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Advances in Research for Horticultural Crops Breeding and Genetics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 December 2023) | Viewed by 15638

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Guest Editor
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, China
Interests: horticultural crop genetics and germplasm enhancement; secondary metabolism; abiotic stress; horticultural crop evolutionary genomics and domestication
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural crops are excellent sources of carbohydrates, protein, dietary fiber, vitamins and minerals, as well as the major source of most dietary antioxidants. With the growing world population and the effects of climate change, there is a need to enhance the production and also the quality of horticultural products. To meet future ecological and economic demands, conventional breeding methods combine with new biological technologies, such as the high throughput technologies, molecular markers, genetic engineering and genome editing, and phenomics, have been widely applied to lead the improvement of yield, quality, abiotic and biotic stresses in horticultural crops, and accelerate the development of new or improved cultivars.

The purpose of this Special Issue is to report the advances research for horticultural crops breeding and genetics. All original research papers or reviews are encouraged, to highlight innovative research aimed at improving horticultural crops, and to enrich the knowledge of various agronomic traits and functions.

Prof. Dr. Aisheng Xiong
Dr. Mengyao Li
Guest Editors

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Keywords

  • horticultural crops
  • breeding

Published Papers (13 papers)

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Research

19 pages, 6447 KiB  
Article
Morphological Analyses and QTL Mapping of Mottled Leaf in Zucchini (Cucurbita pepo L.)
by Kexin Wang, Xinyu Wang, Lijing Zhang, Yichen Chi, Yusong Luo, Wenlong Xu, Yunli Wang and Shuping Qu
Int. J. Mol. Sci. 2024, 25(5), 2491; https://doi.org/10.3390/ijms25052491 - 20 Feb 2024
Viewed by 501
Abstract
The mottled leaf is one of the agronomic traits of zucchini and can be applied as a marker trait in aggregation breeding. However, the genetic mechanism responsible for mottled leaf has yet to be elucidated. In the present study, we used two inbred [...] Read more.
The mottled leaf is one of the agronomic traits of zucchini and can be applied as a marker trait in aggregation breeding. However, the genetic mechanism responsible for mottled leaf has yet to be elucidated. In the present study, we used two inbred lines (line ‘19’: silver mottled leaf; line ‘113’: normal leaf) as parents for the physiological and genetic analysis of mottled leaf. The synthesis and net photosynthetic rate of chlorophyll were not significantly affected in the mottled areas of leaves. However, we detected a large space between the palisade parenchyma in the leaf mottle area of line ‘19’, which may have caused the mottled leaf phenotype. Light also plays an important role in the formation of mottled leaf, and receiving light during the early stages of leaf development is a necessary factor. Genetic analysis has previously demonstrated that mottled leaf is a quantitative trait that is controlled by multiple genes. Based on the strategy of quantitative trait locus sequencing (QTL-seq), two QTLs were identified on chromosomes 1 and 17, named CpML1.1 and CpML17.1, respectively. Two major loci were identified using R/qtl software version 1.66 under greenhouse conditions in April 2019 (2019A) and April 2020 (2020A) and under open cultivation conditions in May 2020 (2020M). The major QTL, CpML1.1, was located in a 925.2-kb interval on chromosome 1 and explained 10.51%-24.15% of the phenotypic variation. The CpML17.1 was located in a 719.7-kb interval on chromosome 17 and explained 16.25%-38.68% of the phenotypic variation. Based on gene annotation, gene sequence alignment, and qRT–PCR analysis, the Cp4.1LG01g23790 at the CpML1.1 locus encoding a protein of the TPX2 family (target protein of Xklp2) may be a candidate gene for mottled leaf in zucchini. Our findings may provide a theoretical basis for the formation of mottled leaf and provide a foundation for the fine mapping of genes associated with mottled leaf. Molecular markers closely linked to mottled leaf can be used in molecular-assisted selection for the zucchini mottled leaf breeding. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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20 pages, 5580 KiB  
Article
Metabonomics and Transcriptomic Analysis of Free Fatty Acid Synthesis in Seedless and Tenera Oil Palm
by Lu Wei, Cheng Yang, Jerome Jeyakumar John Martin, Rui Li, Lixia Zhou, Shuanghong Cheng, Hongxing Cao and Xiaoyu Liu
Int. J. Mol. Sci. 2024, 25(3), 1686; https://doi.org/10.3390/ijms25031686 - 30 Jan 2024
Viewed by 625
Abstract
Oil palm, a tropical woody oil crop, is widely used in food, cosmetics, and pharmaceuticals due to its high production efficiency and economic value. Palm oil is rich in free fatty acids, polyphenols, vitamin E, and other nutrients, which are beneficial for human [...] Read more.
