Literature DB >> 32208137

A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat.

Nikolai M Adamski1, Philippa Borrill2, Jemima Brinton1, Sophie A Harrington1, Clémence Marchal1, Alison R Bentley3, William D Bovill4, Luigi Cattivelli5, James Cockram3, Bruno Contreras-Moreira6, Brett Ford4, Sreya Ghosh1, Wendy Harwood1, Keywan Hassani-Pak7, Sadiye Hayta1, Lee T Hickey8, Kostya Kanyuka7, Julie King9, Marco Maccaferrri10, Guy Naamati6, Curtis J Pozniak11, Ricardo H Ramirez-Gonzalez1, Carolina Sansaloni12, Ben Trevaskis4, Luzie U Wingen1, Brande Bh Wulff1, Cristobal Uauy1.   

Abstract

Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite their importance, a lack of genomic information and resources has hindered the functional characterisation of genes in major crops. The recent release of high-quality reference sequences for these crops underpins a suite of genetic and genomic resources that support basic research and breeding. For wheat, these include gene model annotations, expression atlases and gene networks that provide information about putative function. Sequenced mutant populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources. This review provides a helpful guide for plant scientists, especially those expanding into crop research, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of crops of vital importance for food and nutrition security.
© 2020, Adamski et al.

Entities:  

Keywords:  crop genetics; genomics; plant biology; polyploidy; wheat

Mesh:

Year:  2020        PMID: 32208137      PMCID: PMC7093151          DOI: 10.7554/eLife.55646

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  110 in total

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Journal:  Plant Sci       Date:  2015-01-24       Impact factor: 4.729

2.  Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing.

Authors:  Daniel Rodríguez-Leal; Zachary H Lemmon; Jarrett Man; Madelaine E Bartlett; Zachary B Lippman
Journal:  Cell       Date:  2017-09-14       Impact factor: 41.582

Review 3.  Genomics as the key to unlocking the polyploid potential of wheat.

Authors:  Philippa Borrill; Nikolai Adamski; Cristobal Uauy
Journal:  New Phytol       Date:  2015-06-24       Impact factor: 10.151

4.  An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Authors:  Bernardo J Clavijo; Luca Venturini; Christian Schudoma; Gonzalo Garcia Accinelli; Gemy Kaithakottil; Jonathan Wright; Philippa Borrill; George Kettleborough; Darren Heavens; Helen Chapman; James Lipscombe; Tom Barker; Fu-Hao Lu; Neil McKenzie; Dina Raats; Ricardo H Ramirez-Gonzalez; Aurore Coince; Ned Peel; Lawrence Percival-Alwyn; Owen Duncan; Josua Trösch; Guotai Yu; Dan M Bolser; Guy Namaati; Arnaud Kerhornou; Manuel Spannagl; Heidrun Gundlach; Georg Haberer; Robert P Davey; Christine Fosker; Federica Di Palma; Andrew L Phillips; A Harvey Millar; Paul J Kersey; Cristobal Uauy; Ksenia V Krasileva; David Swarbreck; Michael W Bevan; Matthew D Clark
Journal:  Genome Res       Date:  2017-05       Impact factor: 9.043

5.  Adaptive selection of founder segments and epistatic control of plant height in the MAGIC winter wheat population WM-800.

Authors:  Wiebke Sannemann; Antonia Lisker; Andreas Maurer; Jens Léon; Ebrahim Kazman; Hilmar Cöster; Josef Holzapfel; Hubert Kempf; Viktor Korzun; Erhard Ebmeyer; Klaus Pillen
Journal:  BMC Genomics       Date:  2018-07-31       Impact factor: 3.969

6.  Genetic transformation of wheat via Agrobacterium-mediated DNA delivery.

Authors:  Caroline A Sparks; Angela Doherty; Huw D Jones
Journal:  Methods Mol Biol       Date:  2014

7.  Analysis of the bread wheat genome using whole-genome shotgun sequencing.

Authors:  Rachel Brenchley; Manuel Spannagl; Matthias Pfeifer; Gary L A Barker; Rosalinda D'Amore; Alexandra M Allen; Neil McKenzie; Melissa Kramer; Arnaud Kerhornou; Dan Bolser; Suzanne Kay; Darren Waite; Martin Trick; Ian Bancroft; Yong Gu; Naxin Huo; Ming-Cheng Luo; Sunish Sehgal; Bikram Gill; Sharyar Kianian; Olin Anderson; Paul Kersey; Jan Dvorak; W Richard McCombie; Anthony Hall; Klaus F X Mayer; Keith J Edwards; Michael W Bevan; Neil Hall
Journal:  Nature       Date:  2012-11-29       Impact factor: 49.962

