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1. Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Author

Bellucci, Elisa, Benazzo, Andrea, Xu, Chunming, Bitocchi, Elena, Rodriguez, Monica, Alseekh, Saleh, Di Vittori, Valerio, Gioia, Tania, Neumann, Kerstin, Cortinovis, Gaia, Frascarelli, Giulia, Murube, Ester, Trucchi, Emiliano, Nanni, Laura, Ariani, Andrea, Logozzo, Giuseppina, Shin, Jin Hee, Liu, Chaochih, Jiang, Liang, Ferreira, Juan José, Campa, Ana, Attene, Giovanna, Morrell, Peter L, Bertorelle, Giorgio, Graner, Andreas, Gepts, Paul, Fernie, Alisdair R, Jackson, Scott A, and Papa, Roberto

Subjects
Biological Sciences, Genetics, Human Genome, Humans, Phaseolus, Genetic Variation, Genotype, Biological Evolution, Hybridization, Genetic
Abstract

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

Published
2023

2. The INCREASE project: Intelligent Collections of food‐legume genetic resources for European agrofood systems

Author

Bellucci, Elisa, Aguilar, Orlando Mario, Alseekh, Saleh, Bett, Kirstin, Brezeanu, Creola, Cook, Douglas, De la Rosa, Lucía, Delledonne, Massimo, Dostatny, Denise F, Ferreira, Juan J, Geffroy, Valérie, Ghitarrini, Sofia, Kroc, Magdalena, Agrawal, Shiv Kumar, Logozzo, Giuseppina, Marino, Mario, Mary‐Huard, Tristan, McClean, Phil, Meglič, Vladimir, Messer, Tamara, Muel, Frédéric, Nanni, Laura, Neumann, Kerstin, Servalli, Filippo, Străjeru, Silvia, Varshney, Rajeev K, Vasconcelos, Marta W, Zaccardelli, Massimo, Zavarzin, Aleksei, Bitocchi, Elena, Frontoni, Emanuele, Fernie, Alisdair R, Gioia, Tania, Graner, Andreas, Guasch, Luis, Prochnow, Lena, Oppermann, Markus, Susek, Karolina, Tenaillon, Maud, and Papa, Roberto

Subjects
Plant Biology, Biochemistry and Cell Biology, Biological Sciences, Zero Hunger, Climate Action, Crops, Agricultural, Databases, Genetic, Europe, Fabaceae, Genotype, International Cooperation, Seed Bank, Seeds, plant genetic resources, symbiosis, high-throughput phenotyping, artificial intelligence, metabolomics, Plant Biology & Botany, Biochemistry and cell biology, Plant biology
Abstract

Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.

Published
2021

5. Sequencing of 15 622 gene‐bearing BACs clarifies the gene‐dense regions of the barley genome

Author

Muñoz-Amatriaín, María, Lonardi, Stefano, Luo, MingCheng, Madishetty, Kavitha, Svensson, Jan T, Moscou, Matthew J, Wanamaker, Steve, Jiang, Tao, Kleinhofs, Andris, Muehlbauer, Gary J, Wise, Roger P, Stein, Nils, Ma, Yaqin, Rodriguez, Edmundo, Kudrna, Dave, Bhat, Prasanna R, Chao, Shiaoman, Condamine, Pascal, Heinen, Shane, Resnik, Josh, Wing, Rod, Witt, Heather N, Alpert, Matthew, Beccuti, Marco, Bozdag, Serdar, Cordero, Francesca, Mirebrahim, Hamid, Ounit, Rachid, Wu, Yonghui, You, Frank, Zheng, Jie, Simková, Hana, Dolezel, Jaroslav, Grimwood, Jane, Schmutz, Jeremy, Duma, Denisa, Altschmied, Lothar, Blake, Tom, Bregitzer, Phil, Cooper, Laurel, Dilbirligi, Muharrem, Falk, Anders, Feiz, Leila, Graner, Andreas, Gustafson, Perry, Hayes, Patrick M, Lemaux, Peggy, Mammadov, Jafar, and Close, Timothy J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Chromosomes, Artificial, Bacterial, Genome, Plant, Hordeum, Molecular Sequence Data, Barley, Hordeum vulgare L, BAC sequencing, gene distribution, recombination frequency, synteny, centromere BACs, HarvEST:Barley, Aegilops tauschii, Hordeum vulgare L., Biochemistry and Cell Biology, Plant Biology, Plant Biology & Botany, Biochemistry and cell biology, Plant biology
Abstract

