Epigenetic Modifications and Breeding Application in Horticultural Plants (Closed)

Editors

Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
Interests: plant epigenetics; epigenomics; epigenetic reprogramming; flowering time; tuber development
Department of Biotechnology, Faculty of Crop Production, Sindh Agriculture University, Tandojam 70060, Pakistan
Interests: DNA methylation; RNA methylation; histone modification; flowering time; plant epigenetics; plant breeding; banana; persimmon
Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
Interests: plant flowering; plant development; water stress; low temperature; flowering regulation; flower bud differentiation; leaf development
Special Issues, Collections and Topics in MDPI journals
Department of Pomology, Northwest A & F University, Yangling 712100, China
Interests: germplasm evaluation; plant breeding; genetic diversity; domestication and evolution; biological stress; growth regulation

Topical Collection Information

Dear Colleagues,

In recent years, we have witnessed tremendous advances in techniques and mechanically epigenetic regulation in plant epigenetics, which have been determined to play vital roles in developmental cues and environmental adaptation. Epigenetic modifications that occur toward the central dogma of DNA, RNA, and histone protein, mainly including DNA methylation, RNA modifications, histone post-translational modifications, chromatin remodeling, and non-coding RNAs (small RNAs, long non-coding RNAs), act as major drivers for the regulation of gene transcription and RNA metabolism in plants. As an emerging research field in horticultural plants, epigenetic modifications have already been revealed to regulate various processes, such as fruit development and ripening. In this Topical Collection, we aim to present papers on current progresses of epigenetic regulation and breeding application in horticultural plants. We aim to publish high-impact papers with novelties in (but not limited to) the topics listed below:

  • Epigenomic profiles;
  • Epigenetic regulation of development processes;
  • Epigenetic improvement for environmental adaptation;
  • Genome-wide identification of epigenetic enzymes;
  • Other omics-based profiles;
  • Bioinformatics;
  • Gene expression and regulation;
  • Progresses in breeding approaches;
  • Opinions and future perspectives.

Dr. Pingxian Zhang
Dr. Sadaruddin Chachar
Prof. Dr. Jinzhi Zhang
Dr. Changfei Guan
Collection Editors

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Keywords

  • epigenetic modification
  • DNA methylation
  • RNA modification
  • histone modification
  • epigenetic regulation
  • environmental adaptation
  • development
  • gene expression
  • breeding strategy
  • horticultural plants

Published Papers (22 papers)

2024

Jump to: 2023, 2022, 2021

6 pages, 188 KiB  
Editorial
Epigenetic Modifications and Breeding Applications in Horticultural Plants
by Meiyan Shi, Ziwei Wei, Pingxian Zhang, Changfei Guan, Sadaruddin Chachar and Jinzhi Zhang
Horticulturae 2024, 10(2), 143; https://doi.org/10.3390/horticulturae10020143 - 01 Feb 2024
Viewed by 703
Abstract
Epigenetics is an expansive and rapidly evolving field, fundamentally concerned with heritable changes in gene expression that do not involve alterations to the underlying DNA sequence [...] Full article

