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1. A catalogue of recombination coldspots in interspecific tomato hybrids.

Author

Fuentes, Roven Rommel, Nieuwenhuis, Ronald, Chouaref, Jihed, Hesselink, Thamara, van Dooijeweert, Willem, van den Broeck, Hetty C., Schijlen, Elio, Schouten, Henk J., Bai, Yuling, Fransz, Paul, Stam, Maike, de Jong, Hans, Trivino, Sara Diaz, de Ridder, Dick, van Dijk, Aalt D. J., and Peters, Sander A.

Subjects
TOMATOES, GENETIC variation, TOMATO breeding, GENETIC recombination, CULTIVATED plants, FOOD supply
Abstract

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties. Author summary: Ensuring a stable food supply in a changing climate hinges on enhancing plants' natural defenses and resilience. Breeders achieve this by crossing cultivated plants with their wild counterparts, mixing specific gene variants through genetic recombination. Yet, in some cases, certain genomic areas lack this recombination, particularly when crossing diverse plant types, limiting the mix of beneficial genes. In this study we used a method called pooled-pollen sequencing to map regions where genetic recombination does and doesn't occur when breeding tomatoes with five wild relatives. We discovered specific regions where genetic exchange is rare, mainly due to structural differences in DNA. These regions tend to be rich in repetitive DNA sequences and are less likely to swap genes during reproduction. Importantly, many of these "recombination coldspots" contain genes related to plant health and stress resistance, inadvertently limiting the effectiveness of breeding efforts. By identifying these regions, breeders can now make more informed choices when developing new tomato varieties, potentially by incorporating genes from other wild species to overcome these limitations and improve crop resilience. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Chasing breeding footprints through structural variations in Cucumis melo and wild relatives

Author

Demirci, Sevgin, Fuentes, Roven, van Dooijeweert, Willem, Aflitos, S.A., Schijlen, Elio, Hesselink, Thamara, de Ridder, Dick, van Dijk, Aalt-Jan, Peters, Sander, Demirci, Sevgin, Fuentes, Roven, van Dooijeweert, Willem, Aflitos, S.A., Schijlen, Elio, Hesselink, Thamara, de Ridder, Dick, van Dijk, Aalt-Jan, and Peters, Sander

Abstract

Cucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melon breeding history, analysing structural variations (SV) ranging from 50 bp up to 100kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found 6 mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that the resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development.

Published
2020

8. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Li, Changbao, Shuang, Yang, Xu, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Yi, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Yang, Wencai, Huang, Sanwen, Du, Yongchen, Zhang, Zhonghua, Gao, Jianchang, Guo, Yanmei, Wang, Xiaoxuan, Li, Ying, He, Jun, Li, Chuanyou, Cheng, Zhukuan, Zuo, Jianru, Ren, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Wang, Bao, Li, Hongshuang, Li, Zhenjun, Fu, Fuyou, Chen, Bingtang, Han, Bin, Feng, Qi, Fan, Danlin, Wang, Ying, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, Richard McCombie, W., Lippman, Zachary B., Chia, Jer-Ming, Jiang, Ke, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Xu, Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigó, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Zhang, Junhong, Ye, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, James, Dixit, Rekha, Singh, Manju, Singh, Archana, Kumar Pal, Jitendra, Pandit, Awadhesh, Kumar Singh, Pradeep, Kumar Mahato, Ajay, Dogra, Vivek, Gaikwad, Kishor, Raj Sharma, Tilak, Mohapatra, Trilochan, Kumar Singh, Nagendra, Causse, Mathilde, Rothan, Christophe, Schiex, Thomas, Noirot, Céline, Bellec, Arnaud, Klopp, Christophe, Delalande, Corinne, Berges, Hélène, Mariette, Jérôme, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latché, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Pierre, Osorio, Sonia, Fernandez del Carmen, Asunción, Monforte, Antonio, Granell, Antonio, Fernandez-Muñoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Paolo, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Marco G. M., Feron, Richard M.C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Jo, Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Kim, Sangmi, Koo, Dal-Hoe, Lee, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Alain, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Jöcker, Anika, Warfsmann, Jens, Göbel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Elio G. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Jiang, Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Dong Kim, Byung, Park, Minkyu, Kim, Seungill, Yeom, Seon-In, Lee, Yong-Hwan, Choi, Yang-Do, Li, Guangcun, Gao, Jianwei, Liu, Yongsheng, Huang, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuñiga, Sheila, Wang, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Sandra, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Luis Goicoechea, Jose, Yu, Yeisoo, Kudrna, David, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Bala Gurazada, Aishwarya, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Sharma, Arun K., Khurana, Paramjit, Khurana, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Brad Barbazuk, W., Li, Jingping, Guo, Hui, Lee, Tae-Ho, Wang, Yupeng, Zhang, Dong, Paterson, Andrew H., Wang, Xiyin, Tang, Haibao, Barone, Amalia, Luisa Chiusano, Maria, Raffaella Ercolano, Maria, D’Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Fu, Ying, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Qu, Chunmei, Shi, Ruihua, White, Douglas, White, James, Xing, Yanbo, Yang, Keqin, Yi, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, Alessandro, D’Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Klein Lankhorst, René M., Beasley, Helen, McLaren, Karen, Nicholson, Christine, Riddle, Claire, and Gianese, Giulio

Published
2012
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9. Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing

Author

Rommel Fuentes, Roven, primary, Hesselink, Thamara, additional, Nieuwenhuis, Ronald, additional, Bakker, Linda, additional, Schijlen, Elio, additional, Dooijeweert, Willem, additional, Diaz Trivino, Sara, additional, Haan, Jorn R., additional, Sanchez Perez, Gabino, additional, Zhang, Xinyue, additional, Fransz, Paul, additional, Jong, Hans, additional, Dijk, Aalt D. J., additional, Ridder, Dick, additional, and Peters, Sander A., additional

