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Horticulturae
Special Issues
Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics
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Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 15 May 2024 | Viewed by 13270

Special Issue Editors

Prof. Dr. Zhaohe Yuan

E-Mail Website
Guest Editor
College of Forestry, Nanjing Forestry University, Nanjing 210037, China
Interests: tree fruit and nut crops; pomegranate; developmental biology; flower and fruit development; germplasm; genetics and genomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Gaihua Qin

E-Mail Website
Guest Editor
Institute of Horticultural Research, Anhui Academy of Agricultural Sciences, Hefei 230001, China
Interests: pomegranate; fruit quality evaluation; mechanism of seed coat development; physiology of postharvest fruit
Prof. Dr. Julián Bartual

E-Mail Website
Guest Editor
Agricultural Experiment Station of Elche, CV-855, Km. 1, 03290 Alicante, Spain
Interests: pomegranate breeding; germplasm; pomegranate production; genetics; cultivation

Special Issue Information

Dear Colleagues,

Pomegranate (Punica granatum L.) belongs to the family Lythraceae, native to central Asia. It has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features, such as the bright red appearance and the abundance of valuable compounds in its peel and aril with health-promoting properties due to being ellagitannin-based. In recent years, along with the increase in its cultivation and consumption, research on pomegranate germplasm, genetics, multiomics, cultivation, and postharvest physiology has progressed significantly. Genome sequences of pomegranate varieties and transcriptomic data from fruits, flowers, and leaves is expected to facilitate an understanding of the genetic control of metabolites in pomegranate.

The focus of this Special Issue is to cover pomegranate-related research areas, including germplasm evaluations, innovation and utilization, breeding, genetic map construction, molecular marker development, genomics, transcriptomics, and proteomics, including molecular and physiological mechanisms of fruit quality, fruit seed, flower development, or adaptation to environmental cues. Studies on pomegranate cultivation and postharvest physiology are also welcome. In addition, we aim to invite experts to submit review articles highlighting recent advances and future perspectives of pomegranate germplasm innovation and utilization.

Prof. Dr. Zhaohe Yuan
Prof. Dr. Gaihua Qin
Prof. Dr. Julián Bartual
Guest Editors

Manuscript Submission Information

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

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

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • pomegranate
  • germplasm
  • genetics
  • genomics, transcriptomics
  • proteomics
  • breeding
  • flower and fruit development
  • molecular mechanisms of fruit quality improvement
  • cultivation
  • postharvest physiology

Published Papers (9 papers)