2023

Jump to: 2024, 2022, 2021

17 pages, 2511 KiB  
Article
Multivariate Analysis of the Phenological Stages, Yield, Bioactive Components, and Antioxidant Capacity Effects in Two Mulberry Cultivars under Different Cultivation Modes
by Na Zhang, Jinxin Li, Changyu Qiu, Wei Wei, Sheng Huang, Yong Li, Wen Deng, Rongli Mo and Qiang Lin
Horticulturae 2023, 9(12), 1334; https://doi.org/10.3390/horticulturae9121334 - 12 Dec 2023
Viewed by 802
Abstract
Mulberry fruits are rich in bioactive components renowned for their antioxidant properties and potential health benefits. This study thoroughly investigated the impact of cultivation modes on the phenological stages, yield, bioactive components, and antioxidant activity of two mulberry cultivars, Yueshen Dashi (YS-DS) and [...] Read more.
Mulberry fruits are rich in bioactive components renowned for their antioxidant properties and potential health benefits. This study thoroughly investigated the impact of cultivation modes on the phenological stages, yield, bioactive components, and antioxidant activity of two mulberry cultivars, Yueshen Dashi (YS-DS) and Xinjiang Baisang (XJ-BS). Notably, greenhouse cultivation led to earlier phenology and shorter fruit development maturation durations compared to field cultivation. Despite a decrease in fruit production and firmness, the greenhouse-grown mulberries exhibited higher individual fruit fresh weight. The content of bioactive components, encompassing anthocyanins, polyphenols, flavonoids, and vitamin C, and of antioxidant activity (measured in the FRAP and DPPH radical scavenging assays) was found to be lower in the greenhouse-grown mulberries than in those cultivated in the field. The contents of total polyphenols and flavonoids showed robust positive correlations in the FRAP and DPPH radical scavenging assays, which suggests that the antioxidant activity of mulberry fruit might be primarily attributable to the bioactive components of total polyphenols and flavonoids. Interestingly, the sugar content and hydroxyl radical scavenging activity (HRSA) displayed an inverse relationship between the two cultivars in the greenhouse versus field conditions. The multivariate analysis highlighted distinct patterns for different cultivars under varying cultivation modes. This study underscores the potential to enhance bioactive components and antioxidant activity through effective manipulation of climate conditions, thereby unlocking the full nutritional potential of mulberry fruits on a large scale in greenhouse environments. Full article
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15 pages, 1958 KiB  
Review
Recent Advances in Natural Deastringency and Genetic Improvement of Chinese PCNA Persimmon (Diospyros kaki)
by Sichao Yang, Meng Zhang, Lei Xu, Qinglin Zhang, Chaohua Zhou, Xinlong Hu and Zhengrong Luo
Horticulturae 2023, 9(12), 1273; https://doi.org/10.3390/horticulturae9121273 - 27 Nov 2023
Viewed by 1118
Abstract
Persimmon (Diospyros kaki) is a worldwide fruit cultivated mainly in the East Asia, Mediterranean, Caucasus, Latin America, and Oceania regions. This fruit contains abundant proanthocyanidins (PAs, also called condensed tannins), whose biosynthesis is the main cause of fruit astringency. As the [...] Read more.
Persimmon (Diospyros kaki) is a worldwide fruit cultivated mainly in the East Asia, Mediterranean, Caucasus, Latin America, and Oceania regions. This fruit contains abundant proanthocyanidins (PAs, also called condensed tannins), whose biosynthesis is the main cause of fruit astringency. As the original centre and top producing country, China has discovered a unique type with desirable natural deastringency, the Chinese pollination-constant non-astringent (C-PCNA) persimmon. Studies have revealed that the C-PCNA trait is controlled by a single and dominant locus, which differs from that of another type, the Japanese PCNA type, with recessive loci. In the C-PCNA type, accumulating evidence has shown that the astringency removal process involves two pathways (“dilution effect” and “coagulation effect”). Moreover, molecular marker-assisted selection (MAS) for the natural deastringency trait locus in C-PCNA has been used to test the non-astringency/astringency trait of hybrid offspring at the seedling stage. Importantly, persimmon can bear male flowers, female flowers, and perfect flowers, but sex-linked MAS has been developed for female-only persimmon. This sex-linked MAS, together with astringency-linked MAS and embryo rescue technology, may even shorten the conventional cross-breeding period of about 2–3 years. In addition, recently studies have established a stable genetic transformation system for persimmon transgenic improvement. Despite these efforts, how synthetic PAs and metabolism pathways lead to a deastringent trait remains unclear for persimmon. Thus, our review summarizes the latest research progress on the natural deastringency mechanism in C-PCNA, and we provide a new viewpoint for the genetic improvement of persimmon breeding in China. Full article
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14 pages, 1108 KiB  
Opinion
Harnessing Epigenetics through Grafting: Revolutionizing Horticultural Crop Production
by Qiang Jin, Muzafaruddin Chachar, Nazir Ahmed, Pingxian Zhang, Zaid Chachar, Yuke Geng, Dayong Guo and Sadaruddin Chachar
Horticulturae 2023, 9(6), 672; https://doi.org/10.3390/horticulturae9060672 - 06 Jun 2023
Viewed by 1497
Abstract
Grafting is an ancient agricultural technique that is frequently used to enhance the performance of horticultural plants, including vegetables and woody fruit trees. For successful grafting, genotypes of the compatible scion (the upper part) and the rootstock (the lower part) must interact. Molecular [...] Read more.
Grafting is an ancient agricultural technique that is frequently used to enhance the performance of horticultural plants, including vegetables and woody fruit trees. For successful grafting, genotypes of the compatible scion (the upper part) and the rootstock (the lower part) must interact. Molecular signals, including nutritional and hormonal signals, proteins, and messenger RNAs (mRNAs), are known to be transferred from the rootstock to the scion and vice versa. Nonetheless, there are still numerous mysteries regarding artificial grafts, including the occurrence of genetic/epigenetic alterations due to exchanges between the graft partners, and the long-term ramifications of these alterations on the phenotype are unknown. Recent studies on the interactions between rootstocks and scions suggest that grafting responses have an epigenetic component. In this review, we focus on the current knowledge of epigenetic consequences following grafting. Epigenetic regulations are known to regulate chromatin architecture, alter gene expression, and affect cellular function in plants. Mobile small RNAs, for example, have been shown to modify the DNA methylation pattern of the recipient partner across the graft union. More recently, mRNA 5-methylcytosine (m5C) modification has been shown to elucidate the long-distance transport mechanism of grafting in Arabidopsis thaliana. We also discuss how grafts can cause heritable epigenetic alterations that result in novel plant phenotypes, and how this might help increase horticultural crop quality, yield, and stress resistance in the context of climate change. Full article
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8 pages, 1378 KiB  
Brief Report
Isolation of FLOWERING LOCUS C and Preliminary Characterization in the Floral Transition of Xinjiang Precocious Walnut
by Qiang Jin, Rui Zhang, Liping Chen and Zhengrong Luo
Horticulturae 2023, 9(5), 582; https://doi.org/10.3390/horticulturae9050582 - 14 May 2023
Viewed by 1061
Abstract
Walnut (Juglans regia L.) plants typically flower after eight to ten years of juvenile growth. Precocious germplasm, also known as early-flowering or early-mature genotypes, have shortened juvenile phases of one to two years and are therefore crucial for enhancing breeding efficiency. However, [...] Read more.
