempts to define its phenological stages without an international consensus. A unique criterion to quantify the phenology of quinoa could become a useful tool for researchers and plant breeders in future work by standardising this information for international cooperation. In this article, a proposed scale of the phenological growth stages of quinoa based on the BBCH coding system (Biologische Bundesanstalt Bundessortenamt und CHemische Industrie) was developed. Growth stages were described utilising the decimal code of the BBCH system, and figures were included for the most representative stages.

Wednesday, August 19, 2015

Journal of Agronomy - Current Issue

Journal of Agronomy - Current Issue
  • Quantitative Analysis of Induced Phenotypic Diversity in Chickpea Using Physical and Chemical Mutagenesis
  • Effect of Nitrogen and Phosphorus Fertilizers on Growth, Yield and Yield Components of Black Cumin (Nigella sativa L.) at Konta District, South West Ethiopia
  • Relationship Between some Growth Parameters, Dry Matter Content and Yield of Some Sweet Potato Genotypes Grown under Rainfed Weathered Ultisols in the Humid Tropics
  • Aerial Ramet Dynamics and General Clonal Growth Patterns of Scirpus grossus in Grown at Different Water Depths and Fertilizer Regimes in Paddy Soils
  • Seeder Performance under Different Speeds and its Relation to Soybean Cultivars Yield
  • Study on the Potential of Land Utilization for Energy Plantation as Biodiesel Feedstock: Case Study of Andalas University Campus at Limau Manis
  • Yield Response of Maize to Integrated Soil Fertility Management on Acidic Nitosol of Southwestern Ethiopia
  • Character Association and Path Coefficient Analysis of Maize (Zea mays L.) Grown under Incorporated Legumes and Nitrogen
  • Orange Fleshed Sweet Potato (Ipomoea batatas L.) Varieties Evaluated with Respect to Growth Parameters at Jimma in Southwestern Ethiopia
  • Effects of Water Ozonated and Salinity on Some Properties of Cucumber
  • Agronomic Performance and Genetic Variability among Common Bean Genotypes in Savanna/Pantanal Ecotone

Sunday, July 19, 2015

The impact of the Quinoa boom on Bolivian family farmers

New findings based on survey results from 100 households located in southern Bolivia. 81% of farmers interviewed between December 2012 and March 2013 say quinoa is their primary source of income. Benefits of the increase in Quinoa prices:
  • Guarantees improved incomes and access to credit 
  • Access to additional labour and machinery
  • Increased productivity 
Challenges:
  • Land degradation
  • Reduction of cultivated varieties


Source:

Tuesday, July 07, 2015

Slow Food and FAO launch “Quinoa in the Kitchen”

Recipe book is the first fruit of a partnership that aims to make quinoa a staple of the world’s kitchens
The Slow Food movement and FAO officially launched the book, “Quinoa in the Kitchen,” today to continue to promote awareness about the super-food’s potential as the International Year of Quinoa draws to a close.
The book gives an overview of quinoa’s roots in the history and culture of the central Andean high plateau, geographically extending across the borders of Peru and Bolivia, which together account for the vast majority of quinoa production in the world.
Since quinoa is still new to many beyond the Andes, the book includes a selection of quinoa recipes created by some of the world’s top chefs. The aim is to bring quinoa to kitchens across the world, where it may someday be as commonplace as pasta or rice.
Quinoa is exceptionally versatile, which has drawn it attention as a potential alternative crop that could be an added tool to be able to produce sufficient food for the world’s growing population – expected to grow by 2 billion people by 2050 – as the climate shifts. Different varieties of quinoa can be grown from sea level to 4000 metres in altitude, it can withstand temperatures from below freezing to 38 degrees Celsius, in both humid and arid climates and in a variety of soil conditions.
"Quinoa is part of the effort to recover these lost foods and to promote traditional and forgotten crops. It is also part of the idea that food is not only a commodity. It is a lot more than that. It is also culture, it is also taste, it is also a lot of things that are closely related to our history,” said FAO Director-General José Graziano da Silva.
Slow Food President Carlo Petrini said that the book draws inspiration from the two organizations “shared vision of a sustainable world free from hunger and that safeguards biodiversity for future generations.”
“Central to the process is gastronomy itself and the idea that this holistic, multidisciplinary science, which encompasses everything from agriculture to history, from economics to anthropology, from botany to culinary art, can be a liberating force of the communities most hit by malnutrition,” he added.
Quinoa is higher in protein than grains such as wheat, corn or rice, and it packs in vitamins, minerals and essential amino acids that are important to human nutrition but which many foods lack in just one source.
FAO is currently overseeing a programme in Argentina, Bolivia, Chile, Ecuador and Peru for the sustainable intensification of quinoa farming and food production systems in the Andean region. FAO is assisting countries to respond to a rising demand for quinoa so farmers can benefit from high prices while preserving the environment and biodiversity. Helping farmers to access the organic and fair trade sectors on international markets is one important element of the programme.
FAO is planning a regional project in arid and semi-arid areas of the Near East, where quinoa could prove useful to provide sufficient nutritious food even under extreme climactic conditions. In Algeria, Egypt, Iraq, Iran, Lebanon, Mauritania, Sudan and Yemen, varieties will be selected and field tested to gauge which types of quinoa have the highest yields and nutritional values even under stress, such as drought.
Similar projects are being developed for Bhutan, Brunei and Sri Lanka , as well as for Kygryzstan and Tajikistan.
The United Nations has declared 2013 the “International Year of Quinoa.”

Sunday, December 28, 2014

New insights into origins of agriculture could help shape future of food

Agricultural decisions made by our ancestors more than 10,000 years ago could hold the key to food security in the future, according to new research by the University of Sheffield.

Scientists, looking at why the first arable farmers chose to domesticate some cereal crops and not others, studied those that originated in the Fertile Crescent, an arc of land in western Asia from the Mediterranean Sea to the Persian Gulf.
They grew wild versions of what are now staple foods like wheat and barley along with other grasses from the region to identify the traits that make some plants suitable for agriculture, including how much edible seed the grasses produced and their architecture.
Dr Catherine Preece, who worked on the study with colleagues from the University's Department of Animal and Plant Sciences and Department of Archaeology, said: "Our results surprised us because numerous other grasses that our ancestors ate, but we do not, can produce just as much seed as wild wheat and barley. It is only when these plants are grown at high densities, similar to what we would find in fields, that the advantage of wild wheat and barley is revealed."
The study identified two key characteristics shared by the wild relatives of current crop plants. Firstly they have bigger seeds, which means they grow into bigger seedlings and are able to get more than their fair share of light and nutrients, and secondly, as adult plants they are less bushy than other grasses and package their big seeds onto fewer stems. This means crop wild relatives perform better than the other wild grasses that they are competing with and are better at growing close together in fields, making them ideal for using in agriculture.
"The results are important because our expanding human population is putting increasing demands on food production," said Dr Preece.
"Before humans learnt how to farm, our ancestors ate a much wider variety of grasses. If we can understand what traits have made some grasses into good crops then we can look for those characteristics in other plants and perhaps identify good candidates for future domestication."
She added: "To shape the future we must understand the past, so the more we can discover about the origins of agriculture, the more information we will have to help us tackle the challenges that face modern day food production."
So far the researchers have been conducting their experiments in greenhouses and their results indicate that the traits affecting how plants compete with each other are crucial factors to determining the success of a crop.
The team now plan to observe how the plants interact in their natural environment by growing them in experimental fields in Turkey, the heart of the Fertile Crescent. They hope that their experiments will yield another crop of important results.
"Cereal breeders are taking an increasing interest in modern crops' wild relatives as a source of useful traits that may help to increase yields or increase resilience to climate change, and our work should help in this process," said Dr Preece.
Dr Preece presented the results of this study to the joint British Ecological Society and the French Ecological Society 11 December 2014 in the Grand Palais, Lille.

