Vegetable Breeding, Genetics and Genomics, 2nd Volume

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Agriculture agriculture	3.6	6.3	2011	18.8 Days	CHF 2600	Submit
Agronomy agronomy	3.4	6.7	2011	17 Days	CHF 2600	Submit
Crops crops	1.9	2.4	2021	22.4 Days	CHF 1200	Submit
DNA dna	-	-	2021	36 Days	CHF 1000	Submit
Genes genes	2.8	5.5	2010	14.6 Days	CHF 2600	Submit
Plants plants	4.1	7.6	2012	16.5 Days	CHF 2700	Submit

16 pages, 1892 KB

Open AccessArticle

Genetic Diversity and SNP-Based Fingerprinting of 94 Pumpkin Cultivars: Database Establishment and Population Analysis

by Jiawei Pan, Caochuang Fang, Toheed Anwar and Kun Ma

Plants 2026, 15(11), 1717; https://doi.org/10.3390/plants15111717 - 2 Jun 2026

Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders’ rights enforcement. [...] Read more.

Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders’ rights enforcement. Despite the established utility of SNP markers as the gold standard for genetic analysis, a dedicated high-resolution molecular database for modern pumpkin cultivars remains unavailable. To address this gap, we conducted whole-genome resequencing (WGS) on 94 representative pumpkin cultivars (spanning C. moschata, C. maxima, and C. pepo). Clean reads were mapped to the Cucurbita maxima reference genome. We employed a stringent pipeline to identify genomic variants and utilized STRUCTURE software, Principal Component Analysis (PCA), and Neighbor-Joining (NJ) trees to evaluate population stratification. Linkage disequilibrium (LD) decay and DNA fingerprinting barcodes were also developed. A total of 8,873,150 high-quality variants were identified, including 7,345,007 SNPs and 1,528,143 InDels, with an average SNP density of 21,281.50 SNPs/Mb. Population analysis consistently categorized the 94 cultivars into two primary subpopulations (G1 and G2). The first two PCs accounted for 74.06% of the total genetic variance. Further analysis revealed that G1 possessed a more complex genetic architecture and slower LD decay compared to G2, suggesting distinct selection histories. Finally, we screened for highly informative biallelic SNPs to construct a DNA fingerprinting database, enabling precise sample discrimination through unique chromatic barcodes. This study fills a critical gap in pumpkin genomics by establishing a high-density SNP database and a robust fingerprinting system. These resources provide a definitive tool for variety certification, seed purity testing, and the advancement of molecular-assisted breeding in pumpkin. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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14 pages, 1429 KB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of the PYL Gene Family in Watermelon Under Abiotic Stresses

by Guangpu Lan, Yidong Guo, Jun Hu, Jincan Huang, Ziye Pan, Yingda Chen, Xian Zhang, Zhongyuan Wang, Yongchao Yang and Chunhua Wei

Genes 2026, 17(4), 426; https://doi.org/10.3390/genes17040426 - 4 Apr 2026

Viewed by 643

Abstract

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our [...] Read more.

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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19 pages, 2429 KB

Open AccessArticle

Exploring Molecular Markers Associated with Crumbly in Rubus idaeus L.

by Melissa Y. Oliveira, Teresa Valdiviesso, Francisco Rosado Luz, Amílcar Duarte, Pedro Brás de Oliveira and Ana Rita Varela

Crops 2026, 6(2), 36; https://doi.org/10.3390/crops6020036 - 23 Mar 2026

Viewed by 810

Abstract

The raspberry (Rubus idaeus L.), an economically important crop, is affected by the crumbly fruit disorder, a malformation that leads to fruit disintegration at harvest due to poor drupelet cohesion. Despite previous efforts to identify genetic determinants of this phenotype, its complex [...] Read more.

