Recent progress in DNA marker-assisted selection for vegetable breeding in Japan

Abstract

The development of new cultivars exhibiting high levels of disease resistance and superior quality is critical for vegetable production. Recent advances in genomics and DNA sequencing technologies have facilitated the identification of sequence variants associated with specific phenotypes. This has enabled the development of novel and improved DNA markers for integration into marker-assisted selection (MAS). The application of MAS has significantly enhanced the efficiency of stacking loci responsible for disease resistance and quality characteristics. This paper provides an overview of recent research findings related to DNA markers and their applications in breeding in Japan, focusing primarily on vegetables from Brassicaceae, Solanaceae, Cucurbitaceae, and Allium, as well as strawberries.

Introduction

Vegetables are essential sources of vitamins, minerals, fibers, and other nutrients that maintain a healthy diet. These plants exhibit considerable diversity in biological characteristics, such as reproductive systems (autogamy or allogamy, with self-incompatibility in some cases), generation length, ploidy level, and genome size. Consequently, the development of comprehensive reference genomes and DNA markers has progressed unevenly across vegetable species.

In Japan, the total value of agricultural production was 9.4953 trillion yen, of which vegetables accounted for 2.3243 trillion yen (24.5%) (Ministry of Agriculture, Forestry and Fisheries (2023), https://www.maff.go.jp/j/tokei/kouhyou/nougyou_sansyutu/index.html). The production values of major vegetables were as follows: tomatoes (231.1 billion yen), strawberries (205.5 billion yen), bunching onions (150.3 billion yen), cucumbers (141.3 billion yen), onions (127.3 billion yen), cabbages (100.2 billion yen), eggplants (82.5 billion yen), spinach (78.8 billion yen), lettuce (77.8 billion yen), daikon radishes (77.4 billion yen).

The total demand for vegetables has declined by about 10% over the past two decades. At the same time, demand has gradually shifted from household consumption to processing and food service use, which now accounts for approximately 60% of total vegetable demand. In response to this trend, vegetables are increasingly expected to meet requirements for year-round stable supply and consistent quality.

Vegetable production in Japan is influenced by several distinctive agricultural conditions that present current challenges requiring consideration. These include intensive cultivation on limited farmland, continuous cropping practices, and a rapidly aging farming population. In addition, vegetable production in Japan is expected to respond to the growing demand for processed products and increasing consumer interest in health-promoting traits. These factors have influenced breeding priorities.

Climate change, particularly rising temperatures, has introduced uncertainty in vegetable production conditions. Developing cultivars with resistance to disease and pests, tolerance to heat stress, and adaptability to fluctuating conditions is essential for sustainable production. Bolting in cabbage, radish, and onion is an important breeding trait because it is caused by specific temperature and day-length conditions, resulting in reduced product quality. The demand for a year-round supply of strawberries has expanded breeding efforts, including the development of everbearing cultivars.

Consumer preferences favor vegetables such as tomatoes, melons, and strawberries with superior taste attributes, such as high sugar content and excellent flavor. Growing interest in health has introduced nutritional and functional traits as a new breeding objective. This has prompted the development of cultivars that can accumulate specific beneficial components.

In fruit-bearing vegetables, fruit set occurs through insect pollination or the application of fruit-setting agents. Temperature extremes can reduce insect activity and lead to poor fruit set. Additionally, there is an increasing demand to reduce the labor required for applying fruit-setting agents. To address these issues, parthenocarpic cultivars that set fruit without pollination are being developed for eggplants, tomatoes, sweet peppers, and melons.

In Japan, the development and supply of vegetable cultivars are primarily led by private seed companies, although public research institutions and universities also contribute to the breeding of selected vegetables. Most vegetables currently distributed in the market are F₁ hybrids, reflecting the emphasis on stable quality and yield. As a result, detailed information on commercially developed cultivars is often not publicly disclosed. In this article, we summarize DNA markers commonly used in major vegetable crops (Table 1), review leading cultivars developed through genetic analysis and MAS in Brassicaceae, Solanaceae, Cucurbitaceae, Allium species, and strawberries, examine the current status and challenges of vegetable breeding in Japan.