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

Published
2015

7. Genebank genomics highlights the diversity of a global barley collection

Author

Milner, Sara G., Jost, Matthias, Taketa, Shin, Mazón, Elena Rey, Himmelbach, Axel, Oppermann, Markus, Weise, Stephan, Knüpffer, Helmut, Basterrechea, Martín, König, Patrick, Schüler, Danuta, Sharma, Rajiv, Pasam, Raj K., Rutten, Twan, Guo, Ganggang, Xu, Dongdong, Zhang, Jing, Herren, Gerhard, Müller, Thomas, Krattinger, Simon G., Keller, Beat, Jiang, Yong, González, Maria Y., Zhao, Yusheng, Habekuß, Antje, Färber, Sandra, Ordon, Frank, Lange, Matthias, Börner, Andreas, Graner, Andreas, Reif, Jochen C., Scholz, Uwe, Mascher, Martin, and Stein, Nils

Published
2019
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9. 4th Conference of Cereal Biotechnology and Breeding jointly organized by EUCARPIA Cereal Section November 6–9, 2017 • Budapest, Hungary : BOOK OF ABSTRACTS

Author

Consortium INEW, PPP Barley Consortium, Börner, Andreas, Nagel, Manuela, Tarawneh, Rasha, Arif, Mian Abdur Rehman, Agacka-Mołdoch, Monika, Börner, Mariann, Lohwasser, Ulrike, Rieweach, David, Wieb, Janine, Altmann, Thomas, Góralska, Magdalena, Lenarczyk-Puri, Natalia, Podgórska, Katarzyna, Berdzik, Marcin, Stojałowski, Stefan, Myśków, Beata, Kiss, Tibor, Veisz, Ottó, Karsai, Ildikó, Martín, Antonio, Rasmussen, Søren K., Legzdina, Linda, Fan, Weiyao, Tikhenko, Natalia, Rutten, Twan, Senula, Angelika, Rubtsova, Myroslava, Keller, E. R. Joachim, Vitányi, Beáta, Nagy, Katalin, Fekete, Anna Katalin, Dudás, Brigitta, Lantos, Csaba, Pauk, János, Jenes, Barnabás, Yu, Bianyun, Zhang, Wentao, Gao, Peng, Sidebottom, Christine, Lokuruge, Prabhath, Polley, Brittany, Clarke, Carling, Sharpe, Andrew, Knox, Ron, Cuthbert, Richard, Ruan, Yuefeng, Pozniak, Curtis J., Fobert, Pierre, Dziurka, Kinga, Noga, Angelika, Marcińska, Izabela, Czyczyło-Mysza, Ilona, Warchoł, Marzena, Kapłoniak, Kamila, Warzecha, Tomasz, Sutkowska, Agnieszka, Werwińska, Krystyna, Nita, Zygmunt, Skrzypek, Edyta, Fradgley, Nick, Bentley, Alison, Gardner, Keith, Howell, Phil, Mackay, Ian, Scott, Mike, Mott, Richard, Cockram, James, Galani, Saddia, Sahar, Shagufta, Musharraf, Syed Ghulam, Azhar, Abid, Ferjaoui, Sahbi, Bouslimi, Chadha, Udupa, Sripada M., Hamza, Sonia, Mariana, Ittu, Ciuca, Matilda, Marinciu, Cristina, Cristina, Daniel, Turcu, Alina, Mandea, Vasile, Ittu, Gheorghe, Jabłoński, Bartosz, Onyśk, Agnieszka, Wyszyńska, Renata, Boczkowska, Maja, Przyborowski, Mateusz, Gasparis, Sebastian, Orczyk, Wacław, Nadolska-Orczyk, Anna, Bińkowski, Jan, Kubiś, Jakub, Pogorzelska, Katarzyna, Pellny, Till K, Bolibok-Brągoszewska, Hanna, Idziak-Helmcke, Dominika, Rojek, Magdalena, Hosiawa-Barańska, Marta, Tsai, Hsin-Yuan, Cericola, Fabio, Edriss, Vahid, Andersen, Jeppe, Orabi, Jihad, Jensen, Jens, Jahoor, Ahmed, Janss, Luc, Jensen, Just, Lawrenson, Tom, Hayta, Sadiye, Smedley, Mark, Hinchliffe, Alison, Harwood, Wendy, Gimenez, Guillermo