• DOI:10.1126/science.aar7191
• Corpus ID: 52016579

Shifting the limits in wheat research and breeding using a fully annotated reference genome

@article{Appels2018ShiftingTL,
  title={Shifting the limits in wheat research and breeding using a fully annotated reference genome},
  author={Rudi Appels and Kellye A Eversole and Nils Stein and Catherine Feuillet and Beat Keller and Jane Rogers and Curtis J. Pozniak and Fr{\'e}d{\'e}ric Choulet and Assaf Distelfeld and Jesse A. Poland and Gil Ronen and Andrew G. Sharpe and Omer Barad and Kobi Baruch and Gabriel Keeble-Gagn{\`e}re and Martin Mascher and Gil Ben-Zvi and Ambre-Aurore Josselin and Axel Himmelbach and François Balfourier and Juan J. Gutierrez-Gonzalez and Matthew J. Hayden and Chu Shin Koh and Gary J. Muehlbauer and Raj K. Pasam and Etienne Paux and Philippe Rigault and J Tibbits and Vijay K. Tiwari and Manuel Spannagl and Daniel Lang and Heidrun Gundlach and Georg Haberer and Klaus F. X. Mayer and Danara Ormanbekova and Verena M. Prade and Hana {\vS}imkov{\'a} and Thomas Wicker and David Swarbreck and H{\'e}l{\`e}ne Rimbert and Marius Felder and Nicolas Guilhot and Gemy George Kaithakottil and Jens Keilwagen and Philippe Leroy and Thomas M. Lux and Sven O. Twardziok and Luca Venturini and Ang{\'e}la Juh{\'a}sz and Michael Abrouk and Iris Fischer and Cristobal Uauy and Philippa Borrill and Ricardo H. Ram{\'i}rez-Gonz{\'a}lez and Dominique Arnaud and Smahane Chalabi and Boulos Chalhoub and Aron T. Cory and Raju Datla and M. Davey and John Jacobs and Stephen J. Robinson and Burkhard Steuernagel and F. van Ex and Brande B. H. Wulff and Moussa Benhamed and Abdelhafid Bendahmane and Lorenzo Concia and David Latrasse and Jan Barto{\vs} and Arnaud Bellec and H{\'e}l{\`e}ne Berg{\`e}s and Jaroslav Dole{\vz}el and Zeev Frenkel and Bikram S. Gill and Abraham B. Korol and Thomas Letellier and Odd-Arne Olsen and Kuldeep Singh and Miroslav Val{\'a}rik and Edwin A. G. van der Vossen and Sonia Vautrin and S. Weining and Tzion Fahima and Vladimir Glikson and Dina Raats and Jarmila {\vC}{\'i}hal{\'i}kov{\'a} and Helena Toegelov{\'a} and Jan Vr{\'a}na and Pierre Sourdille and Beno{\^i}t Darrier and Delfina Barabaschi and Luigi Cattivelli and Pilar Hern{\'a}ndez and Sergio G{\'a}lvez and Hikmet Budak and Jonathan D. G. Jones and Kamil Witek and Guotai Yu and Ian D. Small and Joanna Melonek and Ruonan Zhou and Tatiana Belova and Kostya Kanyuka and Robert C. King and Kirby T. Nilsen and Sean Walkowiak and Richard D. Cuthbert and Ron E. Knox and Krystalee Wiebe and Daoquan Xiang and Antje Rohde and Timothy J. Golds and Jana {\vC}{\'i}{\vz}kov{\'a} and Bala Anı Akpınar and Sezgi Biyiklioglu and Liangliang Gao and Amidou N'Daiye and Marie Kubaláková and Jan {\vS}af{\'a}ř and Françoise Alfama and Anne-Françoise Adam-Blondon and Raphael Flores and Claire Guerche and Mika{\"e}l Loaec and Hadi Quesneville and Janet A. Condie and Jennifer Ens and Ron Maclachlan and Yifang Tan and Adriana Alberti and Jean‐Marc Aury and Val{\'e}rie Barbe and Arnaud Couloux and Corinne Cruaud and Karine Labadie and Sophie Mangenot and Patrick Wincker and Gaganpreet Kaur and Mingcheng Luo and Sunish Kumar Sehgal and Parveen Chhuneja and Om Prakash Gupta and Suruchi Jindal and Parampreet Kaur and Palvi Malik and Priti Sharma and Bharat Singh Yadav and Nagendra Kumar Singh and Jitendra Paul Khurana and Chanderkant Chaudhary and Paramjit Khurana and Vinod Kumar and Ajay K. Mahato and Saloni Mathur and Amitha Mithra Sevanthi and Naveen Sharma and Ram Sewak Singh Tomar and Kateřina Holu{\vs}ov{\'a} and Ondřej Pl{\'i}hal and Matthew D. Clark and Darren Heavens and George Kettleborough and Jonathan Wright and Barbora Balc{\'a}rkov{\'a} and Yuqin Hu and Elena A. Salina and Nikolai V. Ravin and Konstantin G. Skryabin and Alexey V. Beletsky and Vitaly V. Kadnikov and Andrey V. Mardanov and Michail A. Nesterov and Andrey L Rakitin and E. M. Sergeeva and Hirokazu Handa and Hiroyuki Kanamori and Satoshi Katagiri and Fuminori Kobayashi and Shuhei Nasuda and Tsuyoshi Tanaka and Jianzhon Wu and Federica Cattonaro and Min Jiumeng and Karl G. Kugler and Matthias Pfeifer and Simen R{\o}d Sandve and Xu Li Xun and Bujie Zhan and Jacqueline Batley and Philipp Emanuel Bayer and David Edwards and Satomi Hayashi and Zuzana Tulpov{\'a} and Paul Visendi and Licao Cui and Xianghong Du and Kewei Feng and Xiaojun Nie and Wei Tong and Le Wang},
  journal={Science},
  year={2018},
  volume={361}
}

• R. Appels, K. Eversole, +198 authors Le Wang
• Published 17 August 2018
• Medicine, Biology
• Science

Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat. Science, this issue p. eaar7191; see also p. eaar6089 The 21 annotated chromosomes of bread wheat provide a foundation for innovation in research and breeding. INTRODUCTION Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. RATIONALE Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. RESULTS An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. CONCLUSION This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing. Wheat genome deciphered, assembled, and ordered. Seeds, or grains, are what counts with respect to wheat yields (left panel), but all parts of the plant contribute to crop performance. With complete access to the ordered sequence of all 21 wheat chromosomes, the context of regulatory sequences, and the interaction network of expressed genes—all shown here as a circular plot (right panel) with concentric tracks for diverse aspects of wheat genome composition—breeders and researchers now have the ability to rewrite the story of wheat crop improvement. Details on value ranges underlying the concentric heatmaps of the right panel are provided in the full article online. An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.