Genetic Breeding and Biotechnology of Garden Plants

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Applied Biosciences applbiosci	-	2.9	2022	22.8 Days	CHF 1200	Submit
Forests forests	2.5	4.6	2010	16.8 Days	CHF 2600	Submit
Genes genes	2.8	5.5	2010	14.6 Days	CHF 2600	Submit
Horticulturae horticulturae	3.0	5.1	2015	16.7 Days	CHF 2200	Submit
International Journal of Molecular Sciences ijms	4.9	9.0	2000	17.8 Days	CHF 2900	Submit
Plants plants	4.1	7.6	2012	16.5 Days	CHF 2700	Submit

20 pages, 9594 KB

Open AccessArticle

Multi-Omics Analysis Identifies SlLhcb13 as a Key Regulator of Tomato Resistance to Botrytis cinerea

by Dan Luo, Xiaojie Peng, Weiqiang Yan, Yujin Wang, Ke Liu, Lixia Li, Zhe Wu, Hongmei Nie, Sheng Sun, Wenhui Sun and Jun Cai

Plants 2026, 15(9), 1360; https://doi.org/10.3390/plants15091360 - 29 Apr 2026

Viewed by 268

Abstract

Gray mold caused by Botrytis cinerea poses a severe threat to tomato production. In this study, physiological, biochemical, transcriptomic, and proteomic analyses were integrated to characterize the dynamic responses of tomato ‘Ailsa Craig’ to B. cinerea infection. During B. cinerea infection, peroxidase (POD) [...] Read more.

Gray mold caused by Botrytis cinerea poses a severe threat to tomato production. In this study, physiological, biochemical, transcriptomic, and proteomic analyses were integrated to characterize the dynamic responses of tomato ‘Ailsa Craig’ to B. cinerea infection. During B. cinerea infection, peroxidase (POD) activity showed a progressive increase, while catalase (CAT) activity was significantly upregulated at 24 hpi and remained stable through 48 hpi. Malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) contents showed a delayed response, increasing significantly only at 48 hpi, whereas SOD activity exhibited a biphasic pattern. Transcriptome and proteome profiling identified 5824 differentially expressed genes and 124 differentially expressed proteins. Functional enrichment analysis highlighted defense-related pathways, including plant–pathogen interaction, flavonoid biosynthesis, and inositol phosphate metabolism. Notably, the chlorophyll a/b-binding protein SlLhcb13 exhibited post-transcriptional upregulation despite transcriptional suppression. Functional validation demonstrated that overexpression of SlLhcb13 enhanced resistance, whereas silencing increased susceptibility. These findings identify SlLhcb13 as a positive regulator linking photosynthesis to immunity and provide new insights into the defense mechanisms of tomato. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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11 pages, 1639 KB

Open AccessArticle

Genetic Diversity Analysis of Cymbidium eburneum Lindl. (Orchidaceae) Based on SSR Markers

by Feilong Hu, Zhe Zhang, Shunjiao Lu, Zhiheng Chen, Haotian Zhong, Liang Xi and Guangsui Yang

Horticulturae 2026, 12(4), 502; https://doi.org/10.3390/horticulturae12040502 - 21 Apr 2026

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Abstract

Cymbidium eburneum Lindl. is a valuable ornamental orchid and breeding parent, but its genetic background remains unclear due to habitat destruction and germplasm mixing. This study developed specific SSR markers to evaluate the genetic diversity and structure of 96 C. eburneum Lindl. accessions [...] Read more.

