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Agronomy
Special Issues
Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition
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Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Horticultural and Floricultural Crops".

Deadline for manuscript submissions: 10 September 2025 | Viewed by 4953

Special Issue Editors

Dr. Guanglong Wang

E-Mail Website
Guest Editor
School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
Interests: vegetable biotechnology; abiotic stress response; vegetable quality regulation; hormones in horticultural plants
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lijun Ou

E-Mail Website
Guest Editor
College of Horticulture, Hunan Agricultural University, Changsha 410128, China
Interests: horticultural crop germplasm enhancement; abiotic stress; organ formation; fruit development
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Ai-Sheng Xiong

E-Mail Website
Guest Editor
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
Interests: plant growth regulators; circadian clock; plant biotechnology; plant genetics and breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the success of the first Special Issue “Progress in Horticultural Crops—from Genotype to Phenotype” (https://www.mdpi.com/journal/agronomy/special_issues/R2ZCWQ40C3), we are pleased to announce the launch of a second series of the Special Issue.

Horticultural plants play an irreplaceable role in satisfying human nutrition, as well as other aspects. Horticultural plants have some excellent traits, including plant type structure, nutrient enrichment, color change, organ development, etc. In recent years, progress has been made in the research on the phenotype variation of horticultural plants and the genotype changes behind it. This progress will effectively accelerate the rate of production of more nutritious, improved and interesting horticultural products for human beings. In recent years, new technologies are increasingly being used to bridge the genotype–phenotype gap in crop selection.

This Special Issue focuses on the progress addressing phenotype variation and its underlying genotype basis in horticultural crops, including the following themes:

  • All types of omics, including genomics, transcriptomics, proteomics, metabolomics and phenomics;
  • Genetic engineering and genome editing;
  • Organ formation and development, and the relevant genetic basis;
  • Genetic analysis of tolerance or resistance;
  • Genome biology and evolution;
  • Genetic basis of quality and production;
  • Stable and transient transformation technology.

Dr. Guanglong Wang
Prof. Dr. Lijun Ou
Prof. Dr. Aisheng Xiong
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • horticultural crop
  • genetics
  • biotechnology
  • genotype
  • phenotype

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Published Papers (5 papers)