Walnut (Juglans regia L.) plants typically flower after eight to ten years of juvenile growth. Precocious germplasm, also known as early-flowering or early-mature genotypes, have shortened juvenile phases of one to two years and are therefore crucial for enhancing breeding efficiency. However, such precocious germplasms are very limited. Here, we isolated and characterized the key flowering-time gene FLOWERING LOCUS C (FLC) in the precocious walnuts of the Xinjiang Uygur Autonomous Region. Sequence alignment showed that Juglans regia FLC (JrFLC)contained a conserved MINICHROMOSOME MAINTENANCE 1 (MCM1), AGAMOUS (AG), DEFICIENS (DEF), and SERUM RESPONSE FACTOR (SRF) (MADS)-box domain. Analysis of an FLC–green fluorescent protein (GFP) fusion protein revealed that JrFLC was localized to the nucleus. Gene expression analysis showed that JrFLC was specifically expressed during the bud dormancy stage of precocious walnut, and that expression levels gradually decreased as the ambient temperature warmed. Exogenous JrFLC overexpression in Arabidopsis thaliana delayed flowering and increased the total leaf number, suggesting a similar function of JrFLC as a floral repressor in walnut and in other plants. Together, these results showed that JrFLC played an important role in regulating the floral transition of Xinjiang precocious walnut. Further studies, including a detailed characterization of JrFLC, are expected to validate JrFLC as a strong target for genetic improvement in flowering time in walnut. Full article
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15 pages, 3685 KiB  
Communication
Phylogeny, Expression Profiling, and Coexpression Networks Reveals the Critical Roles of Nucleotide-BindingLeucine-Rich Repeats on Valsa Canker Resistance
by Yanan Cao, Hongqiang Yu, Dan Tian, E. Sun, Longgang Zuo, Daji Jiang, Cunwu Zuo and Ruiyi Fan
Horticulturae 2023, 9(3), 345; https://doi.org/10.3390/horticulturae9030345 - 06 Mar 2023
Viewed by 1382
Abstract
Rosaceae is one of the major families in the plant kingdom with important economic value. However, many of them are attacked by Valsa canker, resulting in serious loss of production and profits. Nucleotide-binding leucine-rich repeats (NLRs) play a key role in the plant [...] Read more.
Rosaceae is one of the major families in the plant kingdom with important economic value. However, many of them are attacked by Valsa canker, resulting in serious loss of production and profits. Nucleotide-binding leucine-rich repeats (NLRs) play a key role in the plant immune response as the largest class of resistance genes. Currently, we performed a genome-wide identification of NLR genes in Rosaceae and revealed some NLR genes in response to Valsa canker using multispecies bioinformatics including co-expression network analysis and RNASeq data. A total of 3718 NLR genes were identified from genomes of 19 plant species (include 9 Rosaceae plants) and classified them into 15 clades. The NLRs display species- and group-specific expansions that are derived from both the whole genome duplication and the tandem duplication. Additionally, the expression of some NLR members was low under normal growth conditions in various plant tissues, while significantly enhanced after the infection of Valsa canker. Furthermore, co-expression network analysis shows that the 13 NLR members were distributed in key nodes of differentially expressed genes which could be considered as promosing key regulators for the resistance of Valsa canker. Therefore, our findings provide a reference for the evolution of NLR genes in Rosaceae and the key regulators of Valsa canker resistance. Full article
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16 pages, 2454 KiB  
Review
Recent Research Advances of Small Regulatory RNA in Fruit Crops
by Fatima Zaman, Meng Zhang, Rong Wu, Qinglin Zhang, Zhengrong Luo and Sichao Yang
Horticulturae 2023, 9(3), 294; https://doi.org/10.3390/horticulturae9030294 - 22 Feb 2023
Cited by 4 | Viewed by 2133
Abstract
MicroRNAs (miRNAs) are endogenous noncoding small RNAs containing 21–24 nucleotides (nt) that regulate gene expression precisely and efficiently at the posttranscriptional level through the negative regulation of target messenger RNA (mRNA) expression, such as translational inhibition or degradation. Likewise, as a controlling element, [...] Read more.
MicroRNAs (miRNAs) are endogenous noncoding small RNAs containing 21–24 nucleotides (nt) that regulate gene expression precisely and efficiently at the posttranscriptional level through the negative regulation of target messenger RNA (mRNA) expression, such as translational inhibition or degradation. Likewise, as a controlling element, miRNA itself is regulated by a variety of factors when performing its basic purposes, such as SNP detection, miRNA purging, methylation, and the circadian clock in model crops. In current years, miRNA-mediated controls have been intensely investigated in horticultural plants, leading to the discovery of numerous novel mechanisms that exhibit significantly greater mechanistic complexity and distinctive regulatory properties than those explored in model species. In fruit crops, miRNAs play a crucial role corresponding to various biological, metabolic functions and environmental challenges, including growth, expansion, response to biotic and abiotic stress, signaling of growth hormones, and the regulation of secondary product metabolism. In this study, we appraisal the current improvement of small regulatory RNA research in fruit crops, emphasizing miRNA mechanisms and their correlation with key trait rule. Considering that miRNAs engaged in the regulation of all aspects of fruit tree life activities, we focus here on their biosynthesis, target genes, function and regulatory network, as well as the mechanistic connection among them, to provide a theoretic base and breakthrough for upcoming exploration on miRNAs in fruit plants. Full article
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22 pages, 18317 KiB  
Article
Genome-Wide Analysis of the AP2/ERF Family in Oily Persimmon (Diospyros oleifera) and Their Preliminary Roles Exploration in Response to Polyamines for Adventitious Root Formation in Cultivated Persimmon (D. kaki)
by Yanbo Wang, Xiaoyun Du, Minxiao Liu, Xueqing Liu, Lingling Zhao, Luyao Cao, Shuo Zhang, Laiqing Song, Yanxia Sun, Daliang Liu, Xiaoli Yu and Junchi Xu
Horticulturae 2023, 9(2), 191; https://doi.org/10.3390/horticulturae9020191 - 02 Feb 2023
Cited by 4 | Viewed by 1356
Abstract
The AP2/ERF (APETALA2/Ethylene−Responsive element binding factor) family genes play crucial roles in plant growth and development, and responses to environmental factors; however, this family has not been characterized in Diospyros species. In Diospyros, the diploid Oily persimmon (D. oleifera, 2n = [...] Read more.
The AP2/ERF (APETALA2/Ethylene−Responsive element binding factor) family genes play crucial roles in plant growth and development, and responses to environmental factors; however, this family has not been characterized in Diospyros species. In Diospyros, the diploid Oily persimmon (D. oleifera, 2n = 2x = 30) has been released with complete genome assembly, which makes it possible for genome-wide gene family identification and exploration of molecular function in cultivated persimmon (D. kaki, 2n = 6x = 90). Here, we identified the AP2/ERF family in Oily persimmon for the first time and investigated its classification, main physicochemical properties, structural characteristic, chromosome distribution, gene replication and collinearity, cis-factor binding sites deduction, GO term annotation, and PPI interaction, as well as its expression profiles in different tissue and under the treatment of polyamines. A total of 157 AP2/ERF genes, including four subfamilies (AP2, RAV, Soloist, and ERF), were identified with distribution on all 15 chromosomes. DkAP2/ERF gene expression patterns were extensive and diverse. They were detected expression in every examined tissue, with the highest number of DkAP2/ERF genes expressed in the root. DkAP2/ERF gene expression analysis in adventitious root generation and elongation of polyamines showed their different responses to the action of polyamines, and more pairs of DkAP2/ERF genes with high correlation in gene expression were obtained. In addition, some DkAP2/ERF genes were detected remarkably correlated with genes related to polyamine synthesis and cell metabolism, including S-adenosyl-L-methionine Decarboxyla2 (SAMDC2), D-type cyclin1 (CYCD1), and D-type cyclin2 (CYCD2) genes,. indicating that DkAP2/ERF genes may play a synergistic role in adventitious root development This study was the first to analyze the AP2/ERF gene comprehensively in Diospyros on a genome−wide scale and will provide insights into the application of adventitious root formation in cultivated persimmon. Full article
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2022

