Citation: Aci, M.M.; Sidari, R.; Araniti, F.; Lupini, A. Emerging Trends in Allelopathy: A Genetic Perspective for Sustainable Agriculture. Agronomy 2022, 12, 2043. https://doi.org/10.3390/ agronomy12092043 Academic Editor: Andras Cseh Received: 21 July 2022 Accepted: 25 August 2022 Published: 27 August 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). agronomy Review Emerging Trends in Allelopathy: A Genetic Perspective for Sustainable Agriculture Meriem Miyassa Aci 1,† , Rossana Sidari 1,† , Fabrizio Araniti 2 and Antonio Lupini 1, * 1 Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy 2 Department of Agricultural and Environmental Sciences—Production, Territory, Agroenergy, University of Milano, 20133 Milan, Italy * Correspondence: antonio.lupini@unirc.it; Tel.: +39-0965-169-4246 † These authors contributed equally to this work. Abstract: Over the past decades, a growing interest in allelopathy has been recorded due to the effective use of allelochemicals as growth regulators, bioherbicides, insecticides, and antimicrobial crop protection in the sustainable agriculture field. So far, the genetic aspects of the allelopathic effects have been poorly studied, and the identification of allelopathic genes and/or genomic regions (QTLs) has become a challenge to implement specific breeding programs. Here, we review the recent genetic and genome-based research findings in allelopathy, with a particular emphasis on weed control, which is one of the major crop yield-limiting factors. We discuss the key plant–microorganism interactions, including the cross-kingdom RNAi phenomenon and the involvement of microRNAs in allelopathy. Through this review, we wanted to lay the foundation for advancing knowledge in allelopathy and uncover the areas where research is needed. Keywords: allelopathic genes; quantitative trait loci (QTL); weed control; microorganisms; next- generation sequencing (NGS); cross-kingdom RNAi 1. Introduction Allelopathy is an ecological phenomenon, in which the chemicals produced by plants and microorganisms affect the growth, development, and fitness of other organisms [1]. This discipline represents a topic of growing interest due to the sustainability discussion currently in progress [2]. Over the years, several definitions have been adopted, in which “interaction” has been the key common word. Many definitions of allelopathy have been given throughout history [3–5]. More recently, the International Allelopathy Society (IAS) has further expanded the definition as follows: “any process involving secondary metabo- lites produced by plants, microorganisms, viruses, and fungi that influence the growth and development of agricultural and biological systems” (IAS, 1996) (Figure 1). However, although the different definitions mentioned above have tried to include all the possible physiological responses due to allelopathic interactions induced by secondary metabo- lites among organisms, to date the positive or negative effects of allelopathy are not well defined [5]. Indeed, the study of plant responses to allelochemicals is markedly influenced by the used methods, the considered biological traits, and the evolutionary history of the organisms [5]. In addition, the allelopathic phenomenon increases with the genetic distance between the species, and this concept opens a new scenario in which kin recognition takes place among species [6] and where root exudates play a pivotal role [7]. In this context, Crepy and Casal [8] described for the first time the molecular mechanisms of recognition responses in the shoot in which phytochrome B and cryptochrome 1 genes were involved. Moreover, plants can be passive organisms, responding only to environmental fluctuations, or active, transmitting, receiving, and reacting directly with other plants and microorganisms to chemical signals, regardless of environmental variations (Figure 1)[9]. Agronomy 2022, 12, 2043. https://doi.org/10.3390/agronomy12092043 https://www.mdpi.com/journal/agronomy