Source:

Friday, December 26, 2014

More holistic approach needed when studying diets of our ancestors

Researchers have long debated how and what our ancestors ate. Charles Darwin hypothesized that the hunting of game animals was a defining feature of early hominids, one that was linked with both upright walking and advanced tool use and that isolated these species from their closest relatives (such as ancestors of chimpanzees); modified versions of this hypothesis exist to this day. Other scholars insist that while our ancestors' diets did include meat, it was predominantly scavenged and not hunted. Still others argue that particular plant foods such as roots and tubers were of greater importance than meat in the diets of these species.

Research technology has come a long way since Darwin's time, making possible the kind of analysis early scholars could only have imagined. Recent work has presented reconstructions of early hominid diets on the basis of chemical makeups of fossil tooth enamel, evidence of microscopic wear on teeth, and advanced studies of craniodental anatomy, to name a few.
However, according to Ken Sayers (Georgia State University) and C. Owen Lovejoy (Kent State University) in an article published in the December 2014 issue of The Quarterly Review of Biology, although modern-day technology provides valuable insight, such tools alone cannot provide a complete picture of the diet of early hominids. Instead, they should be included -- alongside other methodologies -- in holistic studies grounded in the fundamentals of modern evolutionary ecology.
Sayers and Lovejoy suggest that researchers should examine a species' particular habitat and "whole-body" anatomy, including digestion, locomotion, and possible cognitive abilities. In particular, foraging theory -- a branch of evolutionary ecology that investigates animal feeding decisions through the lens of efficiency principles -- is especially important to consider, as it demonstrates that diet is regulated by the potential value and costs of exploiting individual food items (whether plant, animal, or other) and by the relative abundance of the most profitable foods. In the case of the earliest-known hominids, evidence about their morphology and likely cognitive abilities -- in addition to data obtained from modern technologies -- provide little support for a reliance on any one particular food type. Rather, these species likely had a broadly omnivorous diet that became increasingly generalized over time.
According to Sayers and Lovejoy, the early hominid diet can best be elucidated by considering the entire habitat-specific resource base and by quantifying the potential profitability and abundance of likely available foods. Furthermore, they warn that hypotheses focusing too narrowly on any one food type or foraging strategy -- such as hunting or scavenging or any one particular plant category -- are too restrictive and should be viewed with caution. Modeling these species' diets instead "requires a holistic, interdisciplinary approach that goes beyond merely what we can observe chemically or through a microscope, and draws from ecology, anatomy and physiology, cognitive science, and behavior."

Source:
http://www.sciencedaily.com/
Ken Sayers, C. Owen Lovejoy. Blood, Bulbs, and Bunodonts: On Evolutionary Ecology and the Diets ofArdipithecus,Australopithecus, and EarlyHomo. The Quarterly Review of Biology, 2014; 89 (4): 319 DOI: 10.1086/678568

Wednesday, December 10, 2014

Natural gene selection can produce orange corn rich in provitamin A for Africa, U.S.

Purdue researchers have identified a set of genes that can be used to naturally boost the provitamin A content of corn kernels, a finding that could help combat vitamin A deficiency in developing countries and macular degeneration in the elderly.
Professor of agronomy Torbert Rocheford and collaborators at Cornell University and Michigan State University found gene variations that can be selected to change nutritionally poor white corn into biofortified orange corn with high levels of provitamin A carotenoids - substances that the human body can convert into vitamin A. Vitamin A plays key roles in eye health and the immune system, as well as in the synthesis of certain hormones.
"This study gives us the genetic blueprint to quickly and cost-effectively convert white or yellow corn to orange corn that is rich in carotenoids - and we can do so using natural plant breeding methods, not transgenics," said Rocheford, the Patterson Endowed Chair of Translational Genomics for Crop Improvement.
Vitamin A deficiency causes blindness in 250,000 to 500,000 children every year, half of whom die within a year of losing their eyesight, according to the World Health Organization. The problem most severely affects children in Sub-Saharan Africa, an area in which white corn, which has minimal amounts of provitamin A carotenoids, is a dietary mainstay.
Insufficient carotenoids may also contribute to macular degeneration in the elderly, a leading cause of blindness in older populations in Europe and the U.S.
Identifying the genes that determine carotenoid levels in corn kernels will help plant breeders develop novel biofortifed corn varieties for Africa and the U.S. The dark orange color of these corn varieties also makes them more culturally acceptable to consumers in African countries where yellow corn is generally fed only to animals, Rocheford said.
Previous research by Rocheford and his colleagues identified two genes that contribute to provitamin A carotenoid levels in corn kernels, but "we wanted more cookies in the jar for breeders to pick from," he said.
The researchers used a combination of statistical analysis and prediction models to identify and assess the potential usefulness of genes associated with carotenoid levels in corn. They evaluated data sets from about 200 genetically diverse lines of corn at varying scopes of investigation - from the entire corn genome to stretches of DNA surrounding small sets of genes. They uncovered four genes that had not previously been linked to carotenoid levels in corn kernels.
Though many genes likely contribute to carotenoid levels in corn, "we're pretty confident that our previous and current research has now identified several genes that are the major players," Rocheford said.
Their study found that a combination of visually selecting corn with darker orange kernels and using a number of these favorable genes could be an effective way to rapidly convert white and yellow corn varieties to orange corn with higher levels of provitamin A and total carotenoids.
"We now have the genetic information needed to begin developing a major public-private sector collaboration with the goal of providing orange corn with high levels of provitamin A to farmers throughout Sub-Saharan Africa," he said.
The study also showed that using a more targeted approach to predicting the usefulness of a small set of genes was as effective as evaluating the whole corn genome, said Brenda Owens, doctoral candidate and first author of the study.
"Having this smaller list of genes to select for means that we can make the improvement of carotenoid levels in corn a simpler, faster process for plant breeders," she said.
Their research - with support from the National Science Foundation, HarvestPlus and the International Maize and Wheat Improvement Center, also known as CIMMYT - has yielded varieties of orange corn with markedly higher amounts of provitamin A carotenoids. But further efforts to produce even higher levels will be necessary to offset degradation of nutrients after harvest and reduce the amount of corn African consumers would need to eat to attain enough provitamin A, Rocheford said.
Varieties of orange corn are currently being grown in Zambia, Zimbabwe, Nigeria and Ghana. An open-pollinated variety of orange corn could be available for organic and local grower operations in the U.S. by 2016, he said.