G., Barakate, Abdellah, Russell, Joanne, Stephens, Jennifer, Lampugnani, Edwin R., Doblin, Monika S., Fincher, Geoffrey B., Burton, Rachel A., Waugh, Robbie, Tucker, Matthew, Houston, Kelly, Jouanin, Aurelie, Leigh, Fiona, Wallington, Emma, Schaart, Jan, Smulders, Marinus J.M., Kała, Maciej, Kim, Sung-Yong, Brueggeman, Robert, Åhman, Inger, Zhu, Li-Hua, Bouchet, Sophie, Lemarié, Stéphane, Fugeray-Scarbel, Aline, Auzanneau, Jérôme, Charmet, Gilles, Ali, Ahmad, Mastrangelo, Anna Maria, De Vita, Pasquale, Laido, Giovanni, Marone, Daniale, Arshad, Muhammad, Naqvi, S.M. Sawlan, Sher, Hassan, Rasheed, Awais, Kazi, Abdul Mujeeb, Oakey, Helena, Bayer, Micha, Macaulay, Malcolm, Byrt, Caitlin, Gilliham, Matthew, Salt, David E, István, Monostori, Fruzsina, Szira, Alessandro, Tondelli, Tamás, Árendás, Krisztián, Gierczik, Luigi, Cattivelli, Gábor, Galiba, Attila, Vágújfalvi, Bakuma, Alla, Chebotar, Galyna, Filimonov, Vadim, Kyrylyuk, Tetyana, Chebotar, Sabina, Kristensen, Peter Skov, Andersen, Jeppe Reitan, Guzmán, Carlos, Schurr, Ulrich, Pieruschka, Roland, Neumann, Kerstin, Zhao, Yusheng, Dhanagond, Sidram, Reif, Jochen C., Graner, Andreas, Raymaekers, Dries, Taylor, Mike, Åhman, Inger M., Crespo-Herrera, Leonardo A., Kobiljski, Borislav, Mladenović, Gojko, Jestrović, Zorica, Jancsó, Mihály, Ács, Katalin, Bóna, Lajos, Purgel, Szandra, Békés, Ferenc, Schwember, A.R., Matus, I., Sharma, Dew Kumari, Rosenqvist, Eva, Carl-Otto-Ottosen, Torp, Anna Maria, Andersen, Sven Bode, El-Haddoury, Jamal, Henkrar, Fatima, Grana, Zahra, Nyiraguhirwa, Solange, Gyawali, Sanjaya, Verma, Ramesh, Ouabbou, Hassan, Ibriz, Mohammed, Iraqi, Driss, Forgeois, Paul, Grausgruber, Heinrich, Cuendet, Catherine, Dell’Avo, Franca, Koppel, Reine, Weyermann, Verena, Mikó, Péter, Vida, Gyula, Rakszegi, Marianna, Lafferty, Julia, Lorentz, Bruno, Longin, Carl Friedrich Horst, Megyeri, Mária, Kaskarbayev, Zheksenbay, Zhloba, Ludmila, Kiyas, Aldabergen, Kunanbayev, Kairat, Churkina, Galina, Zueva, Nataliya, Cattivelli, Luigi, Guerra, Davide, Tondelli, Alessandro, Bustos-Korts, D., Rizza, Fulvia, Bretani, Gianluca, Ferrandi, Chiara, Lazzari, Barbara, Rossini, Laura, Ozkan, Hakan, Molnar-Lang, Marta, van Eeuwijk, Fred, Dawson, Ian K, Fricano, Agostino, Azad, Md. Abul Kalam, Kamruzzaman, Md., Yasmine, Fahmina, Islam, Mirza Mofazzal, Jankuloski, Ljupcho, Christopher, John (Jack), Anzooman, Monia, Menzies, Neal, Dalal, Ram, Dang, Yash, Novák, Aliz, Boldizsár, Ákos, Gierczik, Krisztián, Mohamed, Ahres, Ádám, Éva, Bognár, László Kozma, Vágújfalvi, Attila, Båga, Monica, Chibbar, Ravindra, Galiba, Gábor, Gottwald, Sven, Bhandari, Dhaka Ram, Wang, Qing, Li, Bin, Römpp, Andreas, Friedt, Wolfgang, Spengler, Bernhard, Jäger, Katalin, Sáfrán, Eszter, Fábián, Attila, Deák, Csilla, Papp, István, Barnabás, Beáta, Mesterhazy, Akos, Varga, Mónika, Bartók, Tibor, Lehoczki-Krjak, Szabolcs, Toth, Beata, Miloud, Hafsi, Pál, Magda, Szalai, Gabriella, Janda, Tibor, Molnár, István, Lovegrove, Alison, Darkó, Éva, Farkas, András, Láng, László, Bedő, Zoltán, Doležel, Jaroslav, Molnár-Láng, Márta, Shewry, Peter, Tiryakioğlu, Murat, Sakallı, Abdulla, Alloudane, Rajae, El