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1. Prospects for evolution in european tree breeding

Author

European Commission, Fugeray-Scarbel, Aline [0000-0002-2956-6943], Bouffier, L. [0000-0001-7493-5077], Lemarié, Stéphane [0000-0003-1530-3787], Sánchez, Leopoldo [0000-0002-8285-0441], Alía Miranda, Ricardo [0000-0002-9426-0967], Biselli, Chiara [0000-0003-0978-6970], Buiteveld, J. [0000-0003-1892-6760], Cattivelli, L. [0000-0002-6067-4600], Dowkiw, Arnaud [0000-0003-0477-1091], Fricano, Agostino [0000-0003-3715-5834], Gion, J. M. [0000-0003-3958-7796], Grima-Pettenati, J. [0000-0003-4272-9767], Helmersson, Andreas [0000-0001-9043-4002], Lario, F. [0009-0005-2203-0408], Mutke, Sven [0000-0002-6365-7128], Persson, Torgny [0000-0002-5873-5777], Smulders, M. J. M. [0009-0003-6066-1935], Steffenrem, Arne [0000-0001-7116-9151], Vietto, Lorenzo [0000-0003-4489-6227], Haapanen, Matti [0000-0003-3294-501X], Fugeray-Scarbel, Aline, Bouffier, L., Lemarié, Stéphane, Sánchez, Leopoldo, Alía Miranda, Ricardo, Biselli, Chiara, Buiteveld, J., Carra, Andrea, Cattivelli, L., Dowkiw, Arnaud, Fontes, Luis, Fricano, Agostino, Gion, J. M., Grima-Pettenati, J., Helmersson, Andreas, Lario, F., Leal, Luis, Mutke, Sven, Nervo, Giuseppe, Persson, Torgny, Rosso, Laura, Smulders, M. J. M., Steffenrem, Arne, Vietto, Lorenzo, Haapanen, Matti, European Commission, Fugeray-Scarbel, Aline [0000-0002-2956-6943], Bouffier, L. [0000-0001-7493-5077], Lemarié, Stéphane [0000-0003-1530-3787], Sánchez, Leopoldo [0000-0002-8285-0441], Alía Miranda, Ricardo [0000-0002-9426-0967], Biselli, Chiara [0000-0003-0978-6970], Buiteveld, J. [0000-0003-1892-6760], Cattivelli, L. [0000-0002-6067-4600], Dowkiw, Arnaud [0000-0003-0477-1091], Fricano, Agostino [0000-0003-3715-5834], Gion, J. M. [0000-0003-3958-7796], Grima-Pettenati, J. [0000-0003-4272-9767], Helmersson, Andreas [0000-0001-9043-4002], Lario, F. [0009-0005-2203-0408], Mutke, Sven [0000-0002-6365-7128], Persson, Torgny [0000-0002-5873-5777], Smulders, M. J. M. [0009-0003-6066-1935], Steffenrem, Arne [0000-0001-7116-9151], Vietto, Lorenzo [0000-0003-4489-6227], Haapanen, Matti [0000-0003-3294-501X], Fugeray-Scarbel, Aline, Bouffier, L., Lemarié, Stéphane, Sánchez, Leopoldo, Alía Miranda, Ricardo, Biselli, Chiara, Buiteveld, J., Carra, Andrea, Cattivelli, L., Dowkiw, Arnaud, Fontes, Luis, Fricano, Agostino, Gion, J. M., Grima-Pettenati, J., Helmersson, Andreas, Lario, F., Leal, Luis, Mutke, Sven, Nervo, Giuseppe, Persson, Torgny, Rosso, Laura, Smulders, M. J. M., Steffenrem, Arne, Vietto, Lorenzo, and Haapanen, Matti

