Editorial

3 pages, 169 KiB

Open AccessEditorial

Genomics and Biotechnology Empower Plant Science Research

by Yufan Liang, Fei Chen and Jia-Yu Xue

Horticulturae 2023, 9(8), 863; https://doi.org/10.3390/horticulturae9080863 - 28 Jul 2023

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Genomics and biotechnology play crucial roles in biological research, rapidly propelling the field of plant science [...] Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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17 pages, 5562 KiB

Open AccessArticle

Comparative Analyses of Superoxide Dismutase (SOD) Gene Family and Expression Profiling under Multiple Abiotic Stresses in Water Lilies

by Wasi Ullah Khan, Latif Ullah Khan, Dan Chen and Fei Chen

Horticulturae 2023, 9(7), 781; https://doi.org/10.3390/horticulturae9070781 - 08 Jul 2023

Cited by 4 | Viewed by 1557

Abstract

Plants in their natural habitat frequently face different biotic and abiotic stresses, which lead to the production of reactive oxygen species (ROS) that can damage cell membranes, cause peroxidation and deterioration of macromolecules, and ultimately result in cell death. Superoxide dismutase (SOD), a [...] Read more.

Plants in their natural habitat frequently face different biotic and abiotic stresses, which lead to the production of reactive oxygen species (ROS) that can damage cell membranes, cause peroxidation and deterioration of macromolecules, and ultimately result in cell death. Superoxide dismutase (SOD), a class of metalloenzymes, is primarily found in living organisms and serves as the principal line of defense against ROS. The SOD gene family has not yet been characterized in any species of water lily from the genus Nymphaea. The present study aims to conduct a genome-wide study to discover SOD genes in four representative water lily species. In our present comparative study, we discovered 43 SOD genes in the genomes of four water lily species. The phylogenetic investigation results revealed that SOD genes from water lily and closely related plant species formed two distinct groups, as determined by their binding domains with high bootstrap values. Enzymatic ion-binding classified the SOD gene family into three groups, FeSOD, Cu/ZnSOD, and MnSOD. The analysis of gene structure indicated that the SOD gene family exhibited a relatively conserved organization of exons and introns, as well as motif configuration. Moreover, we discovered that the promoters of water lily SODs contained five phytohormones, four stress-responsive elements, and numerous light-responsive cis-elements. The predicted 3D protein structures revealed water lily SODs form conserved protein dimer signatures that were comparable to each other. Finally, the RT-qPCR gene expression analysis of nine NcSOD genes revealed their responsiveness to heat, saline, cold, cadmium chloride, and copper sulphate stress. These findings establish a basis for further investigation into the role of the SOD gene family in Nymphaea colorata and offer potential avenues for genetic enhancement of water lily aquaculture. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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18 pages, 9621 KiB

Open AccessArticle

Characterization of the Passion Fruit (Passiflora edulis Sim) bHLH Family in Fruit Development and Abiotic Stress and Functional Analysis of PebHLH56 in Cold Stress

by Yi Xu, Weidong Zhou, Funing Ma, Dongmei Huang, Wenting Xing, Bin Wu, Peiguang Sun, Di Chen, Binqiang Xu and Shun Song

Horticulturae 2023, 9(2), 272; https://doi.org/10.3390/horticulturae9020272 - 17 Feb 2023

Cited by 6 | Viewed by 2044

Abstract

Abiotic stress is the focus of research on passion fruit characters because of its damage to the industry. Basic helix-loop-helix (bHLH) is one of the Transcription factors (TFs) which can act in an anti-abiotic stress role through diverse biological processes. However, no systemic [...] Read more.

Abiotic stress is the focus of research on passion fruit characters because of its damage to the industry. Basic helix-loop-helix (bHLH) is one of the Transcription factors (TFs) which can act in an anti-abiotic stress role through diverse biological processes. However, no systemic analysis of the passion fruit bHLH (PebHLH) family was reported. In this study, 117 PebHLH members were identified from the genome of passion fruit, related to plant stress resistance and development by prediction of protein interaction. Furthermore, the transcriptome sequencing results showed that the PebHLHs responded to different abiotic stresses. At different ripening stages of passion fruit, the expression level of most PebHLHs in the immature stage (T1) was higher than that in the mature stage (T2 and T3). Eight PebHLHs with differentially expressed under different stress treatments and different ripening stages were selected and verified by qRT-PCR. In this research, the expression of one member, PebHLH56, was induced under cold stress. Further, the promoter of PebHLH56 was fused to β-Galactosidase (GUS) to generate the expression vector that was transformed into Arabidopsis. It showed that PebHLH56 could significantly respond to cold stress. This study provided new insights into the regulatory functions of PebHLH genes during fruit maturity stages and abiotic stress, thereby improving the understanding of the characteristics and evolution of the PebHLH gene family. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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16 pages, 6326 KiB