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Research

14 pages, 2651 KiB  
Article
Exploring MicroRNAs Associated with Pomegranate Pistil Development: An Identification and Analysis Study
by Yujie Zhao, Jingyi Huang, Ming Li, Hongfang Ren, Jian Jiao, Ran Wan, Yu Liu, Miaomiao Wang, Jiangli Shi, Kunxi Zhang, Pengbo Hao, Shangwei Song, Tuanhui Bai and Xianbo Zheng
Horticulturae 2024, 10(1), 85; https://doi.org/10.3390/horticulturae10010085 - 16 Jan 2024
Viewed by 798
Abstract
The interaction between miRNAs (microRNAs) and target genes plays an important role in plant pistil development. MiRNAs related to pistils were explored in pomegranate. The differentially expressed miRNAs were screened at different developmental stages of pomegranate pistils, and their target differentially expressed mRNAs [...] Read more.
The interaction between miRNAs (microRNAs) and target genes plays an important role in plant pistil development. MiRNAs related to pistils were explored in pomegranate. The differentially expressed miRNAs were screened at different developmental stages of pomegranate pistils, and their target differentially expressed mRNAs were further identified to clarify the regulatory effect of miRNAs on pistil development. In our study, 61 conserved miRNAs were identified in 30 families, including miR395, miR394, miR393, miR161, miR162, and miR168. Among them, miR156, miR157, miR159, miR160, miR164, miR165, miR166, miR167, miR169, and miR172 were involved in the development of flower organs. Eight miRNAs were randomly selected and verified for qRT-PCR analysis. The result analysis indicated that miR160, miR164, and miR172 might be positive factors in the regulation of pomegranate pistil development. MiR156 and miR166 might be involved in regulation of pomegranate pistil development as negative factors. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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15 pages, 3141 KiB  
Article
Pomegranate Cultivars with Diverse Origins Exhibit Strong Resistance to Anthracnose Fruit Rot Caused by Colletotrichum gloeosporioides, a Major Disease in Southeast United States
by Alexander Schaller, John M. Chater, Gary E. Vallad, Jeff Moersfelder, Claire Heinitz and Zhanao Deng
Horticulturae 2023, 9(10), 1097; https://doi.org/10.3390/horticulturae9101097 - 03 Oct 2023
Viewed by 2200
Abstract
Pomegranate, a pivotal fruit that is well recognized globally and a rapidly emerging crop in the southeastern United States and other subtropical regions, faces a formidable challenge from Colletotrichum spp., a fungal pathogen causing anthracnose fruit rot, which leads to severe to complete [...] Read more.
Pomegranate, a pivotal fruit that is well recognized globally and a rapidly emerging crop in the southeastern United States and other subtropical regions, faces a formidable challenge from Colletotrichum spp., a fungal pathogen causing anthracnose fruit rot, which leads to severe to complete premature fruit drop. The development and use of disease-resistant cultivars are considered the most cost-effective and sustainable approach to managing this disease. Identifying sources of resistance is essential for developing new cultivars with improved resistance to this disease. This project aimed to expand the scope of evaluation through a 2-year field study in central Florida, examining fruit from 35 cultivars from diverse origins using both artificial inoculation at the petal dehiscent stage and natural infection. Lesion size on the fruit was measured during the growing season in a field setting. Subsequently, seven cultivars were selected for further testing by inoculating detached mature fruit and measuring lesion size to confirm observed resistance and determine the correlation between resistance observed in planta in the field and on detached fruit in the laboratory. The field study revealed significant genetic differences among pomegranate cultivars in susceptibility to naturally occurring and induced anthracnose fruit rot and classified cultivars into five resistance or susceptibility classes. Five cultivars that originated from different regions of the world, including ‘Azadi’, showed consistent resistance to anthracnose fruit rot in the field. Resistance remained strong on detached mature fruit. A strong positive correlation existed between resistance levels on in-planta fruit and on detached mature fruit, suggesting a possible simple, efficient approach to screening breeding populations for anthracnose fruit rot resistance in pomegranate. These findings represent an important step toward developing new anthracnose-resistant cultivars and understanding and improving disease resistance in this increasingly important fruit crop in the world. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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15 pages, 9969 KiB  
Article
Effects of 1–MCP Treatment on Postharvest Fruit of Five Pomegranate Varieties during Low-Temperature Storage
by Ran Wan, Jinhui Song, Zhenyang Lv, Xingcheng Qi, Zhiliang Feng, Zhenfeng Yang, Xinyue Cao, Jiangli Shi, Zaihai Jian, Ruiran Tong, Qingxia Hu and Yanhui Chen
Horticulturae 2023, 9(9), 1031; https://doi.org/10.3390/horticulturae9091031 - 13 Sep 2023
Cited by 1 | Viewed by 1116
Abstract
