Breeding by Design: Advances in Vegetables

1. Introduction

As design breeding has been increasingly adopted in staple crops such as rice and maize, its application in vegetable crops is also rapidly expanding—driven by the continuous identification of functional genes and the completion of genome sequencing for numerous vegetable species. This Special Issue, “Breeding by Design: Advances in Vegetables, highlights recent progress in molecular marker development, genomic variation analysis, functional gene characterization, and genome editing technologies for vegetable crops, providing results that will further advance design breeding in this sector.

2. Regulation of Vegetable Quality from Appearance to Nutrition

Vegetable quality is a key determinant of commercial value, and its assessment involves both appearance-related attributes and nutritional value. Appearance quality traits, including size, shape, and color, directly influence consumers’ purchasing decisions, while nutritional components such as sugars, organic acids, and volatile metabolites further boost consumer satisfaction. To meet evolving consumer demands, researchers have been investigating how functional genes and environmental factors modulate vegetable quality, and accordingly been developing targeted strategies for breeding high-quality vegetable varieties.

Color is a critical aspect of vegetable appearance quality, and green-white color polymorphisms in many species are closely linked to chlorophyll metabolism. The transcriptome profiling of green-versus white-skinned radishes has enabled the identification of RsNAC134 as a key regulator, which modulates radish coloration by targeting the promoters of core genes in the chlorophyll degradation pathway (Contribution 1). Furthermore, in eggplant, the Gv1 locus governing green fruit skin was identified using BSA-seq technology combined with fine mapping. The candidate gene SmAPRR2-like was confirmed to be closely associated with chlorophyll biosynthesis in eggplant, and its mutation results in the white-skinned phenotype. Corresponding molecular markers were also developed to efficiently distinguish between green- and white-skinned eggplant accessions (Contribution 2). Two F₂ segregating populations were developed using the stay-green pepper mutant ‘TNX348’, and BSR-seq mapping enabled the identification of CaSGR1, a gene encoding a senescence-induced chloroplast-localized protein. A single SNP that causes premature translational termination was found to underpin both the stay-green phenotype and extended shelf life; accordingly, a co-segregating SNP marker was developed to facilitate the marker-assisted selection of improved pepper varieties [1].

Sugar content and flavor compounds are key determinants of vegetables’ intrinsic nutritional and sensory quality. In tomato, the plasma membrane-localized sucrose transporter SlSUT2 mediates sucrose influx into cells. SlSUT2 knockout was found to upregulate the sugar accumulation-related gene SlSTP1 while downregulating the sugar repressor genes SlCDPK26 and SlCDPK27, ultimately resulting in a marked increase in sugar content in tomato fruits (Contribution 3). Conversely, loss-of-function mutation in the phytoene synthase gene SlPSY1 reduces carotenoid accumulation and the levels of carotenoid-derived volatile flavor compounds (e.g., MHO and geranylacetone), while increasing flavonoid content and enhancing the expression of corresponding flavonoid pathway genes. Fine-tuning the expression level and pattern of SlPSY1 thus provides a viable strategy for improving multiple quality traits in tomato [2].

Environmental factors exert a profound influence on the growth, development, and nutritional quality of vegetables. Take alfalfa sprouts—a nutrient-dense, high-value vegetable—as an example: dark conditions promote hypocotyl elongation and increase soluble sugar content, whereas specific light spectra can further improve their overall quality. With respect to nutritional composition and antioxidant capacity, the 1R3B light regime (a red-to-blue light ratio of 1:3) is proven most suitable for the industrial-scale cultivation of alfalfa sprouts, effectively enhancing their quality (Contribution 4). Additionally, in grafted watermelon seedlings, far-red light (Fr) treatment activates auxin pathway genes and phytochrome-interacting factors (PIFs). This induction significantly promotes root growth of rootstocks and enhances vascular activity at the graft union, thereby shortening the graft healing period and improving overall seedling quality [3].

3. Identification of Regulatory Genes of Vegetable Stress Response

Plants encounter a wide range of biotic and abiotic stresses throughout their growth and development. Biotic stress stems from biological invaders such as pathogens and pests, whereas abiotic stress is triggered by adverse environmental factors including drought, high salinity, and extreme temperatures. In response to these stresses, plants activate stress-responsive genes and transcription factors, which in turn initiate adaptive defense mechanisms.

Drought stress affects plant growth, development and reproduction, making it a major constraint on agricultural productivity. The JmjC-domain-containing proteins regulate plant growth, development, epigenetic processes, flowering, and stress defense. Wu et al. utilized bioinformatics analysis to identify 23 JmjC-domain genes in tomato. The histone demethylase SlJMJ15 negatively regulates drought tolerance by suppressing ABA signaling genes, thereby establishing it as a promising target for breeding drought-tolerant varieties (Contribution 5).

In recent years, soil salinization, caused by irrational farming and fertilization practices, has emerged as a major stressor that severely constrains plant growth and diminishes crop yield. In eggplant, the expression of SmMYB39 peaked at 12 h after salt stress treatment, reaching a level approximately 50 times that of the control. In SmMYB39-silenced plants, a 12 h salt stress exposure resulted in more severe wilting and a survival rate decrease to approximately 50% that of the control. SmMYB39 is the first MYB transcription factor in eggplant demonstrated to positively regulate salt stress responses (Contribution 6).

