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News Article | April 26, 2017
Site: www.eurekalert.org

Research could lead to better beer, single malt Scotch whiskey and provide tool for scientists to better understand other crops, including rice and wheat RIVERSIDE, Calif. -- Looking for a better beer or single malt Scotch whiskey? A team of researchers at the University of California, Riverside may have you covered. They are among a group of 77 scientists worldwide who have sequenced the complete genome of barley, a key ingredient in beer and single malt Scotch. The research, 10 years in the making, was just published in the journal Nature. "This takes the level of completeness of the barley genome up a huge notch," said Timothy Close, a professor of genetics at UC Riverside. "It makes it much easier for researchers working with barley to be focused on attainable objectives, ranging from new variety development through breeding to mechanistic studies of genes." The research will also aid scientists working with other "cereal crops," including rice, wheat, rye, maize, millet, sorghum, oats and even turfgrass, which like the other food crops, is in the grass family, Close said. Barley has been used for more than 10,000 years as a staple food and for fermented beverages, and as animal feed. It is found in breakfast cereals and all-purpose flour and helps bread rise. Malted barley gives beer color, body, protein to form a good head, and the natural sugars needed for fermentation. And single malt Scotch is made from only water and malted barley. The report in Nature provides new insights into gene families that are key to the malting process. The barley genome sequence also enabled the identification of regions of the genome that have been vulnerable to genetic bottlenecking during domestication, knowledge that helps to guide breeders to optimize genetic diversity in their crop improvement efforts. Ten years ago, the International Barley Genome Sequencing Consortium, which is led by Nils Stein of the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany, set out to assemble a complete reference sequence of the barley genome. This was a daunting task, as the barley genome is almost twice the size of the human genome and 80 percent of it is composed of highly repetitive sequences, which cannot be assigned accurately to specific positions in the genome without considerable extra effort. Multiple novel strategies were used in this paper to circumvent this fundamental limitation. Major advances in sequencing technology, algorithmic design and computing made it possible. Still, this work kept teams around the world - in Germany, Australia, China, Czech Republic, Denmark, Finland, Sweden, Switzerland, United Kingdom and the United State - occupied for a decade. This work provides knowledge of more than 39,000 barley genes. Alcoholic beverages have been made from malted barley since the Stone Age, and some even consider this to be a major reason why humankind adopted plant cultivation, at least in the Fertile Crescent, where barley was domesticated. During malting, amylase proteins are produced by germinated seeds to decompose energy-rich starch that is stored in dry grains, yielding simple sugars. These sugars then are available for fermentation by yeast to produce alcohol. The genome sequence revealed much more variability than was expected in the genes that encode the amylase enzymes. Barley is grown throughout the world, with Russia, Germany, France, Canada, and Spain being among the top producers. In the United States, barley is mainly grown in the northwest. Idaho, Montana, and North Dakota are the leading producers. The Nature paper is called "A chromosome conformation capture ordered sequence of the barley genome." In addition to Close, the following current and former UC Riverside researchers are co-authors of the paper: María Muñoz?Amatriaín, a project scientist and Steve Wanamaker, a programmer, both in the Department of Botany and Plant Sciences; Stefano Lonardi, a professor of computer science in the Bourns College of Engineering; and Rachid Ounit, who earned his Ph.D. earlier this year in computer science after working in Lonardi's lab. The UC Riverside team's contributions were supported by grants from the National Science Foundation and the US Department of Agriculture, and annual support through the UC Riverside Agricultural Experiment Station.


Grant
Agency: European Commission | Branch: H2020 | Program: RIA | Phase: SFS-07b-2015 | Award Amount: 6.89M | Year: 2016