Cymbidium eburneum Lindl. is a valuable ornamental orchid and breeding parent, but its genetic background remains unclear due to habitat destruction and germplasm mixing. This study developed specific SSR markers to evaluate the genetic diversity and structure of 96 C. eburneum Lindl. accessions from China and Vietnam. Transcriptome analysis identified 47,248 SSR loci. Sixteen polymorphic core primer pairs detected 150 alleles (mean Na = 9.375) with an average Polymorphism Information Content (PIC) of 0.444. Observed heterozygosity (Ho = 0.290) was noticeably lower than expected (He = 0.478), indicating heterozygote deficiency. UPGMA clustering identified eight groups strongly correlated with geography. Principal Coordinate Analysis (PCoA) revealed a clear geographical differentiation pattern, featuring the most genetically cohesive group from Guangxi and more differentiated geographically marginal populations from Hainan and Vietnam. STRUCTURE analysis (K = 2) indicated two main gene pools with signals of genetic admixture. Geographical isolation was suggested as a potential driver of genetic differentiation. The Guangxi population represents a genetically consistent major reservoir, while marginal populations harbor unique variations. These findings provide a scientific basis for germplasm identification, conservation, and parental selection in C. eburneum Lindl. breeding. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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19 pages, 6929 KB

Open AccessArticle

Genomic Signatures of Somatic Mutation and Selection Shape Distinct Clonal Lineages in Bougainvillea × buttiana ‘Miss Manila’ Bud Sport

by Hongyan Meng, Qun Zhou, Duchao Chen, Bayan Huang, Mingqiong Zheng and Wanqi Zhang

Genes 2026, 17(4), 471; https://doi.org/10.3390/genes17040471 - 17 Apr 2026

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Abstract

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular [...] Read more.

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular mechanisms behind their formation. This study aimed to characterize the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea × buttiana ‘Miss Manila’. Methods: We employed genotyping by sequencing (GBS) on 39 accessions, including 27 bud sports and 12 conventional varieties. Population genomic analyses, such as principal component analysis (PCA), phylogenetic reconstruction, ADMIXTURE, and diversity statistics (π, He, Tajima’s D), were performed on 64,810 high-quality SNPs. Genome-wide scans for differentiation (FST) and selective sweeps (XP-CLR) were also conducted. Results: Bud sports showed significantly lower genetic diversity (π and He) than conventional varieties, which matches their clonal origin. PCA, phylogenetic, and ADMIXTURE analyses (optimal K = 4) revealed clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed fewer private alleles and a less negative Tajima’s D value. Genomic scans identified regions under selection in bud sports, with functional annotation pointed to genes involved in ubiquitin-mediated proteolysis and RNA transport. Notably, Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showed a high mutation frequency specifically in bud sports. Conclusions: We provide the first population-genomic evidence that bud sports of ‘Miss Manila’ are genetically distinct clonal lineages, shaped by somatic mutation and selection. These findings support bud sports as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for future marker-assisted selection and molecular breeding in bougainvillea. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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21 pages, 5473 KB

Open AccessArticle

The Effect of DNA Methylation on the Depth of Peel Color in ‘Red Fuji’

by Yucheng Liu, Jingyi Su and Wensheng Li

Horticulturae 2026, 12(2), 219; https://doi.org/10.3390/horticulturae12020219 - 10 Feb 2026

Viewed by 402

Abstract

Red pigmentation in apple peel significantly contributes to its commercial value, and bagging treatment contributes to enhancing red coloration in fruits. However, the regulatory mechanisms underlying bagging-induced coloration remain largely unexplored. Through bagging treatment, this study aimed to investigate the role of DNA [...] Read more.

Red pigmentation in apple peel significantly contributes to its commercial value, and bagging treatment contributes to enhancing red coloration in fruits. However, the regulatory mechanisms underlying bagging-induced coloration remain largely unexplored. Through bagging treatment, this study aimed to investigate the role of DNA methylation in anthocyanin biosynthesis in the ‘Nagafu No. 2’ cultivar and its bud mutation variant, which has enhanced red coloration. We compared bagging and unbagging treatments in both the bud mutant (Mt-Bagging and Mt-NoBagging) and the wild type (Control-Bagging and Control-NoBagging). Our results demonstrated that bagging significantly promoted anthocyanin accumulation while reducing chlorophyll content. At 30 days post-bag removal, anthocyanin content was highest in the Mt-Bagging group, followed by the Mt-NoBagging, Control-Bagging, and Control-NoBagging groups, and the highest level of redness (a* values) was detected in the Mt-Bagging group. Genome-wide methylation analysis revealed that differentially methylated regions predominantly targeted structural genes within the anthocyanin biosynthesis pathway, including C4H1, C4H3, C4HL, ANS1, and ANS2. Notably, quantitative PCR analysis confirmed that the upregulation of C4HL, C4H3, and ANS1 in the bagged mutant correlated with its intensified red coloration. These findings offer novel insights into the epigenetic regulation of apple peel pigmentation during bagging cultivation. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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19 pages, 3013 KB

