Capturing Wheat Phenotypes at the Genome Level

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2022-07-04

Author

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

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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 Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for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.

Subject Keywords

abiotic-stress tolerance, CRISPR/Cas9, disease resistance, genome-wide association, genomic selection, QTL cloning, quantitative trait locus mapping, Wheat

URI

https://hdl.handle.net/11511/98506

Journal

Frontiers in Plant Science

DOI

https://doi.org/10.3389/fpls.2022.851079

Collections

Department of Biology, Article

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Citation Formats

B. Hussaın et al., “Capturing Wheat Phenotypes at the Genome Level,” Frontiers in Plant Science, vol. 13, pp. 0–0, 2022, Accessed: 00, 2022. [Online]. Available: https://hdl.handle.net/11511/98506.