Open AccessArticle

Systematic Identification of Long Non-Coding RNAs under Allelopathic Interference of Para-Hydroxybenzoic Acid in S. lycopersicum

by Guoting Liang, Yajie Niu and Jing Guo

Horticulturae 2022, 8(12), 1134; https://doi.org/10.3390/horticulturae8121134 - 02 Dec 2022

Cited by 1 | Viewed by 960

Abstract

The importance of long noncoding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of the lncRNAs expressed during plant allelopathy has not been carried out. We performed RNA-seq experiments on S. lycopersicum subjected to different levels of para-hydroxybenzoic acid [...] Read more.

The importance of long noncoding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of the lncRNAs expressed during plant allelopathy has not been carried out. We performed RNA-seq experiments on S. lycopersicum subjected to different levels of para-hydroxybenzoic acid (PHBA) stress during plant allelopathy and identified 61,729 putative lncRNAs. Of these, 7765 lncRNAs cis-regulated 5314 protein-coding genes (PGs). Among these genes, 1116 lncRNAs and 2239 PGs were involved in a complex web of transcriptome regulation, and we divided these genes into 12 modules. Within these modules, 458 lncRNAs and 975 target genes were found to be highly correlated. Additionally, 989 lncRNAs trans-regulated 1765 PGs, and we classified them into 11 modules, within which 335 lncRNAs were highly correlated with their 633 corresponding target genes. Only 98 lncRNAs in S. lycopersicum had homologs in the lncRNA database of Arabidopsis thaliana, all of which were affected by the PHBA treatments. MiRNAs that interacted with both mRNAs and lncRNAs were selected on the basis of weighted correlation network analysis (WGCNA) results to make lncRNA-miRNA-mRNA triplets. Our study presents a systematic identification of lncRNAs involved in plant allelopathy in S. lycopersicum and provides research references for future studies. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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21 pages, 5199 KiB

Open AccessArticle

Mechanism by Which High Foliar Calcium Contents Inhibit Sugar Accumulation in Feizixiao Lychee Pulp

by Xian Shui, Wenjing Wang, Wuqiang Ma, Chengkun Yang and Kaibing Zhou

Horticulturae 2022, 8(11), 1044; https://doi.org/10.3390/horticulturae8111044 - 07 Nov 2022

Cited by 3 | Viewed by 1408

Abstract

The problem of Feizixiao lychee fruit cracking is typically solved by the application of calcium to the leaves. However, lychee trees are sensitive to excessive amounts of calcium, and in practice, it is easy to spray excessive amounts that result in fertilizer burns. [...] Read more.

The problem of Feizixiao lychee fruit cracking is typically solved by the application of calcium to the leaves. However, lychee trees are sensitive to excessive amounts of calcium, and in practice, it is easy to spray excessive amounts that result in fertilizer burns. This paper intends to explore the effects of excessive calcium fertilizer application on lychee fruit pulp quality and the underlying molecular physiological mechanism. Adult Feizixiao lychee trees were used as test materials; concerning treatment, a 54 μM anhydrous CaCl₂ aqueous solution was sprayed onto the leaves, and water was used as a control (CK). The levels of pulp sugar and the activities of key enzymes involved in glucose metabolism were observed, and transcriptome analysis and genetic screening were performed on the pulp. Spraying excessive amounts of calcium onto the leaf surfaces caused the downregulation of trehalase-encoding genes and SUS-encoding genes, thus inhibiting the activities of trehalase, SS-I and SS-II, and further inhibiting the accumulation of glucose, fructose, and sucrose. Moreover, upregulation of VIN gene expression enhanced AI activity and inhibited sucrose accumulation, thus inhibiting upregulation of NI gene expression during fruit growth and expansion; in turn, this inhibited the increase in NI activity in the fruit pulp, which then decreased the glucose and fructose accumulation in the pulp in the high-calcium treatment group compared with the CK group. The downregulation and expression of CHS family genes may lead to a decrease in chalcone accumulation, which may lead to damage caused by active oxygen production in the fruit pulp, thus inhibiting the accumulation of soluble sugars in that tissue. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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11 pages, 3688 KiB

