Capturing wheat phenotypes at the genome level

Authors: HUSSAIN, BABAR - Middle East Technical University; AKPINAR, BALA - Montana Bioagriculture Inc; ALAUX, MICHAEL - Université Paris-Saclay; ALGHARIB, AHMED - Al-Azhar University; SEHGAL, DEEPMALA - International Maize & Wheat Improvement Center (CIMMYT); ALI, ZULFIQAR - Muhammad Nawaz Shareef University Of Agriculture; ARADOTTIR, GIA - National Institute Of Agricultural Botany (NIAB); BATLEY, JACQUELINE - Agricultural University Of Western Australia; BELLEC, ARNAUD - Institut National De La Recherche Agronomique (INRA); BENTLEY, ALISON - International Maize & Wheat Improvement Center (CIMMYT); CAGIRICI, HALISE - Orise Fellow; CATTIVELLI, LUIGI - Crea - Research Centre For Genomics And Bioinformatics; CHOULET, FRED - French National Institute For Agricultural Research; COCKRAM, JAMES - National Institute Of Agricultural Botany (NIAB); DESIDERIO, FRANCESCA - Crea - Research Centre For Genomics And Bioinformatics; DEVAUX, PIERRE - Florimond Desprez - France; Dogramaci, Munevver; DORADO, GABRIEL - Universidad De Cordoba; DREISIGACKER, SUSANNE - International Maize & Wheat Improvement Center (CIMMYT); EDWARDS, DAVID - University Of Western Australia; EL-HASSOUNI, KHAOULA - University Of Hohenheim; EVERSOLE, KELLYE - International Wheat Genome Sequencing Consortium (IWGSC); FAHIMA, TZION - University Of Haifa; FIGUEROA, MELANIA - Commonwealth Scientific And Industrial Research Organisation (CSIRO); GALVEZ, SERGIO - University Of Malaga; GILL, KULVINDER - Washington State University; GOVTA, LIUBOV - University Of Haifa; GUL, ALVINA - National University Of Sciences And Technology; HENSEL, GOETZ - Heinrich-Heine University; HERNANDEZ, PILAR - Consejo Superior De Investigaciones Cientificas (CSIC); HERRERA, LEONARDO - International Maize & Wheat Improvement Center (CIMMYT); IBRAHIM, AMIR - Texas A&M University; KILIAN, BENJAMIN - Global Crop Diversity Trust; KORZUN, VIKTOR - Kws Saat Ag; KRUGMAN, TAMAR - University Of Haifa; LI, YINGHUI - University Of Haifa; LIU, SHUYU - Texas A&M University; MAHMOUD, AMER - Assiut University; MORGOUNOV, ALEXEY - Food And Agriculture Organization Of The United Nations (FAO); MUSLU, TUGDEM - Sabanci University; NASEER, FAIZA - National University Of Sciences And Technology; ORDON, FRANK - Julius Kuhn Institute; PAUX, ETIENNE - French National Institute For Agricultural Research; PEROVIC, DRAGAN - Julius Kuhn Institute; Reddy, Gadi V.P.; REIF, JOCHEN - Leibniz Institute Of Plant Genetics And Crop Plant Research; REYNOLDS, MATTHEW - International Maize & Wheat Improvement Center (CIMMYT); ROYCHOWDHURY, RAJIB - University Of Haifa; RUDD, JACKIE - Texas A&M University; Sen, Taner; SUKUMARAN, SIVAKUMAR - International Maize & Wheat Improvement Center (CIMMYT); OZDEMIR, BAHAR - Yeditepe University; TIWARI, VIJAY KUMAR - University Of Maryland; ULLAH, NAIMAT - Institute Of Biological Sciences (IBS); UNVER, TURGAY - Ficus Biotechnology; YAZAR, SELAMI - Ministry Of Agriculture - Turkey; APPELS, RUDI - La Trobe University; BUDAK, HIKMET - Montana Bioagriculture Inc

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2022
Publication Date: 6/4/2022
Citation: Hussain, B., Akpinar, B.A., Alaux, M., Algharib, A.M., Sehgal, D., Ali, Z., Aradottir, G.I., Batley, J., Bellec, A., Bentley, A.R., Cagirici, H.B., Cattivelli, L., Choulet, F., Cockram, J., Desiderio, F., Devaux, P., Dogramaci, M., Dorado, G., Dreisigacker, S., Edwards, D., El-Hassouni, K., Eversole, K., Fahima, T., Figueroa, M., Galvez, S., Gill, K.S., Govta, L., Gul, A., Hensel, G., Hernandez, P., Herrera, L.C., Ibrahim, A., Kilian, B., Korzun, V., Krugman, T., Li, Y., Liu, S., Mahmoud, A.F., Morgounov, A., Muslu, T., Naseer, F., Ordon, F., Paux, E., Perovic, D., Reddy, G.V., Reif, J.C., Reynolds, M., Roychowdhury, R., Rudd, J., Sen, T.Z., Sukumaran, S., Ozdemir, B.S., Tiwari, V., Ullah, N., Unver, T., Yazar, S., Appels, R., Budak, H. 2022. Capturing wheat phenotypes at the genome level. Frontiers in Plant Science. 13. Article 851079. https://doi.org/10.3389/fpls.2022.851079.
DOI: https://doi.org/10.3389/fpls.2022.851079

Interpretive Summary: Wheat (Triticum aestivum L.) is the most important crop for feeding the earth´s growing population and a staple food in many regions of the world. Although wheat breeding targets are numerous and varied across the globe, the principle targets are grain yield, quality determinants and tolerance to biotic and abiotic stresses. Breeding programs often utilize genetic markers to identify the plants with desired traits to accelerate the breeding process. But, the complexity of the wheat genome, which consists of three sub-genomes, makes improving qualitative and quantitative traits through molecular approaches challenging. Efforts to sequence the wheat genome have been extremely time consuming due to its large genome size. Consequently, the efficient exploitation of molecular-assisted breeding approaches has lagged behind that achieved in other crop species. Finally, an international gigantic team effort resulted in the releasing of a gold-standard fully annotated wheat genome assembly in 2018. These advances facilitate a new horizon opportunity for marker-assisted selection and genomic selection in wheat. For example, utilizing genotyping arrays, hundreds of wheat lines can be screened for thousands of genetic markers, providing with fast and reliable data for potential exploitation in wheat breeding. Here, we evaluate the advances and perspectives in wheat genetics and genomics studies and make recommendations on the utilization of genomics for next generation wheat breeding.

Technical 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 hexaploid bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, until very recently efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species due to its large polyploidy genome. However, an international public-private effort spanning nine 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 2017. Shortly thereafter, in 2020, the genome of assemblies of an additional fifteen global wheat accessions were released. 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 genotyping 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 a new horizon for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we evaluate 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 enlisted a hundred of reported candidate and cloned genes responsible for the aforesaid 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, (ii) positional cloning methods, and of genomic selection. Finally, we make recommendations on the utilization of genomics for the next-generation wheat breeding and provide a practical example of using the latest, in silico bioinformatics tools that were based on the wheat reference genome sequence.