Abstract

Genetically improved forest reproductive materials are now widely accessible in many European countries due to decades of continuous breeding efforts. Tree breeding does not only contribute to higher-value end products but allows an increase in the rate of carbon capture and sequestration, helping to mitigate the effects of climate change. The usefulness of breeding programmes depends on (i) the relevance of the set of selected traits and their relative weights (growth, drought tolerance, phenology, etc.); (ii) the explicit management of targeted and “neutral” diversity; (iii) the genetic gain achieved; and (iv) the efficiency of transferring diversity and gain to the plantation. Several biological factors limit both operational breeding and mass reproduction. To fully realise the potential of tree breeding, the introduction of new technologies and concepts is pivotal for overcoming these constraints. We reviewed several European breeding programmes, examining their current status and factors that are likely to influence tree breeding in the coming decades. The synthesis was based on case studies developed for the European Union-funded B4EST project, which focused on eight economically important tree species with breeding histories and intensities ranging from low-input breeding (stone pine, Douglas-fir and ash) to more complex programmes (eucalyptus, maritime pine, Norway spruce, poplar, and Scots pine). Tree breeding for these species is managed in a variety of ways due to differences in species’ biology, breeding objectives, and economic value. Most programmes are managed by governmental institutes with full or partial public support because of the relatively late return on investment. Eucalyptus is the only tree species whose breeding is entirely sponsored and managed by a private company. Several new technologies have emerged for both phenotyping and genotyping. They have the potential to speed up breeding processes and make genetic evaluations more accurate, t

Published
2024

4. Prospects for evolution in european tree breeding

Author

Fugeray-Scarbel, Aline, Bouffier, Laurent, Lemarié, Stéphane, Sánchez, Leopoldo, Alia, Ricardo, Biselli, Chiara, Buiteveld, Joukje, Carra, Andrea, Cattivelli, Luigi, Dowkiw, Arnaud, Fontes, Luis, Fricano, Agostino, Gion, Jean Marc, Grima-Pettenati, Jacqueline, Helmersson, Andreas, Lario, Francisco, Leal, Luis, Mutke, Sven, Nervo, Giuseppe, Persson, Torgny, Rosso, Laura, Smulders, Rene, Steffenrem, Arne, Vietto, Lorenzo, Haapanen, Matti, Fugeray-Scarbel, Aline, Bouffier, Laurent, Lemarié, Stéphane, Sánchez, Leopoldo, Alia, Ricardo, Biselli, Chiara, Buiteveld, Joukje, Carra, Andrea, Cattivelli, Luigi, Dowkiw, Arnaud, Fontes, Luis, Fricano, Agostino, Gion, Jean Marc, Grima-Pettenati, Jacqueline, Helmersson, Andreas, Lario, Francisco, Leal, Luis, Mutke, Sven, Nervo, Giuseppe, Persson, Torgny, Rosso, Laura, Smulders, Rene, Steffenrem, Arne, Vietto, Lorenzo, and Haapanen, Matti

Abstract

Genetically improved forest reproductive materials are now widely accessible in many European countries due to decades of continuous breeding efforts. Tree breeding does not only contribute to higher-value end products but allows an increase in the rate of carbon capture and sequestration, helping to mitigate the effects of climate change. The usefulness of breeding programmes depends on (i) the relevance of the set of selected traits and their relative weights (growth, drought tolerance, phenology, etc.); (ii) the explicit management of targeted and “neutral” diversity; (iii) the genetic gain achieved; and (iv) the efficiency of transferring diversity and gain to the plantation. Several biological factors limit both operational breeding and mass reproduction. To fully realise the potential of tree breeding, the introduction of new technologies and concepts is pivotal for overcoming these constraints. We reviewed several European breeding programmes, examining their current status and factors that are likely to influence tree breeding in the coming decades. The synthesis was based on case studies developed for the European Union-funded B4EST project, which focused on eight economically important tree species with breeding histories and intensities ranging from low-input breeding (stone pine, Douglas-fir and ash) to more complex programmes (eucalyptus, maritime pine, Norway spruce, poplar, and Scots pine). Tree breeding for these species is managed in a variety of ways due to differences in species’ biology, breeding objectives, and economic value. Most programmes are managed by governmental institutes with full or partial public support because of the relatively late return on investment. Eucalyptus is the only tree species whose breeding is entirely sponsored and managed by a private company. Several new technologies have emerged for both phenotyping and genotyping. They have the potential to speed up breeding processes and make genetic evaluations more accurate, t