Open AccessArticle

Dynamic Transcriptome Profiling Reveals Key Regulatory Networks Underlying Curd Development in Cauliflower (Brassica oleracea L. botrytis)

by Shuting Qiao, Xiaoguang Sheng, Mengfei Song, Huifang Yu, Jiansheng Wang, Yusen Shen, Sifan Du, Jiaojiao Li, Liang Sun and Honghui Gu

Int. J. Mol. Sci. 2026, 27(3), 1308; https://doi.org/10.3390/ijms27031308 - 28 Jan 2026

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Abstract

Cauliflower (Brassica oleracea var. botrytis) curd formation is a highly complex developmental process governed by tightly coordinated genetic and physiological regulation. Here, we performed transcriptome sequencing of curd and peduncle tissues across multiple developmental stages, generating 171.52 Gb of high-quality data. [...] Read more.

Cauliflower (Brassica oleracea var. botrytis) curd formation is a highly complex developmental process governed by tightly coordinated genetic and physiological regulation. Here, we performed transcriptome sequencing of curd and peduncle tissues across multiple developmental stages, generating 171.52 Gb of high-quality data. Genes associated with photosynthesis and glucosinolate biosynthesis were strongly upregulated in the shoot apical meristem (SAM), highlighting substantial metabolic investment during the pre-initiation phase of curd morphogenesis. Key floral transition regulators, particularly AP2 and MADS-box transcription factors, were activated to drive the vegetative-to-reproductive switch and initiate curd primordia, ultimately giving rise to the arrested inflorescence architecture characteristic of cauliflower. Furthermore, hormone signaling pathways—including auxin (AUX), jasmonic acid (JA), and brassinosteroid (BR)—showed marked activation during SAM proliferation and peduncle elongation, underscoring their crucial roles in structural patterning. Collectively, our findings delineate an integrated regulatory network that links metabolic activity, hormone signaling, and developmental programs, providing novel molecular insights into curd formation and identifying potential breeding targets for the genetic improvement of Brassicaceae crops. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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16 pages, 5029 KB

Open AccessArticle

Genome-Wide Identification of the Zinc Finger-Homeodomain (ZF-HD) Gene Family and Their Response to Cold Stress in Rosa chinensis

by Xiaona Su, Yiting Dong, Yuan Liao, Weijian Li, Zheng Chen, Chao Xu and Shaomei Jiang

Genes 2026, 17(1), 90; https://doi.org/10.3390/genes17010090 - 15 Jan 2026

Viewed by 592

Abstract

Background: The zinc finger-homeodomain (ZF-HD) transcription factor family exerts pivotal regulatory functions in plant development and stress responses, yet a systematic genome-wide survey is lacking for Rosa chinensis. Methods: In this study, we performed a comprehensive genome-wide identification and analysis of RcZF-HD [...] Read more.