Pomegranate fruit production and consumption are restricted by appropriate postharvest handling practices. 1–MCP (1–methylcyclopropene) is a natural preservative of fruits and vegetables; however, its effects on the storage of different pomegranate varieties have not been extensively investigated. Herein, the effects of 1.0 μL [...] Read more.
Pomegranate fruit production and consumption are restricted by appropriate postharvest handling practices. 1–MCP (1–methylcyclopropene) is a natural preservative of fruits and vegetables; however, its effects on the storage of different pomegranate varieties have not been extensively investigated. Herein, the effects of 1.0 μL L−1 1–MCP on postharvest pomegranate fruit of three soft-seed ‘Mollar’, ‘Malisi’, and ‘Tunisan soft seed’ and two semi-soft-seed ‘Moyuruanzi’ and ‘Dongyan’ were investigated over 90 d (days) under low-temperature storage at 4 ± 0.5 °C with a relative humidity of 85–90%. Several indexes of exterior and interior quality were recorded, the sensory quality was evaluated, and the respiration and ethylene production were also determined. The results showed that peel browning was generally more severe in the soft-seed varieties than in the semi-soft-seed varieties. Significantly lighter peel browning presented in the three soft-seed fruits from 45 d after the 1–MCP treatment, with 35%, 19%, and 28% less than those controls at 90 d, correspondingly. However, 1–MCP only significantly decreased peel browning in the semi soft-seed fruits at 60 days. A prominent decrease in weight loss was recorded in all five varieties, with ‘Malisi’ showing the largest and ‘Dongyan’ the smallest difference between the 1–MCP and control treatments. Through the results of color, physiological, and chemical changes, as well as sensory properties, better color and total acceptance were found with higher titratable acids and vitamin C but with decreased anthocyanins in most fruits treated with 1–MCP. In contrast to the control, remarkable suppression of ethylene production peaks in all whole fruits and periodical increase in respiration rates in the soft-seed whole fruits were activated at 30–60 d after storage by the 1–MCP treatment, roughly when peel browning occurred and began increasing. Overall, our findings provided a crucial foundation for extending the application of 1–MCP in postharvest preservation of pomegranates. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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15 pages, 6999 KiB  
Article
Genome-Wide Identification of Laccase Gene Family from Punica granatum and Functional Analysis towards Potential Involvement in Lignin Biosynthesis
by Jiangli Shi, Jianan Yao, Ruiran Tong, Sen Wang, Ming Li, Chunhui Song, Ran Wan, Jian Jiao and Xianbo Zheng
Horticulturae 2023, 9(8), 918; https://doi.org/10.3390/horticulturae9080918 - 11 Aug 2023
Cited by 2 | Viewed by 962
Abstract
Laccase (LAC) is the key enzyme responsible for lignin biosynthesis. Here, 57 PgLACs from pomegranate were identified and distributed on eight chromosomes and one unplaced scaffold. They were divided into six groups containing three typical Cu-oxidase domains. Totally, 51 cis-acting elements in [...] Read more.
Laccase (LAC) is the key enzyme responsible for lignin biosynthesis. Here, 57 PgLACs from pomegranate were identified and distributed on eight chromosomes and one unplaced scaffold. They were divided into six groups containing three typical Cu-oxidase domains. Totally, 51 cis-acting elements in the promoter region of PgLACs are involved in response to ABA, GA, light, stress, etc., indicating diverse functions of PgLACs. The expression profiles of 13 PgLACs during the seed development stage showed that most PgLACs expressed at a higher level earlier than at the later seed development stage in two pomegranate cultivars except PgLAC4. Also, PgLAC1/6/7/16 expressed at a significantly higher level in soft-seed ‘Tunisia’; on the contrary, PgLAC37 and PgLAC50 with a significantly higher expression in hard-seed ‘Taishanhong’. Combined with their distinguishing cis-acting elements, it was concluded that PgLAC1/6/7 may respond to GA via TATC-box and GARE-motif, and PgLAC16 repressed the promotor activity of embryo mid-maturation genes via RY-element so as to contribute to softer seed formation, whereas PgLAC37/50 may participate in seed formation and accelerate seed maturity via ABRE and G-box elements. Collectively, the dramatic gene expressions of PgLAC1/6/7/16/37/50 will provide valuable information to explore the formation of soft- and hard-seed in pomegranate. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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15 pages, 12417 KiB  
Article
Unraveling the Pomegranate Genome: Comprehensive Analysis of R2R3-MYB Transcription Factors
by Heming Suo, Xuan Zhang, Lei Hu, Huihui Ni, Renzeng Langjia, Fangyu Yuan, Maowen Zhang and Shuiming Zhang
Horticulturae 2023, 9(7), 779; https://doi.org/10.3390/horticulturae9070779 - 07 Jul 2023
Cited by 1 | Viewed by 791
Abstract
R2R3-MYB TFs represent one of the most extensive gene families in plants and play a crucial role in regulating plant development, metabolite accumulation, and defense responses. Nevertheless, there has been no systematic investigation into the pomegranate R2R3-MYB family. In this study, 186 R2R3-MYB [...] Read more.