Published
2024

5. A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

Author

Waugh, Robbie, primary, Guo, Wenbin, additional, Schreiber, Miriam, additional, Marosi, Vanda, additional, Bagnaresi, Paolo, additional, Chalmers, Kenneth, additional, Chapman, Brett, additional, Dang, Viet, additional, Dockter, Christoph, additional, Fiebig, Anne, additional, Fricano, Agostino, additional, Fuller, John, additional, Haaning, Allison, additional, Haberer, Georg, additional, Himmelbach, Axel, additional, Jayakodi, Murukarthick, additional, Jia, Yong, additional, Jørgensen, Morten, additional, Kamal, Nadia, additional, Langridge, Peter, additional, Li, Chengdao, additional, Lu, Qiongxian, additional, Lux, Thomas, additional, Mascher, Martin, additional, Mayer, Klaus, additional, McCallum, Nicola, additional, Milne, Linda, additional, Muehlbauer, Gary, additional, Padmarasu, Sudharsan, additional, Pedas, Pai, additional, Pillen, Klaus, additional, Pozniak, Curtis, additional, Sato, Kazuhiro, additional, Schmutzer, Thomas, additional, Scholz, Uwe, additional, Schüler, Danuta, additional, Simkova, Hana, additional, Skadhauge, Birgitte, additional, Stein, Nils, additional, Wang, Penghao, additional, Wonneberger, Ronja, additional, Zhang, Xiao-Qi, additional, Zhang, Guoping, additional, Cattivelli, Luigi, additional, Spannagl, Manuel, additional, Bayer, Micha, additional, Simpson, Craig, additional, and Zhang, Runxuan, additional

Published
2024
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6. Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity.

Author

Civáň, Peter, Fricano, Agostino, Russell, Joanne, Pont, Caroline, Özkan, Hakan, Kilian, Benjamin, and Brown, Terence A.

Subjects
*CHLOROPLAST DNA, *FOSSIL DNA, *GENETIC variation, *HORDEUM, *DNA sequencing
Abstract

Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches – analyses of chloroplast genomes and genome‐wide proportions of private variants – we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north‐eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post‐domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool. [ABSTRACT FROM AUTHOR]

Published
2024
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10. 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

14. Does Plant Breeding for Antioxidant-Rich Foods Have an Impact on Human Health?

Author

Bassolino, Laura, primary, Petroni, Katia, additional, Polito, Angela, additional, Marinelli, Alessandra, additional, Azzini, Elena, additional, Ferrari, Marika, additional, Ficco, Donatella B. M., additional, Mazzucotelli, Elisabetta, additional, Tondelli, Alessandro, additional, Fricano, Agostino, additional, Paris, Roberta, additional, García-Robles, Inmaculada, additional, Rausell, Carolina, additional, Real, María Dolores, additional, Pozzi, Carlo Massimo, additional, Mandolino, Giuseppe, additional, Habyarimana, Ephrem, additional, and Cattivelli, Luigi, additional

Published
2022
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17. 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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18. Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction

Author

Ministero delle Politiche Agricole Alimentari e Forestali, European Commission, Casas Cendoya, Ana María [0000-0003-3484-2655], Igartua Arregui, Ernesto [0000-0003-2938-1719], Puglisi, Damiano, Delbono, Stefano, Visioni, Andrea, Ozkan, Hakan, Kara, Ibrahim, Casas Cendoya, Ana María, Igartua Arregui, Ernesto, Valè, Giampiero, Lo Piero, Angela Roberta, Cattivelli, Luigi, Tondelli, Alessandro, Fricano, Agostino, Ministero delle Politiche Agricole Alimentari e Forestali, European Commission, Casas Cendoya, Ana María [0000-0003-3484-2655], Igartua Arregui, Ernesto [0000-0003-2938-1719], Puglisi, Damiano, Delbono, Stefano, Visioni, Andrea, Ozkan, Hakan, Kara, Ibrahim, Casas Cendoya, Ana María, Igartua Arregui, Ernesto, Valè, Giampiero, Lo Piero, Angela Roberta, Cattivelli, Luigi, Tondelli, Alessandro, and Fricano, Agostino

Abstract

Multi-parent Advanced Generation Inter-crosses (MAGIC) lines have mosaic genomes that are generated shuffling the genetic material of the founder parents following pre-defined crossing schemes. In cereal crops, these experimental populations have been extensively used to investigate the genetic bases of several traits and dissect the genetic bases of epistasis. In plants, genomic prediction models are usually fitted using either diverse panels of mostly unrelated accessions or individuals of biparental families and several empirical analyses have been conducted to evaluate the predictive ability of models fitted to these populations using different traits. In this paper, we constructed, genotyped and evaluated a barley MAGIC population of 352 individuals developed with a diverse set of eight founder parents showing contrasting phenotypes for grain yield. We combined phenotypic and genotypic information of this MAGIC population to fit several genomic prediction models which were cross-validated to conduct empirical analyses aimed at examining the predictive ability of these models varying the sizes of training populations. Moreover, several methods to optimize the composition of the training population were also applied to this MAGIC population and cross-validated to estimate the resulting predictive ability. Finally, extensive phenotypic data generated in field trials organized across an ample range of water regimes and climatic conditions in the Mediterranean were used to fit and cross-validate multi-environment genomic prediction models including G×E interaction, using both genomic best linear unbiased prediction and reproducing kernel Hilbert space along with a non-linear Gaussian Kernel. Overall, our empirical analyses showed that genomic prediction models trained with a limited number of MAGIC lines can be used to predict grain yield with values of predictive ability that vary from 0.25 to 0.60 and that beyond QTL mapping and analysis of epistatic effects, MAGI