Table 1.DNA markers used in marker-assisted breeding in vegetables

Species	Trait	Locus/gene	Chromosome/Linkage group	References
Brassica rapa	Clubroot resistance	Crr2	A01	Suwabe et al. 2003
		CRb	A03	Piao et al. 2004, Kato et al. 2012, 2013
		Crr1a	A08	Suwabe et al. 2003, Hatakeyama et al. 2013
		Crr1b	A08	Hatakeyama et al. 2013
	Late bolting	BrFLC2, BrFLC3	A02, A03	Kitamoto et al. 2014, Kitamoto et al. 2017
Raphanus sativus	Glucosinolate composition	GRS1	R01	Ishida et al. 2015, Kakizaki et al. 2017
Solanum lycopersicum	ToMV resistance	Tm-1	Chr. 2	Ohmori et al. 1995
		Tm-2/Tm-22	Chr. 9	Shi et al. 2011, Panthee et al. 2013
	TYLCV resistance	Ty-1/Ty-3/Ty-3a	Chr. 6	Verlaan et al. 2013, Koeda and Kitawaki 2024
		Ty-2	Chr. 6	Yamaguchi et al. 2018, Kim et al. 2020
	TSWV resistance	Sw-5	Chr. 9	Tong et al. 2023
	Fusarium wilt resistance	I-1	Chr. 11	Sarfatti et al. 1991, Catanzariti et al. 2017
		I-2	Chr. 11	Simons et al. 1998
		I-3	Chr. 7	Catanzariti et al. 2015
	Fusarium crown and root rot resistance	Frl	Chr. 9	Devran et al. 2018
	Leaf mold resistance	Cf-4/Cf-9	Chr. 1	Truong et al. 2011, Thomas et al. 1997
		Cf-2/Cf-5	Chr. 6	Dickinson et al. 1993, Dixon et al. 1998
	Verticillium wilt resistance	Ve1	Chr. 9	Kawchuk et al. 2001
	Corky root rot resistance	py-1	Chr. 3	Doganlar et al. 1998
	Gray leaf spot resistance	Sm	Chr. 11	Yang et al. 2022
	Powdery mildew resistance	Ol-1	Chr. 6	Bai et al. 2005, Lian et al. 2022
	Late blight resistance	Ph-3	Chr. 9	Zhang et al. 2013
	Bacterial wilt resistance	Bwr-6, Bwr-12	Chr. 6, Chr. 12	Kim et al. 2018
	Bacterial canker resistance	Rcm6	Chr. 6	Abebe et al. 2022
	Root-knot nematode resistance	Mi-1.2	Chr. 6	Furumizu and Sawa 2023
	Parthenocarpy	pat-2	Chr. 4	Nunome et al. 2013
		pat-k	Chr. 1	Takisawa et al. 2017
Solanum melongena	Fusarium wilt resistance	Fm1	Chr. 2	Miyatake et al. 2016
	Parthenocarpy	Cop3.1, Cop8.1	Chr. 3, Chr. 8	Miyatake et al. 2012
		pad-1	Chr. 3	Matsuo et al. 2020
	Prickleless	pl	Chr. 6	Miyatake et al. 2020, Li et al. 2024
		PE	Chr. 6	Zhang et al. 2024
Capsicum annuum	PMMoV resistance	L3	Chr. 11	Sugita et al. 2004
		L4	Chr. 11	Matsunaga et al. 2003
	Root-knot nematode resistance	N	Chr. 9	Wang et al. 2009
		Me1	Chr. 9	Wang et al. 2018a
		Me3/Me7	Chr. 9	Liu et al. 2023
	TSWV resistance	Tsw	Chr. 10	Jahn et al. 2000, Moury et al. 2000
	Phytophthora blight resistance	phyt-1, phyt-2, phyt-3	LG7, LG1, LG15	Sugita et al. 2006
			LG15, LG3	Minamiyama et al. 2007
		CaPhyto	Chr. 5	Wang et al. 2016
		Pc5.1	Chr. 5	Bongiorno et al. 2023
Cucumis sativus	downy mildew, anthracnose, angular leaf spot resistance	CsSGR	Chr. 5	Wang et al. 2018b
	powdery mildew resistance	CsMLO1, CsMLO8, CsMLO11	Chr. 1, Chr. 5, Chr. 6	Berg et al. 2017, Dong et al. 2024
	target leaf spot resistance	cca-3	Chr. 6	Wen et al. 2015
	ZYMV resistance	VsVPS4	Chr. 6	Amano et al. 2013
	anthracnose resistance	An5	Chr. 5	Fitriyah et al. 2024
	MYSV resistance	Sws	Chr. 3	Sugiyama et al. 2015
Cucumis melo	CCYV resistance		Chr. 1	Kawazu et al. 2018
	Fusarium wilt resistance	Fom-1, Fom-2	Chr. 11	Oumouloud et al. 2012, 2015
	MNSV resistance	nsv	Chr. 12	Morales et al. 2005, Nieto et al. 2006
	powdery mildew resistance	PMQU2.1, PMQU12.1	Chr. 2, Chr. 12	Fukino et al. 2008, Diaz et al. 2015
	flesh color	CmOr	Chr. 9	Tzuri et al. 2015
Cucurbita spp.	powdery mildew resistance	Pm-0	Chr. 3	Sabharwal et al. 2024
Citrullus lanatus	anthracnose resistance	Cla001017	Chr. 8	Jang et al. 2019, Matsuo et al. 2022
	powdery mildew resistance	ClaPMR2	Chr. 2	Mandal et al. 2020
Allium cepa	CMS	coxI, orf725	mtDNA	Kim et al. 2009
Allium fistulosum	low pungency		2A	Tsukazaki et al. 2012
	bolting time		1A, 2A	Wako et al. 2016
Fragaria × ananassa	flowering habit			Honjo et al. 2016, 2020, Saiga et al. 2023
	anthracnose resistance			Enoki et al. 2014, Iimura et al. 2012
	Fusarium wilt resistance			Iimura et al. 2021
	powdery mildew resistance			Koishihara et al. 2016
	fruit flesh color			Yamakawa et al. 2025
	fruit maturity			Yamakawa et al. 2025