Jump to: 2024, 2023, 2021

14 pages, 7032 KiB  
Article
Identification of Phenological Growth Stages of Four Morus Species Based on the Extended BBCH-Scale and Its Application in Fruit Development with Morphological Profiles and Color Characteristics
by Rongli Mo, Na Zhang, Die Hu, Qiang Jin, Jinxin Li, Zhaoxia Dong, Zhixian Zhu, Yong Li, Cheng Zhang and Cui Yu
Horticulturae 2022, 8(12), 1140; https://doi.org/10.3390/horticulturae8121140 - 03 Dec 2022
Cited by 2 | Viewed by 3592
Abstract
Mulberry (Morus L.; Moraceae; Rosales) is an economically important tree with a long history in China and valued for its rich nutrient, flavor content, medicinal value and useful ecological functions. Morus species are widely distributed in Asia, Europe, North and South America [...] Read more.
Mulberry (Morus L.; Moraceae; Rosales) is an economically important tree with a long history in China and valued for its rich nutrient, flavor content, medicinal value and useful ecological functions. Morus species are widely distributed in Asia, Europe, North and South America and Africa and exhibit obvious differences in morphological characteristics and phenological stages due to being distributed in diverse climate zones. The morphological description of the phenological stages of black mulberry (Morus nigra L.) has been established in Mediterranean climates and this study extended the BBCH scale for application in different Morus species, especially for mulberry trees grown in subtropical monsoon climates. In this study, we used the BBCH (Biologische Bundesanstalt, Bundessortenamt and CHemische Industrie) scale to describe in detail the phenological growth stages for Morus species in Wuhan, China (a subtropical monsoon climate). Based on this general scale, eight principal stages, i.e., bud, leaf and shoot development stage, inflorescence emergence stage, flowering stage, fruit development stage, fruit maturation stage, senescence and beginning of dormancy stage, were described. We provide photographic images of some primary and secondary developmental stages to better define and standardize morphological characteristics and phenological descriptions of these mulberries (Morus spp.). In addition, because the color of mulberry fruit varies from white, purple, black, or pink to red at maturity, with mostly monosexual flowers, we have also presented detailed descriptions of morphological traits of flower sexuality and fruit color among these four species. In addition, two late phenological germplasms (late bud sprouting associated with late blooming and late fruit ripening) were screened out according to the BBCH scale. Overall, this study will contribute to advance the field of mulberry breeding and implementation of agronomic practices and facilitate convenient communication between mulberry cultivators and researchers in different areas. Full article
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15 pages, 2378 KiB  
Article
Identification of the Transcription Factors RAP2-13 Activating the Expression of CsBAK1 in Citrus Defence Response to Xanthomonas citri subsp. citri
by Qi Wu, Mingming Zhao, Yi Li, Dazhi Li, Xianfeng Ma and Ziniu Deng
Horticulturae 2022, 8(11), 1012; https://doi.org/10.3390/horticulturae8111012 - 01 Nov 2022
Viewed by 1324
Abstract
Citrus canker is a quarantined disease caused by the bacterial plant pathogen Xanthomonas citri subsp. citri (Xcc), which causes persistent surface damage, leaf and fruit drop, and tree decline in citrus plants. The citrus cultivar Citron C-05 (Citrus medica L.) [...] Read more.
Citrus canker is a quarantined disease caused by the bacterial plant pathogen Xanthomonas citri subsp. citri (Xcc), which causes persistent surface damage, leaf and fruit drop, and tree decline in citrus plants. The citrus cultivar Citron C-05 (Citrus medica L.) is a disease-resistant genotype identified after years of screening at the National Center for Citrus Improvement (Changsha), which displays allergic, necrotic, and disease-resistant responses to Xcc. In this study, the BAK1 gene was identified in this cultivar to be a disease resistance gene involved in plant-microbe interaction between citrus and Xcc. Functional investigations of this gene revealed that both CsBAK1 (C. sinensis BAK1) or CmBAK1(C. medica BAK1) could inhibit the growth of Xcc to some extent when transiently expressed in the susceptible ‘Bingtang’ genotype of sweet orange. Critical regions of the CmBAK1 promoter sequence were identified by creating downstream deletions and exposing mutants to Xcc to determine effects on the resistance phenotype; a 426 bp region (−2000~–1574) was identified as a key functional region responsible for eliciting the hypersensitive response in plants. Through screening arrayed Citron C-05 cDNA libraries by yeast one-hybrid assays, a basic APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor of CmRAP2-13 that binds directly to the 426 bp key sequence and activates expression of CmBAK1 was identified. Moreover, transcriptional analysis revealed an obvious increase in transcript levels of CsRAP2-13 in Citron C-05, American citron, and Finger citron. In this study, we present the identification of transcriptional activators that are found to interact with BAK1 proteins in response to Xcc. These results reveal a coordinated regulatory mechanism of RAP2-13, which may be involved in defence responses through the regulation of BAK1. Full article
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14 pages, 852 KiB  
Communication
Global Methylation Analysis Using MSAP Reveals Differences in Chilling-Associated DNA Methylation Changes during Dormancy Release in Contrasting Sweet Cherry Varieties
by Gabriela Narváez, Claudia Muñoz-Espinoza, Esteban Soto, Karin Rothkegel, Macarena Bastías, José Gutiérrez, Soraya Bravo, Rodrigo Hasbún, Claudio Meneses and Andrea Miyasaka Almeida
Horticulturae 2022, 8(10), 962; https://doi.org/10.3390/horticulturae8100962 - 18 Oct 2022
Viewed by 1934
Abstract
Dormancy is an adaptive strategy developed by temperate perennial crops to protect overwinter tissues from unfavorable environmental conditions. Sweet cherry (Prunus avium L.), a member of the Rosaceae family, requires chilling to overcome dormancy. The time of harvest is directly correlated with [...] Read more.
