Onions are one of the most important vegetable crops worldwide. However, their production faces many challenges. Genetic improvement is one mechanism to address those challenges. In this review, we discuss recent research pertaining to the diseases Fusarium basal rot and Iris yellow spot, the insect pest onion thrips, onion pungency, and dormancy. Recent research for screening onion bulbs for Fusarium basal rot resistance has resulted in improved screening techniques and germplasm exhibiting less disease when inoculated with the disease-causing pathogen. Improved screening methods have resulted in germplasm exhibiting fewer and less severe Iris yellow spot symptoms when onion thrips and conducive environmental conditions are present. Onion germplasm with less and differing compositions of epicuticular wax on their leaves have shown a nonpreference for thrips feeding and have the potential for developing thrips tolerant cultivars. Conventional breeding efforts and genetic manipulation of the genes producing alliinase and lachrymatory factor synthase has resulted in low pungency, tearless onions. In long-day onions, an annual generation time has been achieved by artificially breaking bulb dormancy early while ensuring proper vernalization has been completed. Genetic improvement of these and many other onion traits will continue and result in better production in the future.

Onion is an important vegetable crop because it adds nutritional value and diversity to food preparation. Understanding recent advancements in onion molecular genetics is essential to improve production, quality, and disease resistance. Cutting-edge genomic technologies like genetic mapping and RNA sequencing reveal important genes and pathways. The review examines the progress in utilizing various molecular markers to study genetic divergence. The exploration extends to understanding the genes and pathways responsible for bulb color and chemical composition and the genetic factors influencing bulbing, flowering, and vernalization. Additionally, the article explores quantitative trait loci associated with resistance to major damaging diseases and delves into the role of different loci in male sterility and hybrid development. The recent publication of the whole genome sequence of onions will lead to further identification of genes and understanding their roles and functions in metabolic pathways.

Allium species are known for their culinary, medicinal, and ornamental purposes. Fusarium basal rot is one of the most damaging soilborne fungal diseases of Allium species and poses a significant threat to yield, quality, and storage life worldwide. Various species of Fusarium have been identified as causal agents for Fusarium basal rot, depending on the Allium species involved. Diverse disease management practices have been implemented to mitigate the impact of Fusarium basal rot. This review article provides a comprehensive overview of the recent progress in detecting different species of Fusarium involved in Fusarium basal rot and strategies to control them in affected Allium species involving chemical, biological, and cultural methods. It covers the latest advancements in host plant resistance research from traditional breeding to modern molecular techniques and studying secondary metabolites involved in defense mechanisms against Fusarium basal rot.

Development of resistant cultivars for Fusarium basal rot (FBR), a fungal disease caused by the soil-borne fungus Fusarium oxysporum f.sp. cepae (FOC), is a major breeding goal for onion breeding programs around the world. Currently, the selection of FBR-resistant bulbs is based on a visual interval or category scale, which is an entirely subjective method. This study aimed to develop an objective approach using digital image analysis to quantify symptom development in the basal plate of dormant bulbs. Digital image analyses were performed after artificially inoculating dormant bulbs of eighty-five United States Department of Agriculture (USDA) Allium cepa accessions with a virulent FOC isolate, ‘CSC-515’. An analysis with confocal microscopy identified bright blue–green autofluorescence from FOC-infected tissue, effectively differentiating diseased from healthy tissue. Visual scoring of the FBR symptom was aided by stereo fluorescence microscopic images captured using a green fluorescence protein dual filter to quantify accurately FBR severity in the basal plate tissue. An automatic stepwise image segmentation method was developed that was relatively more accurate than a visual estimation. This method exhibited comparable reliability and precision to visual scoring, but it tended to underestimate FOC infection. To our best knowledge, this is the first comprehensive study to investigate the potential use of image analysis as a viable alternative to conventional visual scoring for FBR symptom development. This method could be used for developing resistant cultivars for onion breeding programs in the near future.

Fusarium basal rot (FBR) of onion, which is caused by Fusarium oxysporum f.sp. cepae (Hanzawa) Snyder & Hansen (FOC) results in a substantial loss of marketable bulbs worldwide. One of the main reasons for the lack of FBR-resistant short-day cultivars is the unreliable screening methods available for the mature bulb stage when significant economic damage occurs. The objective of this study was to develop an artificial inoculation method with better quantification of inoculum for an effective selection of FBR-resistant mature onion bulbs. Mature bulbs of seven New Mexican short-day onion cultivars, along with susceptible and tolerant controls, were selected and evaluated for FBR resistance using mycelial and conidial inoculation methods, respectively. Transversely cut basal plates of mature bulbs were inoculated artificially with mycelia or conidia (12 × 10 ⁵ spores/mL in 2014 and 3 × 10 ⁵ spores/mL in 2015 embedded in potato dextrose agar plug) of a virulent FOC isolate ‘CSC-515’. Mature bulb evaluation using a visual rating scale (1 = no disease; 9 = >70% basal plate infected) revealed a high degree of FBR severity and incidence irrespective of the genetic background of the cultivars, minimizing the chance of disease escape, which is a significant problem in field inoculation. An attempt to inoculate intact basal plates postharvest resulted in minimal disease development, suggesting that mechanical resistance was conferred by the dry outer layer of the basal plate. The high selection pressure conferred by the conidial inoculation method developed in this study can effectively screen FBR-resistant onion bulbs to replace an unreliable field screening. Concentrations of the conidia lower than 3 × 10 ⁵ spores/mL are recommended to detect subtle genetic differences in FBR resistance among the onion cultivars and their selected population.