High temperature stress is one of the major environmental factors that affect the growth and development of plants. SlWRKY3 has proved to be a crucial transcription factor in the tomato heat stress response, with its expression being upregulated approximately four-fold under heat stress. Overexpression of SlWRKY3 exhibited heat tolerance, along with diminished reactive oxygen species (ROS) accumulation, while knockout of SlWRKY3 showed the opposite behavior. SlWRKY3 directly binds to the promoters of the SlGRXS1 gene cluster and activates its expression, thereby enhancing ROS-scavenging capacity [4]. The bHLH transcription factor CsSPT acts as a positive regulator of thermotolerance in cucumber. Mutants deficient in CsSPT exhibit enhanced heat sensitivity, characterized by impaired photosynthetic capacity and elevated oxidative stress. By coordinating photosynthetic processes, hormone signaling pathways, and various heat-responsive transcriptional cascades, CsSPT orchestrates a sophisticated heat resistance regulatory network, rendering it a valuable target for breeding heat-tolerant cucumber cultivars [5].

Growth regulatory factors (GRFs) and growth-regulating interacting factors (GIFs) play pivotal roles in plant growth and responses to environmental stress. Through bioinformatic analysis and expression profiling, a total of 28 MeGRF genes distributed across 13 chromosomes and 5 MeGIF genes across 4 chromosomes were identified in cassava (Manihot esculenta Crantz). Compared with the control group, MeGRF28- or MeGIF4-silenced lines exhibited a 29% to 57% higher disease incidence. Protein interaction network analysis revealed that these two proteins may form a core GRF-GIF complex, which contributes to enhanced resistance of cassava to bacterial blight (Contribution 7).

Late blight, caused by Phytophthora infestans, is a devastating disease that causes substantial yield losses and severe economic damage in tomato production. Biocontrol strategies mediated by arbuscular mycorrhizal fungi (AMF) exhibit great potential for enhancing plant resistance to this disease. Zhou et al. discovered that AMF colonization enhances tomato resistance to late blight by activating miR319c, which cleaves its target gene TCP1. Overexpression of miR319c or silencing of TCP1 was shown to reduce lesions and enhance ROS scavenging. Furthermore, overexpression of miR319c maintained higher salicylic acid (SA) levels than the wild type both before and after P. infestans inoculation and significantly increased the SA content by 30% at the late stage of infection (5 dpi). miR319c not only regulated the content of SA but also indirectly modulated key genes in the SA signaling pathway by targeting TCP1, thereby systematically enhancing resistance to P. infestans in mycorrhizal tomato [6].

4. Genetic Basis and Heterosis Utilization for Enhancing Yield

Improving crop yield is the central goal of agricultural breeding and a crucial strategy for ensuring food security. This goal relies primarily on the continuous advancement of breeding technologies. Therefore, current research focuses on elucidating the genetic basis of yield, aiming to achieve precise manipulation and efficient utilization of heterosis through the identification of key genes and loci.

In pea breeding, understanding gene action and heterosis is essential for cultivar development. Yadav et al. conducted a diallel design, revealing that yield traits are predominantly governed by non-additive gene effects, thereby indicating the high potential of heterosis utilization for yield improvement. They identified ‘Aman’ and ‘P-1297-97’ as parental lines with superior general combining ability (GCA). Furthermore, specific cross combinations exhibited significant heterosis and specific combining ability (SCA), providing key parental resources and a theoretical foundation for high-yield breeding programs (Contribution 8). To investigate the genetic basis of yield-related heterosis in cabbage, Li et al. constructed two populations by crossing DH lines derived from the ‘01–20’ × ‘96–100’ hybrid with two maternal lines. They identified two key QTL clusters on chromosomes 2 and 3 from ‘01–20’, which significantly influenced yield-related heterosis. DH lines carrying these regions exhibited strong heterosis in hybridization, with candidate genes potentially involved in auxin response and carbohydrate metabolism, which provides crucial genetic loci and materials for high-yield hybrid breeding of cabbage [7].

5. Genome-Assisted Design Breeding

Genome-assisted breeding is a modern approach that leverages high-throughput sequencing and bioinformatics. It utilizes whole-genome data, genetic markers, and association analysis to enhance traditional breeding based on phenotypic selection while also enabling precise breeding through genotypic screening or editing of key genes.

Taro (Colocasia esculenta), a rhizome crop primarily propagated asexually, has accumulated substantial genetic diversity through frequent somatic mutations. Researchers have employed simplified genome resequencing to identify SNP loci in taro, leading to the successful selection of 27 high-efficiency SNP markers using PARMS-SNP technology. These markers were used to construct DNA fingerprinting profiles, which classified 72 taro samples into six evolutionary groups. The results largely aligned with phenotypic clustering patterns, providing valuable insights for germplasm identification, molecular breeding, and the development of new cultivars (Contribution 9).

Brassica contains a variety of edible vegetables, oil crops, and forage plants. To facilitate genome editing in these crops, researchers systematically optimized a protoplast transient gene expression system (PTGE). This optimized system allows rapid validation of CRISPR vector activity and efficient screening of target sites, with transfection efficiency exceeding 50%. It is thus well positioned to accelerate the widespread application of genome editing in Brassica breeding programs [8]. Cabbage (Brassica oleracea), a key species of the genus Brassica, includes a diverse range of vegetable types. Using full-length transcriptome sequencing, researchers re-annotated the JZS genome (designated JZSv3), which enabled the enrichment of untranslated regions (UTRs) and improved the annotation of alternative splicing (AS) events. JZSv3 further revealed that numerous known genes undergo AS, providing valuable genomic resources to advance design breeding and the development of cabbage varieties [9].

In summary, with the in-depth identification of functional genes, increasing refinement of multi-omics maps, and deeper integration of artificial intelligence, vegetable design breeding is poised to enter a new era. This progress will enable breeders to more efficiently develop ideal varieties with integrated traits of high yield, superior quality, and stress tolerance. We are confident that design breeding technology will continue to advance and play a pivotal role in safeguarding food security and advancing sustainable agricultural development.