Dormancy is an adaptive strategy developed by temperate perennial crops to protect overwinter tissues from unfavorable environmental conditions. Sweet cherry (Prunus avium L.), a member of the Rosaceae family, requires chilling to overcome dormancy. The time of harvest is directly correlated with chilling requirements in sweet cherries. Consequently, early and late season varieties have low and high chilling requirements, respectively. There is evidence that the expression of dormancy-related genes is regulated by DNA methylation. In this work, methylation-sensitive amplified polymorphism (MSAP) was applied to study genome-wide DNA methylation changes associated with dormancy in two low-chill varieties, ‘Royal Dawn’ and ‘Glen Red’, and one high-chill variety, ‘Kordia’. Our primary results suggest that the occurrence of progressive DNA demethylation is associated with chilling accumulation during dormancy in the three varieties, independent of their chilling requirements. Genes were identified with different methylation status changes, detected by MSAP, related to cell wall remodeling and energy metabolism. Several MSAP profiles among the varieties were observed, suggesting that fine epigenetic control is required to coordinate hormonal and environmental signals that induce dormancy and its release. Full article
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13 pages, 4140 KiB  
Article
Transcriptomic Analysis Provides Insights into Anthocyanin Accumulation in Mulberry Fruits
by Rongli Mo, Na Zhang, Jinxin Li, Qiang Jin, Zhixian Zhu, Zhaoxia Dong, Yong Li, Cheng Zhang and Cui Yu
Horticulturae 2022, 8(10), 920; https://doi.org/10.3390/horticulturae8100920 - 07 Oct 2022
Cited by 3 | Viewed by 1783
Abstract
Mulberry fruits are rich in anthocyanins, which are important secondary metabolites that give mulberries their bright color, favorable taste and high nutritional quality, making them a popular fruit. However, few studies have focused on the molecular mechanism underlying anthocyanin accumulation in mulberries and [...] Read more.
Mulberry fruits are rich in anthocyanins, which are important secondary metabolites that give mulberries their bright color, favorable taste and high nutritional quality, making them a popular fruit. However, few studies have focused on the molecular mechanism underlying anthocyanin accumulation in mulberries and the gene regulatory networks of anthocyanin biosynthetic pathways remain largely unknown. In this study, we performed RNA sequencing to identify differentially expressed genes (DEGs) associated with anthocyanin accumulation between two mulberry genotypes (‘Zi Jing’, ZJ and ‘Zhen Zhu Bai’, ZZB, with purple and white fruit flesh, respectively) at 5, 18, 27 and 31 days after flower. Using transcriptome analysis, we explored several key DEGs involved in the anthocyanin biosynthetic pathway, including the structural genes: CHS, CHI, F3H, DFR1, DFR2 and ANS, known as MBW complex genes: MYB (M.alba_G0017209), MYB (M.alba_G0017689), bHLH (M.alba_G0012659), bHLH (M.alba_G0009347) and bHLH3 (M.alba_G0016257) and the ethylene response factor: ERF (M.alba_G0016603). Of these, changing trends related to expression pattern and anthocyanin content showed their most positive correlation at the post-flowering stage in both genotypes. Our results indicated that ethylene enhances anthocyanin accumulation in mulberry fruits. Furthermore, qRT-PCR was performed to confirm the above-mentioned genes’ expression (except for MYB (M.alba_G0017689) and bHLH (M.alba_G0009347) was significantly up-regulated under ethylene treatment at 300 mg/L. These findings help uncover the gene regulatory networks of the anthocyanin biosynthetic pathway and will contribute to engineering purposes in future mulberry breeding programs. Full article
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17 pages, 13985 KiB  
Article
Assessment of Fruit Quality and Genes Related to Proanthocyanidins Biosynthesis and Stress Resistance in Persimmon (Diospyros kaki Thunb.)
by Sichao Yang, Meng Zhang, Ming Zeng, Meihua Wu, Qinglin Zhang, Zhengrong Luo and Xinlong Hu
Horticulturae 2022, 8(9), 844; https://doi.org/10.3390/horticulturae8090844 - 14 Sep 2022
Cited by 1 | Viewed by 1585
Abstract
Persimmon (Diospyros kaki Thunb.) is becoming a fruit that is used worldwide because it contains high nutritional and medicinal value. However, the trait evaluation of persimmon is still needed and is critical for marketing and breeding, especially in China. Here, we evaluated [...] Read more.
Persimmon (Diospyros kaki Thunb.) is becoming a fruit that is used worldwide because it contains high nutritional and medicinal value. However, the trait evaluation of persimmon is still needed and is critical for marketing and breeding, especially in China. Here, we evaluated thirteen quality indicators (fruit weight, horizontal length, vertical length, firmness, titratable acid content, vitamin C content, flavonoid content, anthocyanin content, soluble sugar content, pectinase activity, soluble protein content, tannin content, and tannin cell size) in six Chinese pollination-constant, astringent (PCA) persimmon cultivars (‘Jinxi 3′, ‘Ganfang 1′, ‘Poyang 5′, ‘Poyang 6′, ‘Yifeng 1′, and ‘Yifeng 3′) and a Japanese pollination-constant non-astringent (PCNA) persimmon cultivar (‘Youhou’). The quality indicator data were normalized and subjected to variant analysis and principal component analysis (PCA). The results showed that 10 of 13 indicators among the seven persimmon cultivars were significantly different, and the contribution rates of the first principal component reached 40.582%. The principal component comprehensive scores for ‘Poyang 5′ and ‘Ganfang 1′ ranked second and third, respectively, and were clustered with that of ‘Youhou.’ In addition, we also measured the expression levels of three stress resistance genes and three proanthocyanidin (PA, also called condensed tannins) pathway genes in these persimmon cultivars by quantitative reverse transcription PCR (qRT—PCR). The qRT—PCR analysis of DkCBF and DkWRKY3/8 showed low resistance to cold in ‘Ganfang 1′ but stronger resistance to anthracnose. Moreover, the expression of the PA pathway genes demonstrated that the PA content in ‘Ganfang 1′ was at a moderate level in the seven varieties. Together, our study revealed relatively comprehensive profiles of persimmon quality evaluation and demonstrated that ‘Ganfang 1′ may have the potential to be used as a breeding parent for future persimmon breeding programs. Full article
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14 pages, 3145 KiB  
Communication
A Preliminary Study for Identifying Genes Associated with Pellicle Development in Xinjiang Walnut (Juglans regia L.)
by Qiang Jin, Shan Gao, Rongli Mo, Fang Sheng, Qinglin Zhang, Cuiyun Wu, Rui Zhang and Zhengrong Luo
Horticulturae 2022, 8(9), 784; https://doi.org/10.3390/horticulturae8090784 - 29 Aug 2022
Cited by 1 | Viewed by 1561
Abstract
Walnut (Juglans regia L.) is an important nut fruit crop mainly grown for its high nutritional and medicinal value. In walnut fruit, the pellicle is the main source of polyphenols (such as proanthocyanidins), which are natural bioactive compounds but also cause astringency [...] Read more.