Brassicaceae vegetables

Brassicaceae includes widely cultivated vegetables like cabbage, Chinese cabbage, and radish. Most Brassicaceae vegetables require vernalization for bud differentiation, and some require vegetative growth for several weeks to acquire vernalization competence. Therefore, the generation time is relatively long. MAS can eliminate undesirable plants early and is indispensable for Brassicaceae breeding. We developed a clubroot resistant cultivar using DNA marker selection. Clubroot is a soil-borne disease causing significant damage across Japan and is difficult to control. Additionally, we developed DNA markers and cultivars for late bolting in Chinese cabbage, and secondary metabolites in Japanese radish.

Clubroot is a severe soil-borne disease of Brassicaceae caused by the protozoan Plasmodiophora brassicae Woronin. Resting spores in the soil survive long term and are difficult to control through crop rotation, agrochemicals, or other agricultural practices. Resistant cultivars are considered most effective for controlling clubroot. Among the more than 20 clubroot resistance (CR) genes or loci identified in Brassica rapa (Hasan et al. 2021), Crr1, Crr2 and CRb are mainly used for breeding in Japan. The two loci derived from the European turnip ‘Siloga’, Crr1 and Crr2, confer resistance to pathotype groups 1, 2, and 4, especially when combined (Hatakeyama et al. 2004, Suwabe et al. 2003). Crr1 is composed of a major gene Crr1a (encoding a TIR-NB-LRR protein) and a gene Crr1b with minor effects (Hatakeyama et al. 2013, Suwabe et al. 2012). CRb, which is identical to CRa, confers resistance to pathotype groups 3 (Hatakeyama et al. 2017, Kato et al. 2012, 2013, Piao et al. 2004, Ueno et al. 2012). Chinese cabbage F₁ cultivar ‘Akimeki’ was developed using marker-assisted backcrossing. ‘Akimeki’ harbors Crr1, Crr2, and CRb, confers resistance to all four pathotype groups. B. rapa has also been used as CR donor in the breeding of amphidiploid Brassica crops. CR rapeseed cultivar ‘CR nanashikibu’ harboring Crr1 and Crr2 was developed using marker-assisted backcrossing with the resynthesized Brassica napus by interspecific crossing between CR Chinese cabbage line ‘PL9’ and a cabbage cultivar (Kawasaki et al. 2021). The application of MAS has enabled the efficient and precise transfer of CR genes, thereby accelerating the breeding of not only Chinese cabbage cultivars but also amphidiploid rapeseed cultivars.

For Brassicaceae vegetables, bolting time is a critical breeding trait, particularly for cultivars harvested from spring to early summer. Premature bolting in an inappropriate season severely affects harvest quality. The bolting pathway in Brassicaceae plants has been well characterized in Arabidopsis (Niu et al. 2024). FLOWERING LOCUS C (FLC), encodes a MADS-box protein, represses bolting in a dose-dependent manner by binding to the regulatory elements of the floral inducer genes FT and SOC1 (Helliwell et al. 2006, Michaels and Amasino 1999). This pathway is conserved across Brassicaceae species, and FLC function loss results in early flowering (Su et al. 2018). Expression of FLC is suppressed by prolonged low temperatures. Continuous FLC expression that does not respond to low temperatures is known to delay bolting. Large insertions in the first introns of BrFLC2 and BrFLC3 in Chinese cabbage (B. rapa L. ssp. pekinensis), homologs of Arabidopsis FLC, prevent FLC suppression and maintain bolting inhibition (Kitamoto et al. 2014). DNA markers detecting this insertion are used in late bolting breeding programs. The Chinese cabbage F₁ cultivar ‘ITOSAI No. 1’, selected for late bolting BrFLC2 and BrFLC3 alleles, demonstrates the most robust late bolting among commercial cultivars (Kitamoto et al. 2023). In spring cultivation, heating has traditionally been used to prevent bolting caused by exposure to low temperatures. However, ‘ITOSAI No. 1’ exhibits a high vernalization requirement for bolting, allowing cultivation without the need for heating.

