Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guide researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeders by allowing them to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

Phytochemicals with antimicrobial and antioxidant properties have tremendous potential in suppressing both plant and human diseases. Screening and identification of such compounds from diverse plant species is the first step toward realizing their medicinal and agricultural application. In agriculture, application of antimicrobial phytochemicals as part of an Integrated Disease Management strategy would reduce the detrimental residual effect of synthetic chemicals. In the present study, an invasive plant species, i.e., Lantana camara L. was screened for potential antimicrobial and antioxidant phytochemicals. Extracts of leaves (LE) and flowers (FE) from L. camara were tested for their polyphenol content (total phenol, total flavonoid, and total alkaloid) and antioxidant potential [total antioxidant activity, iron chelating activity and enzymatic activity (peroxidase and polyphenol oxidase)]. Both extracts exhibited high antioxidant and free radical scavenging activities with relatively stronger antioxidant activity in the case of whole flower extracts. FTIR and GC-MS also carried out for chemical analysis of crude extracts. FTIR spectral study of LE and FE revealed the presence of different functional groups such as N–H, C–H, OH, C = O indicates the existence of various metabolites in the extracts. GC-MS study revealed the presence of 66 bioactive compounds, of which 19 components were predicted to have various functions like anti-inflammatory, antiandrogenic, anti-tumor, antimicrobial, etc. Furthermore, in vitro antifungal and antibacterial studies confirmed the antimicrobial effect of both LE and FE against phytopathogens like Magnaporthe oryzae, Xanthomonas axonopodis pv. glycines (Xag) and Xanthomonas oryzae pv. oryzae (Xoo). Molecular study further revealed that phytochemicals (Loliolide, Eicosapentaenoic acid, Salicylic Acid Methyl Ester, and Phytol) of Lantana camara could targets MAPK1, PDF, and SUH like enzymes of phytopathogens, which could inhibit their growth. Therefore, L. camara extracts can be an important ingredient in the suppression of plant diseases.

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other -omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).

Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant’s defense response, the contribution of rice resistance genes towards development of disease resistance varieties, identification and characterization of novel, broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the “-omics” technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated thede novodomestication of new crops for sustainable agriculture and food security. In this review, we discuss how “omics” technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.