The paper was published online in Genetics and is available at http://www.genetics.org/content/early/2014/09/25/genetics.114.169979.full.pdf+html
A video presentation of Rocheford discussing the research behind biofortified orange corn and its implications is available at http://docs.lib.purdue.edu/dawnordoom/2014/presentations/11/

Source:

Tuesday, October 21, 2014

Estado del arte de la quinua en el mundo en 2013

Editado por
Bazile, D., Bertero, D. y Nieto, C.

Organización de las Naciones Unidas para la Alimentación y la Agricultura (FAO) Santiago, Chile
Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) Montpellier, France

Resumen
En el 2013 las Naciones Unidas declararon el Año Internacional de la Quinua, situándola en un espacio privilegiado a nivel global, generando expectativas y desafíos.
El "Estado del arte de la quinua en el mundo en 2013" es una publicación conjunta entre el CIRAD y la FAO que reúne en un solo libro toda la información relevante sobre la quinua generada por los más destacados investigadores del mundo, organizaciones de productores, tomadores de decisión, y todos aquéllos que se preocupan por este alimento. El libro tiene como objetivo principal favorecer la difusión de estos conocimientos, promover el dialogo y el debate entre actores del desarrollo de la quinua a nivel mundial y generar nuevas expectativas del cultivo en el mundo, considerando sus aportes a la seguridad alimentaria y a la economía de la agricultura familiar, pero también considerando los riesgos inherentes de una expansión descontrolada, en particular poniendo énfasis: en la necesidad de regulación de la circulación de los recursos fitogenéticos y la redistribución justa y equitativa de los beneficios de su utilización fuera de la zona andina y la sostenibilidad de los sistemas agrícolas. Esperamos que este libro se constituya en una herramienta que impulse el desarrollo de programas y proyectos respetuosos, responsables y éticos de quinua en el mundo manteniendo y preservando la biodiversidad de la quinua.



Thursday, October 16, 2014

Plant variants point the way to improved biofuel production

Manufacturing biofuels from food crop by-products such as straw could be made quicker and cheaper thanks to a new study led by scientists at the University of York.

The research funded by the Biotechnology and Biological Sciences Research Council (BBSRC) discovered variant straw plants whose cell walls are more easily broken down to make biofuels, but which are not significantly smaller or weaker than regular plants.
The discovery by researchers in the Centre for Novel Agricultural Products at York could help ease pressure on global food security as biofuels from non-food crops become easier and cheaper to make.
The impact of carbon emissions on global warming is driving the need for carbon neutral biofuels. Many existing biofuels are produced from crops which can be used for food, and therefore have a negative impact on global food security.
One answer is to make fuels from woody, non-food parts of plants such as straw. These are rich in polysaccharides (sugar chains) which can be broken down into simple sugars and then fermented into ethanol for fuel. However, such biofuels are currently too expensive because of the cost of digesting the woody tissues into simple sugars.
The CNAP researchers led by Professor Simon McQueen-Mason, working with colleagues in France, screened a large collection of variants of the model grass species Brachypodium for digestibility. Screening mutants in this way allows rapid assessment of the range of natural diversity that can be found in a species.
Using this approach, PhD student Poppy Marriott identified 12 independent plant lines with highly digestible straw, but which grew normally and showed no decrease in straw strength. Analysing these plants showed that increased digestibility can be achieved through a range of changes in the cell wall, where the majority of sugar is contained in woody biomass.
In addition the team at York also showed they can identify the gene alterations that give rise to the high digestibility. The new results are published in the latest edition of the Proceedings of the National Academy of Sciences USA.
By identifying these plant variants with straw that is easier to digest, but which retain their size and strength, the cost and complexity of biofuel production could be reduced.
Professor McQueen-Mason said: “This work sets the stage for identifying similar high-digestibility lines in commercial crop species that will pave the way to more cost-effective and sustainable biofuels.
“Using plant by-products such as straw provides a double benefit as we can harvest the food from the plant, then use the straw to produce a carbon neutral fuel.”
Professor Melanie Welham, BBSRC Executive Director for Science, said: “This research is another important step towards making carbon-neutral biofuels both easier and cheaper to produce. Using crop by-products such as straw for biofuels reduces pressure on food supplies and also adds value to the crop, boosting food security and helping farmers.
“It is just one example of how BBSRC investment in world class bioscience is working towards addressing some of the existing and emerging global challenges that we all face.”

Further information:A range of cell wall alterations enhance saccharification in Brachypodium distachyon mutants is published in Proceedings of the National Academy of Sciences USA.
The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Its aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond. Funded by Government, BBSRC invested over £484M in world-class bioscience in 2013-14. It supports research and training in universities and strategically funded institutes. BBSRC research and the people it funds are helping society to meet major challenges, including food security, green energy and healthier, longer lives. BBSRC investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.For more information about BBSRC, its science and impact see:http://www.bbsrc.ac.uk For more information about BBSRC strategically funded institutes see: http://www.bbsrc.ac.uk/institutes
The Centre for Novel Agricultural Products (CNAP) is an award winning strategic research centre based in the Department of Biology at the University of York. CNAP is dedicated to realising the potential of plants as renewable, low-cost factories that produce high-value chemicals and biofuels. Laboratory based discoveries are translated into practice in partnership with industry.www.york.ac.uk/org/cnap/

Source:

Tuesday, October 14, 2014

Natural gene selection can produce orange corn rich in provitamin A for Africa, U.S.