Published
2021

19. Genomic Prediction of Grain Yield in a Barley MAGIC Population Modeling Genotype per Environment Interaction

Author

Puglisi, Damiano, primary, Delbono, Stefano, additional, Visioni, Andrea, additional, Ozkan, Hakan, additional, Kara, İbrahim, additional, Casas, Ana M., additional, Igartua, Ernesto, additional, Valè, Giampiero, additional, Piero, Angela Roberta Lo, additional, Cattivelli, Luigi, additional, Tondelli, Alessandro, additional, and Fricano, Agostino, additional

Published
2021
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22. Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat.

Author

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

Subjects
PLANT germplasm, GENETIC variation, WHEAT breeding, CHROMOSOMAL rearrangement
Abstract

Key message: We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia. [ABSTRACT FROM AUTHOR]

Published
2022
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23. Development of a new tool (4TREE) for adapted genome selection in European tree species

Author

GUILBAUD, Romane, Biselli, Chiara, Buiteveld, Joukje, Cattivelli, Luigi, Copini, Paul, Dowkiw, Arnaud, Esselink, Danny, Fricano, Agostino, Guerin, Vanina, Jorge, Véronique, Kelly, Laura.J., Kodde, Linda, Metheringham, Carey L., Pinosio, Sara, Rogier, Odile, Segura, Vincent, Spanu, Ilaria, Buggs, Richard, Gonzalez-Martinez, Santiago C., Nervo, Giuseppe, Smulders, Rene, Sanchez Rodriguez, Leopoldo, Vendramin, Giovanni, Faivre-Rampant, Patricia, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Unit for Intensive Wood Production, Casale Monferrato (AL), Wageningen University and Research [Wageningen] (WUR), Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office National des Forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AB, School of Biological and Chemical Sciences, Queen Mary University of London, Institute of Biosciences and Bioresources, National Research Council, Biodiversité, Gènes & Communautés (BioGeCo), and Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, fraxinus sp, genotyping, Axiom array, Populus sp, SNP, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Pinus pinaster, Pinus pinea, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, forest tree
Abstract

International audience; Resumé : The 4TREE Axiom 50K SNP array is one of the main deliverables of the H2020 project B4EST which aims at transferring know-how and tools to improve breeding for production, resilience and diversity of forest trees. This array is developed for: Populus sp, Fraxinus sp, Pinus pinaster and Pinus pinea. It is based on de novo sequencing resources and existing genomic resources of loci of interest for breeders. 4TREE is primarily aimed at breeders by providing low genotyping costs for economically important species in Europe, fostering collaboration between breeding programs across Europe. One of its first uses will be genome wide association studies and genomic predictions, being also extremely useful for monitoring and characterizing novel sources of variation. Material/ Methods : The 4Tree array will be designed after the screening of 420K SNP. Except for the orphan species P. pinea, SNP were identified from existing genomic resources: whole genome and RNA sequencing, exome capture, SNP arrays. SNP gathered by these resources were filtered for inclusion in a screening array of 420K (105K/species) and checked over a panel of 480 samples (120/species). SNP without other polymorphisms within 30bp flanking sequences were preferentially selected and those in unique region were prioritized, limiting A/T and C/G which require more space on the array. The selection included several SNP in candidate genes or regions found via transcriptomic, QTL and GWAS analysis. Results : For P. pinea, 128K SNPs were submitted to ThermoFisher, resulting in 37K recommended SNPs for the screening array. P. pinaster submitted 197K SNPs (5K SNPs from Plomion et al. 2016), leading to 140K inclusions in the screening array, including several from candidate genes for abiotic and biotic stress. For Fraxinus sp, 126K SNP were selected from the 327K scored. SNPs were selected in order to prioritize candidate SNPs associated to dieback disease tolerance and incompatibility (Stocks & Metheringham et al. 2019). SNPs were additionally selected according to the genomic coverage (maximum possible representation of genes and scaffolds with respect to the reference genome). For Populus, a subset of SNPs was identified for two species: P. nigra and P. deltoides. These SNPs were either species specific or shared between the two species. For P. nigra, SNPs from a previous array (Faivre-Rampant et al. 2016) and from candidate regions from GWAS were also selected. The final coverage of the genome was 100 SNP/Mb with a ratio of genic and intergenic SNPs of 60/40%. In total, 3 000K SNP were submitted to ThermoFisher for Populus to select 120,500 for the screening array. Conclusion: From this screening genotyping, 12.5K high value SNPs per species will be retained for the final array 4TREE dedicated to gene discovery, pre-breeding monitoring of diversity and genomic selection studies in B4EST. This final array will be a highly valuable genome-assisted breeding tool, made commercially available for cost effective HT genotyping for four important tree species in Europe.

