Recent Advances in Vegetable Genomics and Breeding Research

Vegetables are of critical importance to the human diet, providing the essential vitamins, minerals, and dietary fiber necessary for sustaining health [1]. In light of the rising global population and increasing demand for nutritious vegetables, there is an urgent need to enhance vegetable production, quality, and resilience to environmental challenges. Genomics and breeding research have emerged as powerful tools in achieving these objectives by unraveling the genetic bases of important traits and developing novel technologies and applications to breed new vegetable varieties with desirable characteristics.

This Special Issue, entitled “Vegetable Genomics and Breeding Research”, comprises nine insightful and original research and review articles that aspire to shed light on recent advances in understanding the genetic mechanisms behind quality and stress resistance traits in vegetables and the application of cutting-edge breeding methodologies for vegetable crops.

A key topic in this collection is the advance of modern vegetable breeding technologies, with a focus on ploidy manipulation, haploid technology, and male sterility, as well as their applications in vegetable breeding. Fomicheva et al. (2025) thoroughly reviewed genome doubling in vegetable crops and its potential use in obtaining doubled haploids, which have the potential to be used to produce polyploids and helping to overcome interspecific hybrid sterility and improve agricultural traits [2]. Deng et al. (2025) performed whole-genome identification of DMP-family genes in Solanaceous vegetables, identifying CaDMP8 (pepper) and SmDMP8 (eggplant) as potential targets for developing haploid induction lines, which is critical to accelerating the genetic improvement of Solanaceous crops [3]. Addressing the practical challenges of polyploidization in vegetable breeding, El-Mahrouk et al. (2025) investigated and validated effective morphological markers for the early identification of diploid and tetraploid black cumin (Nigella sativa) seedlings, which offers a cost-effective and accessible tool for polyploid breeding [4]. The use of male sterility has been recognized as an effective strategy for controlling cross-pollination and accelerating the development of hybrids. Chikh-Rouhou et al. (2025) reviewed the current status of molecular markers linked with male sterility and their regulation of genetic and molecular mechanisms in onions, and highlighted the significant role male sterility plays as a transformative tool facilitating efficient hybrid seed production [5].

Due to increasing consumer demand for high-quality, nutrient-dense fresh vegetables, improving the quality of vegetables is of great importance. Yang et al. (2025) identified BrC4H3, BrF3H1, and BrCHS1 as the key genes controlling the biosynthesis of purple leaf traits in pak choi, which provided the genetic basis for breeding anthocyanin-enhanced pak choi cultivars [6]. Moreover, increasing the resilience of vegetables to biotic and abiotic stress is another major focus due to growing demand from growers. For instance, Zhao et al. (2025) performed pan-genome analysis to identify the CsTRM gene family and analyze its expression patterns in response to abiotic and biotic stresses in cucumber. Their results indicate that CsTRM14 responds to salt stress, powdery mildew, gray mold, and downy mildew, while CsTRM21 plays a significant role in regulating abiotic and biotic stress resistance; findings that provide a foundation for the further exploration of the potential role TRMs may play in stress resistance in cucumbers [7]. Oble et al. (2025) revealed that SmPTI6 plays a significant role in the resistance of eggplant to Phytophthora capsica attacks, which insights will assist in the development of resistant eggplant cultivars [8]. Zhang et al. (2025) identified five hub regulatory genes that coordinate the defense response of watermelon against Fusarium oxysporum f. sp. niveum, which provided novel disease-resistant genes for breeding cultivars of watermelon resistant to Fusarium wilt [9]. In addition, Yuan et al. (2025) found that the transcription factor BrNAC19 positively regulates the heat stress response in Chinese cabbage by activating the antioxidant genes BrCSD1 and BrCAT2, thereby mitigating the accumulation of reactive oxygen species (ROS) under heat stress, which exhibited potential as target genes for increasing heat stress tolerance [10].

In conclusion, this Special Issue provides valuable insights into the molecular bases of important quality and resistance traits in vegetables, which underpin the implementation of new breeding technologies to facilitate the development of new cultivars. The development of multi-omics approaches, artificial intelligence, speed breeding, and molecular breeding technologies, along with their applications in vegetable breeding, will enhance the efficiency, precision, and adaptability of vegetable breeding in the future, which promises address the needs of consumers, growers, and the global climate challenge.