The raspberry (Rubus idaeus L.), an economically important crop, is affected by the crumbly fruit disorder, a malformation that leads to fruit disintegration at harvest due to poor drupelet cohesion. Despite previous efforts to identify genetic determinants of this phenotype, its complex inheritance and strong environmental component have limited the development of robust predictive markers. This study assessed the behavior and transferability of previously reported SSR and SNP markers associated with crumbly fruit across plants from a diverse panel of 34 R. idaeus cultivars, including in adjacent genomic regions not screened previously. Phenotyping was based on multi-season fruit performance and drupelet cohesion, and genetic variation was analysed using PCR-based genotyping within a multilocus approach. Consistent clustering patterns were observed across multiple SSR and SNP loci, suggesting a reproducible association between these genomic regions and the crumbly phenotype. Overall, the results support a multilocus genetic architecture underlying crumbly fruit, but also demonstrate that previously reported markers are not universally transferable across genetic backgrounds. These findings highlight the importance of integrated, population-aware marker validation to enable more reliable implementation of marker-assisted strategies in raspberry breeding programs. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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19 pages, 6268 KB

Open AccessReview

Advances in Polyploid Breeding of Cucurbitaceae Crops: From Polyploidy Research to Triploid Seedless Hybrid Breeding

by Alexey Ermolaev, Maria Fomicheva and Elena Domblides

Crops 2026, 6(1), 5; https://doi.org/10.3390/crops6010005 - 25 Dec 2025

Viewed by 1695

Abstract

This literature review systematizes current data on the development of triploid seedless hybrids in the Cucurbitaceae Juss family. The absence of seeds simplifies the consumption and industrial preparation of products from cucurbits. In addition, triploids showed larger plant habitus, field resistance to infections, [...] Read more.

This literature review systematizes current data on the development of triploid seedless hybrids in the Cucurbitaceae Juss family. The absence of seeds simplifies the consumption and industrial preparation of products from cucurbits. In addition, triploids showed larger plant habitus, field resistance to infections, extended shelf life, and higher fruit quality. Phenotypic differences in polyploids can stem from altered chromatin organization and gene regulation, as the nucleus must accommodate a doubled chromosome set. The triploid watermelon cultivation method developed in 1951 failed to gain traction among other crops in the gourd (Cucurbitaceae) family. The challenges of triploid seed production and use include the need for the development of tetraploid and diploid parental lines, as well as bypassing the problem of the low viability of tetraploid parent pollen and the issue of thick seed coats and underdeveloped embryos in triploids. The research findings presented in this review can be applied to the development of triploid seedless hybrids for other members of the Cucurbitaceae family. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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18 pages, 15346 KB

Open AccessArticle

Differential Expression of MYB29 Homologs and Their Subfunctionalization in Glucosinolate Biosynthesis in Allotetraploid Brassica juncea

by Lili Zhang, Jingjing Wang, Shanyi Wang, Youjian Yu, Zhujun Zhu and Liai Xu

Agronomy 2025, 15(12), 2770; https://doi.org/10.3390/agronomy15122770 - 30 Nov 2025

Cited by 2 | Viewed by 616

Abstract

Brassica juncea (L.) Coss. var. foliosa Bailey contains high glucosinolate (GSL) levels that define its flavor and defense properties. However, the regulatory mechanisms controlling GSL biosynthesis in Brassica crops remain unclear. Here, four MYB29 homologs were identified in allotetraploid Brassica juncea. These [...] Read more.

Brassica juncea (L.) Coss. var. foliosa Bailey contains high glucosinolate (GSL) levels that define its flavor and defense properties. However, the regulatory mechanisms controlling GSL biosynthesis in Brassica crops remain unclear. Here, four MYB29 homologs were identified in allotetraploid Brassica juncea. These BjuMYB29 proteins localize to the nucleus and possess transcriptional activation activity. Evolutionary analysis suggests polyploidization-driven expansion of MYB genes contributed to GLS diversification in Brassica species. Expression profiling showed distinct spatiotemporal and herbivory-responsive patterns among BjuMYB29 homologs. Heterologous expression of BjuA03.MYB29 and BjuA10.MYB29 in Arabidopsis enhanced insect resistance via GSL accumulation. Although both homologs upregulate aliphatic GSL biosynthetic genes, they differentially regulate indolic GSLs, with BjuA03.MYB29 suppressing and BjuA10.MYB29 enhancing their accumulation, potentially through differential control of CYP79B2. These results reveal subfunctionalization among MYB29 homologs in GSL regulation. This functional diversification of MYB29 homologs offers novel targets for precision breeding of Brassica crops with customized GSL profiles to optimize pest resistance and nutritional quality. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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15 pages, 2686 KB