Published
2020

24. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm

Author

Fricano Agostino, Bakaher Nicolas, Corvo Marcello, Piffanelli Pietro, Donini Paolo, Stella Alessandra, Ivanov Nikolai V, and Pozzi Carlo

Subjects
Genetics, QH426-470
Abstract

Abstract Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD) in seven genomic regions using simple sequence repeat (SSR) markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA) and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2). The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

Published
2012
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25. Genome-Wide Analysis of japonica Rice Performance under Limited Water and Permanent Flooding Conditions

Author

Volante, Andrea, primary, Desiderio, Francesca, additional, Tondelli, Alessandro, additional, Perrini, Rosaria, additional, Orasen, Gabriele, additional, Biselli, Chiara, additional, Riccardi, Paolo, additional, Vattari, Alessandra, additional, Cavalluzzo, Daniela, additional, Urso, Simona, additional, Ben Hassen, Manel, additional, Fricano, Agostino, additional, Piffanelli, Pietro, additional, Cozzi, Paolo, additional, Biscarini, Filippo, additional, Sacchi, Gian Attilio, additional, Cattivelli, Luigi, additional, and Valè, Giampiero, additional

Published
2017
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26. Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach

Author

Barabaschi, Delfina, primary, Magni, Federica, additional, Volante, Andrea, additional, Gadaleta, Agata, additional, Šimková, Hana, additional, Scalabrin, Simone, additional, Prazzoli, Maria Lucia, additional, Bagnaresi, Paolo, additional, Lacrima, Katia, additional, Michelotti, Vania, additional, Desiderio, Francesca, additional, Orrù, Luigi, additional, Mazzamurro, Valentina, additional, Fricano, Agostino, additional, Mastrangelo, AnnaMaria, additional, Tononi, Paola, additional, Vitulo, Nicola, additional, Jurman, Irena, additional, Frenkel, Zeev, additional, Cattonaro, Federica, additional, Morgante, Michele, additional, Blanco, Antonio, additional, Doležel, Jaroslav, additional, Delledonne, Massimo, additional, Stanca, Antonio M., additional, Cattivelli, Luigi, additional, and Valè, Giampiero, additional

Published
2015
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27. Crossability ofTriticum urartuandTriticum monococcumWheats, Homoeologous Recombination, and Description of a Panel of Interspecific Introgression Lines

Author

Fricano, Agostino, primary, Brandolini, Andrea, additional, Rossini, Laura, additional, Sourdille, Pierre, additional, Wunder, Joerg, additional, Effgen, Sigi, additional, Hidalgo, Alyssa, additional, Erba, Daniela, additional, Piffanelli, Pietro, additional, and Salamini, Francesco, additional

Published
2014
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28. Correction to: Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat.

Author

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

Subjects
GENETIC variation, PUBLISHING
Abstract

The correct name should read as follows: Helmut Knüpffer The original article has been corrected. Correction to: Theoretical and Applied Genetics https://doi.org/10.1007/s00122-021-03912-0 The 3rd author name contained a mistake in the original publication. [Extracted from the article]

Published
2021
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29. Resequencing the barley exome to identify genes controlling plant adaptation to environment.