Background: The zinc finger-homeodomain (ZF-HD) transcription factor family exerts pivotal regulatory functions in plant development and stress responses, yet a systematic genome-wide survey is lacking for Rosa chinensis. Methods: In this study, we performed a comprehensive genome-wide identification and analysis of RcZF-HD genes in R. chinensis using bioinformatics approaches. Nine RcZF-HD loci were mined from the rose genome and comprehensively profiled for physicochemical parameters, phylogenetic affiliations, chromosomal positions, exon–intron architectures, conserved motifs, and spatiotemporal expression landscapes. Results: The results showed that RcZF-HD genes were unevenly distributed across four chromosomes (Chr2, Chr4, Chr6, and Chr7), with tandem duplication events detected on chromosomes 2 and 7, suggesting their contribution to gene family expansion. Maximum-likelihood phylogeny placed RcZF-HD proteins within nine well-supported sub-clades alongside Arabidopsis orthologs, implying both evolutionary conservation and lineage-specific divergence. All members retain canonical zinc-finger domains, yet acquire unique motif signatures predictive of functional specialization. Gene structure analysis revealed considerable diversity in exon–intron organization. Expression profiling across six different tissues (root, stem, leaf, bud, flower, and fruit) demonstrated remarkable tissue-specific expression patterns. Notably, RchiOBHm_Chr2g0168531 exhibited extremely high expression in stem tissue, while RchiOBHm_Chr7g0181371 showed preferential expression in flower tissue, suggesting specialized roles in stem development and floral organ formation, respectively. The cold-stress challenge of ‘Old Blush’ petals further disclosed pronounced up-regulation of seven RcZF-HD genes, attesting to their critical contribution to low-temperature tolerance. Conclusions: Integrative analyses furnish a multidimensional blueprint of the rose RcZF-HD repertoire, providing molecular landmarks for future functional dissection and ornamental trait engineering. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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19 pages, 13272 KB

Open AccessFeature PaperArticle

The MADS-Box Transcription Factor BoAGL8 Is Involved in Regulating Flowering in Broccoli

by Yuanyuan Li, Hanbing Yang, Peini Jia, Zairong Li, Yan Wang, Yajie Jiang, Xia He, Boyue Wen, Chensi Huo, Wei Zhang, Wenchen Chai, Shijiang Yan and Jing Zhang

Horticulturae 2025, 11(10), 1227; https://doi.org/10.3390/horticulturae11101227 - 11 Oct 2025

Cited by 1 | Viewed by 1066

Abstract

Broccoli (Brassica oleracea L. var. italica) is a biennial or annual herbaceous plant belonging to the species Brassica oleracea in the genus Brassica of the Cruciferae family. The green flower curd serves as the primary edible organ, with its development and [...] Read more.

Broccoli (Brassica oleracea L. var. italica) is a biennial or annual herbaceous plant belonging to the species Brassica oleracea in the genus Brassica of the Cruciferae family. The green flower curd serves as the primary edible organ, with its development and preservation critically determining broccoli yield and quality. Given that these processes are regulated by flowering time, understanding the mechanisms underlying floral transition is essential for enhancing broccoli yield and quality. This study aimed to identify the MADS-box family in broccoli and to investigate the function of the BoAGL8 gene in floral induction. We identified a total of 176 MADS-box genes, of which 54 genes were up-regulated and 50 genes were down-regulated under low-temperature treatment. Notably, the expression of BoAGL8 was up-regulated by 6.70-fold under low-temperature induction, prompting us to select and clone this gene for further analysis. Tissue-specific expression profiling further revealed that BoAGL8 is expressed at relatively high level in both mature and young leaves. After 15 days of low-temperature treatment, BoAGL8 expression in shoot tip was significantly upregulated compared to untreated controls. Subcellular localization analysis showed that BoAGL8 protein was located to the nucleus. Ectopic over-expression of BoAGL8 in Arabidopsis exhibited accelerated bolting and flowering, reduced rosette leaf number, and increased seed yield per plant compared to wild-type plants. Furthermore, compared to wild-type controls, transgenic lines exhibited upregulated expression of AtFT, AtAP1 and AtSEP3, alongside downregulation of SVP expression. The above results indicate that BoAGL8 may play a key regulatory role in the process of floral organ development in broccoli, providing an important theoretical basis for future research on flowering time regulation and breeding in broccoli. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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25 pages, 16017 KB

Open AccessArticle

Identification of Key Regulatory Genes Associated with Double-Petaled Phenotype in Lycoris longituba via Transcriptome Profiling

by Zhong Wang, Xiaoxiao Xu, Chuanqi Liu, Fengjiao Zhang, Xiaochun Shu and Ning Wang

Horticulturae 2025, 11(10), 1156; https://doi.org/10.3390/horticulturae11101156 - 26 Sep 2025

Viewed by 1147

Abstract

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared [...] Read more.