Mourabit, Nourdin, Barrijal, Said, Bengtsson, Therése, Manninen, Outi, Bulatova, Kulpash, Mazkirat, Shynar, Babissekova, Dilyara, Aytimbetova, Klara, Goncharova, Anastasiya, Lavrinenko, Yuriy, Bazaliy, Galyna, Cope, Jonathan, Norton, Gareth, George, Timothy, Newton, Adrian, Császár, Orsolya, Lajos, Károly, Szalai, Márk, Dziurka, Michał, Dashkevich, Svetlana, Utebayev, Maral, Chilimova, Irina, Babkenov, Adilchan, Akhmetova, Galiya, Chaimae, Senhaji, Khadija, Ahansal, Rabha, Abdelwahd, Allal, Douira, Driss, Iraqi, Gracz, Joanna, Karłowski, Wojciech, Kuczyński, Jakub, Tyczewska, Agata, Haberle, Jan, Svoboda, Pavel, Neumannová, Adéla, Kurešová, Gabriela, Raimanová, Ivana, Holková, Ludmila, Solařová, Eva, Bradáčová, Marta, Smutná, Pavlína, Horčička, P., Pospíšilová, V., Veškrna, O., Bížova, I., Chrpova, J., Sumíková, T., Ittu, Mariana, Marinciu, Cristina Mihaela, Voica, Maria, Banateanu, Cecilia, Mayer, Marianna, Karsai, Idikó, Mirosavljević, Milan, Momčilović, Vojislava, Mikić, Sanja, Trkulja, Dragana, Denčić, Srbislav, Jocković, Bojan, Aćin, Vladimir, Pržulj, Novo, Nakhoda, Babak, Mohammadi-Nejad, Ghasem, Mardi, Mohsen, Amini, Ashkboos, Tabatabaei, Mohammad-Taghi, Parsayev, Evgeniy, Filippova, Nadezhda, Permana, Hadian, Ishii, Kazuo, Murata, Kazumasa, Yamada, Tetsuya, Kanekatsu, Motoki, Prokesova, Lenka, Smutna, Pavlina, Holkova, Ludmila, Rukavitsina, Irina, Suleimenov, Mechlis, Yerpasheva, Dana, Shtefan, Galina, Ivanova, Galina, Ferderer, Ella, Kalapos, Balázs, Ahres, Mohamed, Székely, András, Gulyás, Zsolt, Kovács, Kristóf, Jones, Huw D, Dalmay, Tamás, Soltész, Alexandra, Trávníčková, Martina, Chrpová, Jana, Martinek, Petr, Hnilička, František, Żywicki, Marek, Twardowski, Tomasz, Végh, Balázs, Marček, Tihana, Wiśniewska, Halina, Kwiatek, Michał, Majka, Maciej, Gawłowska, Magdalena, Korbas, Marek, Danielewicz, Jakub, Belter, Jolanta, Bilgrami, Sayedeh Saba, Sichani, Jalal Sabouri, Zandi, Peiman, Zhunusbayeva, Zhazira, Omirbekova, Nargul, Zhussupova, Aizhan, Mursalieva, Valentina, Nam, Svetlana, Żur, Iwona, Surówka, Ewa, Dubas, Ewa, Nowicka, Anna, Krzewska, Monika, Hura, Tomasz, Rapacz, Marcin, Wójcik-Jagła, Magdalena, Ostrowska, Agnieszka, Malaga, Sabina, Janowiak, Franciszek, Pellny, Till, Patil, Archana, Freeman, Jackie, Plummer, Amy, Hess, Linde, Phillips, Andy, Berry, Simon, Mitchell, Rowan, Larkin, Philip, Tanner, Gregory, Colgrave, Michelle, Blundell, Malcolm, Howitt, Crispin, Morita, Naofumi, Van Hung, Pham, Cegiełko, Małgorzata, Kiecana, Irena, Mielniczuk, Elżbieta, Pastucha, Alina, Perkowski, Juliusz, Áy, Zoltán, Czirle, Csaba, Palágyi, András, Mihály, Róbert, Vermeulen, Philippe, Suman, Michele, Pierna, Juan Antonio Fernández, and Baeten, Vincent