Author

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, Russell, Joanne, Dawson, Ian K., Waugh, Robbie, and Fricano, Agostino

Subjects
BARLEY genetics, PLANT adaptation, BARLEY yields
Abstract

Barley development and actual yield is strongly affected by a number of environmental stress factors that can prevent the plant from expressing its maximum genetic potential. Indeed abiotic stresses (temperatures, drought, anaerobiosis and soil salinity) are often responsible for severe grain losses although they have driven the evolution and the wide distribution of the genus Hordeum in temperate, subtropical and arctic areas. We present a new resource to dissect natural allelic variation at candidate genes controlling key adaptive traits in barley, based on a collection of 500 accessions assembled in the context of the EU-FP7-WHEALBI (Wheat and Barley Legacy for Breeding Improvement) project. The collection comprises 227 old and elite cultivars, 238 landraces and 35 wild barleys (H. spontaneum) from a wide geographical range. Winter and spring nurseries (common garden trials) have been carried out in 4 contrasting environments (Scotland, North Italy, Hungary and Central Anatolia in Turkey, in this last site under both rainfed and irrigated conditions) and several phenological and morphological traits have been evaluated. Moreover, a comprehensive molecular variant analysis by exome sequencing (exome capture arrays) has been carried out, resulting in more than 2 million SNPs and InDels. Plant growth habit and heading-date are the basic traits involved in barley adaptation to the environment since they allow synchronize life cycle with seasonal changes. Several genes involved in these key adaptive traits have been characterized and they can serve as a proof of concept to validate the effectiveness of WHEALBI resource in mining new functional alleles. To this purpose allelic diversity of candidate genes has been evaluated in wild, landraces and cultivated barley to determine the extent of haplotype diversity and build haplotype networks. The genetic diversity of barley CBF and Vrn-H1, two key loci responsible for frost tolerance, have been explored in 403 barley accessions using the exome sequencing information. This dataset along with curated annotation of the CBF genes provided the means to identify unique SNP variants in HvCBF genes and predict functional effects at the protein level. A large proportion of these SNPs were observed in the gene pool of barley landraces and wild relatives, only being fixed in the cultivated germplasm. Similarly, examining diversity at the winter allele of Vrn-H1, from Hordeum vulgare cv. Strider, as reference, several unknown deletions of this gene were identified as well as one accession with two copies of Vrn-H1 gene. To date, the genetic variants (SNPs and CNVs) of coding sequences developed and validated in this project are a snapshot of the existing genetic variability of barley, which will enable the research community to mine interesting alleles for other traits and exploit the untapped genetic diversity of barley. [ABSTRACT FROM AUTHOR]

Published
2017
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30. Crossability of Triticum urartu and Triticum monococcum wheats, homoeologous recombination, and description of a panel of interspecific introgression lines.

Author

Fricano A, Brandolini A, Rossini L, Sourdille P, Wunder J, Effgen S, Hidalgo A, Erba D, Piffanelli P, and Salamini F

Subjects
Breeding, Chromosome Mapping, Diploidy, Genetic Linkage, Genetic Variation, Microsatellite Repeats, Principal Component Analysis, Recombination, Genetic, Genome, Plant, Triticum genetics
Abstract

Triticum monococcum (genome A(m)) and T. urartu (genome A(u)) are diploid wheats, with the first having been domesticated in the Neolithic Era and the second being a wild species. In a germplasm collection, rare wild T. urartu lines with the presence of T. monococcum alleles were found. This stimulated our interest to develop interspecific introgression lines of T. urartu in T. monococcum, a breeding tool currently implemented in several crop species. Moreover, the experiments reported were designed to reveal the existence in nature of A(m)/A(u) intermediate forms and to clarify whether the two species are at least marginally sexually compatible. From hand-made interspecific crosses, almost-sterile F1 plants were obtained when the seed-bearing parent was T. monococcum. A high degree of fertility was, however, evident in some advanced generations, particularly when T. urartu donors were molecularly more related to T. monococcum. Analysis of the marker populations demonstrated chromosome pairing and recombination in F1 hybrid plants. Forty-six introgression lines were developed using a line of T. monococcum with several positive agronomic traits as a recurrent parent. Microsatellite markers were tested on A(u) and A(m) genomes, ordered in a T. monococcum molecular map, and used to characterize the exotic DNA fragments present in each introgression line. In a test based on 28 interspecific introgression lines, the existence of genetic variation associated with T. urartu chromosome fragments was proven for the seed content of carotenoids, lutein, β-cryptoxanthin, and zinc. The molecular state of available introgression lines is summarized., (Copyright © 2014 Fricano et al.)

Published
2014
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