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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20 pages, 6446 KB

Open AccessArticle

The Heavy Metal-Associated Isoprenylated Plant Protein (HIPP) Gene Family Plays a Crucial Role in Cadmium Resistance in Lotus (Nelumbo nucifera G.)

by Chunyan Gao, Yuxuan Zhu, Hualei Xu, Xinyue Peng, Kaili Yu, Xi Gu, Yan Xiao, Jian Cai and Yinjie Wang

Horticulturae 2025, 11(9), 1136; https://doi.org/10.3390/horticulturae11091136 - 18 Sep 2025

Cited by 3 | Viewed by 1668

Abstract

Cadmium (Cd) contamination poses significant threats to aquatic ecosystems. Heavy metal-associated isoprenylated plant proteins (HIPPs) are plant-specific chaperones involved in metal ion homeostasis and stress adaptation. Lotus is an aquatic plant with high biomass and Cd accumulation capacity, showing great potential in water [...] Read more.

Cadmium (Cd) contamination poses significant threats to aquatic ecosystems. Heavy metal-associated isoprenylated plant proteins (HIPPs) are plant-specific chaperones involved in metal ion homeostasis and stress adaptation. Lotus is an aquatic plant with high biomass and Cd accumulation capacity, showing great potential in water remediation. However, the functional characterization of HIPPs in lotus remains unexplored, limiting its application in phytoremediation. We conducted comprehensive characterization of NnHIPP genes in lotus, integrating comparative genomics, Cd-stress transcriptomics, and heterologous expression assays in transgenic yeast. This study identified 33 NnHIPP genes classified into five subfamilies with conserved motifs and structures. Synteny analysis revealed closer evolutionary relationships with dicots (Arabidopsis and Medicago sativa) than monocots. Abundant stress-responsive elements were found in NnHIPPs promoters. Tissue-specific expression profilings indicated functional diversification across organs and developmental stages. Our transcriptome analysis revealed that most NnHIPPs responded to Cd stress, with stronger induction in roots than leaves. Four Cd-induced NnHIPPs (NnHIPP10/14/21/33) showed both plasma membrane and nuclear localization. Notably, NnHIPP14, NnHIPP21, and NnHIPP33 conferred varying degrees of Cd tolerance when overexpressed in yeast. Our study demonstrates that NnHIPPs participate in Cd stress response. Three candidate NnHIPP genes are proposed for genetic engineering to enhance phytoremediation efficiency in lotus. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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19 pages, 3537 KB

Open AccessArticle

Efficient In Vitro Plantlet Regeneration from Stolon Explants and Genetic Stability Assessment Using ISSR Markers in the Ornamental Fern Hypolepis punctata

by Xinyuan Wang, Xuetong Yan, Keyuan Zheng, Hui Shen, Jianguo Cao, Qiang Zhou and Mulan Zhu

Plants 2025, 14(16), 2569; https://doi.org/10.3390/plants14162569 - 18 Aug 2025

Cited by 1 | Viewed by 1394

Abstract

Hypolepis punctata, an aromatic fern with insect-resistant and ornamental potential. Up to date, no studies have reported its micropropagation, particularly using vegetative organs as explants. The optimized stolon sterilization (81.11%) employed 75% ethanol (30 s) and 15% sodium hypochlorite (12 min). The [...] Read more.

