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 Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data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

Atta ur Rahman School of Applied Biosciences National University of Sciences and Technology Islamabad Pakistan

Center of Plant Genome Engineering Heinrich Heine Universität Düsseldorf Germany

Commonwealth Scientific and Industrial Research Organization Agriculture and Food Canberra ACT Australia

Council for Agricultural Research and Economics Research Centre for Genomics and Bioinformatics Fiorenzuola d'Arda Italy

Crop and Soil Science Texas A and M University College Station TX United States

Crop Improvement and Genetics Research USDA Agricultural Research Service Albany CA United States

Department of Biological Sciences Middle East Technical University Ankara Turkey

Department of Bioquímica y Biología Molecular Campus Rabanales C6 1 E17 Campus de Excelencia Internacional Agroalimentario Universidad de Córdoba Córdoba Spain

Department of Biotechnology Faculty of Life Sciences University of Central Punjab Lahore Pakistan

Department of Crop Science Washington State University Pullman WA United States

Department of Environment and Bio Agriculture Faculty of Agriculture Al Azhar University Cairo Egypt

Department of Genetics and Bioengineering Yeditepe University Istanbul Turkey

Department of Languages and Computer Science ETSI Informática Campus de Teatinos Universidad de Málaga Andalucía Tech Málaga Spain

Department of Pathology The National Institute of Agricultural Botany Cambridge United Kingdom

Department of Plant Pathology Faculty of Agriculture Assiut University Assiut Egypt

Division of Molecular Biology Centre of Region Haná for Biotechnological and Agriculture Research Czech Advanced Technology and Research Institute Palacký University Olomouc Czechia

Ficus Biotechnology Ostim Teknopark Ankara Turkey

Food and Agriculture Organization of the United Nations Riyadh Saudi Arabia

French National Research Institute for Agriculture Food and the Environment INRAE GDEC Clermont Ferrand France

French Plant Genomic Resource Center INRAE CNRGV Castanet Tolosan France

General Directorate of Research Ministry of Agriculture Ankara Turkey

Global Crop Diversity Trust Bonn Germany

Institute for Resistance Research and Stress Tolerance Julius Kühn Institute Quedlinburg Germany

Institute for Sustainable Agriculture Córdoba Spain

Institute of Biological Sciences Gomal University D 1 Khan Pakistan

Institute of Evolution and Department of Environmental and Evolutionary Biology University of Haifa Haifa Israel

Institute of Plant Breeding and Biotechnology MNS University of Agriculture Multan Pakistan

International Maize and Wheat Improvement Center Texcoco Mexico

International Wheat Genome Sequencing Consortium Bethesda MD United States

KWS SAAT SE and Co KGaA Einbeck Germany

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Germany

Molecular Biology Genetics and Bioengineering Sabanci University Istanbul Turkey

Montana BioAgriculture Inc Missoula MT United States

Murdoch University Perth WA Australia

Research and Innovation Florimond Desprez Group Cappelle en Pévèle France

School of Biological Sciences and Institute of Agriculture University of Western Australia Perth WA Australia

State Plant Breeding Institute The University of Hohenheim Stuttgart Germany

The John Bingham Laboratory The National Institute of Agricultural Botany Cambridge United Kingdom

Université Paris Saclay INRAE URGI Versailles France

University of Maryland Baltimore MD United States

University of Western Australia Perth WA Australia

USDA Agricultural Research Service Edward T Schafer Agricultural Research Center Fargo ND United States

USDA Agricultural Research Service Southern Insect Management Research Unit Stoneville MS United States

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