Oil palm, a tropical woody oil crop, is widely used in food, cosmetics, and pharmaceuticals due to its high production efficiency and economic value. Palm oil is rich in free fatty acids, polyphenols, vitamin E, and other nutrients, which are beneficial for human health when consumed appropriately. Therefore, investigating the dynamic changes in free fatty acid content at different stages of development and hypothesizing the influence of regulatory genes on free fatty acid metabolism is crucial for improving palm oil quality and accelerating industry growth. LC-MS/MS is used to analyze the composition and content of free fatty acids in the flesh after 95 days (MS1 and MT1), 125 days (MS2 and MT2), and 185 days (MS3 and MT3) of Seedless (MS) and Tenera (MT) oil palm species fruit pollination. RNA-Seq was used to analyze the expression of genes regulating free fatty acid synthesis and accumulation, with differences in genes and metabolites mapped to the KEGG pathway map using the KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis method. A metabolomics study identified 17 types of saturated and 13 types of unsaturated free fatty acids during the development of MS and MT. Transcriptomic research revealed that 10,804 significantly different expression genes were acquired in the set differential gene threshold between MS and MT. The results showed that FabB was positively correlated with the contents of three main free fatty acids (stearic acid, myristate acid, and palmitic acid) and negatively correlated with the contents of free palmitic acid in the flesh of MS and MT. ACSL and FATB were positively correlated with the contents of three main free fatty acids and negatively correlated with free myristate acid. The study reveals that the expression of key enzyme genes, FabB and FabF, may improve the synthesis of free myristate in oil palm flesh, while FabF, ACSL, and FATB genes may facilitate the production of free palmitoleic acid. These genes may also promote the synthesis of free stearic acid and palmitoleic acid in oil palm flesh. However, the FabB gene may inhibit stearic acid synthesis, while ACSL and FATB genes may hinder myristate acid production. This study provides a theoretical basis for improving palm oil quality. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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21 pages, 10106 KiB  
Article
Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants (Camellia sinensis)
by Zhihang Hu, Nan Zhang, Zhiyuan Qin, Jinwen Li, Ni Yang, Yi Chen, Jieyu Kong, Wei Luo, Aisheng Xiong and Jing Zhuang
Int. J. Mol. Sci. 2024, 25(1), 657; https://doi.org/10.3390/ijms25010657 - 04 Jan 2024
Viewed by 967
Abstract
The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible ‘clock’ in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor [...] Read more.
The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible ‘clock’ in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant ‘Baiyeyihao’ were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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0 pages, 2039 KiB  
Article
Comprehensive Analysis of Highbush Blueberry Plants Propagated In Vitro and Conventionally
by Marzena Mazurek, Aleksandra Siekierzyńska, Tomasz Piechowiak, Anna Spinardi and Wojciech Litwińczuk
Int. J. Mol. Sci. 2024, 25(1), 544; https://doi.org/10.3390/ijms25010544 - 30 Dec 2023
Cited by 1 | Viewed by 943
Abstract
In vitro culture allows the production of numerous plants with both desirable and undesirable traits. To investigate the impact of the propagation method on highbush blueberry plants, an analysis was performed on four groups of differentially propagated plants: in vitro with axillary (TC-Ax) [...] Read more.