Hypolepis punctata, an aromatic fern with insect-resistant and ornamental potential. Up to date, no studies have reported its micropropagation, particularly using vegetative organs as explants. The optimized stolon sterilization (81.11%) employed 75% ethanol (30 s) and 15% sodium hypochlorite (12 min). The optimal conditions for GGB induction (75.56%) and proliferation (8.46 mm) were achieved using Murashige and Skoog (MS) medium + 2.0 mg/L 6-benzylaminopurine (BA) + 0.2 mg/L 1-naphthaleneacetic acid (NAA). The optimal plant growth regulator (PGR) formula for sporophyte regeneration was 0.5 mg/L BA + 0.1 mg/L NAA + 2 g/L activated charcoal (AC), achieving a 98.89% induction rate and 49.19 buds per explant. The 1/4 MS medium had the greatest promoting effect on biomass accumulation and leaf expansion. Optimal shoot elongation (97.78% success, 4.83 cm) was achieved in 1/4 MS + 0.5 mg/L BA + 0.1 mg/L NAA + 2 g/L AC, and optimized rooting (92.22%) was achieved using 1/4 MS + 0.5 mg/L indole-3-butyric acid (IBA) + 0.1 mg/L NAA + 2 g/L AC, producing 25.27 roots per plantlet. Crucially, ISSR analysis confirmed the genetic stability of all regenerants. This optimized protocol establishes a scalable micropropagation system, enhancing both commercial cultivation and genetic improvement potential in Hypolepis punctata. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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19 pages, 3510 KB

Open AccessArticle

Transcriptomics Integrated with Metabolomics Reveals the Accumulation Mechanism of Flavones in Jinsi Huangju

by Yanan Liu, Xinnan Huang, Xinran Chong, Shasha Huang, Changshuai Yu, Hongbin Yu, Yan Wu, Sheng Zeng, Hua Cheng and Guizhen Chen

Horticulturae 2025, 11(8), 948; https://doi.org/10.3390/horticulturae11080948 - 11 Aug 2025

Viewed by 1328

Abstract

Chrysanthemum morifolium Ramat. is an important ornamental plant, holding dual economic value as a medicinal and edible plant. Jinsi Huangju is a popular healthy tea drink prepared from the large and elegant shaped flowers of C. morifolium. However, the suboptimal accumulation of [...] Read more.

Chrysanthemum morifolium Ramat. is an important ornamental plant, holding dual economic value as a medicinal and edible plant. Jinsi Huangju is a popular healthy tea drink prepared from the large and elegant shaped flowers of C. morifolium. However, the suboptimal accumulation of bioactive flavonoids during conventional harvest (full bloom stage) limits its commercial potential. To elucidate the molecular mechanisms governing flavonoid biosynthesis in Jinsi Huangju flowers and identify key genetic regulators for metabolic engineering, we performed integrated metabolomic and transcriptomic analyses of flowers at distinct developmental stages using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) and RNA-seq. Differential metabolites were screened, and candidate genes were validated via transient transformation assays. Among 2146 identified metabolites, flavonoids were the predominant differential compounds, with accumulation patterns being strongly stage dependent. Thirty-eight flavonoid biosynthetic genes and key transcription factors from the MYB, bHLH, and WD40 families exhibited dynamic expression. The CmMYB8a was confirmed as a positive regulator of flavonoid biosynthesis through transient overexpression. This study deciphers the stage-specific flavonoid accumulation in Jinsi Huangju and identifies CmMYB8a as a pivotal regulatory target. Our findings provide genetic resources for breeding high-flavonoid cultivars via molecular design. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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15 pages, 8047 KB

Open AccessArticle

Comparison of Chloroplast Genome Sequences of Saxifraga umbellulata var. pectinata in Qinghai–Xizang Plateau

by Cui Wang, Kaidi Su, Qiwen Li, Rui Sun, Haoyu Liu, Jingxuan Du, Jinping Li and Likuan Liu

Genes 2025, 16(7), 789; https://doi.org/10.3390/genes16070789 - 30 Jun 2025

Cited by 1 | Viewed by 1024

Abstract

Background: Saxifraga umbellulata var. pectinata (Saxifragaceae) is recognized as a genuine medicinal material from the Qinghai–Tibet Plateau in China. This paper presents the chloroplast (cp) genome of S. umbellulata var. pectinata, marking the first report for this genus. The Tibetan medicinal plants [...] Read more.

