The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.

Centre for Plant Genome Engineering Institute of Plant Biochemistry Heinrich Heine University 40225 Dusseldorf Germany

Centre of the Region Haná for Biotechnological and Agricultural Research Czech Advanced Technology and Research Institute Palacký University Olomouc 78371 Olomouc Czech Republic

Department of Biological Sciences University of Lethbridge Lethbridge AB T1K 3M4 Canada

Faculty of Engineering and Natural Sciences Sabanci University 34956 Istanbul Turkey

Federal Research Center Kazan Scientific Center of Russian Academy of Sciences Kazan Institute of Biochemistry and Biophysics 420111 Kazan Russia

Federal Research Center Kazan Scientific Center of Russian Academy of Sciences Laboratory of Plant Infectious Diseases 420111 Kazan Russia

Institute of Biological Sciences University of Talca 1 Poniente 1141 Talca 3460000 Chile

KWS SAAT SE and Co KGaA Grimsehlstr 31 37555 Einbeck Germany

Laboratory of Cellular and Molecular Mechanisms of Plant Development Komarov Botanical Institute of the Russian Academy of Sciences 197376 Saint Petersburg Russia

Montana BioAg Inc Missoula MT 59802 USA

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