Published
2017

10. Development and implementation of high-throughput SNP genotyping in barley

Author

Close, Timothy J, Bhat, Prasanna R, Lonardi, Stefano, Wu, Yonghui, Rostoks, Nils, Ramsay, Luke, Druka, Arnis, Stein, Nils, Svensson, Jan T, Wanamaker, Steve, Bozdag, Serdar, Roose, Mikeal L, Moscou, Matthew J, Chao, Shiaoman, Varshney, Rajeev K, Szűcs, Péter, Sato, Kazuhiro, Hayes, Patrick M, Matthews, David E, Kleinhofs, Andris, Muehlbauer, Gary J, DeYoung, Joseph, Marshall, David F, Madishetty, Kavitha, Fenton, Raymond D, Condamine, Pascal, Graner, Andreas, and Waugh, Robbie

Abstract

Abstract Background High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Results Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. Conclusion The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

Published
2009

11. Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice.

Author

Thiel, Thomas, Graner, Andreas, Waugh, Robbie, Grosse, Ivo, Close, Timothy J, and Stein, Nils

Subjects
Hordeum, Gene Duplication, Synteny, Genome, Plant, Biological Evolution, Oryza, Oryza sativa, Genome, Plant, Evolutionary Biology, Genetics
Abstract

BackgroundWell preserved genomic colinearity among agronomically important grass species such as rice, maize, Sorghum, wheat and barley provides access to whole-genome structure information even in species lacking a reference genome sequence. We investigated footprints of whole-genome duplication (WGD) in barley that shaped the cereal ancestor genome by analyzing shared synteny with rice using a approximately 2000 gene-based barley genetic map and the rice genome reference sequence.ResultsBased on a recent annotation of the rice genome, we reviewed the WGD in rice and identified 24 pairs of duplicated genomic segments involving 70% of the rice genome. Using 968 putative orthologous gene pairs, synteny covered 89% of the barley genetic map and 63% of the rice genome. We found strong evidence for seven shared segmental genome duplications, corresponding to more than 50% of the segmental genome duplications previously determined in rice. Analysis of synonymous substitution rates (Ks) suggested that shared duplications originated before the divergence of these two species. While major genome rearrangements affected the ancestral genome of both species, small paracentric inversions were found to be species specific.ConclusionWe provide a thorough analysis of comparative genome evolution between barley and rice. A barley genetic map of approximately 2000 non-redundant EST sequences provided sufficient density to allow a detailed view of shared synteny with the rice genome. Using an indirect approach that included the localization of WGD-derived duplicated genome segments in the rice genome, we determined the current extent of shared WGD-derived genome duplications that occurred prior to species divergence.

Published
2009

12. 454 sequencing put to the test using the complex genome of barley

Author

Wicker, Thomas, Schlagenhauf, Edith, Graner, Andreas, Close, Timothy J, Keller, Beat, and Stein, Nils

Subjects
Microbiology, Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Generic health relevance, Base Pairing, Base Sequence, Chromosomes, Artificial, Bacterial, Genes, Plant, Genome, Plant, Hordeum, Molecular Sequence Data, Repetitive Sequences, Nucleic Acid, Sequence Analysis, DNA, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundDuring the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising an approximately 100-fold increase in throughput over Sanger technology--an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley.ResultsTo study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences.ConclusionOur data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence analysis can result in large regions of high-quality finished genomic sequences.