Open AccessArticle

Overexpression of AgDREBA6b Gene Significantly Increases Heat Tolerance in Arabidopsis thaliana

by Fangjie Xie, Shengyan Yang, Zexi Peng, Yonglu Li, Zhenchao Yang and Ruiheng Lv

Agronomy 2025, 15(7), 1565; https://doi.org/10.3390/agronomy15071565 - 27 Jun 2025

Cited by 2 | Viewed by 1441

Abstract

The APETALA2/ethylene response factor (AP2/ERF) is a class of plant-specific transcription factors, among which the dehydration-responsive element-binding protein (DREB) subfamily has been widely reported to enhance plant resistance to abiotic stresses. A high-temperature-related gene, Apium graveolens DREBA6b (AgDREBA6b; accession number: OR727346), was [...] Read more.

The APETALA2/ethylene response factor (AP2/ERF) is a class of plant-specific transcription factors, among which the dehydration-responsive element-binding protein (DREB) subfamily has been widely reported to enhance plant resistance to abiotic stresses. A high-temperature-related gene, Apium graveolens DREBA6b (AgDREBA6b; accession number: OR727346), was previously cloned from a heat-tolerant celery variety. In this study, we transformed this gene into Arabidopsis thaliana using an Agrobacterium rhizogenes-mediated method to explore its function. The results showed that overexpressing AgDREBA6b in Arabidopsis thaliana significantly improved plant growth under high-temperature stress (38 °C) compared to the dreb mutant and wild-type (WT) plants. The anatomical structure of the leaves revealed that the number and degree of stomatal openings in the overexpressed plants were significantly higher than those in the WT and dreb plants, suggesting that AgDREBA6b enhances stomatal opening. Additionally, the chlorophyll content, chlorophyll fluorescence properties, proline (Pro), malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities were higher in the transgenic plants, indicating better stress tolerance. qPCR analysis showed that four heat tolerance-related genes (AtHSP98.7, AtHSP70-1, AtAPX1, and AtGOLS1) were upregulated in the transgenic plants, with higher expression levels than in WT and mutant plants. This study provides valuable genetic resources for understanding the molecular mechanisms of celery’s heat tolerance and offers insights for breeding heat-tolerant celery varieties. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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21 pages, 5835 KB

Open AccessArticle

Transcriptome and Metabolome Analysis of Low-Pressure Regulation in Saussurea involucrata Leaves

by Xinyu Quan, Fenggui Fan, Hanbo Cao, Na Tang, Changgen Xu and Changhe Wang

Genes 2025, 16(3), 328; https://doi.org/10.3390/genes16030328 - 11 Mar 2025

Cited by 4 | Viewed by 2347

Abstract

Saussurea involucrata, an endangered medicinal plant, thrives in high mountain regions at altitudes ranging from 3500 to 5000 m. Being a plant that grows at high altitudes means it possesses unique physiological mechanisms and stress-responsive genes that regulate and adapt to the [...] Read more.

Saussurea involucrata, an endangered medicinal plant, thrives in high mountain regions at altitudes ranging from 3500 to 5000 m. Being a plant that grows at high altitudes means it possesses unique physiological mechanisms and stress-responsive genes that regulate and adapt to the high-altitude environment. While many cold-resistant genes have been cloned and their mechanisms studied, the genes and molecular mechanisms involved in adaptation to hypobaric hypoxia remain largely unexplored. This study conducted transcriptomic and metabolomic analyses on the leaves of S. involucrata under normal atmosphere (101 kPa) and low pressure (60 kPa). A total of 2383 differentially expressed genes (DEGs) and 336 differentially accumulated metabolites (DAMs) were identified utilizing RNA-seq and UPLS-MS techniques. The results indicated that S. involucrata exhibits responses to hypobaric hypoxia environments by engaging in DNA repair, membrane transport, hypoxic response, reproductive processes, and various metabolic activities associated with nutrient uptake and the effective utilization of chemical components. It is worth noting that under low-pressure treatment, flavonoids are predominantly negatively regulated, whereas terpenoids are primarily positively regulated. These findings identify key genes and metabolites in S. involucrata that respond to hypobaric hypoxia treatment, providing a theoretical basis for the development of its medicinal value and for low-altitude cultivation. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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15 pages, 4363 KB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of the SPL Gene Family in Solanum melongena (Eggplant)

by Hefen Cheng, Zhiliang Li, Baojuan Sun, Wei Zhao, Songyuan Zhang, Tao Li, Qian You and Dinggang Zhou