Glucosinolates (GSLs) are secondary metabolites in Brassicaceae vegetables that contribute to odor and pigmentation of harvested and processed products (Ishida et al. 2014). Glucoraphasatin, the primary GSL in radishes (Raphanus sativus L.), is responsible for the distinct smell and yellow color of Takuan-zuke (Takahashi et al. 2015). The GSL composition of radish has been uniform, with cultivars containing high glucoraphasatin levels. However, screening of radish genetic resources revealed a mutant where glucoerucin was the dominant GSL (Ishida et al. 2015). Genetic analysis revealed that this strain carries a mutation in GLUCORAPHASATIN SYNTHASE 1 (GRS1), the enzyme that converts glucoerucin into glucoraphasatin (Kakizaki et al. 2017). Radish plants homozygous for the defective GRS1 allele exhibit minimal glucoraphasatin accumulation. Using this defective allele of GRS1, it is possible to modify the GSL biosynthetic pathway in radishes, enabling breeding of cultivars lacking characteristic odors and pigments. Developing a DNA marker to detect GRS1 mutations will enable the rapid breeding of radish cultivars without glucoraphasatin production, eliminating the need for GSL analysis. Using these DNA markers, several F₁ cultivars without glucoraphasatin have been developed since 2015. One cultivar, ‘Sarah White’, has high dry matter content in roots, making it suitable for processed ingredients like grated daikon radish (daikon-oroshi) and dried strips (kiriboshi-daikon) (Ishida and Morimitsu 2020). Given its non-discoloring and odorless properties, development of glucoraphasatin-free cultivars for various processing applications is expected to continue.

Solanaceae vegetables

Solanaceae includes important vegetables like tomatoes (Solanum lycopersicum L.), eggplants (Solanum melongena L.), and sweet peppers (Capsicum annuum L.). In Japan, vegetables grown in open fields during spring/summer and are forced from autumn to summer, enabling year-round supply. Solanaceae vegetables have been bred in Japan for a long time with private seed companies and public institutions have developed many excellent cultivars.

As listed in Table 1, tomatoes face various pathogens, including viruses, fungi, and bacteria, and resistance genes have been studied using DNA markers. According to private seed company catalogs, these characteristics are actively introduced. Resistance to Tomato yellow leaf curl virus (TYLCV) is the most significant viral challenge. TYLCV resistance gene 1 (Ty-1) is widely used for TYLCV-resistant breeding in Japan, and resistant cultivars have been developed by Japanese seed companies. Koeda and Kitawaki (2024) used DNA marker analysis to reveal the introduced genes. Although MAS usage for cultivars was not explicitly stated by private seed companies, multiple companies developing multiple resistant cultivars with the same genes suggests that DNA markers were used.

Although Tomato mosaic virus (ToMV) resistance is an essential trait, ToMV resistance gene 2² (Tm-2²) shows stable resistance in various races, which can be addressed using the markers currently in use (Koeda and Kitawaki 2024, Verlaan et al. 2013).

Root-knot nematodes resistance is another important trait. The root-knot nematode resistance gene Mi-1.2 is widely used in most tomato cultivars (Furumizu and Sawa 2023). Nematodes bypassing this resistance gene are emerging as threats (Marques de Carvalho et al. 2015).

Bacterial diseases pose a major threat to Solanaceae vegetable production. Among them, bacterial wilt, caused by Ralstonia solanacearum, is one of the most serious diseases. The most well-known resistance quantitative trait loci (QTLs) are bacterial wilt resistance on chromosomes 6 (Bwr-6) and 12 (Bwr-12) (Genin and Denny 2012). Even when these two QTLs are introduced, the resistance of current rootstock cultivars falls short of the desired level, suggesting multiple genes are involved and identifying causative genes is challenging. Attempts to introduce resistance genes into rootstock cultivars have resulted in cultivars with various levels of resistance to bacterial wilt.

There are examples of selection markers for resistance genes in sweet peppers. The most common application of MAS is breeding for resistance to tobamoviruses, including Pepper mild mottle virus (PMMoV). Four resistance genes, L¹, L², L³, and L⁴, have been identified, conferring resistance to pathotypes P₀, P₁, P_1,2, and P_1,2,3, respectively (Matsunaga et al. 2003). Recently developed cultivars have specified resistance gene types, suggesting marker utilization.

This provides examples of disease resistance-selective markers in Solanaceae vegetables. We have introduced examples of viral resistance. However, when breeding Solanaceae vegetables using viral resistance genes, an important issue must be considered. In Solanaceae vegetables, grafting onto rootstocks is common to confer resistance against soil-borne diseases. When using rootstocks, if scion and rootstock have different resistance genotypes, the graft interface may exhibit hypersensitivity reactions owing to the resistance response to viruses, leading to plant death. Therefore, identifying resistance gene types using markers is important in breeding, not only for conferring resistance but also for avoiding graft incompatibility. This eliminates labor-intensive inoculation of multiple standard viruses, improving breeding efficiency.