Published
2006

18. Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Author

Khodaeiaminjan, Mortaza, primary, Knoch, Dominic, additional, Ndella Thiaw, Marie Rose, additional, Marchetti, Cintia F., additional, Kořínková, Nikola, additional, Techer, Alexie, additional, Nguyen, Thu D., additional, Chu, Jianting, additional, Bertholomey, Valentin, additional, Doridant, Ingrid, additional, Gantet, Pascal, additional, Graner, Andreas, additional, Neumann, Kerstin, additional, and Bergougnoux, Véronique, additional

Published
2023
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20. Genome-wide association mapping in a diverse spring barley collection reveals the presence of QTL hotspots and candidate genes for root and shoot architecture traits at seedling stage

Author

Abdel-Ghani, Adel H., Sharma, Rajiv, Wabila, Celestine, Dhanagond, Sidram, Owais, Saed J., Duwayri, Mahmud A., Al-Dalain, Saddam A., Klukas, Christian, Chen, Dijun, Lübberstedt, Thomas, von Wirén, Nicolaus, Graner, Andreas, Kilian, Benjamin, and Neumann, Kerstin

Published
2019
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23. Aegilops

Author

Kilian, Benjamin, Mammen, Kerstin, Millet, Eitan, Sharma, Rajiv, Graner, Andreas, Salamini, Francesco, Hammer, Karl, Özkan, Hakan, and Kole, Chittaranjan, editor

Published
2011
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24. Precision phenotyping across the life cycle to validate and decipher drought-adaptive QTLs of wild emmer wheat (Triticum turgidum ssp. dicoccoides) introduced into elite wheat varieties

Author

Lauterberg, Madita, primary, Saranga, Yehoshua, additional, Deblieck, Mathieu, additional, Klukas, Christian, additional, Krugman, Tamar, additional, Perovic, Dragan, additional, Ordon, Frank, additional, Graner, Andreas, additional, and Neumann, Kerstin, additional

Published
2022
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25. Selection and adaptive introgression guided the complex evolutionary history of the European common bean

Author

Bellucci, Elisa, primary, Benazzo, Andrea, additional, Xu, Chunming, additional, Bitocchi, Elena, additional, Rodriguez, Monica, additional, Alseekh, Saleh, additional, Vittori, Valerio Di, additional, Gioia, Tania, additional, Neumann, Kerstin, additional, Cortinovis, Gaia, additional, Frascarelli, Giulia, additional, Murube, Ester, additional, Trucchi, Emiliano, additional, Nanni, Laura, additional, Ariani, Andrea, additional, Logozzo, Giuseppina, additional, Shin, Jin Hee, additional, Liu, Chaochih, additional, Jiang, Liang, additional, Ferreira, Juan José, additional, Campa, Ana, additional, Attene, Giovanna, additional, Morrell, Peter Laurent, additional, Bertorelle, Giorgio, additional, Graner, Andreas, additional, Gepts, Paul, additional, Fernie, Alisdair Robert, additional, Jackson, Scott Allen, additional, and Papa, Roberto, additional

Published
2022
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27. A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

Author

Ariyadasa, Ruvini, Mascher, Martin, Nussbaumer, Thomas, Schulte, Daniela, Frenkel, Zeev, Poursarebani, Naser, Zhou, Ruonan, Steuernagel, Burkhard, Gundlach, Heidrun, Taudien, Stefan, Felder, Marius, Platzer, Matthias, Himmelbach, Axel, Schmutzer, Thomas, Hedley, Pete E., Muehlbauer, Gary J., Scholz, Uwe, Korol, Abraham, Mayer, Klaus F. X., Waugh, Robbie, Langridge, Peter, Graner, Andreas, and Stein, Nils