Open AccessEditor’s ChoiceArticle

Development of InDel Markers for Gypsophila paniculata Based on Genome Resequencing

by Chunlian Jin, Bin Liu, Jiwei Ruan, Chunmei Yang and Fan Li

Horticulturae 2022, 8(10), 921; https://doi.org/10.3390/horticulturae8100921 - 07 Oct 2022

Cited by 3 | Viewed by 1435

Abstract

Gypsophila paniculata is the only species in the genus Gypsophila that has been used as cut flowers, and the sequencing of its genome has just been completed, opening a new chapter in its molecular genetic breeding. The molecular marker system is the basis [...] Read more.

Gypsophila paniculata is the only species in the genus Gypsophila that has been used as cut flowers, and the sequencing of its genome has just been completed, opening a new chapter in its molecular genetic breeding. The molecular marker system is the basis for genetic molecular research in the era of genomics, whereas it is still a gap for G. paniculata. In this study, we constructed a genome-wide InDel marker system of G. paniculata after genome resequencing of another wild-type accession with white flowers. Consequently, 407 InDel markers at a distance of ~2 Mb were designed for all 17 chromosomes. Later, the validation of these markers by PCR revealed that 289 markers could distinguish alleles of the two wild-type alleles clearly. The predicted polymorphisms of two wild-type alleles were then transferred to the commercial cultivars, which displayed a rich polymorphism among four commercial cultivars. Our research established the first genome-level genetic map in G. paniculata, providing a comprehensive set of marker systems for its molecular research. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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13 pages, 2780 KiB

Open AccessArticle

Genetic Diversity and Genome-Wide Association Study of Architectural Traits of Spray Cut Chrysanthemum Varieties

by Daojin Sun, Luyao Zhang, Jiangshuo Su, Qi Yu, Jiali Zhang, Weimin Fang, Haibin Wang, Zhiyong Guan, Fadi Chen and Aiping Song

Horticulturae 2022, 8(5), 458; https://doi.org/10.3390/horticulturae8050458 - 19 May 2022

Cited by 4 | Viewed by 2117

Abstract

The architecture of spray cut chrysanthemum is crucial for the quality and quantity of cut flower production. However, the mechanism underlying plant architecture still needs to be clarified. In this study, we measured nine architecture-related traits of 195 spray cut chrysanthemum varieties during [...] Read more.

The architecture of spray cut chrysanthemum is crucial for the quality and quantity of cut flower production. However, the mechanism underlying plant architecture still needs to be clarified. In this study, we measured nine architecture-related traits of 195 spray cut chrysanthemum varieties during a two-year period. The results showed that the number of upper primary branches, number of lateral flower buds and primary branch length widely varied. Additionally, plant height had a significant positive correlation with number of leaf nodes and total number of lateral buds. Number of upper primary branches had a significant negative correlation with primary branch diameter, primary branch angle and primary branch length. Plant height, total number of lateral buds, number of upper primary branches, stem diameter, primary branch diameter and primary branch length were vulnerable to environmental impacts. All varieties could be divided into five categories according to cluster analysis, and the typical plant architecture of the varieties was summarized. Finally, a genome-wide association study (GWAS) was performed to find potential functional genes. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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13 pages, 4359 KiB

Open AccessArticle

C-CorA: A Cluster-Based Method for Correlation Analysis of RNA-Seq Data

by Jianpu Qian, Wenli Liu, Yanna Shi, Mengxue Zhang, Qingbiao Wu, Kunsong Chen and Wenbo Chen

Horticulturae 2022, 8(2), 124; https://doi.org/10.3390/horticulturae8020124 - 29 Jan 2022

Cited by 1 | Viewed by 3616

Abstract

Correlation analysis is a routine method of biological data analysis. In the process of RNA-Seq analysis, differentially expressed genes could be identified by calculating the correlation coefficients in the comparison of gene expression vs. phenotype or gene expression vs. gene expression. However, due [...] Read more.