In vitro culture allows the production of numerous plants with both desirable and undesirable traits. To investigate the impact of the propagation method on highbush blueberry plants, an analysis was performed on four groups of differentially propagated plants: in vitro with axillary (TC-Ax) or adventitious shoots (TC-Ad), conventionally (SC) and using a mixed method (TC/SC). The analysis included plant features (shoot length and branching, chlorophyll and fluorescence and DNA methylation) and fruit properties (antioxidant compounds). The data obtained indicated significant differences between plants propagated conventionally and in vitro, as well as variations among plants derived from in vitro cultures with different types of explants. SC plants generally exhibited the lowest values of morphological and physiological parameters but produced fruits richest in antioxidant compounds. TC/SC plants were dominant in length, branching and fluorescence. Conversely, TC-Ax plants produced fruits with the lowest levels of antioxidant compounds. The methylation-sensitive amplified polymorphism (MSAP) technique was employed to detect molecular differences. TC-Ad plants showed the highest methylation level, whereas SC plants had the lowest. The overall methylation level varied among differentially propagated plants. It can be speculated that the differences among the analysed plants may be attributed to variations in DNA methylation. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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18 pages, 5155 KiB  
Article
Genome-Wide Identification of Catalase Gene Family and the Function of SmCAT4 in Eggplant Response to Salt Stress
by Lei Shen, Xin Xia, Longhao Zhang, Shixin Yang and Xu Yang
Int. J. Mol. Sci. 2023, 24(23), 16979; https://doi.org/10.3390/ijms242316979 - 30 Nov 2023
Cited by 1 | Viewed by 700
Abstract
Salinity is an important abiotic stress, damaging plant tissues by causing a burst of reactive oxygen species (ROS). Catalase (CAT) enzyme coded by Catalase (CAT) genes are potent in reducing harmful ROS and hydrogen peroxide (H2O2) produced. Herein, we [...] Read more.
Salinity is an important abiotic stress, damaging plant tissues by causing a burst of reactive oxygen species (ROS). Catalase (CAT) enzyme coded by Catalase (CAT) genes are potent in reducing harmful ROS and hydrogen peroxide (H2O2) produced. Herein, we performed bioinformatics and functional characterization of four SmCAT genes, retrieved from the eggplant genome database. Evolutionary analysis CAT genes revealed that they are divided into subgroups I and II. The RT-qPCR analysis of SmCAT displayed a differential expression pattern in response to abiotic stresses. All the CAT proteins of eggplant were localized in the peroxisome, except for SmCAT4, which localized in the cytomembrane and nucleus. Silencing of SmCAT4 compromised the tolerance of eggplant to salt stress. Suppressed expression levels of salt stress defense related genes SmTAS14 and SmDHN1, as well as increase of H2O2 content and decrease of CAT enzyme activity was observed in the SmCAT4 silenced eggplants. Our data provided insightful knowledge of CAT gene family in eggplant. Positive regulation of eggplant response to salinity by SmCAT4 provides resource for future breeding programs. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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14 pages, 3618 KiB  
Article
Comprehensive Analysis of the Pectate Lyase Gene Family and the Role of FaPL1 in Strawberry Softening
by Yuanxiu Lin, Hao He, Yanling Wen, Shuaipeng Cao, Zisen Wang, Ziqing Sun, Yunting Zhang, Yan Wang, Wen He, Mengyao Li, Qing Chen, Yong Zhang, Ya Luo, Xiaorong Wang and Haoru Tang
Int. J. Mol. Sci. 2023, 24(17), 13217; https://doi.org/10.3390/ijms241713217 - 25 Aug 2023
Cited by 3 | Viewed by 921
Abstract
Fruit softening is a crucial factor that controls shelf life and commercial value. Pectate lyase (PL) has a major role in strawberry fruit softening. However, the PL gene family in strawberry has not been comprehensively analyzed. In this study, 65 FaPL genes were [...] Read more.