G2P-SOL is a research alliance bringing together the major European and International repositories of germplasm with public and private institutions active in genomics, phenotyping and breeding in the four major Solanaceous crops: potato, tomato, pepper and eggplant. These four crops constitute 66% of the value of European horticultural production, and over 65,000 accessions are available within the consortium. By harnessing the available global biodiversity, novel genotyping and phenotyping concepts and data analysis tools, the G2P-SOL project will link the genetic code underlying Solanaceae biodiversity with the traits that improve productivity, adaptation and human health. By making this information accessible to end-users, the awareness of the available diversity will be increased and use of this genetic diversity in breeding programs will be stimulated, resulting in diversified production chains. The phenotypes and traits of material held in European and major international collections will be described using common ontology terms developed in this project and this information will be housed in an open source software platform, allowing easy interfacing with existing platforms for germplasm cataloguing. G2P-SOL will develop shared values in science and education in the following areas: 1) Defining and maintaining genetic pools for crop improvement. 2) Phenomic and genomic data: generation, analysis, storage, and linkage with gene banks. 3) Pre-breeding and germplasm enhancement. 4) Training, workshops and public outreach. G2P-SOL will redefine how to manage and organize genetic resources and linked genomic and phenomic information in a manner that will make them accessible to naturalists, geneticists and breeders for conservation, scientific research, and breeding in the post genomic era, in compliance with the objectives of the International Treaty on Plant Genetic Resources and the Nagoya Protocol.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.65M | Year: 2013

Global population stands at 7 billion and is predicted to reach 9 billion by 2050. It is anticipated that food production will need to increase by at least 50% to meet the demand arising from this increase in population. This will require a sustained improvement in crop yield. The nature of this challenge is exacerbated by the likely impact of climate change. These factors combine to make Food Security one the key challenges for the 21st century. To deliver improvement and sustainability in crop production it will be necessary to harness a broad spectrum approaches. Crop improvement will be crucial and a major part in the delivery of this will be based on classical breeding. This harnesses the genetic variation that is generated by homologous recombination during meiosis. Meiotic recombination creates new combinations of alleles that confer new phenotypes that can be tested for enhanced performance. It is also crucial in mapping genetic traits and in the introgression of new traits from sources such as wild-crop varieties. Despite the central role played by meiosis in crop production we are remarkably ignorant as to how the process is controlled in these species. For example, it is not known why recombination in cereals and forage grasses is skewed towards the ends of the chromosomes such that an estimated 30-50% of genes rarely, if ever, recombine thereby limiting the genetic variation that is available to plant breeders. Moreover, as many crop species are polyploid a further level of complexity is added to the meiotic process. Over the past 15 years studies in Arabidopsis, many conducted in the laboratories in the COMREC consortium, have provided both insights into the control of meiosis in plants and generated the tools to analyze this process in crop species. It is now timely, to translate this knowledge, training a new generation of young scientists who will gain the expertise to understand and develop strategies to modify recombination in crops.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: KBBE.2012.1.1-01 | Award Amount: 3.83M | Year: 2013

Seed quality is of paramount importance to agriculture, food security and the conservation of wild species. Considerable economic losses result from sub-optimal seed performance, undermining food security and livelihoods. Seed quality is strongly influenced by the environmental stresses experienced by the mother plant. Climate change will further exacerbate economic losses and decrease the predictability of seed yield and quality for the farmer. The looming challenges of climate change and food security require new knowledge of how stress impacts on seed quality, as well as a re-appraisal of optimal storage conditions. EcoSeed addresses these challenges by bringing together a group of distinguished European experts in seed science and converging sciences to characterise seed quality and resilience to perturbation. EcoSeed combines state-of the-art omics, epigenetics, and post-omics approaches, such as nuclear and chromatin compaction, DNA repair, oxidative and post-translational modifications to macromolecules, to define regulatory switchboards that underpin the seed phenotype. Special emphasis is placed on the stress signalling hub that determines seed fate from development, through storage, germination and seedling development, with a particular focus on seed after-ripening, vigour, viability and storability. Translation of new knowledge gained in model to crop and wild species is an integral feature of EcoSeed project design, which will create a step-change in our understanding of the regulatory switchboards that determine seed fate. Novel markers for seed quality and new omics information generated in this project will assist plant breeders, advise the seed trade and conservationists alike. In this way, EcoSeed will not only be proactive in finding solutions to problems of ensuring seed quality and storability but also play a leading role in enabling associated industries to better capture current and emerging markets.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: KBBE.2013.1.2-03 | Award Amount: 6.90M | Year: 2014

