Plant-microbe interactions can be either beneficial or harmful depending on the nature of the interaction. Multifaceted benefits of plant-associated microbes in crops are well documented. Specifically, the management of plant diseases using beneficial microbes is considered to be eco-friendly and the best alternative for sustainable agriculture. Diseases caused by various phytopathogens are responsible for a significant reduction in crop yield and cause substantial economic losses globally. In an ecosystem, there is always an equally daunting challenge for the establishment of disease and development of resistance by pathogens and plants, respectively. In particular, comprehending the complete view of the complex biological systems of plant-pathogen interactions, co-evolution and plant growth promotions (PGP) at both genetic and molecular levels requires novel approaches to decipher the function of genes involved in their interaction. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein 9) is a fast, emerging, precise, ecofriendly and efficient tool to address the challenges in agriculture and decipher plant-microbe interaction in crops. Nowadays, the CRISPR/Cas9 approach is receiving major attention in the field of functional genomics and crop improvement. Consequently, the present review updates the prevailing knowledge in the deployment of CRISPR/Cas9 techniques to understand plant-microbe interactions, genes edited for the development of fungal, bacterial and viral disease resistance, to elucidate the nodulation processes, plant growth promotion, and future implications in agriculture. Further, CRISPR/Cas9 would be a new tool for the management of plant diseases and increasing productivity for climate resilience farming.

Phytophthora gummosis, foot rot, and root rot are considered major challenges to the citrus industry worldwide. Little is known about the Phytophthora–microbiome interaction, despite several studies demonstrating changes in the microbial composition of the rhizosphere following challenges by a pathogen. In the present study, we studied the microbial diversity and community structure in healthy rhizospheres and Phytophthora-infected rhizospheres of Khasi mandarin (Citrus reticulata Blanco), a commercial cultivar extensively grown in the northeast of India. An exploratory study was conducted to identify Phytophthora-infected orchards of Khasi mandarin, and the isolated pathogen was confirmed as P. nicotianae based on its morpho-cultural and molecular characteristics coupled with pathogenicity tests. This study on culturable microbes established the dominance of Trichoderma spp. in the healthy rhizosphere, while the diseased rhizosphere showed the presence of Fusarium spp. A metagenomic study further revealed that the rhizospheres of Phytophthora-infected plants were dominated by species such as Bacteroidia spp., Patescibacteria spp., and Pythium spp., while the healthy Khasi mandarin rhizospheres had a more diverse community predominantly represented by Trichoderma, Penicillium, Linnemannia, Mortierella, Talaromyces, Saitozyma, Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Terrabacteria and FCB (Fibrobacterota, Chlorobiota, and Bacteroidota groups) were found to exist in higher relative abundance in disease-free soils than in Phytophthora-infected soils, while phylum Proteobacteria showed identical relative abundance in all soil types. The phyla represented by Pseudomonas, Flavobacteriia, Candidatus, Mycobacterium, Rhizobium, Mesorhizobium, Sphingomonas, and Cytophagia were the most common bacterial phyla in all soil samples, but healthy soil exhibited a greater abundance of Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Our study suggests that the presence of Phytophthora spp. in the rhizosphere alters microbial community structure, having potentially strong implications for plant health and productivity. These rhizosphere microbiome-derived citrus responses shed light on exploring effective management strategies for Phytophthora gummosis disease ailing Khasi mandarin.

The sweet oranges [C. sinensis (L.) Osbeck] produced in India are mainly consumed fresh as a table fruit and in the form of freshly extracted juice. Currently, a fraction of the fruit is processed into products like orange juice, concentrates, pulp, and other value-added products. Seedless varieties are preferred both by the consumers and by the processing industry; however, indigenously developed seedless sweet orange cultivars are not available. Citrus triploids are usually seedless due to their abnormal meiosis and embryo abortion. A research study was undertaken at CCRI Nagpur to develop triploid seedless plants of the local sweet orange cultivar Mosambi through endosperm culture in the shortest possible time by dovetailing various techniques. Various steps, viz., endosperm excision, standardization of media for callus initiation, somatic embryogenesis, shoot/root differentiation, mini-grafting, and validation of the triploid status through flow cytometry, chromosome counting, and other morphological parameters, were standardized, and seven confirmed triploid plants were finally produced. An evaluation of fruit quality parameters during the 2022 and 2023 fruiting seasons revealed that the fruits of the triploid sweet orange trees were commercially seedless. This is the first reported comprehensive study on the successful development of commercially seedless plants of the sweet orange cultivar Mosambi. The fruits of the triploid plants showed desirable fruit quality parameters in terms of their seed number (3 to 5.9/fruit), higher vitamin C content (34.4 to 42.66 mg), and lower limonene content (7.77 to 11.34 µg/mL). These triploid plants have the potential to gain recognition as a distinct variety.

Sweet orange ( Citrus sinensis (L.) Osbeck) is an important commercial citrus fruit crop, cultivated in India and across the world. In India most of the cultivated sweet orange species were introduced varieties. In this study, we used two molecular markers,SSR and InDels, to understand the genetic diversity and population structure of seventy-two sweet orange genotypes. Genetic parameters consisted of total number of alleles, number of polymorphic alleles (effective alleles); genetic diversity (G.D.), expected heterozygosity (He) and polymorphic information content (PIC) were calculated based on molecular data. Two dendrograms were constructed based on the InDels and SSR. In the both the cases they formed three major clusters showing various degrees of variations with respect to members of the clusters. Population structure analysis revealed presence of two distinct sub populations. Therefore, in order to address various challenges and develop sweet orange varieties with desirable traits, there is a need to broaden the genetic base of sweet orange through intensive collection in the northeastern region. These results of intra-specific genetic variability of the collections will dictate the path for the sweet orange breeding and conservation programs in India.

<!----> <!----> The enigma surrounding life always makes humans inquisitive towards understanding their mechanism. With the developments in the past decades, science has witnessed rapid strides in terms of high-throughput technologies, including sequencing, genotyping, targeted genome technologies and computational methods. This played a major role towards probing various molecular mechanisms in plants. The availability of the draft genome sequences of the plant genomes enhances the scope for systematic studies for understanding the functions of the genes. Identifying the function of a particular gene is crucial to understand the underlying mechanism in the life process. Thus, the generation of mutants on a large scale is inevitable to understand the complete process or cycle. Several methods, including T-DNA insertion, TILLING (targeting-induced local lesions in genomes) and RNAi (RNA interference), were commonly used to create large-scale mutant libraries. Each of these methods has their own drawbacks like random insertions, difficulty to locate the inserted position and reduction in expression rather than the total knockout. Recent advances in genome engineering led to the development of precise genome editing methods, including CRISPR-Cas9, which has a high success rate in editing genome at the desired position, including the introduction of biallelic mutation. CRISPR/Cas9-based screening is target-specific and helps in identifying both functional genes and mutant phenotypes. CRISPR/Cas9-based robust methods would help to decode the functions of several hundred genes; in due course, it will be used to understand the genome function rather than the gene function. <!----> <!---->