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Genetics and Breeding of Horticulture Crops
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Genetics and Breeding of Horticulture Crops

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 10 May 2024 | Viewed by 6015

Special Issue Editors

Dr. Jun Tang

E-Mail
Guest Editor
Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
Interests: horticultural crop; biotechnology; genetics; genomics; genotype; phenotype
Dr. Liwei Gao

E-Mail Website
Guest Editor
College of Life Sciences, Gannan Normal University (Golden Campus), Ganzhou 341000, China
Interests: horticultural crop; abiotic stress; gene cloning; genomics, biotechnology

Special Issue Information

Dear Colleagues,

Horticultural crops contain numerous health-promoting phytochemicals, such as vitamins, flavonoids, polyphenols, and other secondary metabolites, that play an important role in the global food supply and human health. The yield and quality of horticultural crops depends on the intrinsic genetics and genome characteristics as well as environmental conditions. The discovery of genes for horticultural crop yield, quality, and resistance has unlocked the potential to accelerate horticultural crop molecular breeding, with continuous advancement in genome data, molecular marker, gene discovery, gene editing and multi-omics technology, e.g., genomics, transcriptomics, proteomics, metabolomics, interactomics, and phenomics. The utilization of all these new techniques in combination with the analysis of genomic data using bioinformatics tools contributes to a better understanding of the function of various agronomic traits of interest as well as horticultural crop breeding.

The goal of this Special Issue is to collect the latest advances in understanding the genetics and breeding of horticulture crops by integration with multi-omics, revealing molecular mechanisms of agronomically important traits in horticultural crops, such as yield, quality, and resistance to abiotic and biotic stresses. We particularly encourage research derived from the development or application of new omics technologies in horticultural crops as well as new methods for the analysis, mining, and visualization of horticultural crop omics datasets.

We welcome submissions of all article types on, but are not limited to, the following subtopics:

  • Genetic and functional characterization of genes regulating horticultural crop growth and development;
  • Development of novel omics technologies for horticultural crop improvement, software, and algorithms;
  • Genetic improvement in horticultural crops using gene editing and other modern biotechnologies;
  • Integration with multi-omics revealing the molecular basis of important agronomic traits in horticultural crops.

Dr. Jun Tang
Dr. Liwei Gao
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. Genes 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
  • biotechnology
  • gene function
  • genetics
  • genomics
  • genotype
  • phenotype

Published Papers (5 papers)