Purdue researchers have identified a set of genes that can be used to naturally boost the provitamin A content of corn kernels, a finding that could help combat vitamin A deficiency in developing countries and macular degeneration in the elderly.
Professor of agronomy Torbert Rocheford and fellow researchers found gene variations that can be selected to change nutritionally poor white corn into biofortified orange corn with high levels of provitamin A carotenoids - substances that the human body can convert into vitamin A. Vitamin A plays key roles in eye health and the immune system, as well as in the synthesis of certain hormones.
"This study gives us the genetic blueprint to quickly and cost-effectively convert white or yellow corn to orange corn that is rich in carotenoids - and we can do so using natural plant breeding methods, not transgenics," said Rocheford, the Patterson Endowed Chair of Translational Genomics for Crop Improvement.
Vitamin A deficiency causes blindness in 250,000 to 500,000 children every year, half of whom die within a year of losing their eyesight, according to the World Health Organization. The problem most severely affects children in Sub-Saharan Africa, an area in which white corn, which has minimal amounts of provitamin A carotenoids, is a dietary mainstay.
Insufficient carotenoids may also contribute to macular degeneration in the elderly, a leading cause of blindness in older populations in Europe and the U.S.
Identifying the genes that determine carotenoid levels in corn kernels will help plant breeders develop novel biofortifed corn varieties for Africa and the U.S. The dark orange color of these corn varieties also makes them more culturally acceptable to consumers in African countries where yellow corn is generally fed only to animals, Rocheford said.
Previous research by Rocheford and his colleagues identified two genes that contribute to provitamin A carotenoid levels in corn kernels, but "we wanted more cookies in the jar for breeders to pick from," he said.
The researchers used a combination of statistical analysis and prediction models to identify and assess the potential usefulness of genes associated with carotenoid levels in corn. They evaluated data sets from about 200 genetically diverse lines of corn at varying scopes of investigation - from the entire corn genome to stretches of DNA surrounding small sets of genes. They uncovered four genes that had not previously been linked to carotenoid levels in corn kernels.
Though many genes likely contribute to carotenoid levels in corn, "we're pretty confident that our previous and current research has now identified several genes that are the major players," Rocheford said.
Their study found that a combination of visually selecting corn with darker orange kernels and using a number of these favorable genes could be an effective way to rapidly convert white and yellow corn varieties to orange corn with higher levels of provitamin A and total carotenoids.
"We now have the genetic information needed to begin developing a major public-private sector collaboration with the goal of providing orange corn with high levels of provitamin A to farmers throughout Sub-Saharan Africa," he said.
The study also showed that using a more targeted approach to predicting the usefulness of a small set of genes was as effective as evaluating the whole corn genome, said Brenda Owens, doctoral candidate and first author of the study.
"Having this smaller list of genes to select for means that we can make the improvement of carotenoid levels in corn a simpler, faster process for plant breeders," she said.
Their research - in collaboration with HarvestPlus and the International Maize and Wheat Improvement Center, also known as CIMMYT - has yielded varieties of orange corn with markedly higher amounts of provitamin A carotenoids. But further efforts to produce even higher levels will be necessary to offset degradation of nutrients after harvest and reduce the amount of corn African consumers would need to eat to attain enough provitamin A, Rocheford said.
Varieties of orange corn are currently being grown in Zambia, Zimbabwe, Nigeria and Ghana. An open-pollinated variety of orange corn could be available for organic and local grower operations in the U.S. by 2016, he said.
The paper was published online in Genetics and is available at http://www.genetics.org/content/early/2014/09/25/genetics.114.169979.full.pdf+html
A video presentation of Rocheford discussing the research behind biofortified orange corn and its implications is available athttp://docs.lib.purdue.edu/dawnordoom/2014/presentations/11/
Funding for the research was provided by the National Science Foundation; HarvestPlus; Purdue University startup and Patterson Chair funds; the U.S. Department of Agriculture-Agricultural Research Service; Cornell University startup funds; a U.S. Department of Agriculture National Needs Fellowship; and a Borlaug Fellowship.

ABSTRACT
A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels
Brenda F. Owens 1; Alexander E. Lipka 2; Maria Magallanes-Lundback 3; Tyler Tiede 1; Christine H. Diepenbrock 4; Catherine B. Kandianis 3, 4; Eunha Kim 3; Jason Cepela 5; Maria Mateos-Hernandez 1; C. Robin Buell 1; Edward S. Buckler 2, 4, 6; Dean DellaPenna 3; Michael A. Gore 4; Torbert Rocheford 1

1 Purdue University, Department of Agronomy, West Lafayette, IN 47907
2 Cornell University, Institute for Genomic Diversity, Ithaca, NY 14853
3 Michigan State University, Department of Biochemistry and Molecular Biology, East Lansing, MI 48824
4 Cornell University, Department of Plant Breeding and Genetics, Ithaca, NY 14853
5 Michigan State University, Department of Plant Biology, East Lansing, MI 48824
6 United States Department of Agriculture-Agricultural Research Service (ARS), Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853

Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci (QTL) associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on our GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A.

Source:

Wednesday, October 01, 2014

Future of our crops is at risk in conflict zones, say scientists

Wild species related to our crops, which are crucial as potential future food resources, have been identified by scientists, however, a significant proportion are found in conflict zones in the Middle East, where their conservation is increasingly comprised.

Wild species related to our crops which are crucial as potential future food resources have been identified by University of Birmingham scientists, however, a significant proportion are found in conflict zones in the Middle East, where their conservation is increasingly comprised.
The scientists have identified 'hotspots' around the globe where crop wild relatives (CWR) -- species closely related to our crops which are needed for future crop variety development -- could be conserved in the wild in order to secure future global food resources.
The hotspot where CWR are most concentrated is in the so-called 'Fertile Crescent', which is situated in the Middle East, arcing around the Arabian desert from Jordan, Palestine, Israel, Syria, Lebanon, Turkey and ending in Iraq and Iran.
Climate change, along with a steady rise in the human population is forecast to have a detrimental impact on crops that are grown for food. The wild relatives of crops, however, contain many useful traits such as drought tolerance, yield improvement, and resilience to pests and diseases. These wild species can be used by plant breeders to create stronger, more resilient crop varieties which will help to underpin future food security.
Now a comprehensive database of globally important CWR exists, thanks to this study. The inventory lists 173 crops and their 1667 priority wild relatives, along with their particular traits. For example, the crop wild relative of the wheat crop, Aegilops tauschii, is resistant to Hessian Fly which is pest of cereal crops; Saccharum arundinaceum is a relative of sugar cane and can survive very low temperatures, andPrunus ferganensis, the crop wild relative of peach, is tolerant to drought conditions. Globally, the highest concentration of CWR per unit area is found in Syria and Lebanon.
Research at Birmingham has shown that 12 per cent of CWRs are threatened with extinction and all are likely to be already suffering a loss of genetic diversity due to habitat loss and alteration, conflict, intensive agriculture, urbanisation, and mismanagement of the environment. However, until now, there has been no attempt to systematically conserve the diversity of this important global resource.
A new initiative led by the Food and Agriculture Organisation of the UN, with help from scientists at the University of Birmingham, will, for the first time, plan and implement effective conservation of these priority plant species in the countries where they are found. The Birmingham scientists are now working on a strategy to conserve CWRs by identifying and promoting the establishment of managed conservation sites in the wild, while taking samples and placing them in gene banks as a safety back up, where the genetic material can be kept for up to 300 years.
The team is currently negotiating with governments in the Fertile Crescent to highlight the plight of these species and to try to implement 'in situ' conservation in the hotspot areas.
Dr Nigel Maxted, lead investigator from the University of Birmingham's School of Biosciences, said: 'There has previously been no opportunity to systematically conserve and use CWR as there was a lack of clarity over their identities and distribution. By creating an inventory of globally important CWR we can discover which countries and regions are the richest in terms of priority CWR, and more efficiently plan and coordinate conservation efforts to ensure their survival.
'It is very important that we conserve these species in secure gene banks, but it is critical to conserve them in their natural habitat as they will continue to adapt to changes in the climate as well as threats from pests and diseases.'
'The global population is now 7 billion and by 2050 it will be 9 billion so it is now even more crucial that we conserve crop wild relatives as part of the wider need to address global food security issues.'
As well as the abundance of CWR in the Fertile Crescent, many CWR can be found in the UK including the wild relatives of sugarbeet, asparagus, raddish and wild garlic. The Birmingham team is now working with Natural England to identify an area where CWR can be conserved in their natural habitat in the UK.