WHEALBI will combine genomics, genetics and agronomy to improve European wheat and barley production in competitive and sustainable cropping systems. Germplasm representing the species diversity will be selected and characterised in unprecedented detail by next-generation-sequencing. Life history and adaptive traits will be evaluated in both transnational field experiments and a state-of-the-art precision phenotyping platform. Germplasm will be stored in a specialised and accessible bio-repository and associated data in knowledge bases that will represent a valuable legacy to the community. Whole genome association scans will be conducted for several traits, signatures of adaptive selection will be explored, and allele mining of candidate genes will reveal new variation associated with specific phenotypes. Pre-breeding tools and pipelines will be developed to optimize the efficiency of allele transfer from unadapted germplasm into elite breeding lines. New methodologies will explore how to optimally exploit the large amount of new genotypic and phenotypic data available. They will focus on the design of ideotypes with improved yield stability and tolerance to biotic and climatic stresses and provide proof of concept of the efficiency of genome and phenome assisted selection. Ideotypes and reference varieties will be evaluated in innovative cropping systems, particularly organic farming and no-till agriculture, and an economic evaluation of these approaches will be conducted. The results will be disseminated to a broad user community, highlighting the benefits and issues associated with the adoption of what is considered sustainable and environmentally friendly wheat and barley crop production in a European context. WHEALBI aims to help the EU remain a major actor in world small grain cereal production while addressing the pressing global priorities of increasing and stabilising primary production, improving food quality and safety, and reducing environmental impact.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.07M | Year: 2013

The YEASTCELL ITN will train 11 Early Stage Researchers for productive careers as research scientists and leaders in the public or private yeast biotechnology sectors. Yeast biotechnology spans fundamental and applied research and is an area with an immediate need for highly trained researchers to advance knowledge and to develop new applications. The training consortium comprises 9 Public Sector (6 Universities, 3 Research Institutes) and 4 Private Sector (2 large companies and 2 SME) partners. A research training programme embracing the philosophy of use-inspired fundamental research has been designed to provide all 11 ESRs with interdisciplinary research training in both the public and private sectors. The research themes include yeast physiology and metabolism, metabolic engineering, mathematical modeling, genomics and bioinformatics, fermentation, synthetic biology and systems biology. In addition to training via collaborative research projects, ESRs will participate in courses at local and network levels to enhance their technical and academic skills. All ESRs will register for PhD degrees and will also take a separate postgraduate certificate course in commercialisation and entrepreneurship. Industry-led workshops, research secondments and site visits will provide specific training that prepares ESRs for research in the private sector. A comprehensive programme of advanced training in complementary topics and skills of relevance to both the public and private sectors is provided at the network level. As well as directly training 11 ESRs, the network training activities will provide opportunities for ~40 additional researchers and will promote long-term interactions between research groups at the partner Institutions. The major impact of YEASTCELL will be a cohort of highly-trained ESRs with excellent career prospects in the yeast biotechnology sector and a lasting European training and research collaboration between public and private sector partners.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2015-ETN | Award Amount: 4.01M | Year: 2015

There is a massive and urgent effort needed to ensure security of food supply for the growing world population. This challenge of doubling crop yields by 2050 provides the motivation for this project, entitled Cereal Pathology training in innovative and integrated control of cereal diseases (CEREALPATH). Cereals are the most important source of human calories, but we lose billions of euro worth of grain annually due to diseases that reduce yield. CEREALPATH is a multidisciplinary, multisectoral training programme built using the complimentary expertise from 22 participants from 8 European countries, including 7 Universities, 3 research institutes, 11 industry and one regulatory agency. The consortium will combine and share expertise in different approaches to disease control to offer standardized, high quality doctoral training at an advanced level to 15 ESRs. CEREALPATH will expose researchers to research and innovation in both industry and academia. The training equips researchers with the skills and opportunities to develop innovative methods contributing to integrated disease control programmes, thus matching their potential to the jobs of the future and helping Europe and the world meet the critical need of global food security.