Walnut (Juglans regia L.) is an important nut fruit crop mainly grown for its high nutritional and medicinal value. In walnut fruit, the pellicle is the main source of polyphenols (such as proanthocyanidins), which are natural bioactive compounds but also cause astringency and bitterness for walnut fruit consumption. However, the gene regulatory networks of phenolic biosynthetic pathways remain largely unknown in walnut pellicles. Here, we performed RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs) associated with pellicle development in walnut. In this study, seven developmental stages (8-, 9-, 11-, 13-, 15-, 17-, and 19-week after pollination) of ‘Xinwen179’ pellicle tissues were harvested to conduct further transcriptome-wide profiles. Via RNA-seq, we explored several key DEGs involved in the phenolic biosynthetic pathway, such as dihydroflavonol-4-reductase (DFR), leucoanthocyanidin reductase (LAR), anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR), which are dynamically expressed at developmental stages of the walnut pellicle. Among them, ANR may directly contribute to proanthocyanidins accumulation during walnut development. Taken together, our preliminary investigation on DEGs associated with pellicle development will not only elucidate the gene regulatory networks of the phenolic biosynthetic pathway for pellicle development, but also contribute to the broad spectrum of RNA-seq data resources for further genetic improvement of walnut. Full article
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20 pages, 8544 KiB  
Article
Analysis of Relative Expression of Key Enzyme Genes and Enzyme Activity in Nitrogen Metabolic Pathway of Two Genotypes of Potato (Solanum tuberosum L.) under Different Nitrogen Supply Levels
by Zhijun Han, Yue Lu, Yanfei Zhao, Yaping Wang, Zhongcai Han, Yuzhu Han and Jingying Zhang
Horticulturae 2022, 8(9), 769; https://doi.org/10.3390/horticulturae8090769 - 26 Aug 2022
Cited by 3 | Viewed by 1167
Abstract
Nitrogen (N) plays an important role in the growth cycle of the potato, and is an important guarantee of yield and quality. Rational N application is one of the key ways to improve a crop’s high and stable yield and economic and environmental [...] Read more.
Nitrogen (N) plays an important role in the growth cycle of the potato, and is an important guarantee of yield and quality. Rational N application is one of the key ways to improve a crop’s high and stable yield and economic and environmental benefits. The N nutrition level of potato regulates the gene expression of enzymes related to the N metabolism pathway, which shows the change of the activity of key enzymes in N metabolism, and finally realizes the regulation of N absorption and utilization. In this study, the key enzyme genes and enzyme activity of different genotypes of potato under different N supply treatments were identified, which laid a foundation for further exploration of the functions of each gene in the potato N metabolism pathway and provided theoretical basis for rational N application. The results showed that the relative expression levels of StNRT1.5, StNR, StNiR in leaves, StNRT2.5, StNRT2.4, StGS1-2 in roots and StNRT2.7, StGS1-3, StGS2, StGS1-4, StFd-GOGAT in leaves and roots showed that the levels of N-inefficient potato Atlantic (A) were higher than the N-efficient potato Yanshu 4 (Y), while the relative expression levels of StNRT2.5, StGS1-2 in leaves, StNRT1.5StNR, StNiR in roots and StGDH, StNADH-GOGAT in leaves and roots showed that levels in Yanshu 4 (Y) were higher than in Atlantic (A). At the same time, we especially found that the GDH activity in the leaves of the two genotypes of potato were higher at low N levels. Additionally, the activity of NR and NiR, and the activity of GS and GOGAT were correlated. In addition, the changes of key enzymes in different N metabolism showed a certain continuity with the advancement of growth and development, and some gene expression rules and enzyme activity changes also showed a certain consistency. Full article
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18 pages, 4726 KiB  
Article
Cell Division Controls Final Fruit Size in Three Apple (Malus x domestica) Cultivars
by Siti Khadijah A. Karim, Andrew C. Allan, Robert J. Schaffer and Karine M. David
Horticulturae 2022, 8(7), 657; https://doi.org/10.3390/horticulturae8070657 - 19 Jul 2022
Cited by 4 | Viewed by 3791
Abstract
Apple (Malus x domestica) fruit size is dependent on cell division and cell expansion, processes that are subsequently regulated by plant hormones such as auxins, gibberellins, and cytokinins. In this study, we investigated the role of cell division and cell expansion [...] Read more.
Apple (Malus x domestica) fruit size is dependent on cell division and cell expansion, processes that are subsequently regulated by plant hormones such as auxins, gibberellins, and cytokinins. In this study, we investigated the role of cell division and cell expansion in apple growth and identified which of the two was more deterministic of final fruit size. Three cultivars of different sizes were selected, namely, “Twenty Ounce” (large-sized), “Royal Gala” (medium-sized), and “Crabapple” (small-sized). Gene expression and cell size analyses were conducted over the course of two consecutive seasons. The expression patterns of three classes of genes were markedly similar across all cultivars. Two cell division markers, namely MdCDKB2;2 and MdANT2, were discovered to be correlatively expressed, as both displayed initially high expression levels, which gradually declined from the early to late stages of the growth time course. For cell expansion markers, MdEXP3 was upregulated as the cells expanded, while MdARF106 was expressed in both the cell division and expansion stages. Meanwhile, the ripening-related gene MdACO1 was expectedly expressed only during the ending stages associated with ripening. Interestingly, the cell measurements taken regularly from each cultivar throughout the same experimental timespan showed that cell sizes were unaltered and remained constant from initial pollination at the zeroth Day After Pollination (DAP) to ripening at 120 Days After Full Bloom (DAFB). Full article
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28 pages, 838 KiB  
Review
Recent Advances in DNA Methylation and Their Potential Breeding Applications in Plants
by Aamir Ali Shaikh, Sadaruddin Chachar, Muzafaruddin Chachar, Nazir Ahmed, Changfei Guan and Pingxian Zhang
Horticulturae 2022, 8(7), 562; https://doi.org/10.3390/horticulturae8070562 - 21 Jun 2022
Cited by 6 | Viewed by 3125
Abstract
