Capturing Wheat Phenotypes at the Genome Level
Authors: Hussain 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 
Published: July 2022

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 Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data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