Source:

http://www.sciencedaily.com/

Monday, September 29, 2014

'Most famous wheat gene' discovered, clears way for non-GMO breeding

Researchers have found 'the most famous wheat gene,' a reproductive traffic cop of sorts that can be used to transfer valuable genes from other plants to wheat. The discovery clears the way for breeders to develop wheat varieties with the disease- and pest-resistance traits of other grasses, using a legion of genetic tools that can reduce crop losses and pesticide use while foregoing the cost, regulatory hurdles and controversy of genetically modified organisms.
The discovery clears the way for breeders to develop wheat varieties with the disease- and pest-resistance traits of other grasses, using a legion of genetic tools that can reduce crop losses and pesticide use while foregoing the cost, regulatory hurdles and controversy of Genetically Modified Organisms, or GMOs.
"The real exciting part of this gene is that it has tremendous potential for application," said Kulvinder Gill, a WSU professor, who reports his findings in the journalProceedings of the National Academy of Sciences.
For some 35 million years, the wild ancestors of wheat routinely traded genes as they accidentally cross-bred with each other. But with the rise of agriculture and cultivated wheat 10,000 years ago, the plant's genetic structure changed. Instead of being diploid, with two sets of chromosomes like humans and most other living things, it became polyploid, with, in the case of bread wheat, seven sets of six related chromosomes.
Starting in 1958, just five years after the discovery of DNA's double-helix structure, researchers suspected that a specific gene controls the orderly pairing of wheat chromosomes during reproduction.
"If this gene was not present, there would be chaos in the nucleus," said Gill. "Six chromosomes would pair with each other, and sometimes five chromosomes would go to one cell and one to the other, resulting in a sterile plant. Because of this gene, wheat can be fertile. Without this gene, it would be more like sugar cane, where it is a mess in the nucleus and it can only be vegetatively propagated."
But the gene also prevents wheat from breeding with related ancestors that can contain a vast array of traits preferred by growers.
"This gene would not allow rye chromosomes to pair with wheat," said Gill. "We cannot get a single gene transfer into wheat as long as this gene is present."
Interest in the gene, called Ph1, has spawned scores of research papers, making it what Gill called, "the most famous wheat gene."
In 2006, British researchers writing in the journal Nature said they identified the gene.
"In this paper," said Gill, "we show that their gene is not the Ph1." Knowing their findings would be controversial, Gill and his colleagues spent a year repeating the experiments that led to their conclusion. They are now moving on.
"Now that we have the gene, we can actually use that gene sequence to temporarily silence the gene and make rye and other chromosomes pair with wheat and transfer genes by a natural method into wheat without calling it GMO," Gill said.
Their first effort involves transferring a gene from jointed goatgrass, a wild relative of wheat, to confer resistance to stripe rust. The fungus is considered the world's most economically damaging wheat pathogen, costing U.S. farmers alone some $500 million in lost productivity in 2012.
While facilitated by technology, the actual exchange of genetic material is similar to what has long taken place in nature, only faster. Incorporating the gene transfer into the overall breeding process, researchers can develop a new variety in five years, said Gill.
"If we let wheat evolve for another few millions years in the wild, maybe it will develop enough variation, but we don't have that kind of time," said Gill. "We need to solve this problem today."

Source:
http://www.sciencedaily.com/

Ramanjot Bhullar, Ragupathi Nagarajan, Harvinder Bennypaul, Gaganpreet K. Sidhu, Gaganjot Sidhu, Sachin Rustgi, Diter Von Wettstein, and Kulvinder S. Gill.Silencing of a metaphase I-specific gene results in a phenotype similar to that of the Pairing homeologous 1 (Ph1) gene mutations. PNAS, September 2014 DOI: 10.1073/pnas.1416241111

Thursday, September 25, 2014

Plant diversity in China vital for global food security

With climate change threatening global food supplies, new research claims the rich flora of China could be crucial to underpin food security in the future. A team has identified 871 wild plant species native to China that have the potential to adapt and maintain 28 globally important crops, including rice, wheat, soybean, sorghum, banana, apple, citrus fruits, grape, stone fruits and millet. 42% of these wild plant species, known as crop wild relatives occur nowhere else in the world.

With climate change threatening global food supplies, new research claims the rich flora of China could be crucial to underpin food security in the future.
A team from the University of Birmingham and partners in China have identified 871 wild plant species native to China that have the potential to adapt and maintain 28 globally important crops, including rice, wheat, soybean, sorghum, banana, apple, citrus fruits, grape, stone fruits and millet. 42% of these wild plant species, known as crop wild relatives (CWR) occur nowhere else in the world.
CWR are wild plant species closely related to crops which grow under a broad range of environmental conditions in their natural habitats and are therefore much more genetically variable. Their adaptive traits can be transferred to crops to improve tolerance to extreme environmental conditions and exposure to different pests and diseases, which helps sustain food production. Furthermore, they can be utilised to improve the nutritional and marketing qualities of crops.
Examples of China's CWR successfully used to improve crops include: Oryza rufipogon, a wild relative of rice, utilised to confer tolerance to drought and aluminium toxicity; Glycine soja, used to improve protein content in soybean; and Vitis amurensis, a wild relative of grape, which has been used to improve cold tolerance.
Worryingly, of these 871 CWR native to China, at least 17% are threatened with extinction in China and require urgent conservation action. This includes wild relatives of 16 crops that are globally threatened because they do not occur anywhere else in the world.
The flora of China comprises more than 20,000 native higher plant species, a proportion of which have value as gene donors for crop improvement. However, until now, the full range of these potentially valuable CWR species had not been identified.
The research carried out by academics from the University of Birmingham represents a significant contribution to global research in plant genetic resources for food and agriculture, particularly in the fight against the detrimental impacts of climate change on food security. The research in China is based upon methodologies developed and applied by the University's research team in Europe, but it is the first survey of its kind anywhere else in the world.
Now a comprehensive database of CWR for China exists and the priority species have been identified, the next step is to systematically conserve their diversity in situ and via gene banks to ensure their wealth of resilient characteristics are available to plant breeders.
Shelagh Kell, Research Fellow, School of Biosciences said "China has remarkable wild plant diversity. With more plant species than Europe and CWR of globally important food crops, its position as a provider of plant genetic resources for crop improvement is crucial to us all globally. Now that we have identified China's priority CWR and some of the hotspots in which they occur, stakeholders need to implement a strategy to secure their future.
"Conservation planning and plant breeding knowledge is very advanced but the politics of establishing a network for in situ protection of CWR and for accessing plant material for crop improvement is incredibly complex. However, urgent attention needs to be paid to China's CWR to ensure that they are adequately conserved, so that this diversity is available for use in crop improvement programmes before it is lost forever."

Tuesday, September 23, 2014

Coffee genome sheds light on the evolution of caffeine

An international research team has sequenced the genome of the coffee plant Coffea canephora. By comparing genes in the coffee, tea and chocolate plants, the scientists show that enzymes involved in making caffeine likely evolved independently in these three organisms. More than 8.7 million tons of coffee was produced in 2013; it is the principal agricultural product of many tropical nations.

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 appeared on Sept. 5 in the journalScience.

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.