Another important trait is the conferral of labor-saving properties. We introduce parthenocarpy, extensively studied in tomato and eggplant. These characteristics freed farmers from regular fruit-setting agent treatment. Since the causative genes, parthenocarpic fruit 2 (pat-2) and k (pat-k), have been isolated and markers published (Nunome et al. 2013, Takisawa et al. 2018), their use is expected to increase to alleviate labor shortages. In eggplant, the effect of parthenocapy is more pronounced because fruits develop singly rather than in clusters like tomatoes. Many cultivars developed in Japan recently exhibit parthenocarpy. The first research on parthenocarpy in Japan used the parthenocarpic eggplant cultivar ‘Talina’ from Europe. With DNA marker development advancement in eggplant, research progressed rapidly, leading to two highly effective QTLs, controlling parthenocarpy 3.1 (Cop3.1) and 8.1 (Cop8.1) (Miyatake et al. 2012), which are utilized in the breeding parthenocarpic cultivars, such as ‘YAMAGATA N 1GO’, developed by the National Agriculture and Food Research Organization (NARO) and Yamagata Prefecture. The parthenocarpic gene, parental advice-1, found in cultivar, ‘PC Chikuyo’ (Takii & Co., Ltd.), exhibits highly stable parthenocarpy as a single factor and has been introduced into commercial cultivars, leading to cultivar replacement in major production areas. This gene has been isolated (Matsuo et al. 2020) and can be introduced into any genetic background.

The absence of prickles on calyxes, stems, and leaves, is a desirable trait in eggplant, contributing to improved handling efficiency and can be selected using a DNA marker (Miyatake et al. 2020). The development of new prickleless eggplant cultivars has been reported, and the use of this DNA marker is expected to facilitate further breeding.

Cucurbitaceae vegetables

Cucurbitaceae vegetables, including cucumber (Cucumis sativus L.), melon (Cucumis melo L.), squash (Cucurbita spp.), and watermelon (Citrullus lanatus (Thunb.) Matsum. et Nakai), are cultivated in open fields from spring to autumn, and in greenhouses throughout the year in Japan. Diseases have caused major problems, reducing yield and fruit quality. Genetically conferred host resistance is ideal for overcoming disease control problems worldwide. The development of resistant cultivars is a primary objective of modern breeding programs. DNA markers are widely used for disease resistance breeding in Japanese Cucurbitaceae vegetables. Traits for high fruit quality and labor-saving cultivation are important, and genetic analysis and DNA marker development have been conducted in Japan.

The whole-genome sequence of cucumbers was first reported in 2009 (Huang et al. 2009), and various cucumber lines have been resequenced. A high-grade genome reference of ‘Tokiwa’, a Japanese old cultivar, was reported in 2025 (Seiko et al. 2025). Numerous genetic studies have identified resistance genes and loci in various wild and cultivated cucumbers (Wang et al. 2020).

Major fungal and oomycete diseases infecting cucumber cause significant yield losses in Japan. These include powdery mildew (PM), mainly caused by Podosphaera xanthii; downy mildew (DM), caused by Pseudoperonospora cubensis; target leaf spot (TLS) caused by Corynespora cassiicola; and anthracnose (AR), caused by Colletotrichum orbiculare. Cucumber is susceptible to soil-borne fungal diseases like Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. melonis. However, cucumbers are commonly grafted onto squash in Japan; soil-borne diseases resistance is not prioritized. Angular leaf spot (ALS), caused by Pseudomonas syringae, is a bacterial disease that is a major problem in the cucumber-producing areas of Japan. Additionally, various viral diseases caused by Cucumber mosaic virus (CMV), Zucchini yellow mosaic virus (ZYMV), Melon yellow spot virus (MYSV), and Cucurbit chlorotic yellows virus (CCYV) have increased in recent years.

Genetic mapping studies for resistance to PM, DM, AR, ZYMV, and MYSV have been conducted in Japan, identifying several resistance loci (Amano et al. 2013, Fitriyah et al. 2024, Fukino et al. 2013, Sugiyama et al. 2015, Yoshioka et al. 2014). Genetic analyses of fruit shape and texture traits (firmness and crispness) have been conducted (Shimomura et al. 2017, 2021), and DNA polymorphisms near QTLs could be used as DNA markers in breeding.

Many major diseases in melons are similar to those in cucumbers with some differences. Unlike cucumbers, melons in Japan are almost unaffected by TLS and relatively unaffected by DM and AR. FW resistance is crucial for developing melon rootstock cultivars. The whole-genome sequence of melon was reported in 2012 (Garcia-Mas et al. 2012), and a high quality genome reference of ‘Earl’s Favorite Harukei 3’, was reported in 2020 (Yano et al. 2020). This genomic information has facilitated genetic mapping and DNA marker development. Similar to cucumber, MAS has been commonly adopted in melon breeding. The following are important DNA markers and examples of disease-resistant cultivars recently developed using DNA markers in Japan.