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Research

13 pages, 4175 KiB  
Article
Identification of Volatile Compounds and Terpene Synthase (TPS) Genes Reveals ZcTPS02 Involved in β-Ocimene Biosynthesis in Zephyranthes candida
by Guo Wei, Yang Xu, Mengmeng Xu, Xinwei Shi, Jianwen Wang and Liguo Feng
Genes 2024, 15(2), 185; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15020185 - 30 Jan 2024
Viewed by 839
Abstract
Zephyranthes candida is a frequently cultivated ornamental plant containing several secondary metabolites, including alkaloids, flavonoids, and volatile organic compounds (VOCs). However, extensive research has been conducted only on non-VOCs found in the plant, whereas the production of VOCs and the molecular mechanisms underlying [...] Read more.
Zephyranthes candida is a frequently cultivated ornamental plant containing several secondary metabolites, including alkaloids, flavonoids, and volatile organic compounds (VOCs). However, extensive research has been conducted only on non-VOCs found in the plant, whereas the production of VOCs and the molecular mechanisms underlying the biosynthesis of terpenes remain poorly understood. In this study, 17 volatile compounds were identified from Z. candida flowers using gas chromatography–mass spectrometry (GC-MS), with 16 of them being terpenoids. Transcriptome sequencing resulted in the identification of 17 terpene synthase (TPS) genes; two TPS genes, ZcTPS01 and ZcTPS02, had high expression levels. Biochemical characterization of two enzymes encoded by both genes revealed that ZcTPS02 can catalyze geranyl diphosphate (GPP) into diverse products, among which is β-ocimene, which is the second most abundant compound found in Z. candida flowers. These results suggest that ZcTPS02 plays a vital role in β-ocimene biosynthesis, providing valuable insights into terpene biosynthesis pathways in Z. candida. Furthermore, the expression of ZcTPS02 was upregulated after 2 h of methyl jasmonate (MeJA) treatment and downregulated after 4 h of the same treatment. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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22 pages, 9497 KiB  
Article
Genome-Wide Identification of BrCAX Genes and Functional Analysis of BrCAX1 Involved in Ca2+ Transport and Ca2+ Deficiency-Induced Tip-Burn in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)
by Shuning Cui, Hong Liu, Yong Wu, Lugang Zhang and Shanshan Nie
Genes 2023, 14(9), 1810; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14091810 - 17 Sep 2023
Viewed by 1121
Abstract
Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ [...] Read more.
Calcium (Ca2+) plays essential roles in plant growth and development. Ca2+ deficiency causes a physiological disorder of tip-burn in Brassiceae crops and is involved in the regulation of cellular Ca2+ homeostasis. Although the functions of Ca2+/H+ exchanger antiporters (CAXs) in mediating transmembrane transport of Ca2+ have been extensively characterized in multiple plant species, the potential roles of BrCAX genes remain unclear in Chinese cabbage. In this study, eight genes of the BrCAX family were genome-widely identified in Chinese cabbage. These BrCAX proteins contained conserved Na_Ca_ex domain and belonged to five members of the CAX family. Molecular evolutionary analysis and sequence alignment revealed the evolutionary conservation of BrCAX family genes. Expression profiling demonstrated that eight BrCAX genes exhibited differential expression in different tissues and under heat stress. Furthermore, Ca2+ deficiency treatment induced the typical symptoms of tip-burn in Chinese cabbage seedlings and a significant decrease in total Ca2+ content in both roots and leaves. The expression changes in BrCAX genes were related to the response to Ca2+ deficiency-induced tip-burn of Chinese cabbage. Specially, BrCAX1-1 and BrCAX1-2 genes were highly expressed gene members of the BrCAX family in the leaves and were significantly differentially expressed under Ca2+ deficiency stress. Moreover, overexpression of BrCAX1-1 and BrCAX1-2 genes in yeast and Chinese cabbage cotyledons exhibited a higher Ca2+ tolerance, indicating the Ca2+ transport capacity of BrCAX1-1 and BrCAX1-2. In addition, suppression expression of BrCAX1-1 and BrCAX1-2 genes reduced cytosolic Ca2+ levels in the root tips of Chinese cabbage. These results provide references for functional studies of BrCAX genes and to investigate the regulatory mechanisms underlying Ca2+ deficiency disorder in Brassiceae vegetables. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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14 pages, 4879 KiB  
Article
Alternative Splicing for Leucanthemella linearis NST1 Contributes to Variable Abiotic Stress Resistance in Transgenic Tobacco
by Hai Wang, Yuning Guo, Xueying Hao, Wenxin Zhang, Yanxia Xu, Wenting He, Yanxi Li, Shiyi Cai, Xiang Zhao and Xuebin Song
Genes 2023, 14(8), 1549; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14081549 - 28 Jul 2023
Cited by 2 | Viewed by 871
Abstract
Leucanthemella linearis is a marsh plant in the family Compositae. It has good water and moisture resistance and ornamental properties, which makes it one of the important materials for chrysanthemum breeding and genetic improvement. The NST1 (NAC secondary wall enhancement factor 1) [...] Read more.