Agronomy 2025, 15(2), 471; https://doi.org/10.3390/agronomy15020471 - 14 Feb 2025

Cited by 1 | Viewed by 1538

Abstract

The SPL (SQUAMOSA promoter-binding protein-like) transcription factor gene family plays a crucial role in the growth of plants, including fruit development. Although the SPL gene family has been widely studied in many plants, it remains unexplored in eggplant, an important Solanaceae vegetable crop. [...] Read more.

The SPL (SQUAMOSA promoter-binding protein-like) transcription factor gene family plays a crucial role in the growth of plants, including fruit development. Although the SPL gene family has been widely studied in many plants, it remains unexplored in eggplant, an important Solanaceae vegetable crop. In this study, we performed a genome-wide analysis and identified 11 SmSPL genes with 10 motifs in the eggplant genome, which were assigned to five groups based on the amino acid sequences and the gene structure of the SBP domain. In addition, the expression patterns of 11 SmSPL genes were analyzed in different tissue types and at four different fruit development stages in eggplant. The results showed that all SmSPL genes were expressed differently in various tissues, suggesting that they may play different roles in the regulation of the development of different organs. Specifically, the expression level of SmSPL_5 was increased at the fruit expansion stage and showed the highest expression levels at 16 and 24 days after pollination, suggesting that it may be involved in regulating fruit development at both the fruit expansion and commercial fruit stages. Overall, this study provides an important basis for further exploring the function of the SmSPL gene family in eggplant. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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16 pages, 2124 KB

Open AccessArticle

Genotype-Driven Phenotype Prediction in Onion Breeding: Machine Learning Models for Enhanced Bulb Weight Selection

by Junhwa Choi, Sunghyun Cho, Subin Choi, Myunghee Jung, Yu-jin Lim, Eunchae Lee, Jaewon Lim, Han Yong Park and Younhee Shin

Agriculture 2024, 14(12), 2239; https://doi.org/10.3390/agriculture14122239 - 6 Dec 2024

Cited by 2 | Viewed by 3000

Abstract

Onions (Allium cepa L.) are a globally significant horticultural crop, ranking second only to tomatoes in terms of cultivation and consumption. However, due to the crop’s complex genome structure, lengthy growth cycle, self-incompatibility, and susceptibility to disease, onion breeding is challenging. To [...] Read more.

Onions (Allium cepa L.) are a globally significant horticultural crop, ranking second only to tomatoes in terms of cultivation and consumption. However, due to the crop’s complex genome structure, lengthy growth cycle, self-incompatibility, and susceptibility to disease, onion breeding is challenging. To address these issues, we implemented digital breeding techniques utilizing genomic data from 98 elite onion lines. We identified 51,499 high-quality variants and employed these data to construct a genomic estimated breeding value (GEBV) model and apply machine learning methods for bulb weight prediction. Validation with 260 new individuals revealed that the machine learning model achieved an accuracy of 83.2% and required only thirty-nine SNPs. Subsequent in silico crossbreeding simulations indicated that offspring from the top 5% of elite lines exhibited the highest bulb weights, aligning with traditional phenotypic selection methods. This approach demonstrates that early-stage selection based on genotypic information followed by crossbreeding can achieve economically viable breeding results. This methodology is not restricted to bulb weight and can be applied to various horticultural traits, significantly improving the efficiency of onion breeding through advanced digital technologies. The integration of genomic data, machine learning, and computer simulations provides a powerful framework for data-driven breeding strategies, accelerating the development of superior onion varieties to meet global demand. Full article

(This article belongs to the Topic Vegetable Breeding, Genetics and Genomics, 2nd Volume)

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