The melon cultivars of ‘Earl’s Aporon’ series with CCYV resistance were developed through MAS using simple sequence repeat (SSR) markers in 2024 (Kawazu et al. 2024). CCYV was first reported in Japan and is transmitted by the sweet potato whitefly, Bemisia tabaci (Gyoutoku et al. 2009). I-10 (JP 138332) has been reported resistant to CCYV (Okuda et al. 2013) and was crossed with ‘Earl’s Favorite Harukei No. 3’ to develop the ‘Melon Chukanbohon Nou 5 Go’, with CCYV resistance (Sugiyama et al. 2019). QTL analysis using I-10 identified one locus on chromosome 1, and SSR markers linked to the resistance gene were developed (Kawazu et al. 2018). ‘Melon Chukanbohon Nou 5 Go’ was crossed with Earl’s Favorite type cultivars, and backcrossing introduced the resistance genes using MAS and CCYV resistance tests. The CCYV resistance to I-10 is recessive; therefore, phenotypic identification is impossible in individuals heterozygous for resistance genes. MAS has been effectively used in backcross breeding to develop these cultivars.

The genes Fom-1 and Fom-2 confer resistance to FW caused by races 0 and 1, and 0 and 2, respectively (Oumouloud et al. 2012, 2015). The nsv gene confers resistance to MYSV (Morales et al. 2005, Nieto et al. 2006), and PMQU2.1 and PMQU12.1 confer resistance to PM caused by P. xanthii pxA and pxB strains (Diaz et al. 2015, Fukino et al. 2008). DNA markers that identify fruit flesh color (the gene CmOr) have been used (Tzuri et al. 2015). Genetic analyses of parthenocarpy and pistil-bearing flowers on the main stem have been conducted (Nashiki et al. 2023, https://doi.org/10.1101/2023.02.16.528896). DNA polymorphisms near these QTLs have been used or could be used as DNA markers in melon breeding in Japan.

Among Cucurbitaceae vegetables, squash (especially C. maxima) and watermelon are also important in Japan. Genomic information for these crops has accumulated, and genetic analyses of disease resistance have progressed. Major diseases of squash include PM, gummy stem blight, phytophthora rot, and mosaic diseases, such as CMV, ZYMV, and Watermelon mosaic virus. Disease resistance studies have focused on C. moschata and C. pepo, but not C. maxima, which is the most important species in Japan. The major PM resistance locus (Pm-0) in several C. moschata and C. pepo cultivars were introduced from a wild relative by interspecific hybridization long ago. The location of Pm-0 and candidate genes have been reported for each species (Sabharwal et al. 2024). A Japanese seed company patented a DNA marker for PM resistance in C. maxima and developed a new PM-resistant cultivar. The source of the resistance gene is unclear; however, resistance may be conferred by the above or a homologous gene. Although several DNA markers exists for C. pepo and C. moschata, a few reports cover C. maxima.

Common diseases in Japanese watermelon fields include AR, PM, and CCYV. Genetic analyses were conducted for AR and PM resistance. Race differentiation exists for AR (races 1 and 2 appear are most common). A non-synonymous single nucleotide polymorphism (SNP) in Cla001017, encoding a coiled-coil nucleotide binding site leucine-rich repeat (CC-NBS-LRR) protein, confers strong resistance to race 1 (Jang et al. 2019). This mutation is conserved among cultivars resistant to race 1 (Matsuo et al. 2022), including the commercial cultivars in Japan. No promising source was found in race 2.

Most improvements in Cucurbitaceae vegetables rely on conventional breeding methods. The superiority of the current cultivars is a testament to the success of these methods. However, there are several problems with this approach, such as being time-consuming and less precise, particularly when aiming to improve complex traits governed by multiple QTLs. Genetic analyses of useful traits of Cucurbitaceae vegetables have been conducted in Japan to address this issue. Several effective sources of resistance against major diseases have been discovered, and effective DNA markers for resistance have been developed (Table 1). Further discovery of useful gene sources and establishment of a MAS system should progress in the future, leading to the development of new cultivars with multiple disease resistance and other favorable agronomic traits.

Allium vegetables

Conventional breeding of Allium vegetables takes many years because these are annual or biennial. Therefore, the development of practical DNA markers can reduce the effort required for breeding. However, genome research has made little progress until approximately 2020 because of their large genome size (Ricroch et al. 2005), the outcrossing of plants, and their proneness to inbreeding depression. Thus, most developments have been conducted using conventional selection rather than DNA marker selection.