Background: Saxifraga umbellulata var. pectinata (Saxifragaceae) is recognized as a genuine medicinal material from the Qinghai–Tibet Plateau in China. This paper presents the chloroplast (cp) genome of S. umbellulata var. pectinata, marking the first report for this genus. The Tibetan medicinal plants documented in ‘Chinese Medicinal Plant Resources’ are associated with their chloroplast genomes and medicinal mechanisms. Objective: In order to resolve any potential ambiguity in conventional classifications, this study reconstructs the evolutionary position of S. umbellulata var. pectinata within the genus by comparing its chloroplast genetic information with that of other groupings. Methods: The chloroplast genome of S. umbellulata var. pectinata was sequenced using the Illumina NovaSeq 6000 platform. Subsequent sequence assembly, annotation, and characterization were performed using bioinformatics analysis. The NJ phylogenetic tree was constructed using MEGA 7.0 software. Results: The complete chloroplast genome of S. umbellulata var. pectinata is 146,549 bp in length, comprising four subregions: a large single-copy (LSC) region of 79,318 bp and a small single-copy (SSC) region of 16,390 bp, separated by a pair of inverted repeat (IR) regions each 25,421 bp long. This cp genome contains 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 38.1%. Phylogenetic analysis based on 20 cp genomes indicates that S. umbellulata var. pectinata is closely related to Saxifraga sinomontana and Saxifraga stolonifera. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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13 pages, 5319 KB

Open AccessArticle

The Mining for Flowering-Related Genes Based on De Novo Transcriptome Sequencing in the Endangered Plant Phoebe chekiangensis

by Qinglin Sun, Yan Liu, Mingyang Ni, Yandong Song, Qi Yang, Junhong Zhang, Yuting Zhang and Zaikang Tong

Int. J. Mol. Sci. 2025, 26(3), 1000; https://doi.org/10.3390/ijms26031000 - 24 Jan 2025

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Abstract

Phoebe chekiangensis is an indigenous, endangered, and valuable timber and garden tree species in China, which is notable for having a short juvenile phase (early flowering), unique among the Phoebe genus. However, the molecular mechanisms regulating the flowering of P. chekiangensis remain unexplored, [...] Read more.

Phoebe chekiangensis is an indigenous, endangered, and valuable timber and garden tree species in China, which is notable for having a short juvenile phase (early flowering), unique among the Phoebe genus. However, the molecular mechanisms regulating the flowering of P. chekiangensis remain unexplored, primarily due to the lack of transcriptomic or genomic data. In the present study, transcriptome sequencing yielded 53 million RNA reads, resulting in 111,250 unigenes after de novo assembly. Of these, 47,525 unigenes (42.72%) were successfully annotated in the non-redundant (Nr) database. Furthermore, 15,605 unigenes were assigned to Clusters of Orthologous Groups (KOGs), and 36,370 unigenes were classified into Gene Ontology (GO) categories. A total of 16,135 unigenes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, involving 298 pathways. Based on the expression levels, Gibberellin signaling pathway-related genes were the most predominant expression levels. Hormonal analysis showed that gibberellin (GA) levels varied across tissues and flowering stages, as GA20 levels in leaves were low during full bloom, while GA1 and GA5 levels peaked in flowers. Furthermore, several key genes involved in gibberellin biosynthesis, including CPS, GID1, GA20ox, GA3ox, and GA2ox, exhibited stage-specific expression patterns. Certain genes were highly expressed during the initial phases of flowering, while others, like GA3ox and GA2ox, reached peak expression at full bloom. These findings provide valuable insights into the molecular mechanisms underlying flowering in P. chekiangensis, laying the foundation for future breeding efforts. This transcriptome dataset will serve as an important public resource for molecular research on this species, facilitating the discovery of functional genes related to its growth, development, and flowering regulation. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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12 pages, 1049 KB

Open AccessArticle

An Exploration of Candidate Korean Native Poaceae Plants for Breeding New Varieties as Garden Materials in the New Climate Regime Based on Existing Data

by Sang Heon Kim and Wonwoo Cho

Horticulturae 2024, 10(11), 1158; https://doi.org/10.3390/horticulturae10111158 - 31 Oct 2024

Cited by 3 | Viewed by 2438

Abstract

There is an increasing demand for low-maintenance public garden models, and environmental stress on plants due to climate change is growing. As a result, the demand for developing new plant varieties based on native species for use in gardens in response to climate [...] Read more.