Source:
http://www.sciencedaily.com/

France Denoeud et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, September 2014 DOI:10.1126/science.1255274

Monday, August 04, 2014

Evaluation of Unintended Effects in the Composition of Tomatoes Expressing a Human Immunoglobulin A against Rotavirus

The production of neutralizing immunoglobulin A (IgA) in edible fruits as a means of oral passive immunization is a promising strategy for the inexpensive treatment of mucosal diseases. This approach is based on the assumption that the edible status remains unaltered in the immunoglobulin-expressing fruit, and therefore extensive purification is not required for mucosal delivery. However, unintended effects associated with IgA expression such as toxic secondary metabolites and protein allergens cannot be dismissed a priori and need to be investigated. This paper describes a collection of independent transgenic tomato lines expressing a neutralizing human IgA against rotavirus, a mucosal pathogen producing severe diarrhea episodes. This collection was used to evaluate possible unintended effects associated with recombinant IgA expression. A comparative analysis of protein and secondary metabolite profiles using wild type lines and other commercial varieties failed to find unsafe features significantly associated with IgA expression. Preliminary, the data indicate that formulations derived from IgA tomatoes are as safe for consumption as equivalent formulations derived from wild type tomatoes. 

Saturday, July 26, 2014

"Quinoa" magazine on Flipboard

Quinoa
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Source: https://flipboard.com/section/quinoa-bOjVX9

Wednesday, June 25, 2014

BT crops: To plant or not to plant

Scientists, through genetic engineering, have taken the Bt gene responsible for the production of the insecticidal protein from the bacterium and incorporated it into the genome of plants. As such, the plants have a built-in mechanism of protection against targeted pests.
Aside from corn, Bt is also introduced in cotton, poplar, potato, rice, soybean, tomato, and more recently eggplant. “The protein produced by the plants does not get washed away, nor is it destroyed by sunlight,” said a briefing paper published by the Global Knowledge Center on Crop Biotechnology. “The plants are protected from the insects round the clock regardless of the situation.”
Since Bt crops are able to defend themselves against pests, the use of chemical insecticides is significantly reduced. A study conducted by the United States Department of Agriculture showed that 8.2 million pounds of pesticide active ingredients were eliminated by the farmers who planted Bt crops in 1998.
“Aside from being effective against insect pests, Bt crops have lower incidences of opportunistic microbial pathogens, such as the fungus Fusarium,” the briefing paper said. “This fungus produces mycotoxins that can be deadly to livestock and also cause cancer in humans.”
The briefing paper shares this information on how Bt operates: “When ingested by larva of the target insect, the Bt protein is activated in the gut’s alkaline condition and punctures the mid-gut leaving the insect unable to eat. The insect dies within a few days.”
It is for this reason why much research has been done to exploit the organism’s agronomic value. To date, there are more than 200 types of Bt proteins identified with varying degrees of toxicity to some insects.
The International Service for the Acquisition of Agri-Biotech
Applications (Isaaa) recently released a report which indicates more than 18 million farmers in 27 countries planted biotech crops in 2013, reflecting a five million, or three percent, increase in global biotech crop hectarage.
“Accumulated hectarage of biotech crops planted worldwide to-date stands at 1.6 billion hectares or 150 percent of the total landmass of China,” said Clive James, author of the report and ISAAA Founder and Chairman Emeritus.
In Asia, Bt corn is now planted not only in the Philippines but also in China, Indonesia, Japan, Malaysia, South Korea, and Taiwan. It is also grown in the United States, Canada, Switzerland, and in some parts of South America and Africa.
But there are some issues against Bt crops. Critics claim that Bt proteins could target predatory and other beneficial or harmless insects as well as the targeted pest. The University of California reported that the Bt proteins have been used as organic sprays for insect control in France since 1938 and the USA since 1958 with no ill effects on the environment reported.
“The specificity of Bt for its target insects is one of the characteristics that make it an ideal method of biological pest control,” the briefing paper explained. “The specificity rests on the fact that the toxicity of the Bt protein is receptor-mediated. This means that for an insect to be affected by the Bt protein, it must have specific receptor sites in its gut where the proteins can bind. Fortunately, humans and majority of beneficial insects do not have these receptors.”
A 1999 study, which appeared in Nature, showed that in a lab environment, pollen from Bt corn dusted onto milkweed could harm the monarch butterfly. Several groups later studied the phenomenon in both the field and the laboratory, resulting in a risk assessment that concluded that any risk posed by the corn to butterfly populations under real-world conditions was negligible, according to a study published in the Proceedings of Natural Academy Science.
A 2002 review of the scientific literature also concluded that “the commercial large-scale cultivation of current Bt–maize hybrids did not pose a significant risk to the monarch population” to quote a study entitled, “The case of the monarch butterfly: a verdict is returned,” which appeared in Trends Genet.
What about among human beings? The US Environment Protection Agency has reportedly administered toxicology assessments. Bt proteins have already been tested even at relatively higher dosages.
According to the Extension Toxicology Network (Extonet), a pesticide information project of several universities in the US, “no complaints were made after 18 humans ate one gram of commercial Bt preparation daily for five days, on alternate days… Humans also ate one gram per day for three consecutive days were not poisoned or infected.”
On tests conducted on dogs, guinea pigs, rats, fish, frogs, salamanders and birds, the Bt protein was found not to have any harmful effects. What was interesting about the study was that the no toxic effects were found on beneficial or predator insects, such as honeybees and lady beetles, Extonet reports.
The ISAAA claimed that Bt crops have benefitted food security, sustainability and the environment. “Between 1996 and 2012, biotech crops have made positive contributions through decreased production costs and increased productivity (estimated at 377 million tons) valued at US $117 billion,” it reported.
Its environmental benefits included: eliminating the need for 497 million kilograms of pesticides; reducing carbon dioxide emissions by 27 billion kilograms in 2012 alone (equivalent to removing 12 million cars from the road for one year); and conserving biodiversity by saving 123 million hectares of land from being placed in agricultural production during the period 1996 to 2012.
“Bt crops are an addition to our arsenal against plant pests,” the briefing paper concludes. “With an increasing population and decreasing arable land, it is necessary to exploit all options with as little compromise to produce more crops. When used side by side with proper agricultural practices, Bt insect resistance technology can bring many benefits to crops, farmers, and consumers alike.”