Correlation analysis is a routine method of biological data analysis. In the process of RNA-Seq analysis, differentially expressed genes could be identified by calculating the correlation coefficients in the comparison of gene expression vs. phenotype or gene expression vs. gene expression. However, due to the complicated genetic backgrounds of perennial fruit, the correlation coefficients between phenotypes and genes are usually not high in fruit quality studies. In this study, a cluster-based correlation analysis method (C-CorA) is presented for fruit RNA-Seq analysis. C-CorA is composed of two main parts: the clustering analysis and the correlation analysis. The algorithm is described and then integrated into the MATLAB code and the C# WPF project. The C-CorA method was applied to RNA-Seq datasets of loquat (Eriobotrya japonica) fruit stored or ripened under different conditions. Low temperature conditioning or heat treatment of loquat fruit can alleviate the extent of lignification that occurs because of postharvest storage under low temperatures (0 °C). The C-CorA method generated correlation coefficients and identified many candidate genes correlated with lignification, including EjCAD3 and EjCAD4 and transcription factors such as MYB (UN00328). C-CorA is an effective new method for the correlation analysis of various types of data with different dimensions and can be applied to RNA-Seq data for candidate gene detection in fruit quality studies. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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21 pages, 7304 KiB

Open AccessArticle

QTL Mapping of Resistance to Bacterial Wilt in Pepper Plants (Capsicum annuum) Using Genotyping-by-Sequencing (GBS)

by Soo-Young Chae, Kwanuk Lee, Jae-Wahng Do, Sun-Cheul Hong, Kang-Hyun Lee, Myeong-Cheoul Cho, Eun-Young Yang and Jae-Bok Yoon

Horticulturae 2022, 8(2), 115; https://doi.org/10.3390/horticulturae8020115 - 27 Jan 2022

Cited by 8 | Viewed by 3501

Abstract

Bacterial wilt (BW) disease, which is caused by Ralstonia solanacearum, is one globally prevalent plant disease leading to significant losses of crop production and yield with the involvement of a diverse variety of monocot and dicot host plants. In particular, the BW [...] Read more.

Bacterial wilt (BW) disease, which is caused by Ralstonia solanacearum, is one globally prevalent plant disease leading to significant losses of crop production and yield with the involvement of a diverse variety of monocot and dicot host plants. In particular, the BW of the soil-borne disease seriously influences solanaceous crops, including peppers (sweet and chili peppers), paprika, tomatoes, potatoes, and eggplants. Recent studies have explored genetic regions that are associated with BW resistance for pepper crops. However, owing to the complexity of BW resistance, the identification of the genomic regions controlling BW resistance is poorly understood and still remains to be unraveled in the pepper cultivars. In this study, we performed the quantitative trait loci (QTL) analysis to identify genomic loci and alleles, which play a critical role in the resistance to BW in pepper plants. The disease symptoms and resistance levels for BW were assessed by inoculation with R. solanacearum. Genotyping-by-sequencing (GBS) was utilized in 94 F₂ segregating populations originated from a cross between a resistant line, KC352, and a susceptible line, 14F6002-14. A total of 628,437 single-nucleotide polymorphism (SNP) was obtained, and a pepper genetic linkage map was constructed with putative 1550 SNP markers via the filtering criteria. The linkage map exhibited 16 linkage groups (LG) with a total linkage distance of 828.449 cM. Notably, QTL analysis with CIM (composite interval mapping) method uncovered pBWR-1 QTL underlying on chromosome 01 and explained 20.13 to 25.16% by R² (proportion of explained phenotyphic variance by the QTL) values. These results will be valuable for developing SNP markers associated with BW-resistant QTLs as well as for developing elite BW-resistant cultivars in pepper breeding programs. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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14 pages, 4551 KiB

Open AccessArticle

GDS: A Genomic Database for Strawberries (Fragaria spp.)

by Yuhan Zhou, Yushan Qiao, Zhiyou Ni, Jianke Du, Jinsong Xiong, Zongming Cheng and Fei Chen

Horticulturae 2022, 8(1), 41; https://doi.org/10.3390/horticulturae8010041 - 31 Dec 2021

Cited by 4 | Viewed by 3523

Abstract

Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale [...] Read more.

Strawberry species (Fragaria spp.) are known as the “queen of fruits” and are cultivated around the world. Over the past few years, eight strawberry genome sequences have been released. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. To promote the reuse and exploration of strawberry genomic data and enable extensive analyses using various bioinformatics tools, we have developed the Genome Database for Strawberry (GDS). This platform integrates the genome collection, storage, integration, analysis, and dissemination of large amounts of data for researchers engaged in the study of strawberry. We collected and formatted the eight published strawberry genomes. We constructed the GDS based on Linux, Apache, PHP and MySQL. Different bioinformatic software were integrated. The GDS contains data from eight strawberry species, as well as multiple tools such as BLAST, JBrowse, synteny analysis, and gene search. It has a designed interface and user-friendly tools that perform a variety of query tasks with a few simple operations. In the future, we hope that the GDS will serve as a community resource for the study of strawberries. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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12 pages, 1763 KiB