Traditional plant breeding encompasses repetitive crossing and selection based on morphological traits, while phenotypic selection has been complemented by molecular methods in recent decades. Genome editing with techniques like the CRISPR-Cas9 system is still a novel approach that is being used to make [...] Read more.
Traditional plant breeding encompasses repetitive crossing and selection based on morphological traits, while phenotypic selection has been complemented by molecular methods in recent decades. Genome editing with techniques like the CRISPR-Cas9 system is still a novel approach that is being used to make direct modifications to nucleotide sequences of crops. In addition to these genetic alterations, an improved understanding of epigenetic variations such as DNA methylation on the phenotype of plants has led to increased opportunities to accelerate crop improvement. DNA methylation is the most widely studied epigenetic mark in plants and other eukaryotes. These epigenetic marks are highly conserved and involved in altering the activities and functions of developmental signals by catalyzing changes in the chromatin structure through methylation and demethylation. Cytosine methylation (5mC) is the most prevalent modification found in DNA. However, recent identification of N6-methyladenosine (6mA) in plants starts to reveal their critical role in plant development. Epigenetic modifications are actively involved in creating the phenotype by controlling essential biological mechanisms. Epigenetic modifications could be heritable and metastable causing variation in epigenetic status between or within species. However, both genetic and heritable epigenetic variation has the potential to drive natural variation. Hence, epigenome editing might help overcome some of the shortcomings of genome editing (such as gene knockout), which can have significant off-target effects and only enables the loss of a gene’s function. In this review, we have discussed the mechanism underlying DNA methylation and demethylation in plants. Methyltransferases and demethylases are involved in catalyzing specific types of modification. We also discuss the potential role of DNA modifications in crop improvement for meeting the requirements of sustainable and green agriculture. Full article
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14 pages, 2957 KiB  
Article
Comprehensive Analysis of N6-Methyladenosine Regulatory Genes from Citrus grandis and Expression Profilings in the Fruits of “Huajuhong” (C. grandis “Tomentosa”) during Various Development Stages
by Yuzhen Tian, Jiwu Zeng and Ruiyi Fan
Horticulturae 2022, 8(5), 462; https://doi.org/10.3390/horticulturae8050462 - 20 May 2022
Cited by 3 | Viewed by 1817
Abstract
Citrus grandis “Tomentosa” (“Huajuhong”) is a famous traditional Chinese medicine. The aim of the present study is to provide a comprehensive characterization of the m6A regulatory genes from C. grandis, and examine their expression patterns in fruits of C. grandis [...] Read more.
Citrus grandis “Tomentosa” (“Huajuhong”) is a famous traditional Chinese medicine. The aim of the present study is to provide a comprehensive characterization of the m6A regulatory genes from C. grandis, and examine their expression patterns in fruits of C. grandis “Tomentosa” during various developmental stages. A total of 26 N6-methyladenosine (m6A) regulatory proteins were identified from the genome of C. grandis, which were distributed across nine chromosomes in C. grandis. Phylogenetic relationships revealed that all m6A regulatory genes were divided into groups of m6A writers, erasers, and readers. The m6A writer groups included CgMTA, CgMTB, and CgMTC three MTs (methyltransferases), one CgVIR (virilizer), one CgHAKAI (E3 ubiquitin ligase HAKAI), and one CgFIP37 (FKBP interacting protein 37). Moreover, 10 CgALKBH (α-ketoglutarate-dependent dioxygenase homolog) members (numbered from CgALKBH1 to CgALKBH10) and 10 CgECT (C-terminal region) members (numbered from CgECT1 to CgECT10) in C. grandis were identified as m6A erasers and readers, respectively. The domain structures and motif architectures among the groups of m6A writers, erasers, and readers were diverse. Cis-acting elements in the promoters of the 26 m6A regulatory genes predicted that the abscisic acid-responsive (ABA) element (ABRE) was present on the promoters of 19 genes. In addition, the expression profiles of all m6A regulatory genes were examined in the fruits of two varieties of C. grandis “Tomentosa” during different growth stages to give basic hints for further investigation of the function of the N6-methyladenosine regulatory genes in C. grandis “Tomentosa”. Full article
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12 pages, 1978 KiB  
Article
Identification and Comparative Analysis of Genes and MicroRNAs Involved in the Floral Transition of the Xinjiang Early-Flowering Walnut (Juglans regia L.)
by Qiang Jin, Rongli Mo, Wenxing Chen, Qinglin Zhang, Fang Sheng, Cuiyun Wu, Rui Zhang and Zhengrong Luo
Horticulturae 2022, 8(2), 136; https://doi.org/10.3390/horticulturae8020136 - 05 Feb 2022
Cited by 4 | Viewed by 2349
Abstract
For tree crops, shortening the juvenile phase is a vital strategy to advance fruit bearing and enhance the breeding efficiency. Walnut (Juglans regia L.) seedlings usually take at least eight to 10 years to flower, but early-flowering (EF) types can flower one [...] Read more.
For tree crops, shortening the juvenile phase is a vital strategy to advance fruit bearing and enhance the breeding efficiency. Walnut (Juglans regia L.) seedlings usually take at least eight to 10 years to flower, but early-flowering (EF) types can flower one or two years after planting. In this study, RNA sequencing (RNA-Seq) and microRNA sequencing (miRNA-Seq) were used for a transcriptome-wide analysis of gene and miRNA expression in hybrids of the Xinjiang EF walnut variety ‘Xinwen 81’ and later-flowering (LF) walnut. Based on a high-quality chromosome-scale reference genome, a total of 3009 differentially expressed genes (DEGs) were identified, of which 933 were upregulated (accounting for 31%) and 2076 were downregulated (accounting for 69%). DEGs were functionally annotated, and the flowering-related genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), and LEAFY (LFY) showed remarkable upregulation in EF compared with in the LF walnut. In addition, miRNAs associated with floral transition were screened as candidates for flowering time regulation in the walnut. This work provides new insights into walnut floral transition, which may ultimately contribute to genetic improvement of the walnut. Full article
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2021