Source:

Tuesday, June 24, 2014

Enter halophytes: We are running out of land for traditional agriculture. Time to figure out what saltwater plants can do for us

Ever since ancient times, the sowing of salt has been synonymous with severe and deadly retribution. The Roman general Scipio Africanus the Younger was said to have ended the Third Punic War in 146BC by razing Carthage, enslaving its population and spreading salt on its fields. In the biblical book of Judges (9:45), the brutal and unprincipled King Abimelech laid siege to the Canaanite city of Shechem. ‘He took the city,’ the biblical story says, ‘and slew the people that was therein, and beat down the city, and sowed it with salt.’
Salt kills most plants. In fact, it attacks them in much the same way that carbon monoxide kills humans. In cases of carbon monoxide poisoning, CO molecules exhaust the carrying capacity of your red blood cells, depriving your body of the oxygen it needs. Likewise, most terrestrial plants soak up the sodium ions and sodium chloride from salt much faster than they can absorb essential nutrients such as potassium, calcium and magnesium. Without those nutrients, they perish. Spread salt on the fields of your enemies and their crops will fail.
More than 97 per cent of the water on Earth is saline. Wouldn’t it be cruel if nature had locked up the vast bulk of the planet’s vital fluids in a form that no plant could drink? Well, as it happens nature is not quite that cruel. Of the 400,000 flowering plant species around the world, 2,600 do drink seawater. They are halophytes, meaning ‘salt-plant’, and they might just be the answer to a question surprisingly few governments have yet asked: namely, how can we put our planet’s practically infinite volumes of saltwater to good use?
It might not be immediately obvious why such a question is worth our time. But consider: between sea-level rise and the increase in droughts and floods, the acreage available for conventional, freshwater agriculture is shrinking rapidly. Freshwater aquifers are becoming increasingly salty: among them, the Ogallala Aquifer, which covers a quarter of the irrigated land in the US. And so one of the world’s most important breadbaskets is under threat. Elsewhere, one-sixth of the world’s population relies on Eurasian rivers that trace back to Himalayan glaciers, which are themselves disappearing because of climate change.
While the global supply of arable land is shrinking, demand keeps rising. The United Nations has calculated that, if we are to feed the 9 billion people on Earth by the middle of this century, we will have to increase agricultural productivity by as much as 70 per cent. How on earth are we going to do that? Perhaps we’ll discover some ultra-productive new crops or farming techniques; we’ve been lucky before. But even if we manage that, our crops will still have to withstand the projected spike in extreme weather caused by climate change.
Meanwhile, we are trying to replace our fossil fuels with bio alternatives. The trouble with fossil fuels, you might or might not be aware, is the ‘fossil’ part: burning them returns a lot of carbon into the atmosphere that had been locked away underground for millions of years. Biofuels, by contrast, are made from plants whose carbon was for the most part only recently pulled out of the air, so they don’t increase the atmospheric carbon count by very much. That is to say, we need them. The only catch is, they come from plants that also have to be grown and cultivated. With limited arable land and increasingly limited freshwater supplies, conventional biofuel crops have to fight for space with our own food and water. Whichever way you cut it, we are running out of land.
Enter halophytes. Edward Glenn, an environmental scientist at the University of Arizona, has been promoting the plants for the best part of two decades. Above all, he sees them as an effective way to tackle climate change itself. Deforestation generates an astonishing 20 per cent of greenhouse gas emissions today – exceeding the total carbon emissions from all cars, trucks, ships and planes around the world – and most felling takes place in order to clear ground for freshwater agriculture. ‘If you can develop new cropland using seawater and saline water and coastal deserts,’ Glenn explains, ‘and preserve all those forested lands, that’d really make a contribution to the carbon balance and climate change.’
Dennis Bushnell, chief scientist at NASA’s Langley Research Center, has been working on his own high-level analysis, and he shares Glenn’s enthusiasm for the plants, though he emphasises another aspect of the overall picture. Bushnell is one of the agency’s ‘big thinkers’, concerned not only with rocket launches but also with global-scale problems. He predicts that by developing saline agriculture on waste ground, we could get our water issues under control within ‘15 to 20 years’, freeing up as much as 70 per cent of the water that we’re using now for conventional farming. ‘The beauty of halophytes,’ says Bushnell, ‘is you can do it wherever you have wastelands and some saline water. We have a surfeit of that.’
Encouraging as these global estimates might be, what the halophyte campaign really needs are concrete business proposals. So how about this one: according to researchers at the University of Delaware, a perennial species called seashore mallow (Kosteletzkya pentacarpos) could work in desert and salty-soil regions of North America, the Middle East, southeast Asia and western Australia. Seashore mallow can grow in salty soil, using saltwater irrigation. It is non-invasive and tolerant of both droughts and waterlogging. And its seeds are 18-20 per cent oil, making it a plausible biofuel candidate.
Those researchers are John Gallagher and Denise Seliskar – respectively, professor and research scientist at Delaware’s College of Earth, Ocean and Environment. They have been championing seashore mallow for many years. Last year they published a paper in the journal Renewable Energy, co-written with a group from the US Department of Agriculture, that analysed the plant’s potential as a biodiesel and ethanol source. By their calculations, it comes out roughly on par with soybeans, one of the commonest sources of biofuel now in use. A second paper, in Biomass and Bioenergy,examined the perennial’s stems’ absorbency, revealing commercial potential as mulch, erosion control and even kitty litter and animal bedding.
That variety of applications is important. ‘The thing that became apparent to us is it wasn’t going to run economically just on the oil you squeezed out of it,’ Gallagher says. ‘It’s taken 8,000 years to evolve corn from the teosinte [wild grass] found in the Mexican highlands to the Iowa cornfields. I just don’t have that long. So we thought we’d try to come up with an array of things we can get from the plant.’ Gallagher and Seliskar estimate that the entire crop can be harvested for products that could compete with existing markets of conventionally farmed commodities. The absorbency of its inner stem makes it attractive for animal bedding, while the outer bark has been developed into a thread for cloth. The seed, as noted, is a promising stock for ethanol and biodiesel. And the seedmeal offers a spread of amino acids that make it attractive as animal feed. Roots, spent flowers and the biopolymers in the plant are also being investigated for everything from gums to industrial chemicals.
It’s pretty straightforward to cultivate, too. According to the sales pitch that the duo sends out to interested farmers, this wild cousin of cotton is at home in brackish marshes and has adapted to both soggy and salty soils. That means it might be worth considering for farmers near estuaries, for instance, or near ocean dunes or deltas that are becoming too saline for traditional crops. Planting, they say, requires only the same row planter used for soybeans or corn. Harvesting can be done with traditional tools such as a combine harvester. It sounds almost too good to be true, doesn’t it? Farmers should be beating down their door.
And yet, somehow they aren’t.
In fact, despite the halophyte family’s dazzling promise, its champions have had to be remarkably patient. The catch, says Jeannette Hoek, president of the company OceanDesertFood in the Netherlands, is creating a demand in the marketplace for halophyte food, fodder and products. Hoek’s company contracts with halophyte farmers in Mexico who grow a vegetable called salicornia, also known as glasswort or pickleweed. It looks something like a green bean crossed with a stalk of asparagus, and has become a favourite of food bloggers and locavore enthusiasts. It is, of course, rather salty. OceanDesertFood makes salicornia crackers, as well as seaweed chips. ‘These things build a market,’ she says. ‘And as soon as the farmers see they can sell something, they will do it. But as long as they don’t see that, they will be very hesitant.’
Edward Glenn was beating the halophyte drum fully 16 years ago, notably talking up the advantages of saltwater agriculture in a landmark 1998 article for Scientific American. Today, he says he’s not surprised that the ambitious changes he and his co-authors proposed – greening the world’s deserts, transforming lands with brackish water tables into sites of commercial agriculture – have not yet come to pass. ‘These kinds of changes take much longer than people think they’ll take,’ he says. ‘But if you develop the technology and the resources – and there’s a place for them – eventually they’ll be utilised.’ Agriculture, after all, is as old as human civilisation. Perhaps it has earned the right to be a slow-moving industry.
Even so, there are some peculiarly modern reasons why uptake should be slow. The greatest opportunity for halophytes, both commercially and environmentally, is fuel. But bringing halophyte biofuel up to commercial scale would require the support of big energy – and perhaps big agribusiness – corporations. ‘The oil companies would have to become agriculturalists instead of hole drillers,’ says NASA’s Bushnell. This, of course, would take them a long way out of their comfort zones. ‘We have had contacts with several big corporations,’ says Bushnell. ‘And my impression of the big energy companies is they’re trying to squeeze the last dollops of profit out of their sunk costs and investments. However, in the back room they’re like the duck, paddling like hell underwater, trying to make sure they’re on to the next thing. So they are looking at this.’
J Alan Weber is the vice president of MARC-IV, a Missouri-based biofuel consulting firm. Though seashore mallow hasn’t yet secured much in the way of attention and research funding, it remains, in his opinion, a promising biodiesel and ethanol feedstock. But how to help it break through? ‘You probably wouldn’t anticipate seeing mallow grown on acres in Indiana,’ he says. On the other hand, ‘change the story, and start talking about a piece of ground that is high in salinity, where other crops wouldn’t perform very well, then the economics change.’ In the meantime, pilot programmes on non-traditional farmlands might draw in the research dollars. Weber recommends trials on federal lands, military bases, highway right-of-ways, or municipal county lands such as airports.
Air travel, in fact, might just be the factor that forces the issue. In 2015, the world’s airplanes are projected to consume 75 billion gallons of jet fuel, and consumption is expected to keep growing some 3-4 per cent per year through the next two decades. At NASA’s Glenn Research Center in Cleveland, Ohio, Bilal Bomani runs the Green Lab, a research and teaching lab that investigates both halophyte- and algae-based biofuels in aviation. He guesses that actual shortages will drive the industry to look to new resources. ‘We do not have fuel that will sustain us for the next 50 years,’ Bomani says. ‘You’re either going to do it now, or you’re going to be forced to do it later. And it’s a longer-term process. You’re not going to get running on halophytes in two to three years. But in five to 10 years? Absolutely positively.’
As far as Edward Glenn is concerned, the situation reminds him of another saltwater venture that no one paid attention to, until suddenly it took over its industry. In the late 1970s, he was working at a pilot shrimp farm in Mexico. ‘Us postdocs would get together in the evenings and say: ugh, this is hopeless – this aquaculture is never going to replace wild fisheries,’ he recalls. ‘But now aquaculture is a multi-multi-multi billion dollar industry around the world. And it’s where most of the world’s shrimp comes from. So change is slow, but it’s possible.’
Indeed, Glenn points to a possible synergy between aquaculture and halophyte agriculture. Shrimp farms produce copious amounts of ‘effluent’ – waste-laden water from the shrimp. This water can be a toxic hazard if it’s just dumped back into the ocean or back into the shrimp ponds. ‘You pump the water out of the ocean – or out of wells near the ocean – and you grow your shrimp,’ he says. ‘They require quite a bit of turnover of water to keep them healthy and growing. And you have to do something with the effluent water.’ The problem is that the effluent is also saltwater, which makes it useless for nearly any conventional agricultural use: crops choke on it as we would on carbon monoxide. But for halophyte-based agriculture, it is perfect: free irrigation plus free fertiliser. This opens the door for a symbiotic relationship that, Glenn says, shrimp farms in southeast Asia in particular have now begun to look into.
Even if halophytes do take off, we should temper our optimism. If there’s any single lesson to draw from the many problems that climate change poses, it’s that any single lesson is deceiving. There is no magic switch to make it all go away, and halophytes won’t save the planet any sooner than solar power, fuel cells or genetic engineering.
All the same, as a key that unlocks agriculture across four-tenth’s of the world’s land mass, they clearly deserve our close attention. Salted fields were synonymous with severe and deadly retribution, and it’s common today to think of climate change in similar terms: a harsh punishment for human hubris. Well, we might not be able to escape what’s coming to us altogether, but we should learn to roll with the punches.