Shi R.,Leibniz Institute of Plant Genetics and Crop Plant Research
The New phytologist | Year: 2012

• Retranslocation of iron (Fe) from source leaves to sinks requires soluble Fe binding forms. As much of the Fe is protein-bound and associated with the leaf nitrogen (N) status, we investigated the role of N in Fe mobilization and retranslocation under N deficiency- vs dark-induced leaf senescence. • By excluding Fe retranslocation from the apoplastic root pool, Fe concentrations in source and sink leaves from hydroponically grown barley (Hordeum vulgare) plants were determined in parallel with the concentrations of potential Fe chelators and the expression of genes involved in phytosiderophore biosynthesis. • N supply showed opposing effects on Fe pools in source leaves, inhibiting Fe export out of source leaves under N sufficiency but stimulating Fe export from source leaves under N deficiency, which partially alleviated Fe deficiency-induced chlorosis. Both triggers of leaf senescence, shading and N deficiency, enhanced NICOTIANAMINE SYNTHASE2 gene expression, soluble Fe pools in source leaves, and phytosiderophore and citrate rather than nicotianamine concentrations. • These results indicate that Fe mobilization within senescing leaves is independent of a concomitant N sink in young leaves and that phytosiderophores enhance Fe solubility in senescing source leaves, favoring subsequent Fe retranslocation. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.


Sreenivasulu N.,Leibniz Institute of Plant Genetics and Crop Plant Research | Wobus U.,Leibniz Institute of Plant Genetics and Crop Plant Research
Annual Review of Plant Biology | Year: 2013

Seeds develop differently in dicots and monocots, especially with respect to the major storage organs. High-resolution transcriptome data have provided the first insights into the molecular networks and pathway interactions that function during the development of individual seed compartments. Here, we review mainly recent data obtained by systems biology-based approaches, which have allowed researchers to construct and model complex metabolic networks and fluxes and identify key limiting steps in seed development. Comparative coexpression network analyses define evolutionarily conservative (FUS3/ABI3/LEC1) and divergent (LEC2) networks in dicots and monocots. Finally, we discuss the determination of seed size-an important yield-related characteristic-as mediated by a number of processes (maternal and epigenetic factors, fine-tuned regulation of cell death in distinct seed compartments, and endosperm growth) and underlying genes defined through mutant analyses. Altogether, systems approaches can make important contributions toward a more complete and holistic knowledge of seed biology and thus support strategies for knowledge-based molecular breeding. © Copyright ©2013 by Annual Reviews. All rights reserved.


Grant
Agency: European Commission | Branch: H2020 | Program: ERC-COG | Phase: ERC-CoG-2015 | Award Amount: 2.00M | Year: 2016

Meeting the forecasted world demand for food remains a crucial challenge for plant scientists in this century. One promising avenue for improving grain yield of cereal crops, including wheat and barley, involves reducing spikelet mortality. Spikelets, the grain-bearing units of cereal spikes, usually form in excess and subsequently abort during development; increased spikelet survival is linked to increased numbers of grains per spike. Therefore, reducing spikelet mortality is an intriguing approach to improve grain yield. In barley, the number of spikelets per spike at the awn primordium (AP) stage represents the maximum yield potential per spike. After the AP stage, significant spikelet mortality results in fewer grains per spike. Our previous results clearly indicated that spikelet survival in barley is highly genetically controlled (broad-sense heritability >0.80) and that the period from AP to tipping represents the most critical pre-anthesis phase related to spikelet reduction and grain yield per spike. However, the underlying genetic and molecular determinants of spikelet survival remain to be discovered. I therefore propose this ambitious research program with an emphasis on using available genetic resources. Our specific aims during the LUSH SPIKE project are to: (i) discover quantitative trait loci (QTL) for spikelet survival and grain number per spike and validate these QTL in bi-parental doubled-haploid mapping populations, (ii) isolate and functionally characterize Mendelized QTL using a map-based approach, (iii) reveal gene regulatory networks determining spikelet survival during the critical spike growth period from AP to heading, and (iv) elucidate spatio-temporal patterns of metabolite and phytohormone distributions in spike and spikelet sections during the critical growth period, using mass spectrometric imaging. The results we obtain will advance our understanding of how to improve yields of cereal crops.

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