R2R3-MYB TFs represent one of the most extensive gene families in plants and play a crucial role in regulating plant development, metabolite accumulation, and defense responses. Nevertheless, there has been no systematic investigation into the pomegranate R2R3-MYB family. In this study, 186 R2R3-MYB genes were identified from the pomegranate genome and grouped into 34 subgroups based on phylogenetic analysis. Gene structure analysis showed that the PgR2R3-MYB family in the same subgroup had a similar structure. Gene duplication event analysis revealed that the amplification of the PgMYB family was driven by Whole Genome Duplication (WGD) and dispersed duplication. In the upstream promoter sequence of the PgMYB gene, we identified a large number of plant hormones and environmental response elements. Using phylogenetic analysis and RNA-seq analysis, we identified three PgMYB TFs that may be involved in the regulation of lignin synthesis. Their expression patterns were verified by qPCR experiments. This study provides a solid foundation for further studies on the function of the R2R3-MYB gene and the molecular mechanism of lignin synthesis. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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17 pages, 4171 KiB  
Article
Molecular Identification and Characterization of UDP-glycosyltransferase (UGT) Multigene Family in Pomegranate
by Xueqing Zhao, Yingyi Feng, Ding Ke, Yingfen Teng, Ying Chen and Renzeng Langjia
Horticulturae 2023, 9(5), 540; https://doi.org/10.3390/horticulturae9050540 - 28 Apr 2023
Cited by 1 | Viewed by 1755
Abstract
Pomegranate (Punica granatum L.) is regarded as one of the functional fruits because of its large amounts of secondary metabolites. The glycosylation processes mediated by UDP-glycosyltransferases (UGTs) play a decisive role in regulating secondary metabolite availability. In this study, a genome-wide search [...] Read more.
Pomegranate (Punica granatum L.) is regarded as one of the functional fruits because of its large amounts of secondary metabolites. The glycosylation processes mediated by UDP-glycosyltransferases (UGTs) play a decisive role in regulating secondary metabolite availability. In this study, a genome-wide search identified 145 UGT genes in pomegranate, and further phylogenetic analysis defined 17 distinct groups: A to P and R. PgUGTs were dispersed unevenly across all eight chromosomes. Duplication events analysis revealed that both segmental and tandem duplications were the main mechanisms leading to gene family expansions. The comparison of exon–intron patterns identified 53 intron-less genes. A total of 24 types of cis-acting elements related to hormone, stress, and developmental responses were predicted in the promoter regions. Expression analysis of PgUGT genes using RNA-seq data and quantitative real-time PCR (qRT-PCR) verification suggested that PgUGT genes were expressed at specific stages of fruit development, and different PgUGT members likely played different roles in specific fruit developmental stages. In an attempt to identify the UGTs involved in the glycosylation of flavonoids, 44 PgUGTs were putatively determined, and 5 well-defined orthologous groups (OGs) were characterized by the regioselectivity of these enzymes. These results provide significant insight into the UGT multi-gene family in pomegranate, and will be helpful to further elucidate their roles involved in secondary and specialized metabolism in pomegranate. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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16 pages, 11088 KiB  
Article
Uncovering the Expansin Gene Family in Pomegranate (Punica granatum L.): Genomic Identification and Expression Analysis
by Xintong Xu, Yuying Wang, Xueqing Zhao and Zhaohe Yuan
Horticulturae 2023, 9(5), 539; https://doi.org/10.3390/horticulturae9050539 - 28 Apr 2023
Cited by 2 | Viewed by 1516
Abstract
Expansins, which are important components of plant cell walls, act as loosening factors to directly induce turgor-driven cell wall expansion, regulate the growth and development of roots, leaves, fruits, and other plant organs, and function essentially under environmental stresses. In multiple species, many [...] Read more.
Expansins, which are important components of plant cell walls, act as loosening factors to directly induce turgor-driven cell wall expansion, regulate the growth and development of roots, leaves, fruits, and other plant organs, and function essentially under environmental stresses. In multiple species, many expansin genes (EXPs) have been cloned and functionally validated but little is known in pomegranate. In this study, a total of 33 PgEXPs were screened from the whole genome data of ‘Taishanhong’ pomegranate, belonging to the EXPA(25), EXPB(5), EXLA(1), and EXLB(2) subfamilies. Subsequently, the composition and characteristics were analyzed. Members of the same branch shared similar motif compositions and gene structures, implying they had similar biological functions. According to cis-acting element analysis, PgEXPs contained many light and hormone response elements in promoter regions. Analysis of RNA-seq data and protein interaction network indicated that PgEXP26 had relatively higher transcription levels in all pomegranate tissues and might be involved in pectin lyase protein synthesis, whilst PgEXP5 and PgEXP31 might be involved in the production of enzymes associated with cell wall formation. Quantitative real-time PCR (qRT-PCR) results revealed that PgEXP expression levels in fruit peels varied considerably across fruit developmental phases. PgEXP23 was expressed highly in the later stages of fruit development, suggesting that PgEXP23 was essential in fruit ripening. On the other hand, the PgEXP28 expression level was minimal or non-detected. Our work laid a foundation for further investigation into pomegranate expansin gene functions. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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16 pages, 3865 KiB  