Source:

Saturday, June 14, 2014

Perennial corn crops? It could happen with new plant-breeding tool

Since the first plant genome sequence was obtained for the plant Arabidopsis in 2000, scientists have gene-sequenced everything from cannabis to castor bean. They have now unveiled a new tool that will help all plant scientists label genes far more quickly and accurately and is expected to give a big boost to traditional and nontraditional plant breeders.

University of Florida scientists were part of a research team that this week unveiled a new tool that will help all plant scientists label ("annotate" in researcher parlance) genes far more quickly and accurately and is expected to give a big boost to traditional and nontraditional plant breeders.
Christopher Henry, a computational biologist at the University of Chicago who had a leading role in creating the database, called PlantSEED, said it is an important step toward the engineering of improved crops, such as creating rice that grows more efficiently or is more drought resistant.

Or creating perennial corn.
"Imagine if you didn't have to plant seeds for crops -- if crops were just like your flowers and your maize just came up year after year," he said.
Andrew Hanson, a UF eminent scholar in horticultural sciences, said he believes PlantSEED -- the capstone of the team's three-year effort -- will prove even more of a boon to traditional breeders and should help them create better cultivars, faster.
"It's really the future. It'll be a new tool in the hands of the next generation of plant breeders, just as similar tools for bacteria are now widely used in microbial metabolic engineering," he said.
While scientists have been documenting and annotating genome sequences for plants at an amazing clip since breaking through with Arabidopsis, the work has not been without challenges.
In documenting genome sequences, scientists must sort through millions of bits of genetic code to identify what function each gene is responsible for (such as telling a plant how tall to grow or how to transport an amino acid throughout the plant). They base those identifications on evidence from previous studies.
That can be an imperfect process, Hanson said, because with 20,000 to 30,000 genes in a typical plant, scientists can't possibly conduct experiments to find out what each and every gene is responsible for. And they don't.

That is where the team's PlantSEED system comes in.
The open-access system, described in a paper published online by Proceedings of the National Academy of Sciences, integrates data from plant scientists around the world into a common platform, which should result in better, more quickly-updated plant models for everyone using them.
PlantSEED will help plant scientists begin to make better use of genome information by helping them create consistently accurate models for all plant genomes contained in the database.
Hanson, a faculty member with UF's Institute of Food and Agricultural Sciences, likens the new tool to models aeronautical engineers use when testing new equipment. They don't build a brand new jet every time they want to test a new material, but instead, test it by plugging information into computer models.
Because of tools like PlantSEED, plant scientists will eventually be able to do the same, he said.
"You can't really make as much use of the genome information as we should be able to until you can do that kind of modeling for plants, as well," he said. "And that's pretty much what this project is about."

Source:
http://www.sciencedaily.com/

S. M. D. Seaver, S. Gerdes, O. Frelin, C. Lerma-Ortiz, L. M. T. Bradbury, R. Zallot, G. Hasnain, T. D. Niehaus, B. El Yacoubi, S. Pasternak, R. Olson, G. Pusch, R. Overbeek, R. Stevens, V. de Crecy-Lagard, D. Ware, A. D. Hanson, C. S. Henry.High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proceedings of the National Academy of Sciences, 2014; DOI: 10.1073/pnas.1401329111