Published
2014

35. Unlocking the Barley Genome by Chromosomal and Comparative Genomics

Author

Mayer, Klaus F.X., Martis, Mihaela, Hedley, Pete E., Šimková, Hana, Liu, Hui, Morris, Jenny A., Steuernagel, Burkhard, Taudien, Stefan, Roessner, Stephan, Gundlach, Heidrun, Kubaláková, Marie, Suchánková, Pavla, Murat, Florent, Felder, Marius, Nussbaumer, Thomas, Graner, Andreas, Salse, Jerome, Endo, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, ltoh, Takeshi, Sato, Kazuhiro, Platzer, Matthias, Matsumoto, Takashi, Scholz, Uwe, Doležel, Jaroslav, Waugh, Robbie, and Stein, Nils

Published
2011
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36. Gene Content and Virtual Gene Order of Barley Chromosome 1H

Author

Mayer, Klaus EX., Taudien, Stefan, Martis, Mihaela, Šimková, Hana, Suchánková, Pavla, Gundlach, Heidrun, Wicker, Thomas, Petzold, Andreas, Felder, Marius, Steuernagel, Burkhard, Scholz, Uwe, Graner, Andreas, Platzer, Matthias, Doležel, Jaroslav, and Stein, Nils

Published
2009
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43. Towards Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Lupins

Author

Kroc, Magdalena, Tomaszewska, Magdalena, Czepiel, Katarzyna, Bitocchi, Elena, Oppermann, Markus, Neumann, Kerstin, Guasch, Luis, Bellucci, Elisa, Alseekh, Saleh, Graner, Andreas, Fernie, Alisdair R., Papa, Roberto, and Susek, Karolina

Subjects
genetic resources, intelligent collections, lupin, food and beverages, plant standardized phenotyping, germplasm, INCREASE, single-seed descent line
Abstract

Well-characterized genetic resources are fundamental to maintain and provide the various genotypes for pre-breeding programs for the production of new cultivars (e.g., wild relatives, unimproved material, landraces). The aim of the current article is to provide protocols for the characterization of the genetic resources of two lupin crop species: the European Lupinus albus and the American Lupinus mutabilis. Intelligent nested collections of lupins derived from homozygous lines (single-seed descent) are being developed, established, and exploited using cutting-edge approaches for genotyping, phenotyping, data management, and data analysis within the INCREASE project (EU Horizon 2020). This will allow us to predict the phenotypic performance of genotyped lines, and will further boost research and development in lupins. Lupins stand out due to their high-quality seed protein (∼40% of seed dry weight) and other primary components in the seeds, which include fatty acids, dietary fiber, and minerals. The potential of lupins as a crop is highlighted by the multiple benefits of plant-based food in terms of food security, nutrition, human health, and sustainable production. The use of lupins in foods, along with other well-studied and widely used food legumes, will also provide a greatly diversified plant-based food palette to meet the Global Goals for Sustainable Development to improve people’s lives by 2030.

Published
2021

49. Contributors

Author

Baik, Byung-Kee, primary, Fincher, Geoffrey B., additional, Finnie, Christine, additional, Gibson, B.R., additional, Gils, Mario, additional, Graner, Andreas, additional, Gubatz, Sabine, additional, Hicks, Kevin B., additional, Izydorczyk, Marta S., additional, Montanti, Justin, additional, Morell, Matthew, additional, Nghiem, Nhuan P., additional, Olsen, Odd-Arne, additional, Ritala, A., additional, Shewry, Peter R., additional, Sreenivasulu, Nese, additional, Svensson, Birte, additional, Swanston, J.S., additional, Topping, David, additional, Trafford, Kay, additional, Ullrich, Steven E., additional, Wilhelmson, A., additional, and Weschke, Winfriede, additional

Published
2014
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50. Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

Author

Badaeva, Ekaterina D., primary, Konovalov, Fedor A., additional, Knüpffer, Helmut, additional, Fricano, Agostino, additional, Ruban, Alevtina S., additional, Kehel, Zakaria, additional, Zoshchuk, Svyatoslav A., additional, Surzhikov, Sergei A., additional, Neumann, Kerstin, additional, Graner, Andreas, additional, Hammer, Karl, additional, Filatenko, Anna, additional, Bogaard, Amy, additional, Jones, Glynis, additional, Özkan, Hakan, additional, and Kilian, Benjamin, additional

Published
2021
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