Open AccessArticle

Frequent Gene Duplication/Loss Shapes Distinct Evolutionary Patterns of NLR Genes in Arecaceae Species

by Xiao-Tong Li, Guang-Can Zhou, Xing-Yu Feng, Zhen Zeng, Yang Liu and Zhu-Qing Shao

Horticulturae 2021, 7(12), 539; https://doi.org/10.3390/horticulturae7120539 - 02 Dec 2021

Cited by 6 | Viewed by 1565

Abstract

Nucleotide-binding leucine-rich repeat (NLR) genes play a key role in plant immune responses and have co-evolved with pathogens since the origin of green plants. Comparative genomic studies on the evolution of NLR genes have been carried out in several angiosperm lineages. However, most [...] Read more.

Nucleotide-binding leucine-rich repeat (NLR) genes play a key role in plant immune responses and have co-evolved with pathogens since the origin of green plants. Comparative genomic studies on the evolution of NLR genes have been carried out in several angiosperm lineages. However, most of these lineages come from the dicot clade. In this study, comparative analysis was performed on NLR genes from five Arecaceae species to trace the dynamic evolutionary pattern of the gene family during species speciation in this monocot lineage. The results showed that NLR genes from the genomes of Elaeis guineensis (262), Phoenix dactylifera (85), Daemonorops jenkinsiana (536), Cocos nucifera (135) and Calamus simplicifolius (399) are highly variable. Frequent domain loss and alien domain integration have occurred to shape the NLR protein structures. Phylogenetic analysis revealed that NLR genes from the five genomes were derived from dozens of ancestral genes. D. jenkinsiana and E. guineensis genomes have experienced “consistent expansion” of the ancestral NLR lineages, whereas a pattern of “first expansion and then contraction” of NLR genes was observed for P. dactylifera, C. nucifera and C. simplicifolius. The results suggest that rapid and dynamic gene content and structure variation have shaped the NLR profiles of Arecaceae species. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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16 pages, 2835 KiB

Open AccessEssay

RNA-Seq Based Transcriptomic Analysis of Bud Sport Skin Color in Grape Berries

by Wuwu Wen, Haimeng Fang, Lingqi Yue, Muhammad Khalil-Ur-Rehman, Yiqi Huang, Zhaoxuan Du, Guoshun Yang and Yanshuai Xu

Horticulturae 2023, 9(2), 260; https://doi.org/10.3390/horticulturae9020260 - 15 Feb 2023

Cited by 1 | Viewed by 1329

Abstract

The most common bud sport trait in grapevines is the change in color of grape berry skin, and the color of grapes is mainly developed by the composition and accumulation of anthocyanins. Many studies have shown that MYBA is a key gene regulates [...] Read more.

The most common bud sport trait in grapevines is the change in color of grape berry skin, and the color of grapes is mainly developed by the composition and accumulation of anthocyanins. Many studies have shown that MYBA is a key gene regulates the initiation of bud sport color and anthocyanin synthesis in grape peels. In the current study, we used berry skins of ‘Italia’, ‘Benitaka’, ‘Muscat of Alexandria’, ‘Flame Muscat’, ‘Rosario Bianco’, ‘Rosario Rosso’, and ‘Red Rosario’ at the véraison stage (10 weeks post-flowering and 11 weeks post-flowering) as research materials. The relative expressions of genes related to grape berry bud sport skin color were evaluated utilizing RNA-Seq technology. The results revealed that the expressions of the VvMYBA1/A2 gene in the three red grape varieties at the véraison stage were higher than in the three white grape varieties. The VvMYBA1/A2 gene is known to be associated with UFGT in the anthocyanin synthesis pathway. According to the results, VvMYBA1/A2 gene expression could also be associated with the expression of LDOX. In addition, a single gene (gene ID: Vitvi19g01871) displayed the highest expressions in all the samples at the véraison stage for the six varieties. The expression of this gene was much higher in the three green varieties compared to the three red ones. GO molecular function annotation identified it as a putative metallothionein-like protein with the ability to regulate the binding of copper ions to zinc ions and the role of maintaining the internal stable state of copper ions at the cellular level. High expression levels of this screened gene may play an important role in bud sport color of grape berry skin at the véraison stage. Full article

(This article belongs to the Special Issue Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants)

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