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Journal Articles Frontiers in Plant Science Year : 2022

Capturing Wheat Phenotypes at the Genome Level

Michael Alaux
Zulfiqar Ali
  • Function : Author
Gudbjorg I Aradottir
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Jacqueline Batley
  • Function : Author
Alison R Bentley
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Halise B Cagirici
  • Function : Author
Luigi Cattivelli
  • Function : Author
James Cockram
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Francesca Desiderio
  • Function : Author
Pierre Devaux
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Munevver Dogramaci
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Gabriel Dorado
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Susanne Dreisigacker
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David Edwards
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Khaoula El-Hassouni
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Kellye Eversole
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Tzion Fahima
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Melania Figueroa
  • Function : Author
Sergio Gálvez
  • Function : Author
Kulvinder S Gill
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Liubov Govta
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Alvina Gul
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Goetz Hensel
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Pilar Hernandez
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Leonardo Abdiel Crespo-Herrera
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Amir Ibrahim
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Benjamin Kilian
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Viktor Korzun
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Tamar Krugman
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Yinghui Li
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Shuyu Liu
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Amer F Mahmoud
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Alexey Morgounov
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Tugdem Muslu
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Faiza Naseer
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Frank Ordon
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Dragan Perovic
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Gadi V P Reddy
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Jochen Christoph Reif
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Matthew Reynolds
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Rajib Roychowdhury
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Jackie Rudd
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Taner Z Sen
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Sivakumar Sukumaran
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Bahar Sogutmaz Ozdemir
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Vijay Kumar Tiwari
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Naimat Ullah
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Turgay Unver
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Selami Yazar
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Rudi Appels
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Hikmet Budak
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Abstract

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat ( Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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hal-03740520 , version 1 (29-07-2022)

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Babar Hussain, Bala A Akpınar, Michael Alaux, Ahmed M Algharib, Deepmala Sehgal, et al.. Capturing Wheat Phenotypes at the Genome Level. Frontiers in Plant Science, 2022, 13, ⟨10.3389/fpls.2022.851079⟩. ⟨hal-03740520⟩
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