Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.

Some broccoli (Brassica oleracea L. italic) accessions have purple sepals and cold weather would deepen the purple color, while the sepals of other broccoli lines are always green even in cold winter. The related locus or gene is still unknown. In this study, a high-density genetic map was constructed based on specific locus amplified fragment (SLAF) sequencing in a doubled-haploid segregation population with 127 individuals. And mapping of the purple sepal trait in flower heads based on phenotypic data collected during three seasons was performed. A genetic map was constructed, which contained 6694 SLAF markers with an average sequencing depth of 81.37-fold in the maternal line, 84-fold in the paternal line, and 15.76-fold in each individual population studied. In all of the annual data recorded, three quantitative trait loci (QTLs) were identified that were all distributed within the linkage group (LG) 1. Among them, a major locus, qPH.C01–2, located at 36.393 cM LG1, was consistently detected in all analysis. Besides this locus, another two minor loci, qPH.C01–4 and qPH.C01–5, were identified near qPH.C01–2, based on the phenotypic data from spring of 2018. The purple sepal trait could be controlled by a major single locus and two minor loci. The genetic map and location of the purple sepal trait of flower heads provide an important foundation for mapping other compound traits and the identification of the genes related to purple sepal trait in broccoli.

Black rot is a destructive disease that affects B. oleracea crops, causing significant losses to growers throughout the world. The purpose of this study was to screen out new sources resistant to Xanthomonas campestris pv. campestris race 4 (Xcc4) in 26 cauliflower and six related wild species, and to assess the inheritance of resistance. The results indicate that most of the tested accessions were susceptible or had intermediate resistance, except the Boc4601 (a cauliflower stable inbred line) and PI435896, UNICT5168, and UNICT5169 (wild accessions). Among them, UNICT5169 (Brassica montana) and PI435896 (Brassica balearica) showed the strongest resistance to Xcc4, with significantly lower disease index (DI), area of the infected part (AIP) and proportion of the infected part to the total leaf area (PTL) values. UNICT 5169 was selected as an Xcc4-resistant parent because of its relatively good cross seed-setting rate with cauliflower cultivars. F₁ hybrids were successfully produced between this wild resistant accession (UNICT 5169) and one susceptible cauliflower breeding line (Boc3202-4), indicating the potential transferability of this resistance to cauliflower. The results of the symptoms severity evaluation of the F₂ population indicate that Xcc4 resistance in UNICT5169 is a quantitative trait, which guides future resistance gene location and black rot resistance breeding.

Most broccoli cultivars or accessions exhibit green buds under appropriate growth conditions, which turn purple at cold temperatures. However, certain cultivars consistently maintain green buds both during normal growth and at cold temperatures. In this study, we used BSA-seq (bulked segregation analysis-sequencing), along with fine mapping and transcriptome analysis to identify a candidate gene (flavonoid 3′-hydroxylase, F3′H) responsible for reducing anthocyanin accumulation in the mutant GS and HX-16 broccoli (Brassica oleracea L. var. italica), which could retain green buds even at low temperatures. A 43-bp deletion was detected in the coding sequence (CDS) of the F3′H gene in HX-16 and the mutant GS, which significantly decreased F3′H expression and the accumulation of cyanidin and delphinidin in the mutant GS. Furthermore, the expression of F3′H was upregulated at low temperatures in the wild line PS. Our results demonstrated the efficacy of utilizing the 43-bp InDel (Insertion–Deletion) in predicting whether buds in B. oleracea L. will turn purple or remain green at cold temperatures across forty-two germplasm materials. This study provides critical genetic and molecular insights for the molecular breeding of B. oleracea and sheds light on the molecular mechanisms underlying the effect of low temperatures on bud color in broccoli.

Variations in the concentration of glucoraphanin (GRA) and glucoerucin (GER), as well as the corresponding breakdown products, isothiocyanates (ITCs) and nitriles, were investigated during the growth of broccoli sprouts. The concentrations of GRA and GER decreased sharply from 33.66 µmol/g to 11.48 µmol/g and 12.98 µmol/g to 8.23 µmol/g, respectively, after seed germination. From the third to the seventh day, both GRA and GER were maintained as relatively stable. The highest concentrations of sulforaphane (17.16 µmol/g) and erucin (12.26 µmol/g) were observed on the first day. Hereafter, the concentrations of nitrile hydrolyzed from GRA or GER were higher than those of the corresponding ITCs. Moreover, the ratio of sulforaphane to sulforaphane nitrile decreased from 1.35 to 0.164 from 1 d to 5 d, with a similar trend exhibited for erucin/erucin nitrile after 2 d. RNA-seq analysis showed that BolMYB28 and BolCYP83A1, involved in aliphatic glucosinolate (GSL) biosynthesis, remained largely unexpressed until the third day. In contrast, the genes operating within the GSL-myrosinase hydrolysis pathway were highly expressed right from the beginning, with their expression levels increasing significantly after the third day. Additionally, we identified two BolESPs and six BolNSPs that might play important roles in promoting the production of nitriles during the development of broccoli sprouts.

Broccoli is rich in glucosinolates (GSLs), secondary metabolites that contribute to both plant defense and human health. Optimizing the composition of major aliphatic GSLs is an important breeding objective, yet robust molecular markers for marker-assisted selection (MAS) remain limited. In this study, candidate gene-based kompetitive allele-specific PCR (KASP) markers were developed from conserved GSL biosynthesis genes, focusing on AOP2 and GSL-OH selected from 19 GSL-related genes. Marker–trait associations were evaluated in a natural broccoli population and further validated in an independent F₂ population. Among the tested markers, S101, located in AOP2, exhibited consistent genotype-dependent effects on GNA and PRO across both populations, supporting its stable predictive value. Receiver operating characteristic (ROC) analysis further confirmed strong classification performance of S101 for distinguishing high- and low-content genotypes of these traits in the F₂ population. In contrast, S074 and S035 showed population-dependent effects, with significant associations detected only in the natural population. Although association signals were reduced under mixed linear model (MLM) analysis with false discovery rate (FDR) correction, major loci identified under the general linear model (GLM) framework remained detectable. Overall, these results demonstrate the potential of candidate gene-based KASP markers for improving aliphatic GSL composition in broccoli through marker-assisted selection.