Fruit softening is a crucial factor that controls shelf life and commercial value. Pectate lyase (PL) has a major role in strawberry fruit softening. However, the PL gene family in strawberry has not been comprehensively analyzed. In this study, 65 FaPL genes were identified in the octoploid strawberry genome. Subcellular localization prediction indicated that FaPLs are mostly localized to the extracellular and cytoplasmic spaces. Duplication event analysis suggested that FaPL gene family expansion is mainly driven by whole genome or segmental duplication. The FaPL family members were classified into six groups according to the phylogenetic analysis. Among them, FaPL1, 3, 5, 20, 25, 42, and 57 had gradually increased expressions during strawberry fruit development and ripening and higher expression levels in the fruits with less firmness than that in firmer fruit. This result suggested that these members are involved in strawberry softening. Furthermore, overexpression of FaPL1 significantly reduced the fruit firmness, ascorbic acid (AsA), and malondialdehyde (MDA) content but obviously increased the anthocyanins, soluble proteins, and titratable acidity (TA), while it had no apparent effects on flavonoids, phenolics, and soluble sugar content. These findings provide basic information on the FaPL gene family for further functional research and indicate that FaPL1 plays a vital role in strawberry fruit softening. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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21 pages, 9328 KiB  
Article
Genome-Wide Exploration and Expression Analysis of the CNGC Gene Family in Eggplant (Solanum melongena L.) under Cold Stress, with Functional Characterization of SmCNGC1a
by Zheng Jiang, Lihui Du, Lei Shen, Jie He, Xin Xia, Longhao Zhang and Xu Yang
Int. J. Mol. Sci. 2023, 24(17), 13049; https://doi.org/10.3390/ijms241713049 - 22 Aug 2023
Cited by 1 | Viewed by 1021
Abstract
Eggplant (Solanum melongena L.) is an important economic crop, and to date, there has been no genome-wide identification and analysis of the cyclic nucleotide-gated channel (CNGC) gene family in eggplant. In this study, we identified the CNGC gene family in eggplant, and [...] Read more.
Eggplant (Solanum melongena L.) is an important economic crop, and to date, there has been no genome-wide identification and analysis of the cyclic nucleotide-gated channel (CNGC) gene family in eggplant. In this study, we identified the CNGC gene family in eggplant, and the results showed that 29 SmCNGC genes were classified into five groups, unevenly distributed across the 12 chromosomes of eggplant. The gene structure and motif analysis indicated that the SmCNGC family proteins may exhibit apparent preferences during evolution. Furthermore, our study revealed the presence of numerous light-responsive elements, hormone-responsive elements, and transcription factor binding sites in the promoter regions of SmCNGC genes, suggesting their significant role in environmental adaptability regulation. Finally, we analyzed the expression patterns of all SmCNGC genes under cold stress and found that SmCNGC1a was significantly upregulated under cold stress. Subcellular localization experiments indicated that this gene is located on the plasma membrane. Subsequently, its importance in the low-temperature response of eggplant was validated through virus-induced gene silencing (VIGS), and its protein interactome was predicted. In summary, our study provides a comprehensive understanding of the function and regulatory mechanisms of the CNGC gene family in eggplant, laying an important foundation for further research on cold adaptation in eggplant. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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14 pages, 11939 KiB  
Article
FaMYB5 Interacts with FaBBX24 to Regulate Anthocyanin and Proanthocyanidin Biosynthesis in Strawberry (Fragaria × ananassa)
by Lianxi Zhang, Yiping Wang, Maolan Yue, Leiyu Jiang, Nating Zhang, Ya Luo, Qing Chen, Yong Zhang, Yan Wang, Mengyao Li, Yunting Zhang, Yuanxiu Lin and Haoru Tang
Int. J. Mol. Sci. 2023, 24(15), 12185; https://doi.org/10.3390/ijms241512185 - 29 Jul 2023
Cited by 1 | Viewed by 1366
Abstract
MYB and BBX transcription factors play important roles in flavonoid biosynthesis. Here, we obtained transgenic woodland strawberry with stable overexpression of FaMYB5, demonstrating that FaMYB5 can increase anthocyanin and proanthocyanidin content in roots, stems and leaves of woodland strawberry. In addition, bimolecular [...] Read more.