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13 pages, 4032 KiB  
Article
Comprehensive Analysis of Jumonji Domain C Family from Citrus grandis and Expression Profilings in the Exocarps of “Huajuhong” (Citrus grandis “Tomentosa”) during Various Development Stages
by Yuzhen Tian, Ruiyi Fan and Jiwu Zeng
Horticulturae 2021, 7(12), 592; https://doi.org/10.3390/horticulturae7120592 - 20 Dec 2021
Cited by 5 | Viewed by 2547
Abstract
Citrus grandis “Tomentosa” (“Huajuhong”) is a famous Traditional Chinese Medicine. In this study, a total of 18 jumonji C (JMJC) domain-containing proteins were identified from C. grandis. The 18 CgJMJCs were unevenly located on six chromosomes of C. grandis. Phylogenetic [...] Read more.
Citrus grandis “Tomentosa” (“Huajuhong”) is a famous Traditional Chinese Medicine. In this study, a total of 18 jumonji C (JMJC) domain-containing proteins were identified from C. grandis. The 18 CgJMJCs were unevenly located on six chromosomes of C. grandis. Phylogenetic analysis revealed that they could be classified into five groups, namely KDM3, KDM4, KDM5, JMJC, and JMJD6. The domain structures and motif architectures in the five groups were diversified. Cis-acting elements on the promoters of 18 CgJMJC genes were also investigated, and the abscisic acid-responsive element (ABRE) was distributed on 15 CgJMJC genes. Furthermore, the expression profiles of 18 CgJMJCs members in the exocarps of three varieties of “Huajuhong”, for different developmental stages, were examined. The results were validated by quantitative real-time PCR (qRT-PCR). The present study provides a comprehensive characterization of JMJC domain-containing proteins in C. grandis and their expression patterns in the exocarps of C. grandis “Tomentosa” for three varieties with various development stages. Full article
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18 pages, 4029 KiB  
Article
Rootstock-Mediated Transcriptional Changes Associated with Cold Tolerance in Prunus mume Leaves
by Faisal Hayat, Chengdong Ma, Shahid Iqbal, Xiao Huang, Ouma Kenneth Omondi, Zhaojun Ni, Ting Shi, Rezwan Tariq, Ummara Khan and Zhihong Gao
Horticulturae 2021, 7(12), 572; https://doi.org/10.3390/horticulturae7120572 - 13 Dec 2021
Cited by 10 | Viewed by 2945
Abstract
Japanese apricot (Prunus mume) is remarkably valuable for its high ornamental and economic importance due to its distinctive features. Low temperature is a serious environmental constraint for this species, restricting its cultivation and dispersal in the north of China. To address [...] Read more.
Japanese apricot (Prunus mume) is remarkably valuable for its high ornamental and economic importance due to its distinctive features. Low temperature is a serious environmental constraint for this species, restricting its cultivation and dispersal in the north of China. To address this issue, breeding requires an understanding of the molecular mechanisms underlying responses to cold stress. We examined the leaf physiological and transcriptome profile by RNA sequencing in ‘Bungo’ scion cultivar grafted onto Prunus mume (cold-sensitive) and Prunus armeniaca (cold-tolerant) rootstocks at 4 °C for 0, 6, and 24 h. Our results revealed that the increased MDA concentration in the leaves of P. mume cultivar (cold-sensitive) suggests that cold stress might cause oxidative damage and increased sensitivity. Moreover, the cold-tolerant cultivar (P. armeniaca) considerably enhances the enzyme activities (i.e., SOD, POD, and CAT), as well as osmo-protectants (soluble sugars and proline) compared with sensitive cultivar, which helps plants to withstand oxidative damage caused by cold stress. Additionally, differentially expressed genes were shown to be enriched in plant hormone signal transduction, ribosome, MAPK signaling, and circadian rhythm pathway. After 24 h of cold stress, genes related to PYL4, histidine kinase 1, SAUR36, bHLH130, bHLH123, TIFY 6B-like, WRKY 40, WRKY 57, and 60S acidic ribosomal protein P1 were differentially expressed, implying that these DEGs involved in multiple pathways are involved in cold tolerance in Japanese apricot. This study improved our current understanding of the mechanism of cold tolerance in Japanese apricot, and the findings could be utilized for other related fruit species. Full article
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16 pages, 5094 KiB  
Article
Identification of Long Non-Coding RNAs Associated with Tomato Fruit Expansion and Ripening by Strand-Specific Paired-End RNA Sequencing
by Jinyu Wang, Yan Feng, Xiaotao Ding, Jingtian Huo and Wen-Feng Nie
Horticulturae 2021, 7(12), 522; https://doi.org/10.3390/horticulturae7120522 - 25 Nov 2021
Cited by 4 | Viewed by 1751
Abstract
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. [...] Read more.
As emerging essential regulators in plant development, long non-coding RNAs (lncRNAs) have been extensively investigated in multiple horticultural crops, as well as in different tissues of plants. Tomato fruits are an indispensable part of people’s diet and are consumed as fruits and vegetables. Meanwhile, tomato is widely used as a model to study the ripening mechanism in fleshy fruit. Although increasing evidence shows that lncRNAs are involved in lots of biological processes in tomato plants, the comprehensive identification of lncRNAs in tomato fruit during its expansion and ripening and their functions are partially known. Here, we performed strand-specific paired-end RNA sequencing (ssRNA-seq) of tomato Heinz1706 fruits at five different developmental stages, as well as flowers and leaves. We identified 17,674 putative lncRNAs by referencing the recently released SL4.0 and annotation ITAG4.0 in tomato plants. Many lncRNAs show different expression patterns in fleshy fruit at different developmental stages compared with leaves or flowers. Our results indicate that lncRNAs play an important role in the regulation of tomato fruit expansion and ripening, providing informative lncRNA candidates for further studies in tomato fruits. In addition, we also summarize the recent advanced progress in lncRNAs mediated regulation on horticultural fruits. Hence, our study updates the understanding of lncRNAs in horticultural plants and provides resources for future studies relating to the expansion and ripening of tomato fruits. Full article
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