Background: The genusAllium(Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of theAlliumis not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for variousAlliumspecies; it will help in understanding the key traits inAlliumcrops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding inAlliumcrops.Method: In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.Results: Here, we have discussed the recent progress made inAlliumresearch using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated withAlliumcrops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.Conclusion: All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research ofAlliumcrops. We also mentioned a few research areas inAlliumcrops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research inAlliumspecies.

Background: Trichoderma asperellum and T. harzianum were assessed in this study as a potential biological control against Colletotrichum truncatum. C. truncatum is a hemibiotrophic fungus that causes anthracnose disease in chilli thereby affecting plant growth and fruit yield. Scanning electron microscope (SEM) technique showed the beneficial interaction between chilli root-Trichoderma spp. inducing the plant growth promotion, mechanical barrier, and defense network under C. truncatum challenged conditions. Methods: Seeds bio-primed with T. asperellum, T. harzianum, and T. asperellum + T. harzianum promoted the plant growth parameters and strengthening of physical barrier via lignification on the wall of vascular tissues. Seed primed with bioagents were used for exploring the molecular mechanism of defense response in pepper against anthracnose to assess the temporal expression of six defense genes in the Surajmukhi variety of Capsicum annuum. QRT-PCR demonstrated induction of defense responsive genes in chilli pepper bioprimed with Trichoderma spp. such as plant defensin 1.2 (CaPDF1.2), superoxide dismutase (SOD), ascorbate peroxidase (APx), guaiacol peroxidase (GPx), pathogenesis related proteins PR-2 and PR-5. Results: The results showed that bioprimed seeds were assessed for T. asperellum, T. harzianum, and T. asperellum + T. harzianum-chilli root colonization interaction under in vivo conditions. The results of the scanning electron microscope revealed that T. asperellum, T. harzianum and T. asperellum + T. harzianum interact with chilli roots directly via the development of plant-Trichoderma interaction system. Seeds bio-primed with bioagents promoted the plant growth parameters, fresh and dry weight of shoot and root, plant height, leaf area index, number of leaves, stem diameter and strengthening of physical barrier via lignification on the wall of vascular tissues and expression of six defense related genes in pepper against anthracnose. Conclusions: Application of T. asperellum and T. harzianum and in combination of treatments enhanced the plant growth. Further, as seeds bioprimed with T. asperellum, T. harzianum and in combination with treatment of T. asperellum + T. harzianum induced the strengthening of the cell wall by lignification and expression of six defense related genes CaPDF1.2, SOD, APx, GPx, PR-2 and PR-5 in pepper against C. truncatum. Our study contributed for better disease management through biopriming with T. asperellum, T. harzianum and T. asperellum + T. harzianum. The biopriming possess enormous potential to promote plant growth, modulate the physical barrier, and induced the defense related genes in chilli pepper against anthracnose.

Globally, abiotic stresses, such as temperature (heat or cold), water (drought and flooding), and salinity, cause significant losses in crop production and have adverse effects on plant growth and development. A variety of DNA-based molecular markers, such as SSRs, RFLPs, AFLPs, SNPs, etc., have been used to screen germplasms for stress tolerance and the QTL mapping of stress-related genes. Such molecular-marker-assisted selection strategies can quicken the development of tolerant/resistant cultivars to withstand abiotic stresses. Oilseeds such as rapeseed, mustard, peanuts, soybeans, sunflower, safflower, sesame, flaxseed, and castor are the most important source of edible oil worldwide. Although oilseed crops are known for their capacity to withstand abiotic challenges, there is a significant difference between actual and potential yields due to the adaptation and tolerance to severe abiotic pressures. This review summarizes the applications of molecular markers to date to achieve abiotic stress tolerance in major oilseed crops. The molecular markers that have been reported for genetic diversity studies and the mapping and tagging of genes/QTLs for drought, heavy metal stress, salinity, flooding, cold and heat stress, and their application in the MAS are presented.