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Journal:  PLoS One       Date:  2007-08-08       Impact factor: 3.240

9.  Enabling reusability of plant phenomic datasets with MIAPPE 1.1.

Authors:  Evangelia A Papoutsoglou; Daniel Faria; Daniel Arend; Elizabeth Arnaud; Ioannis N Athanasiadis; Inês Chaves; Frederik Coppens; Guillaume Cornut; Bruno V Costa; Hanna Ćwiek-Kupczyńska; Bert Droesbeke; Richard Finkers; Kristina Gruden; Astrid Junker; Graham J King; Paweł Krajewski; Matthias Lange; Marie-Angélique Laporte; Célia Michotey; Markus Oppermann; Richard Ostler; Hendrik Poorter; Ricardo Ramı Rez-Gonzalez; Živa Ramšak; Jochen C Reif; Philippe Rocca-Serra; Susanna-Assunta Sansone; Uwe Scholz; François Tardieu; Cristobal Uauy; Björn Usadel; Richard G F Visser; Stephan Weise; Paul J Kersey; Célia M Miguel; Anne-Françoise Adam-Blondon; Cyril Pommier
Journal:  New Phytol       Date:  2020-04-25       Impact factor: 10.323

10.  Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

Authors:  Shichen Wang; Debbie Wong; Kerrie Forrest; Alexandra Allen; Shiaoman Chao; Bevan E Huang; Marco Maccaferri; Silvio Salvi; Sara G Milner; Luigi Cattivelli; Anna M Mastrangelo; Alex Whan; Stuart Stephen; Gary Barker; Ralf Wieseke; Joerg Plieske; Morten Lillemo; Diane Mather; Rudi Appels; Rudy Dolferus; Gina Brown-Guedira; Abraham Korol; Alina R Akhunova; Catherine Feuillet; Jerome Salse; Michele Morgante; Curtis Pozniak; Ming-Cheng Luo; Jan Dvorak; Matthew Morell; Jorge Dubcovsky; Martin Ganal; Roberto Tuberosa; Cindy Lawley; Ivan Mikoulitch; Colin Cavanagh; Keith J Edwards; Matthew Hayden; Eduard Akhunov
Journal:  Plant Biotechnol J       Date:  2014-03-20       Impact factor: 9.803

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  28 in total

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2.  Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species.

Authors:  Noorhariza Mohd Zaki; Trude Schwarzacher; Rajinder Singh; Maria Madon; Corey Wischmeyer; Nordiana Hanim Mohd Nor; Muhammad Azwan Zulkifli; J S Pat Heslop-Harrison
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3.  The mosaic oat genome gives insights into a uniquely healthy cereal crop.

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Journal:  Nature       Date:  2022-05-18       Impact factor: 69.504

4.  Trend, population structure, and trait mapping from 15 years of national varietal trials of UK winter wheat.

Authors:  Oluwaseyi Shorinola; James Simmonds; Luzie U Wingen; Cristobal Uauy
Journal:  G3 (Bethesda)       Date:  2022-02-04       Impact factor: 3.542

5.  Exploring the diversity of promoter and 5'UTR sequences in ancestral, historic and modern wheat.

Authors:  Michael C U Hammond-Kosack; Kim E Hammond-Kosack; Robert King; Kostya Kanyuka
Journal:  Plant Biotechnol J       Date:  2021-09-16       Impact factor: 9.803

6.  A consensus on the Aquaporin Gene Family in the Allotetraploid Plant, Nicotiana tabacum.

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Journal:  Plant Direct       Date:  2021-05-07

7.  Annotation and Molecular Characterisation of the TaIRO3 and TaHRZ Iron Homeostasis Genes in Bread Wheat (Triticum aestivum L.).

Authors:  Oscar Carey-Fung; Jesse T Beasley; Alexander A T Johnson
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Review 8.  Wheat root systems as a breeding target for climate resilience.

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9.  An Efficient Brome mosaic virus-Based Gene Silencing Protocol for Hexaploid Wheat (Triticum aestivum L.).

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Journal:  Front Plant Sci       Date:  2021-06-18       Impact factor: 5.753

10.  Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles.

Authors:  H Busra Cagirici; Taner Z Sen
Journal:  G3 (Bethesda)       Date:  2020-06-01       Impact factor: 3.154

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