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Research

17 pages, 6994 KiB  
Article
Integrative Transcriptomic and Metabolomic Analysis Reveals Regulatory Networks and Metabolite Dynamics in Gastrodia elata Flower Development
by Hongyu Chen, Ying Yu, Jiehong Zhao and Jian Zhang
Agronomy 2025, 15(2), 441; https://doi.org/10.3390/agronomy15020441 - 11 Feb 2025
Viewed by 605
Abstract
Flower development, a vital phase in the plant life cycle, involves intricate physiological and morphogenetic processes driven by dynamic molecular and metabolic processes. However, the specific molecular mechanisms and metabolite accumulation patterns during Gastrodia elata flower development remain largely unknown. This study utilized [...] Read more.
Flower development, a vital phase in the plant life cycle, involves intricate physiological and morphogenetic processes driven by dynamic molecular and metabolic processes. However, the specific molecular mechanisms and metabolite accumulation patterns during Gastrodia elata flower development remain largely unknown. This study utilized Illumina’s next-generation sequencing to analyze the G. elata flower transcriptome across three critical developmental stages, capturing gene expression changes, particularly those related to transcription factors that regulate flower formation and metabolite accumulation. FPKM analysis showed significant transcriptomic changes during G. elata flower development, while targeted metabolomics identified key metabolites with stage-specific variations via widely targeted metabolic profiling. Here, integrative transcriptome and metabolome analyses were performed to investigate floral genes and compounds in G. elata flowers at three different developmental stages. The differentially expressed genes (DEGs) and significant changes in metabolites (SCMs) involved in key biological pathways were identified. This approach aimed to identify functional genes or pathways jointly enriched in metabolites, thereby defining pathways linked to crucial biological phenotypes. By mapping DEGs and SCMs to KEGG pathways, the comprehensive network was constructed, uncovering functional relationships between gene expression and metabolite accumulation. This study proposes dynamic models of transcriptomic and metabolite changes, revealing key regulatory networks that govern G. elata flower development and potential applications. Full article
(This article belongs to the Special Issue Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition)
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20 pages, 3891 KiB  
Article
Identification and Analysis of Melon (Cucumis melo L.) SHMT Gene Family Members and Their Functional Studies on Tolerance to Low-Temperature Stress
by Yanmin Liu, Dandan He, Yizhou Wu, Kangqi Zhao, Changyi Yang, Yulu Zhong, Liuyang Yang, Haiyue Niu and Sushuang Liu
Agronomy 2025, 15(1), 203; https://doi.org/10.3390/agronomy15010203 - 15 Jan 2025
Viewed by 966
Abstract
Melon (Cucumis melo L.) is a significant cash crop globally and is cherished for its sweet and flavorful fruits, as well as its high nutritional values. However, its yield and quality are limited by various factors, including drought, salinity, and low temperatures. [...] Read more.
Melon (Cucumis melo L.) is a significant cash crop globally and is cherished for its sweet and flavorful fruits, as well as its high nutritional values. However, its yield and quality are limited by various factors, including drought, salinity, and low temperatures. Low temperatures are one of the primary factors influencing the growth and development of melons, diminishing the viability, germination, and growth rate of melon seeds. Concurrently, low temperatures also reduce light absorption efficiency and fruit yields, thereby affecting melon growth and development. Serine hydroxymethyltransferase (SHMT), a conserved phosphopyridoxal-dependent enzyme, plays a crucial role in plant resistance to abiotic stressors. In this study, eight CmSHMT family genes were identified from the melon genome. We predicted their chromosomal locations, physicochemical properties, gene structures, evolutionary relationships, conserved motifs, cis-acting elements of promoters, and tissue-specific expression patterns. The expression levels of CmSHMT family genes in response to low-temperature stress was then analyzd using qRT-PCR. The phylogenetic results indicated that these CmSHMT genes were classified into four subfamilies and were unevenly distributed across five chromosomes, with relatively high conservation among them. Furthermore, our investigation revealed that the promoter regions of the CmSHMT family genes contain many cis-acting elements related to phytohormones, growth, and various stress responses. The relative expression levels of CmSHMT3, CmSHMT4, CmSHMT6, and CmSHMT7 were higher under low-temperature stress compared to the control group. Notably, the promoter region of CmSHMT3 contains cis-acting elements associated with low-temperature response (LTR) and abscisic acid response (ABRE). It is suggested that the mechanism through which CmSHMT3 responds to low-temperature stress treatments may be associated with hormonal regulation. These findings provide a foundation for the further exploration of CmSHMT family genes in melon and their functional roles in response to low-temperature stress, and they provide a theoretical basis for the targeted breeding of superior melon varieties with enhanced tolerance to low temperatures. Full article
(This article belongs to the Special Issue Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition)
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19 pages, 18851 KiB  
Article
Analysis of Transcriptional and Metabolic Differences in the Petal Color Change Response to High-Temperature Stress in Various Chrysanthemum Genotypes
by Zhimei Li, Hougao Zhou, Yan Chen, Minyi Chen, Yutong Yao, Honghui Luo, Qing Wu, Fenglan Wang and Yiwei Zhou
Agronomy 2024, 14(12), 2863; https://doi.org/10.3390/agronomy14122863 - 30 Nov 2024
Viewed by 897
Abstract
Flower color is one of the most important ornamental traits of chrysanthemums. Previous studies have shown that high temperatures can cause the petals of some chrysanthemum varieties to fade; however, the molecular mechanisms behind this phenomenon remain poorly understood. This study examines the [...] Read more.
