Publications

Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice

Parthiban Thathapalli Prakash, Dmytro Chebotarov, Jianwei Zhang, David A. Kudrna, Rolando O. Torres, Mignon A. Natividad, Marinell R. Quintana, Jiaming Song, Carlos E. Maldonado, Sherry Lou Hechanova, Kshirod Jena, Rod A. Wing, and Amelia Henry

**Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud**

Fabrice Ntakirutimana, Christine Tranchant-Dubreuil, Philippe Cubry, Kapeel Chougule, Jianwei Zhang, Rod A. Wing, Hélène Adam, Mathias Lorieux, Stefan Jouannic

(preprint) HPC-based genome variant calling workflow (HPC-GVCW)

Yong Zhou, Nagarajan Kathiresan, Zhichao Yu, Luis F. Rivera, Manjula Thimma, Keerthana Manickam, Dmytro Chebotarov, Ramil Mauleon, Kapeel Chougule, Sharon Wei, Tingting Gao, Carl D. Green, Andrea Zuccolo, Jianwei Zhang, Doreen Ware, Kenneth L. McNally,

Multi-omics resources for targeted agronomic improvement of pigmented rice

Khalid Sedeek, Andrea Zuccolo, Alice Fornasiero, Annika M. Weber, Krishnaveni Sanikommu, Sangeetha Sampathkumar, Luis F. Rivera, Haroon Butt, Saule Mussurova, Abdulrahman Alhabsi, Nurmansyah Nurmansyah, Elizabeth P. Ryan, Rod A. Wing & Magdy M. Mahfou

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Yong Zhou, Zhichao Yu, Dmytro Chebotarov, Kapeel Chougule, Zhenyuan Lu, Luis F. Rivera, Nagarajan Kathiresan, Noor Al-Bader, Nahed Mohammed, Aseel Alsantely, Saule Mussurova, João Santos, Manjula Thimma, Maxim Troukhan, Alice Fornasiero, Carl D. Green,

Dario Copetti, David Kudrna, Victor Llaca, Mathias Lorieux, Andrea Zuccolo, Doreen Ware, Kenneth McNally, Jianwei Zhang & Rod A. Wing

Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice

Zhichao Yu (于志超), Yongming Chen (陈永明), Yong Zhou (周勇), Yulu Zhang (张雨露), Mengyuan Li (李梦圆), Yidan Ouyang (欧阳亦聃), Dmytro Chebotarov, Ramil Mauleon, Hu Zhao (赵虎), Weibo Xie (谢为博), Kenneth L. McNally, Rod A. Wing, Weilong Guo (郭伟龙), Jianwei Zhang (张建伟)

Prediction of crossover recombination using parental genomes

Mauricio Peñuela, Camila Riccio-Rengifo, Jorge Finke, Camilo Rocha, Anestis Gkanogiannis, Rod A. Wing, Mathias Lorieux

(preprint) Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice

Zhichao Yu (于志超), Yongming Chen (陈永明), Yong Zhou (周勇), Yulu Zhang (张雨露), Mengyuan Li (李梦圆), Yidan Ouyang (欧阳亦聃), Dmytro Chebotarov, Ramil Mauleon, Hu Zhao (赵虎), Weibo Xie (谢为博), Kenneth L. McNally, Rod A. Wing, Weilong Guo (郭伟龙), Jianwei Zhang (张建伟)

**The gyrfalcon (Falco rusticolus) genome**

Andrea Zuccolo, Sara Mfarrej, Mirko Celii, Saule Mussurova, Luis F Rivera, Victor Llaca, Nahed Mohammed, Arnab Pain, Abdulmajeed Fahad Alrefaei, Abdulwahed Fahad Alrefaei, Rod A Wing

**The International Oryza Map Alignment Project (IOMAP): The Americas - Past achievements and future directions**

Aseel Alsantely, Rafal Gutaker, María E Navarrete Rodríguez, Griselda Arrieta-Espinoza, Eric J Fuchs, Antonio Costa de Oliveira, Joe Tohme, Andrea Zuccolo, Rod A Wing, Alice Fornasiero

What lies behind a fruit crop variety name? A case study of the barnī date palm from al-‘Ulā oasis, Saudi Arabia

Muriel Gros-Balthazard, Vincent Battesti, Jonathan M Flowers, Sylvie Ferrand, Matthieu Breil, Sarah Ivorra, Jean-Frédéric Terral, Michael D. Purugganan, Rod A. Wing, Nahed Mohammed, Yann X C Bourgeois

Gene fusion as an important mechanism to generate new genes in the genus Oryza

Yanli Zhou, Chengjun Zhang, Li Zhang, Qiannan Ye, Ningyawen Liu, Muhua Wang, Guangqiang Long, Wei Fan, Manyuan Long & Rod A. Wing

Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Naveenkumar Athiyannan, Michael Abrouk, Willem H. P. Boshoff, Stéphane Cauet, Nathalie Rodde, David Kudrna, Nahed Mohammed, Jan Bettgenhaeuser, Kirsty S. Botha, Shannon S. Derman, Rod A. Wing, Renée Prins & Simon G. Krattinger

Rice domestication

Alice Fornasiero, Rod A. Wing, Pamela Ronald

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass)

Van de Peer, Y.; Ma, X.; Olsen, J.L.; Reusch, T.B.H.; Procaccini, G.; Kudrna, D.; Williams, M.; Grimwood, J.; Rajasekar, S.; Jenkins, J.; Schmutz, J.

**Evolution and diversification of reproductive phased small interfering RNAs in Oryza species**

Peng Tian, Xuemei Zhang, Rui Xia, Yang Liu, Meijiao Wang, Bo Li, Tieyan Liu, Jinfeng Shi, Rod A. Wing, Blake C. Meyers, Mingsheng Chen

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Matthew B. Hufford, Arun S. Seetharam, Margaret R. Woodhouse, Kapeel M. Chougule, Shujun Ou, Jianing Liu, William A. Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas Tittes, Asher I. Hudson, Alexandre P. Marand, Sharon Wei,

Zhenyuan Lu, Bo Wang, Marcela K. Tello-Ruiz, Rebecca D. Piri, Na Wang, Dong won Kim, Yibing Zeng, Christine H. O’Connor, Xianran Li, Amanda M. Gilbert, Erin Baggs, Ksenia V. Krasileva, John L. Portwood II, Ethalinda K.S. Cannon, Carson M. Andorf,

Nancy Manchanda, Samantha J. Snodgrass, David E. Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L. Syring, David A. Kudrna, Victor Llaca, Kevin Fengler, Robert J. Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I. Gent, Candice N. Hirsch,

Doreen Ware, R. Kelly Dawe

Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping

Huang Li, Xiao Hu, John T Lovell, Paul P Grabowski, Sujan Mamidi, Cindy Chen, Mojgan Amirebrahimi, Indika Kahanda, Brendan Mumey, Kerrie Barry, David Kudrna, Jeremy Schmutz, Jennifer Lachowiec, Chaofu Lu

***Starch Synthesis-Related Genes (SSRG)* Evolution in the Genus *Oryza***

Karine E. Janner de Freitas, Railson Schreinert dos Santos, Carlos Busanello, Filipe de Carvalho Victoria, Jennifer Luz Lopes, Rod A. Wing and Antonio Costa de Oliveira

**Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) [version 1; peer review: awaiting peer review]**

Xiao Ma, Jeanine L. Olsen, Thorsten B.H. Reusch, Gabriele Procaccini, Dave Kudrna, Melissa Williams, Jane Grimwood, Shanmugam Rajasekar, Jerry Jenkins, Jeremy Schmutz, Yves Van de Peer

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