Frontiers in Plant Science (Jul 2022)
Capturing Wheat Phenotypes at the Genome Level
- Babar Hussain,
- Babar Hussain,
- Bala A. Akpınar,
- Michael Alaux,
- Ahmed M. Algharib,
- Deepmala Sehgal,
- Zulfiqar Ali,
- Gudbjorg I. Aradottir,
- Jacqueline Batley,
- Arnaud Bellec,
- Alison R. Bentley,
- Halise B. Cagirici,
- Luigi Cattivelli,
- Fred Choulet,
- James Cockram,
- Francesca Desiderio,
- Pierre Devaux,
- Munevver Dogramaci,
- Gabriel Dorado,
- Susanne Dreisigacker,
- David Edwards,
- Khaoula El-Hassouni,
- Kellye Eversole,
- Tzion Fahima,
- Melania Figueroa,
- Sergio Gálvez,
- Kulvinder S. Gill,
- Liubov Govta,
- Alvina Gul,
- Goetz Hensel,
- Goetz Hensel,
- Pilar Hernandez,
- Leonardo Abdiel Crespo-Herrera,
- Amir Ibrahim,
- Benjamin Kilian,
- Viktor Korzun,
- Tamar Krugman,
- Yinghui Li,
- Shuyu Liu,
- Amer F. Mahmoud,
- Alexey Morgounov,
- Tugdem Muslu,
- Faiza Naseer,
- Frank Ordon,
- Etienne Paux,
- Dragan Perovic,
- Gadi V. P. Reddy,
- Jochen Christoph Reif,
- Matthew Reynolds,
- Rajib Roychowdhury,
- Jackie Rudd,
- Taner Z. Sen,
- Sivakumar Sukumaran,
- Bahar Sogutmaz Ozdemir,
- Vijay Kumar Tiwari,
- Naimat Ullah,
- Turgay Unver,
- Selami Yazar,
- Rudi Appels,
- Hikmet Budak
Affiliations
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Babar Hussain
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
- Bala A. Akpınar
- Montana BioAgriculture, Inc., Missoula, MT, United States
- Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
- Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
- Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
- Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Arnaud Bellec
- 0French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
- Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Halise B. Cagirici
- 1Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
- Luigi Cattivelli
- 2Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
- Fred Choulet
- 3French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
- James Cockram
- 4The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
- Francesca Desiderio
- 2Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
- Pierre Devaux
- 5Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
- Munevver Dogramaci
- 6USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
- Gabriel Dorado
- 7Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
- Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- David Edwards
- 8University of Western Australia, Perth, WA, Australia
- Khaoula El-Hassouni
- 9State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
- Kellye Eversole
- 0International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
- Tzion Fahima
- 1Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
- Melania Figueroa
- 2Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
- Sergio Gálvez
- 3Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
- Kulvinder S. Gill
- 4Department of Crop Science, Washington State University, Pullman, WA, United States
- Liubov Govta
- 1Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
- Alvina Gul
- 5Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Goetz Hensel
- 6Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Goetz Hensel
- 7Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
- Pilar Hernandez
- 8Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
- Leonardo Abdiel Crespo-Herrera
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Amir Ibrahim
- 9Crop and Soil Science, Texas A&M University, College Station, TX, United States
- Benjamin Kilian
- 0Global Crop Diversity Trust, Bonn, Germany
- Viktor Korzun
- 1KWS SAAT SE & Co. KGaA, Einbeck, Germany
- Tamar Krugman
- 1Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
- Yinghui Li
- 1Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
- Shuyu Liu
- 9Crop and Soil Science, Texas A&M University, College Station, TX, United States
- Amer F. Mahmoud
- 2Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
- Alexey Morgounov
- 3Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
- Tugdem Muslu
- 4Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
- Faiza Naseer
- 5Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Frank Ordon
- 5Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
- Etienne Paux
- 3French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
- Dragan Perovic
- 5Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
- Gadi V. P. Reddy
- 6USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
- Jochen Christoph Reif
- 7Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Rajib Roychowdhury
- 1Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
- Jackie Rudd
- 9Crop and Soil Science, Texas A&M University, College Station, TX, United States
- Taner Z. Sen
- 1Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
- Sivakumar Sukumaran
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Bahar Sogutmaz Ozdemir
- 8Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey
- Vijay Kumar Tiwari
- 9University of Maryland, Baltimore, MD, United States
- Naimat Ullah
- 0Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
- Turgay Unver
- 1Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
- Selami Yazar
- 2General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
- Rudi Appels
- 3Murdoch University, Perth, WA, Australia
- Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
- DOI
- https://doi.org/10.3389/fpls.2022.851079
- Journal volume & issue
-
Vol. 13
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.
Keywords
- Wheat
- genome-wide association
- quantitative trait locus mapping
- abiotic-stress tolerance
- genomic selection
- QTL cloning