Leucanthemella linearis is a marsh plant in the family Compositae. It has good water and moisture resistance and ornamental properties, which makes it one of the important materials for chrysanthemum breeding and genetic improvement. The NST1 (NAC secondary wall enhancement factor 1) gene is associated with the thickening of the secondary walls of fiber cells in the plant ducts and the secondary xylem and plays an important role in plant stress resistance. In this study, two variable spliceosomes of the NST1 gene were identified from a chrysanthemum plant by using bioinformatics, qRT-PCR, transgene, and paraffin section methods to explore the molecular mechanism of the variable splicing of NST1 under abiotic stress. The results show that only three amino acids were found to be different between the two LlNST1 variants. After being treated with salt, drought, and low temperatures, analysis of the expression levels of the LlNST1 and LlNST1.1 genes in Ll showed that LlNST1.1 could respond to low temperatures and salt stress and had a weak response to drought stress. However, the expression level of LlNST1 under the three treatments was lower than that of LlNST1.1. LlNST1 transgenic tobacco showed increased saline–alkali resistance and low-temperature resistance at the seedling stage. LlNST1.1 transgenic tobacco also showed enhanced saline–alkali resistance and drought resistance at the seedling stage. In conclusion, the functions of the two variable spliceosomes of the NST1 gene are very different under abiotic stress. Therefore, this study verified the function of the variable spliceosome of NST1 and improved the stress resistance of the chrysanthemum plant under examination by regulating the expression of the NST protein, which lays a material foundation for the improvement of plant stress resistance materials and has important significance for the study of the resistance of chrysanthemum plants to abiotic stress. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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22 pages, 5031 KiB  
Article
Integrated Transcriptomics and Metabolomics Analysis of the Fructan Metabolism Response to Low-Temperature Stress in Garlic
by Haiyan Bian, Qianyi Zhou, Zhongping Du, Guangnan Zhang, Rui Han, Laisheng Chen, Jie Tian and Yi Li
Genes 2023, 14(6), 1290; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14061290 - 19 Jun 2023
Cited by 2 | Viewed by 1410
Abstract
As the main reserve carbohydrate in garlic, fructan contributes to garlic’s yield and quality formation. Numerous studies have shown that plant fructan metabolism induces a stress response to adverse environments. However, the transcriptional regulation mechanism of garlic fructan in low-temperature environments is still [...] Read more.
As the main reserve carbohydrate in garlic, fructan contributes to garlic’s yield and quality formation. Numerous studies have shown that plant fructan metabolism induces a stress response to adverse environments. However, the transcriptional regulation mechanism of garlic fructan in low-temperature environments is still unknown. In this study, the fructan metabolism of garlic seedlings under low-temperature stress was revealed by transcriptome and metabolome approaches. With the extension of stress time, the number of differentially expressed genes and metabolites increased. Using weighted gene co-expression network analysis (WGCNA), three key enzyme genes related to fructan metabolism were screened (a total of 12 transcripts): sucrose: sucrose 1-fructosyltransferase (1-SST) gene; fructan: fructan 6G fructosyltransferase (6G-FFT) gene; and fructan 1-exohydrolase (1-FEH) gene. Finally, two hub genes were obtained, namely Cluster-4573.161559 (6G-FFT) and Cluster-4573.153574 (1-FEH). The correlation network and metabolic heat map analysis between fructan genes and carbohydrate metabolites indicate that the expression of key enzyme genes in fructan metabolism plays a positive promoting role in the fructan response to low temperatures in garlic. The number of genes associated with the key enzyme of fructan metabolism in trehalose 6-phosphate was the highest, and the accumulation of trehalose 6-phosphate content may mainly depend on the key enzyme genes of fructan metabolism rather than the enzyme genes in its own synthesis pathway. This study not only obtained the key genes of fructan metabolism in garlic seedlings responding to low temperatures but also preliminarily analyzed its regulatory mechanism, providing an important theoretical basis for further elucidating the cold resistance mechanism of garlic fructan metabolism. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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18 pages, 6684 KiB  
Article
Ectopic Expression of BcCUC2 Involved in Sculpting the Leaf Margin Serration in Arabidopsis thaliana
by Wanqi Li, Tongtong Wang, Yu Ma, Nan Wang, Wenjing Wang, Jun Tang, Changwei Zhang, Xilin Hou and Hualan Hou
Genes 2023, 14(6), 1272; https://0-doi-org.brum.beds.ac.uk/10.3390/genes14061272 - 15 Jun 2023
Viewed by 1097
Abstract
Leaf margin serration is a morphological characteristic in plants. The CUC2 (CUP-SHAPED COTYLEDON 2) gene plays an important role in the outgrowth of leaf teeth and enhances leaf serration via suppression of growth in the sinus. In this study, we isolated [...] Read more.
Leaf margin serration is a morphological characteristic in plants. The CUC2 (CUP-SHAPED COTYLEDON 2) gene plays an important role in the outgrowth of leaf teeth and enhances leaf serration via suppression of growth in the sinus. In this study, we isolated the BcCUC2 gene from Pak-choi (Brassica rapa ssp. chinensis), which contains a 1104 bp coding sequence, encoding 367 amino acid residues. Multiple sequence alignment exhibited that the BcCUC2 gene has a typical conserved NAC domain, and phylogenetic relationship analysis showed that the BcCUC2 protein has high identity with Cruciferae plants (Brassica oleracea, Arabidopsis thaliana, and Cardamine hirsuta). The tissue-specific expression analysis displayed that the BcCUC2 gene has relatively high transcript abundance in floral organs. Meanwhile, the expression profile of BcCUC2 was relatively higher in the ‘082’ lines with serrate leaf margins than the ‘001’ lines with smooth leaf margins in young leaves, roots, and hypocotyls. In addition, the transcript level of BcCUC2 was up-regulated by IAA and GA3 treatment, especially at 1–3 h. The subcellular localization assay demonstrated that BcCUC2 was a nuclear-target protein. Furthermore, leaf serration occurred, and the number of the inflorescence stem was increased in the transgenic Arabidopsis thaliana plants’ overexpressed BcCUC2 gene. These data illustrated that BcCUC2 is involved in the development of leaf margin serration, lateral branches, and floral organs, contributing to further uncovering and perfecting the regulation mechanism of leaf serration in Pak-choi. Full article
(This article belongs to the Special Issue Genetics and Breeding of Horticulture Crops)
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