Flower color is one of the most important ornamental traits of chrysanthemums. Previous studies have shown that high temperatures can cause the petals of some chrysanthemum varieties to fade; however, the molecular mechanisms behind this phenomenon remain poorly understood. This study examines the mechanisms of color change in purple chrysanthemums under high-temperature stress using combined metabolomic and transcriptomic analyses. Four chrysanthemum varieties—two heat-stable (‘Zi Feng Che’ and ‘Chrystal Regal’) and two heat-sensitive (‘Zi Hong Tuo Gui’ and ‘Zi Lian’)—were analyzed. High-temperature conditions (35 °C) significantly downregulated key anthocyanins in heat-sensitive varieties, particularly cyanidin-3-O-(3″,6″-O-dimalonyl)glucoside and pelargonidin-3-O-(3″,6″-O-dimalonyl)glucoside. Transcriptome analysis revealed differential gene expression involved in anthocyanin biosynthesis and degradation, with significant enrichment in the MAPK signaling, phenylpropanoid biosynthesis, flavonoid biosynthesis, and anthocyanin biosynthesis pathways. The study highlighted the differential expression of CHS, DFR, ANS, GT1, 3AT, and UGT75C1 genes in anthocyanin synthesis between heat-sensitive and heat-tolerant varieties. Compared to heat-stable varieties, the petals of heat-sensitive varieties exhibited greater differential expression of heat-responsive transcription factors, including HSFs, ERFs, MYBs, and WRKYs. Genes that show a significant negative correlation with the downregulated anthocyanins, including Cse_sc012959.1_g030.1 (βG), Cse_sc001798.1_g020.1 (MYB), Cse_sc006944.1_g010.1 (MYB), and Cse_sc000572.1_g090.1 (HSF), might regulate anthocyanin accumulation in chrysanthemums in response to high-temperature stress. These results provide guidance for the cultivation management and variety selection of chrysanthemums under high-temperature conditions. Additionally, they lay the foundation for elucidating the molecular mechanisms of flower color stability under heat stress and for breeding new heat-tolerant varieties. Full article
(This article belongs to the Special Issue Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition)
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19 pages, 6978 KiB  
Article
Phenotypic Characters and Inheritance Tendency of Agronomic Traits in F1 Progeny of Chinese Cherry
by Zhenshan Liu, Shuaiwei Yang, Lisu Hao, Hao Wang, Jing Zhang, Wen He, Mengyao Li, Yuanxiu Lin, Yunting Zhang, Qing Chen, Yong Zhang, Ya Luo, Haoru Tang, Yan Wang and Xiaorong Wang
Agronomy 2024, 14(12), 2862; https://doi.org/10.3390/agronomy14122862 - 30 Nov 2024
Cited by 1 | Viewed by 664
Abstract
Chinese cherry [Prunus. pseudocerasus Lindl., syn. Cerasus. pseudocerasus (Lindl.) G.Don], an economically important tetraploid fruit crop native to southwestern China, is celebrated as “the earliest fruit of spring”. Understanding the inheritance and heterosis of major agronomical traits is essential for advancing its [...] Read more.
Chinese cherry [Prunus. pseudocerasus Lindl., syn. Cerasus. pseudocerasus (Lindl.) G.Don], an economically important tetraploid fruit crop native to southwestern China, is celebrated as “the earliest fruit of spring”. Understanding the inheritance and heterosis of major agronomical traits is essential for advancing its breeding. In this study, we conducted a three-year observation and inheritance analysis of 32 economic traits in the reciprocal F1 populations (NH, n = 114; HN, n = 87) derived from Chinese cherry landraces “Nanzaohong” and “Hongfei”. The results revealed a broad segregation for all traits in F1 offspring. Fruit size exhibited an inheritance tendency toward smaller dimensions, with some individuals displaying extreme values (Fruit weight, HH = 3.90~12.15%) that highlighted the potential for selecting larger fruits. The hybrids showed a tendency for sweeter fruit flavor, with total soluble solids (RHm = 7.00~19.35%) and soluble sugar (RHm = 11.09% and 17.47%) exhibiting hybrid vigor, along with a decreasing tendency in titratable acid (RHm = −16.08~−1.05%). The flowering and fruiting phenology tended to occur earlier, with extremely early and late flowering lines offering the potential to extend the ornamental and harvesting periods. Fruit bitterness (H2 = 0.98 and 0.95) and fruit skin color (H2 = 0.93 and 0.89) displayed the highest heritability. Correlation analysis revealed strong internal correlations among trait categories, confirming the reliability of the data collection and analysis. Moreover, no significant differences were observed between the maternal and the paternal effect on the inheritance for agronomic traits attributes. This study systematically clarifies the inheritance trends of agronomic traits in Chinese cherry, providing a foundation for the rational selection of parental lines in breeding strategies and laying the groundwork for future molecular genetic research. Full article
(This article belongs to the Special Issue Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition)
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14 pages, 3592 KiB  
Article
Characterization of Superoxide Dismutase (SOD) Gene Family and Their Responses to Salinity Stress and Fruit Development in Octoploid Strawberry
by Yunting Zhang, Yan Chen, Weiliang Gao, Su Tian, Bangyu Lin, Xianjie Gu, Yuanxiu Lin, Mengyao Li, Yan Wang, Wen He, Yong Zhang, Qing Chen, Ya Luo, Xiaorong Wang and Haoru Tang
Agronomy 2024, 14(11), 2514; https://doi.org/10.3390/agronomy14112514 - 26 Oct 2024
Cited by 1 | Viewed by 1205
Abstract
Superoxide dismutases (SODs), as the first line of defense against reactive oxygen species (ROS), play an essential role in protecting plants from adverse elicitors during plant growth and development. However, little is known about the SOD gene family and their response to salinity [...] Read more.
Superoxide dismutases (SODs), as the first line of defense against reactive oxygen species (ROS), play an essential role in protecting plants from adverse elicitors during plant growth and development. However, little is known about the SOD gene family and their response to salinity stress and fruit development in cultivated strawberries (Fragaria × ananassa). In this study, 32 SOD genes consisting of 16 Cu/ZnSODs, 11 FeSODs, and 5 MnSOD were identified, which presented three well-resolved clades in the phylogenetic tree. Each clade had similar motifs, and exon–intron structures, which in turn supported the evolutionary classification. Cis-acting element analysis suggested that FaSOD genes might be involved in the plant response to abiotic and biotic stresses, hormones, and light. The analysis of previously published transcriptome data revealed that FaSOD genes are expressed variably under salt stress. Among these SODs, FaMSD5 was expressed at relatively high levels in strawberry root and leaf, and its transcript abundance significantly increased after salt treatment. Some transcription factors related to photomorphogenesis, hormone signaling pathways, and hyperosmotic salinity response were predicted to bind to the FaMSD5 promoter. These outcomes implied that FaMSD5 might play an important role in protection against salt stress. In addition, the comprehensive transcriptome analysis of FaSOD genes in strawberry fruit showed that almost all FaCSDs and FaMSDs were more highly expressed than FaFSDs at different developmental stages, and the expression patterns of FaCSD1, FaCSD2, FaCSD7, FaCSD8, and FaCSD10 suggested that they were likely to be involved in fruit development and ripening. This study provides a basis for further exploration of the function of the FaSOD gene family in strawberry and provides candidate FaSOD genes for enhancing salinity tolerance and regulating fruit development and ripening. Full article
(This article belongs to the Special Issue Progress in Horticultural Crops—from Genotype to Phenotype—2nd Edition)
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