Even in such a situation, analyses have been conducted to develop DNA markers linked to the traits of vegetables of the Allium genus using bulb onions and shallots, where it is possible to produce genetically fixed doubled haploids and a complete set of Allium fistulosum L.- Allium. cepa monosomic addition lines (MALs) (Abdelrahman et al. 2015, Shigyo et al. 1996) as materials. MALs are strains in which one chromosome from shallots has been added to the Japanese bunching onion, and the expression of traits from each shallot chromosome makes it possible to perform genetic analysis of anthocyanin and flavonoid production in the leaf sheath (Shigyo et al. 1997) and rust resistance traits (Wako et al. 2015). A high-density linkage map was constructed from the expressed gene information for each chromosome obtained using these MALs and the F₂ population between the doubled haploid bulb onion and doubled haploid shallot. Information on these expressed genes has been compiled in AlliumTDB (https://alliumtdb.kazusa.or.jp/) (Fujito et al. 2021), and later effectively utilized in the analysis of the whole genome sequence of bulb onions and the development of chromosomal markers for useful traits. A research group centered at Wageningen University and Research succeeded in linking the genome information of doubled haploid bulb onions into a pseudomolecule for each chromosome, and contributed to verifying the validity of the sequence using this information as an anchor marker (Finkers et al. 2021).

Additionally, a DNA marker set was developed in bulb onions to efficiently perform linkage analysis of the entire chromosome (Sekine et al. 2022). It is possible to develop DNA markers linked to desired traits efficiently by utilizing this DNA marker set. At the time, there was no chromosome-level reference genome assembly; therefore, Sekine et al. (2022) comprehensively examined the sequence information of expressed genes in the leaves of two cultivars that differed in traits such as bulb size and identified expressed genes whose sequences differed between the cultivars. Next, by utilizing the information on expressed genes for each chromosome mentioned above, they selected expressed genes such that they were uniformly distributed across the entire chromosome and developed DNA markers that could be used to analyze DNA polymorphisms between cultivars.

Bulb onion genomic information has been used to create DNA markers and linkage maps for Japanese bunching onions. In Japanese bunching onions, markers linked to multiple traits have been developed through QTL analysis, reducing the labor required for selecting traits that are time-consuming and labor-intensive to investigate by using markers. DNA markers that identify low pungency have been developed for Japanese bunching onions (Tsukazaki et al. 2012), because it is difficult to directly quantify sulfur-containing compounds, which are the pungent components of Japanese bunching onions, and conduct sensory tests at a large scale. The markers can only be used with some breeding materials, and that low-pungency QTLs are homozygous in the parental lines of F₁ cultivars. The cultivars distinguishable by these markers are limited to the specific cultivars used in each test; therefore, it is desirable that marker development becomes available for a greater number of cultivars in the future.

DNA markers have been developed to assess the bolting time of Japanese bunching onions (Wako et al. 2016). In Japan, bunching onion flower bolts from spring to early summer and late-bolting cultivars are in high demand to prevent the loss of commercial value. When the main QTL for late bolting is homozygous, the bolting date is delayed compared to when it is heterozygous or when it does not have QTL for late bolting.

The number of cultivars developed using these markers for breeding Allium vegetables is limited. It is important to provide markers linked to more important traits and develop markers that can be used for a wide range of breeding materials in a simple and easy-to-use manner to increase the efficiency of MAS. In recent years, the development of long-read sequencing technologies has enabled the construction of high-accuracy genomes at a low cost, even for crops with large genome sizes, leading to the release of reference genomes for three species of Allium plants (Liao et al. 2022). The development of DNA markers is expected to accelerate as it has become easier to develop them using genomic information.

Strawberry

More than 90% of strawberry fruits are produced from winter to spring by forcing culture of June-bearing cultivars. However, because strawberries are in demand throughout the year, everbearing cultivars, which can bear fruit in summer and autumn when June-bearing cultivars do not bear fruit under natural conditions, are used for fruit production. Because cultivation continues for a long period of time, pest control is an important issue. Therefore, important breeding targets for strawberries include flowering characteristics, such as early/late flowering and everbearing, which affect the harvest period, disease resistance, yield characteristics, and fruit traits, such as flavor, color, firmness, and shape.

The use of DNA markers is expected to improve strawberry breeding efficiency. However, cultivated strawberries possess a highly heterozygous octoploid genome (2n = 8x = 56, Bringhurst 1990, Edger et al. 2019, Kunihisa 2011), and this complex genome structure has hindered the construction of comprehensive reference genome sequences and the development of DNA markers linked to agronomically significant traits.

DNA markers have been developed in Japan for agriculturally important qualitative traits, such as the everbearing flowering trait (Honjo et al. 2016, 2020, Saiga et al. 2023), anthracnose resistance (Enoki et al. 2014, Iimura et al. 2012), Fusarium wilt resistance (Iimura et al. 2021) and PM race 0 resistance (Koishihara et al. 2016), where the presence of major genes is suggested by phenotypic segregation patterns. Various breeding programs in Japan are starting to use these markers, and the development of excellent breeding materials is progressing (Saido et al. 2024).