MYB and BBX transcription factors play important roles in flavonoid biosynthesis. Here, we obtained transgenic woodland strawberry with stable overexpression of FaMYB5, demonstrating that FaMYB5 can increase anthocyanin and proanthocyanidin content in roots, stems and leaves of woodland strawberry. In addition, bimolecular fluorescence complementation assays and yeast two-hybridization demonstrated that the N-terminal (1-99aa) of FaBBX24 interacts with FaMYB5. Transient co-expression of FaBBX24 and FaMYB5 in cultivated strawberry ‘Xiaobai’ showed that co-expression strongly promoted the expression of F3′H, 4CL-2, TT12, AHA10 and ANR and then increased the content of anthocyanin and proanthocyanidin in strawberry fruits. We also determined that FaBBX24 is also a positive regulator of anthocyanin and proanthocyanidin biosynthesis in strawberry. The results reveal a novel mechanism by which the FaMYB5–FaBBX24 module collaboratively regulates anthocyanin and proanthocyanidin in strawberry fruit. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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13 pages, 8344 KiB  
Article
Transcriptome and Metabolome Reveal Distinct Sugar Accumulation Pattern between PCNA and PCA Mature Persimmon Fruit
by Weijuan Han, Yiru Wang, Huawei Li, Songfeng Diao, Yujing Suo, Taishan Li, Peng Sun, Fangdong Li and Jianmin Fu
Int. J. Mol. Sci. 2023, 24(10), 8599; https://doi.org/10.3390/ijms24108599 - 11 May 2023
Cited by 1 | Viewed by 1232
Abstract
Persimmon (Diospyros kaki) fruit have significant variation between pollination-constant non-astringent (PCNA) and pollination-constant astringent (PCA) persimmons. The astringency type affects not only the soluble tannin concentration but also the accumulation of individual sugars. Thus, we comprehensively investigate the gene expression and [...] Read more.
Persimmon (Diospyros kaki) fruit have significant variation between pollination-constant non-astringent (PCNA) and pollination-constant astringent (PCA) persimmons. The astringency type affects not only the soluble tannin concentration but also the accumulation of individual sugars. Thus, we comprehensively investigate the gene expression and metabolite profiles of individual sugars to resolve the formation of flavor differences in PCNA and PCA persimmon fruit. The results showed that soluble sugar, starch content, sucrose synthase, and sucrose invertase were significantly different between PCNA and PCA persimmon fruit. The sucrose and starch metabolism pathway was considerably enriched, and six sugar metabolites involving this pathway were significantly differentially accumulated. In addition, the expression patterns of diferentially expressed genes (such as bglX, eglC, Cel, TPS, SUS, and TREH genes) were significantly correlated with the content of deferentially accumulated metabolites (such as starch, sucrose, and trehalose) in the sucrose and starch metabolism pathway. These results indicated that the sucrose and starch metabolism pathway maintained a central position of sugar metabolism between PCNA and PCA persimmon fruit. Our results provide a theoretical basis for exploring functional genes related to sugar metabolism and provide useful resources for future studies on the flavor differences between PCNA and PCA persimmon fruit. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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20 pages, 4605 KiB  
Article
Genome-Wide Investigation and Functional Analysis Reveal That CsGeBP4 Is Required for Tea Plant Trichome Formation
by Hao Zhou, Wei Zhou, Xinzhuan Yao, Qi Zhao and Litang Lu
Int. J. Mol. Sci. 2023, 24(6), 5207; https://doi.org/10.3390/ijms24065207 - 08 Mar 2023
Cited by 1 | Viewed by 1613
Abstract
Tea plant trichomes not only contribute to the unique flavor and high quality of tea products but also provide physical and biochemical defenses for tea plants. Transcription factors play crucial roles in regulating plant trichome formation. However, limited information about the regulatory mechanism [...] Read more.