Published
2020
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12. Additional file 16: of Correcting palindromes in long reads after whole-genome amplification

Author

Warris, Sven, Schijlen, Elio, Geest, Henri Van De, Rahulsimham Vegesna, Hesselink, Thamara, Hekkert, Bas Te Lintel, Perez, Gabino Sanchez, Medvedev, Paul, Makova, Kateryna, and Ridder, Dick De

Subjects
food and beverages
Abstract

The number of duplication or inversion events that were observed on contigs/scaffolds when aligned to human X-degenerate genes. (DOCX 26 kb)

Published
2018
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16. A 'footprint' of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria-Cecília D., Artur, Mariana A. S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F. L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, Jose M., Elio, Schijlen, Hesselink, Thamara, Schijlen, Elio G. W. M., Ligterink, Wilco, Oliver, Melvin J., Farrant, Jill M., Jill, Farrant, Henk, Hilhorst, and Hilhorst, Henk W. M.

Subjects
food and beverages
Abstract

Desiccation tolerance is common in seeds and various other organisms but only a few Angiosperm species possess vegetative desiccation tolerance. These 'resurrection species' may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration. Data revealed induction of transcripts typically associated with desiccation tolerance in seeds, and involvement of orthologues of ABI3 and ABI5, both key regulators of seed maturation. Dehydration resulted in both increased, but predominantly reduced transcript abundance of genomic 'clusters of desiccation-associated genes' (CoDAGs), reflecting the cessation of growth that allows for the expression of desiccation tolerance. Vegetative desiccation tolerance in X. viscosa was found to be uncoupled from drought-induced senescence. We provide strong support for the hypothesis that vegetative desiccation tolerance arose by redirection of genetic information from desiccation tolerant seeds.

Published
2017

17. Correcting palindromes in long reads after whole-genome amplification

Author

Warris, Sven, primary, Schijlen, Elio, additional, van de Geest, Henri, additional, Vegesna, Rahulsimham, additional, Hesselink, Thamara, additional, te Lintel Hekkert, Bas, additional, Sanchez Perez, Gabino, additional, Medvedev, Paul, additional, Makova, Kateryna D., additional, and de Ridder, Dick, additional

Published
2018
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18. A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria Cecília D., Artur, Mariana A.S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F.L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, José M., Hesselink, Thamara, Schijlen, Elio G.W.M., Ligterink, Wilco, Oliver, Melvin J., Farrant, Jill M., Hilhorst, Henk W.M., Costa, Maria Cecília D., Artur, Mariana A.S., Maia, Julio, Jonkheer, Eef, Derks, Martijn F.L., Nijveen, Harm, Williams, Brett, Mundree, Sagadevan G., Jiménez-Gómez, José M., Hesselink, Thamara, Schijlen, Elio G.W.M., Ligterink, Wilco, Oliver, Melvin J., Farrant, Jill M., and Hilhorst, Henk W.M.

Published
2017

19. A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Author

Costa, Maria Cecilia, Artur, Mariana, Maia, Julio, Jonkheer, Eef, Derks, Martijn, Nijveen, Harm, Williams, Brett, Mundree, Sagadevan, Jimenez-Gomez, Jose, Hesselink, Thamara, Schijlen, Elio, Ligterink, Wilco, Oliver, Melvin, Farrant, Jill, Hilhorst, Henk, Costa, Maria Cecilia, Artur, Mariana, Maia, Julio, Jonkheer, Eef, Derks, Martijn, Nijveen, Harm, Williams, Brett, Mundree, Sagadevan, Jimenez-Gomez, Jose, Hesselink, Thamara, Schijlen, Elio, Ligterink, Wilco, Oliver, Melvin, Farrant, Jill, and Hilhorst, Henk

Abstract

Desiccation tolerance is common in seeds and various other organisms but only a few Angiosperm species possess vegetative desiccation tolerance. These ‘resurrection species’ may serve as ideal models for the ultimate design of crops with enhanced drought tolerance. To understand the molecular and genetic mechanisms enabling vegetative desiccation tolerance we produced a high-quality whole-genome sequence for the resurrection plant Xerophyta viscosa and assessed transcriptome changes during its dehydration. Data revealed induction of transcripts typically associated with desiccation tolerance in seeds, and involvement of orthologues of ABI3 and ABI5, both key regulators of seed maturation. Dehydration resulted in both increased, but predominantly reduced transcript abundance of genomic ‘clusters of desiccation-associated genes’ (CoDAGs), reflecting the cessation of growth that allows for the expression of desiccation tolerance. Vegetative desiccation tolerance in X. viscosa was found to be uncoupled from drought-induced senescence. We provide strong support for the hypothesis that vegetative desiccation tolerance arose by redirection of genetic information from desiccation tolerant seeds.

Published
2017

25. Chasing breeding footprints through structural variations in Cucumis melo and wild relatives.

Author

Demirci, Sevgin, Fuentes, Roven Rommel, Dooijeweert, Willem van, Aflitos, Saulo, Schijlen, Elio, Hesselink, Thamara, Ridder, Dick de, van Dijk, Aalt D. J., and Peters, Sander

Subjects
*MUSKMELON, *CHROMOSOME inversions, *GENETIC variation, *WATERMELONS, *FRUIT ripening, *CROP development, *PLANT species
Abstract

Cucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melonbreeding history, analyzing structural variations ranging from 50 bp up to 100 kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found six mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance, and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives, and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
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