Recent advances in genome sequencing technology and analysis protocols, such as long-read sequencing techniques, have yielded comprehensive reference genome sequences and high-quality haplotype-phased genomes of octoploid strawberries. (Edger et al. 2019, Han et al. 2025, Hirakawa et al. 2014, Isobe et al. 2020, Jin et al. 2025, https://doi.org/10.1101/2021.11.03.467115). In addition to these precedents, the reference sequence for one of the major cultivars in Japan, i.e., ‘Koiminori’, is scheduled to be released soon. Moreover, a genetic analysis method for ploidy QTLs applicable to octoploid strawberries has been established, which is expected to facilitate the genetic analysis of significant traits (Yamakawa et al. 2021). Yamakawa et al. (2025) identified three QTLs associated with red fruit flesh color based on the above-mentioned procedure; by selecting individuals that retained all three DNA markers, a high selection frequency of 92% for red-fleshed individuals was achieved. Red flesh color is important for processed products such as jams, purees, and cakes. Yamakawa et al. (2025) identified an early maturity QTL and a de-maturity QTL that alleviated the early maturity effects. By selecting individuals that retained the DNA marker for the former QTL, but lacked the marker for the latter QTL, a selection frequency of 90% was attained for early maturing individuals. Early maturing cultivars are in high demand for forcing culture because they can produce fruit on time to meet the demand for strawberries for Christmas cakes.

Currently, strawberry cultivars developed using MAS are not commercially available in Japan. Although cultivars with diverse flowering traits and disease resistance have been developed, they have been selected based on phenotypic evaluation. The development of DNA markers is expected to accelerate breeding efforts, including the selection of cultivars with improved flowering characteristics and disease resistance.

Future perspective

Exploration of genetic resources possessing novel and beneficial traits is essential for future breeding efforts, and the development of unique resources is actively underway. However, developing these populations requires the long-term cultivation of large populations and trait evaluation. A core collection is a representative subset of accessions selected from a vast collection of genetic resources to cover genetic diversity efficiently. In Japan, core collections have been established for vegetables such as eggplants, cucumbers, and melons (Miyatake et al. 2019, Shigita et al. 2023, 2024). The eggplant core collection, accompanied by genomic data, has been characterized for practical agricultural traits, including disease resistance. Since these accessions have been confirmed for local culinary use, the introduction of useful traits can proceed without significant barriers. A four-way cross-population derived from the F₂ population of two commercial F₁ tomato cultivars has been developed (Ohyama et al. 2017). This population originated from four parental lines of the original F₁ tomato cultivars and exhibited higher genetic diversity than the population derived from a cross between two parental lines. Multi-parent advanced generation intercross (MAGIC) populations are created by intercrossing multiple parental lines to promote extensive genome-wide recombination. This process yields a population that combines high genetic diversity with a minimal population structure and a broad spectrum of recombinant haplotypes. MAGIC populations have been established in strawberries, demonstrating significant value for both genetic analysis and breeding applications (Tasaki et al. 2020, Wada et al. 2017).

In Japan, DNA markers and whole-genome sequence data for vegetables have been curated and are widely accessible through databases such as Plant Garden (https://plantgarden.jp/ja/index), Melonet-DB (https://melonet-db.dna.affrc.go.jp/), and AlliumTDB (https://alliumtdb.kazusa.or.jp/). These resources facilitate genetic analyses based on genome-wide polymorphism data, thereby accelerating the identification of novel genes for valuable traits using core collections. Genome-wide association study (GWAS) have been conducted on vegetables such as tomatoes (Yamamoto et al. 2024) and strawberries (Wada et al. 2020). Moreover, genomic prediction, which estimates phenotypic performance from genome-wide polymorphism data, has enabled genomic selection for breeding purposes. Genomic selection has been implemented in vegetables such as tomatoes (Yamamoto et al. 2017) and strawberries (Nagano et al. 2018), contributing to improved selection accuracy for complex traits, including yield and fruit quality. These advanced genomic approaches are expected to significantly enhance breeding efficiency and precision of trait selection.

Recent advances in genome-related technologies have significantly expanded vegetable breeding possibilities. Progress in long-read sequencing technologies has enabled the establishment of high-quality reference genome assemblies, including haplotype phasing. This advances the analysis of how genomic structural variation influences trait expression. Furthermore, automation of phenotyping data collection is expected to enhance the speed and precision of breeding processes. The integration of these technologies is expected to accelerate the identification of valuable genetic resources and the establishment of MAS systems, leading to the more efficient development of new cultivars.

Author Contribution Statement

MK and TK wrote the draft for the section on Brassicaceae vegetables; KM for the section on Solanaceae vegetables; MS and YY for the section on Cucurbitaceae vegetables; SF for the section on Allium vegetables; MH and TN for the section on strawberries; and TN integrated all the sections of the text. All the authors have reviewed and approved the final manuscript.

 Acknowledgments

We thank M. Yoshida of TARC/NARO, S. Kataoka of NIVFS, M. Ogura of NIVFS, and M. Misumi of KARC/NARO for their technical insights on strawberries. We would like to thank Editage for the English language editing.

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