Article
Genome-Wide Identification and Characterization of the ANS Gene Family in Pomegranate (Punica granatum L.)
by Huihui Ni, Heming Suo, Xuan Zhang, Lei Hu, Fangyu Yuan, Maowen Zhang and Shuiming Zhang
Horticulturae 2023, 9(4), 468; https://doi.org/10.3390/horticulturae9040468 - 07 Apr 2023
Cited by 1 | Viewed by 1271
Abstract
Anthocyanidin Synthase (ANS) is a key enzyme in the later stages of the anthocyanin biosynthetic pathway, and its role is to convert colorless leucoanthocyanidins to colored anthocyanidins. In this study, a total of 75 members of the pomegranate ANS family were identified and [...] Read more.
Anthocyanidin Synthase (ANS) is a key enzyme in the later stages of the anthocyanin biosynthetic pathway, and its role is to convert colorless leucoanthocyanidins to colored anthocyanidins. In this study, a total of 75 members of the pomegranate ANS family were identified and divided into four groups (Group I, Group Ⅱ, Group Ⅲ and Group Ⅳ) based on evolutionary relationships. The 75 ANS gene family members were unevenly distributed on seven of the eight chromosomes of pomegranate. The results of the physical and chemical property analysis showed that 93.33% of the proteins were acidic proteins, 6.67% were alkaline proteins, 28% of the proteins were stable proteins and 72% were unstable proteins. Protein secondary structure analysis showed that α-Spiral and irregular curl are the main structural elements. Analysis of the conserved structural domains of the proteins showed that all 75 ANS family members contained one DIOX -N subfamily structural domain and one 2OG-FeII_Oxy subfamily structural domain. The results of subcellular localization showed that all 75 ANS family members of pomegranate were localized in the cytoplasm. Analysis of the transcriptome data showed that the expression of the pomegranate ANS genes were variety-specific and period-specific. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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16 pages, 12110 KiB  
Article
Exploring the Relationship between Genomic Variation and Phenotype in Ornamental Pomegranate: A Study of Single and Double-Petal Varieties
by Yan Huo, Han Yang, Wenjie Ding, Zhaohe Yuan and Zunling Zhu
Horticulturae 2023, 9(3), 361; https://doi.org/10.3390/horticulturae9030361 - 09 Mar 2023
Cited by 1 | Viewed by 1174
Abstract
The double-petal varieties of ornamental pomegranate have higher ornamental value and garden development potential than the single-petal varieties but there has been no study on the genomic variation between them. This study aimed to determine the genomic variation between the two kinds of [...] Read more.
The double-petal varieties of ornamental pomegranate have higher ornamental value and garden development potential than the single-petal varieties but there has been no study on the genomic variation between them. This study aimed to determine the genomic variation between the two kinds of varieties and the relationship between the variation and phenotype by identifying the DNA variation of three single-petal varieties and three double-petal varieties using re-sequencing technology. The results showed that the variation number of each variety was in the order of single nucleotide polymorphisms (SNPs) > insertions and deletions (InDels) > structural variations (SVs) > copy number variations (CNVs). The number of SNPs and InDels in the double-petal varieties was significantly higher than that in the single-petal varieties, and there was no significant difference in the number of SVs and CNVs. The number of non-synonymous SNPs in the coding region (Nonsyn_CDS_SNPs) and InDels with a 3X length in the coding region (3X_shiftMutation_CDS_InDel) was significantly higher in the double-petal varieties than that in the single-petal varieties. The number of the two variants was strongly positively correlated with each morphological index that was related to the phenotypic difference between the two varieties. Nonsyn_CDS_SNPs and 3X_shiftMutation_CDS_InDel were enriched in the cell membrane system, cell periphery, and signal transduction, from which 15 candidate genes were screened. Our results provide genomic data for the study of the formation mechanism of the double-petal flower and lay a theoretical foundation for new variety breeding of ornamental pomegranate. Full article
(This article belongs to the Special Issue Research on Pomegranate Germplasm, Breeding, Genetics and Multiomics)
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