There is an increasing demand for low-maintenance public garden models, and environmental stress on plants due to climate change is growing. As a result, the demand for developing new plant varieties based on native species for use in gardens in response to climate change has increased significantly. Many plants in the Poaceae family are applied for various purposes, including food crops, fodder grasses, ornamental plants, and medicinal plants. Additionally, native plants provide economic and ecological benefits, making them advantageous for use in gardens. However, there are some difficulties in Poaceae breeding studies and the utilization of wild native plants for breeding. Model plants can be utilized in breeding studies of Poaceae plant species. In this study, to identify Korean native Poaceae species with the potential for use not only as garden materials but also as model plants for breeding research in response to climate change, candidate species were selected from the Korean Plant Names Index (KPNI). A total of three Korean native plants in the Poaceae family, including Brachypodium sylvaticum, Setaria viridis, and Zoysia japonica, were selected, and their properties and genome information were compared with the existing representative model plants, Arabidopsis thaliana and Brachypodium distachyon. The current research status of B. sylvaticum, S. viridis, and Z. japonica has been summarized, and the genome size and other characteristics of these model plants have been compared and discussed. As a result, both A. thaliana (2n = 2x = 10) and B. distachyon (2n = 2x = 10) are annual C₃ plants, but B. sylvaticum (2n = 2x = 18) is a perennial C₃ plant, and S. viridis (2n = 2x = 18) is an annual C₄ plant. Thus, B. sylvaticum and S. viridis can be utilized as model plants for perennial C₃ plants and annual C₄ plants, respectively. Z. japonica (2n = 4x = 40) is a perennial C₄ plant, but it can be unsuitable as a model plant because it is an allotetraploid. The application of these newly selected candidate plants in breeding research can build a foundation for breeding native Poaceae plants in Korea in the new climate regime. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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Open AccessArticle

A Plasma Membrane Intrinsic Protein Gene OfPIP2 Involved in Promoting Petal Expansion and Drought Resistance in Osmanthus fragrans

by Xinke Lu, En Kong, Lixiao Shen, Yong Ye, Yiguang Wang, Bin Dong and Shiwei Zhong

Int. J. Mol. Sci. 2024, 25(19), 10716; https://doi.org/10.3390/ijms251910716 - 5 Oct 2024

Cited by 5 | Viewed by 1926

Abstract

Osmanthus fragrans, a native to China, is renowned as a highly popular gardening plant. However, this plant faces significant challenges from drought stress, which can adversely affect its flowering. In this study, we found that the plasma membrane-localized gene OfPIP2 exhibited a [...] Read more.

Osmanthus fragrans, a native to China, is renowned as a highly popular gardening plant. However, this plant faces significant challenges from drought stress, which can adversely affect its flowering. In this study, we found that the plasma membrane-localized gene OfPIP2 exhibited a substantial upregulation during the flowering stages and in response to drought stress. GUS staining has illustrated that the OfPIP2 promoter can drive GUS activity under drought conditions. The overexpression of OfPIP2 was found to enhance petal size by modulating epidermal cell dimensions in Petunia and tobacco. Moreover, this overexpression also bolstered drought tolerance, as evidenced by a reduction in stomatal aperture in both species. Furthermore, yeast one-hybrid (Y1H) and dual-luciferase (Dual-LUC) assays have indicated that the transcription factor OfMYB28 directly binds to the OfPIP2 promoter, thereby regulating its expression. Together, we speculated that a module of OfMYB28-OfPIP2 was not only involved in the enhancement of petal size but also conferred the improvement of drought tolerance in O. fragrans. These results contribute valuable insights into the molecular function of the OfPIP2 gene and lay a foundation for molecular breeding strategies in O. fragrans. Full article

(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)

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