Genomics-Assisted Analysis and Exploitation of Barley Diversity (ERA-PG 061)
Final Report Abstract
Our project aimed to identify new gene variants (‘alleles’) that occur naturally in wild barley and ultimately to transfer them into the cultivated crop. Useful gene alleles have been lost by selective breeding and are needed to deal with the challenges of climate change and reduced use of pesticides and fertiliser. The project used an ‘association genetics’ approach to identify new alleles, which screens hundreds of plant lines both for their detailed genetic fingerprints and their crop performances, then compares these two sets of data to identify the particular genetic segments conferring advantageous properties. The first phase of the research involved careful selection and growth of the large numbers of experimental plants needed for the project. In total, more than 1300 different genetically pure barley lines were selected, in-bred seed obtained from each, plants grown up and each plant line was genetically characterised for at least 1536 different genes, completing the first half of the work needed for association genetics analysis. The other main task of measuring crop performance was carried out in field trials on 887 of the barley lines at four different locations across Europe during 2009 and 2010. These plants were harvested and an extensive set of measurements were taken to exactly define their crop properties, such as total grain yield, plant height, resistance to microbial infection etc. In all, 14 such traits were recorded, constituting the second half of the data needed for the association genetics methodology. Putting these two very large data sets and thus discovering useful genetic loci that confer beneficial properties to the plants containing them comprised the most important goal of the project. 9 research publications in high impact refereed research journals and two book chapters describing these activities have been published by our partnership so far. We have identified a wide variety of highly promising new gene loci that control the important traits studied by us. These will be freely accessible for use by European barley breeders to aid crop improvement. Looking to the future of this kind of experimental approach, a new population of ca 1400 barley plant lines containing defined segments of wild barley-derived DNA replacing the corresponding segments of a popular cultivar was developed in the Exbardiv project, to explore directly the beneficial effects of our crop improvement strategy.
Publications
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2008. Effects of the growth stage and hardening conditions on the association between frost resistance and the expression of the cold induced protein COR14b in barley. Environmental and Experimental Botany, 62: 93-100
Crosatti C, Pagani D, Cattivelli L, Stanca A M, Rizza F
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2009. Genetic variants of HvCbf14 are statistically associated with frost tolerance in a European germplasm collection of Hordeum vulgare. Theoretical and Applied Genetics, 119: 1335-1348
Fricano A, Rizza F, Faccioli P, Pagani D, Pavan P, Stella A, Rossini L, Piffanelli P, Cattivelli L
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2009. The International Barley Sequencing Consortium (IBSC) – at the threshold of efficient access to the barley genome. Plant Physiology, 49: 142-147
Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N
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An incremental approach for association mapping of useful traits in barley - The EXBARDIV Project. 2nd Intl Symposium on Genomics of Plant Resources 24-27.04-2010 Bologna, Italy
Flavell AJ, X Xu , Comadran J, Thomas W, Marshall D, Russell J, Waugh R, Tondelli A, Cattivelli L, Schnaithmann F, Pillen K, Schulman A, Ingvardsen C, Rasmussen S, Sharma R, Kilian B
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Genome wide association studies for plant architecture traits in different barley genepools. Genomics Based Breeding Conference, Giessen, 26-28.10.2010
Sharma R, Pasam RK, Kilian B, Graner A
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2011. Abiotic stress in barley: problems and solutions. In: Ullrich S (ed) Barley: improvement, production, and uses. Wiley-Blackwell, Ames, USA pp 282-306. ISBN: 9780813801230
Cattivelli L, Ceccarelli S, Romagosa I, Stanca A M
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2011. Diversity in the response to low temperature in a set of representative barley genotypes cultivated in Europe. Crop Science, 51: 2759–2779
Rizza F, Pagani D, Gut M, Prasil IT, Lago C, Tondelli A, Orrù L, Mazzucotelli E, Francia E, Badeck FW, Crosatti C, Terzi V, Cattivelli L, Stanca AM
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(2012) Comparing genetic diversity within a crop and its wild progenitor: a case study for barley. In: Maxted N et al. (editors). Agrobiodiversity Conservation: Securing the Diversity of Crop Wild Relatives and Landraces. CABI pp. 186-192
Kilian B, Özkan H, Shaaf S, Hübner S, Pasam RK, Sharma R, Neumann K, Weißgerber W, Konovalov FA, Keilwagen J, Friedel S, Knüpffer H, von Korff M, Coupland G, Graner, A
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Genome-wide association study of resistant starch (RS) phenotypes in a barley variety collection. J. Agric. Food Chem. 2012, 60, 10302−10311
Shu, X., Backes, G., Rasmussen, S. K.
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Structural and Temporal Variation in the Genetic Diversity of a European Collection of Barley Cultivars and Utility for Association Mapping of Quantitative Traits. Plant and Animal Genome Conference 2012 XX P0346
A Tondelli, X Xu, F Schnaithmann, R Sharma … A Flavell
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(2013) Detection of exotic QTLs controlling nitrogen stress tolerance among wild barley introgression lines. Euphytica 189: 67-88
Schnaithmann F, Pillen K
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(2013) Structural and temporal variation in genetic diversity of European spring 2-row barley cultivars and association mapping of quantitative traits. The Plant Genome 6
Tondelli A, Xin X, Moragues M, Sharma R, Schnaithmann F, Ingvardsen C, Manninen O, Comadran J, Russell J, Waugh R, Schulman AH, Pillen K, Rasmussen SK, Kilian B, Cattivelli L, Thomas WTB and Flavell AJ
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(2014) Allelic variation at Fr-H1/Vrn-H1 and Fr-H2 loci is the main determinant of frost tolerance in spring barley. Environmental and Experimental Botany
Tondelli A, Pagani D, Ghafoori IN, Ataei MRR, Rizza F, Flavell AJ, Cattivelli L
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(2014). Quantification of amylose, amylopectin and β-glucan in the search for genes controlling the three major quality traits in barley using genome-wide association studies. Front. Plant Sci. 5:197
Shu X and Rasmussen SK