Tea plant trichomes not only contribute to the unique flavor and high quality of tea products but also provide physical and biochemical defenses for tea plants. Transcription factors play crucial roles in regulating plant trichome formation. However, limited information about the regulatory mechanism of transcription factors underlying tea plant trichome formation is available. Here, the investigation of trichome phenotypes among 108 cultivars of Yunwu Tribute Tea, integrated with a transcriptomics analysis of both hairy and hairless cultivars, revealed the potential involvement of CsGeBPs in tea trichome formation. In total, six CsGeBPs were identified from the tea plant genome, and their phylogenetic relationships, as well as the structural features of the genes and proteins, were analyzed to further understand their biological functions. The expression analysis of CsGeBPs in different tissues and in response to environmental stresses indicated their potential roles in regulating tea plant development and defense. Moreover, the expression level of CsGeBP4 was closely associated with a high-density trichome phenotype. The silencing of CsGeBP4 via the newly developed virus-induced gene silencing strategy in tea plants inhibited trichome formation, indicating that CsGeBP4 was required for this process. Our results shed light on the molecular regulatory mechanisms of tea trichome formation and provide new candidate target genes for further research. This should lead to an improvement in tea flavor and quality and help in breeding stress-tolerant tea plant cultivars. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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20 pages, 10849 KiB  
Article
Integrated Transcriptome and Metabolome Analyses Provide Insights into the Coloring Mechanism of Dark-red and Yellow Fruits in Chinese Cherry [Cerasus pseudocerasus (Lindl.) G. Don]
by Yan Wang, Zhiyi Wang, Jing Zhang, Zhenshan Liu, Hao Wang, Hongxia Tu, Jingting Zhou, Xirui Luo, Qing Chen, Wen He, Shaofeng Yang, Mengyao Li, Yuanxiu Lin, Yunting Zhang, Yong Zhang, Ya Luo, Haoru Tang and Xiaorong Wang
Int. J. Mol. Sci. 2023, 24(4), 3471; https://doi.org/10.3390/ijms24043471 - 09 Feb 2023
Cited by 7 | Viewed by 1487
Abstract
Chinese cherry [Cerasus pseudocerasus (Lindl.) G. Don] is an important fruit tree from China that has excellent ornamental, economic, and nutritional values with various colors. The dark-red or red coloration of fruit, an attractive trait for consumers, is determined by anthocyanin pigmentation. [...] Read more.
Chinese cherry [Cerasus pseudocerasus (Lindl.) G. Don] is an important fruit tree from China that has excellent ornamental, economic, and nutritional values with various colors. The dark-red or red coloration of fruit, an attractive trait for consumers, is determined by anthocyanin pigmentation. In this study, the coloring patterns during fruit development in dark-red and yellow Chinese cherry fruits were firstly illustrated by integrated transcriptome and widely-targeted metabolome analyses. Anthocyanin accumulation in dark-red fruits was significantly higher compared with yellow fruits from the color conversion period, being positively correlated to the color ratio. Based on transcriptome analysis, eight structural genes (CpCHS, CpCHI, CpF3H, CpF3’H, CpDFR, CpANS, CpUFGT, and CpGST) were significantly upregulated in dark-red fruits from the color conversion period, especially CpANS, CpUFGT, and CpGST. On contrary, the expression level of CpLAR were considerably higher in yellow fruits than in dark-red fruits, especially at the early stage. Eight regulatory genes (CpMYB4, CpMYB10, CpMYB20, CpMYB306, bHLH1, CpNAC10, CpERF106, and CpbZIP4) were also identified as determinants of fruit color in Chinese cherry. Liquid chromatography-tandem mass spectrometry identified 33 and 3 differential expressed metabolites related to anthocyanins and procyanidins between mature dark-red and yellow fruits. Cyanidin-3-O-rutinoside was the predominant anthocyanin compound in both fruits, while it was 6.23-fold higher in dark-red than in yellow fruits. More accumulated flavanol and procyanidin contents resulted in less anthocyanin content in flavonoid pathway in yellow fruits due to the higher expression level of CpLAR. These findings can help understand the coloring mechanism of dark-red and yellow fruits in Chinese cherry, and provide genetic basis for breeding new cultivars. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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17 pages, 5763 KiB  
Article
Genome-Wide Identification and Evolution Analysis of R2R3-MYB Gene Family Reveals S6 Subfamily R2R3-MYB Transcription Factors Involved in Anthocyanin Biosynthesis in Carrot
by Ao-Qi Duan, Shan-Shan Tan, Yuan-Jie Deng, Zhi-Sheng Xu and Ai-Sheng Xiong
Int. J. Mol. Sci. 2022, 23(19), 11859; https://doi.org/10.3390/ijms231911859 - 06 Oct 2022
Cited by 6 | Viewed by 1850
Abstract
The taproot of purple carrot accumulated rich anthocyanin, but non-purple carrot did not. MYB transcription factors (TFs) condition anthocyanin biosynthesis in many plants. Currently, genome-wide identification and evolution analysis of R2R3-MYB gene family and their roles involved in conditioning anthocyanin biosynthesis in carrot [...] Read more.
The taproot of purple carrot accumulated rich anthocyanin, but non-purple carrot did not. MYB transcription factors (TFs) condition anthocyanin biosynthesis in many plants. Currently, genome-wide identification and evolution analysis of R2R3-MYB gene family and their roles involved in conditioning anthocyanin biosynthesis in carrot is still limited. In this study, a total of 146 carrot R2R3-MYB TFs were identified based on the carrot transcriptome and genome database and were classified into 19 subfamilies on the basis of R2R3-MYB domain. These R2R3-MYB genes were unevenly distributed among nine chromosomes, and Ka/Ks analysis suggested that they evolved under a purified selection. The anthocyanin-related S6 subfamily, which contains 7 MYB TFs, was isolated from R2R3-MYB TFs. The anthocyanin content of rhizodermis, cortex, and secondary phloem in ‘Black nebula’ cultivar reached the highest among the 3 solid purple carrot cultivars at 110 days after sowing, which was approximately 4.20- and 3.72-fold higher than that in the ‘Deep purple’ and ‘Ziwei’ cultivars, respectively. The expression level of 7 MYB genes in purple carrot was higher than that in non-purple carrot. Among them, DcMYB113 (DCAR_008994) was specifically expressed in rhizodermis, cortex, and secondary phloem tissues of ‘Purple haze’ cultivar, with the highest expression level of 10,223.77 compared with the control ‘DPP’ cultivar at 70 days after sowing. DcMYB7 (DCAR_010745) was detected in purple root tissue of ‘DPP’ cultivar and its expression level in rhizodermis, cortex, and secondary phloem was 3.23-fold higher than that of secondary xylem at 110 days after sowing. Our results should be useful for determining the precise role of S6 subfamily R2R3-MYB TFs participating in anthocyanin biosynthesis in carrot. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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16 pages, 3557 KiB  
Article
BrWAX3, Encoding a β-ketoacyl-CoA Synthase, Plays an Essential Role in Cuticular Wax Biosynthesis in Chinese Cabbage
by Shuangjuan Yang, Hao Tang, Xiaochun Wei, Yanyan Zhao, Zhiyong Wang, Henan Su, Liujing Niu, Yuxiang Yuan and Xiaowei Zhang
Int. J. Mol. Sci. 2022, 23(18), 10938; https://doi.org/10.3390/ijms231810938 - 19 Sep 2022
Cited by 6 | Viewed by 1444
Abstract
In this study, we identified a novel glossy mutant from Chinese cabbage, named SD369, and all wax monomers longer than 26 carbons were significantly decreased. Inheritance analysis revealed that the glossy trait of SD369 was controlled by a single recessive locus, BrWAX3. [...] Read more.
In this study, we identified a novel glossy mutant from Chinese cabbage, named SD369, and all wax monomers longer than 26 carbons were significantly decreased. Inheritance analysis revealed that the glossy trait of SD369 was controlled by a single recessive locus, BrWAX3. We fine-mapped the BrWAX3 locus to an interval of 161.82 kb on chromosome A09. According to the annotated genome of Brassica rapa, Bra024749 (BrCER60.A09), encoding a β-ketoacyl-CoA synthase, was identified as the candidate gene. Expression analysis showed that BrCER60.A09 was significantly downregulated in all aerial organs of glossy plants. Subcellular localization indicated that the BrCER60.A09 protein functions in the endoplasmic reticulum. A 5567-bp insertion was identified in exon 1 of BrCER60.A09 in SD369, which lead to a premature stop codon, thus causing a loss of function of the BrCER60.A09 enzyme. Moreover, comparative transcriptome analysis revealed that the ‘cutin, suberine, and wax biosynthesis’ pathway was significantly enriched, and genes involved in this pathway were almost upregulated in glossy plants. Further, two functional markers, BrWAX3-InDel and BrWAX3-KASP1, were developed and validated. Overall, these results provide a new information for the cuticular wax biosynthesis and provide applicable markers for marker-assisted selection (MAS)-based breeding of Brassica rapa. Full article
(This article belongs to the Special Issue Advances in Research for Horticultural Crops Breeding and Genetics)
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