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Identification and Functional Analysis of CAD Gene Family in Pomegranate ( Punica granatum). Genes (Basel) 2022; 14:genes14010026. [PMID: 36672766 PMCID: PMC9858471 DOI: 10.3390/genes14010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
[Objective] Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. The aim of this study was to identify CAD gene family members in pomegranate and its expression correlation with seed hardness. [Methods] Based on the reported CAD sequence of Arabidopsis, the CAD gene family of pomegranate was identified by homologous comparison, and then phylogenetic, molecular characterization, and expression profile analysis were performed. [Results] Pomegranate CAD gene family has 25 members, distributed on seven chromosomes of pomegranate. All pomegranate CAD proteins have similar physical and chemical properties. We divide the family into four groups based on evolutionary relationships. The member of group I, called bona fide CAD, was involved in lignin synthesis. Most of the members of group II were involved in stress resistance. The functions of groups III and IV need to be explored. We found four duplicated modes (whole genome duplication or segmental (WGD), tandem duplication (TD), dispersed duplication (DSD), proximal duplication (PD) in this family; TD (36%) had the largest number of them. We predicted that 20 cis-acting elements were involved in lignin synthesis, stress resistance, and response to various hormones. Gene expression profiles further demonstrated that the PgCAD gene family had multiple functions. [Conclusions] Pomegranate CAD gene family is involved in lignin synthesis of hard-seeded cultivar Hongyushizi and Baiyushizi, but its role in seed hardness of soft-seeded cultivar Tunisia needs to be further studied.
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In Vitro and In Planta Antagonistic Effect of Endophytic Bacteria on Blight Causing Xanthomonas axonopodis pv. punicae: A Destructive Pathogen of Pomegranate. Microorganisms 2022; 11:microorganisms11010005. [PMID: 36677297 PMCID: PMC9860609 DOI: 10.3390/microorganisms11010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Pomegranate bacterial blight caused by Xanthomonas axonopodis pv. punicae (Xap) is a highly destructive disease. In the absence of host resistance to the disease, we aimed to evaluate the biocontrol potential of endophytic bacteria against Xap. Thus, in this study, we isolated endophytes from pomegranate plants, identified them on the basis of 16S rDNA sequencing, tested them against Xap, and estimated the endophyte-mediated host defense response. The population of isolated endophytes ranged from 3 × 106 to 8 × 107 CFU/g tissue. Furthermore, 26 isolates were evaluated for their biocontrol activity against Xap, and all the tested isolates significantly reduced the in vitro growth of Xap (15.65% ± 1.25% to 56.35% ± 2.66%) as compared to control. These isolates could reduce fuscan, an uncharacterized factor of Xap involved in its aggressiveness. Lower blight incidence (11.6%) and severity (6.1%) were recorded in plants sprayed with endophytes 8 days ahead of Xap spray (Set-III) as compared to control plants which were not exposed to endophytes (77.33 and 50%, respectively%) during in vivo evaluation. Moreover, significantly high phenolic and chlorophyll contents were estimated in endophyte-treated plants as compared to control. The promising isolates mostly belonged to the genera Bacillus, Burkholderia, and Lysinibacillus, and they were deposited to the National Agriculturally Important Microbial Culture Collection, India.
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Parashuram S, Singh NV, Gaikwad NN, Corrado G, Roopa Sowjanya P, Basile B, Devaraja NS, Chandra R, Babu KD, Patil PG, Kumar P, Singh A, Marathe RA. Morphological, Biochemical, and Molecular Diversity of an Indian Ex Situ Collection of Pomegranate ( Punica granatum L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:3518. [PMID: 36559629 PMCID: PMC9781629 DOI: 10.3390/plants11243518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Pomegranate (Punica granatum, L.) is a fruit tree that is increasingly popular worldwide due to the health-related properties of the fruit juice. While several studies highlighted the rich phytochemical diversity, few efforts have been devoted to an integrative understanding of the level of diversity of this species. This study investigated the diversity of 40 pomegranate accessions in an Indian ex situ collection by using twenty-nine morphological traits, six biochemical parameters, and twenty-nine Simple Sequence Repeats (SSR) markers. Among the evaluated traits, fruit volume (23.34% CV), fruit weight (21.12% CV), and fruit color (*a) (22.69 % CV) largely contributed to the morphological classification. Based on Mahalanobis D2 distance and Tocher's clustering, the 40 pomegranate accessions were grouped into eight clusters, partly consistent with their origin. Specifically, cultivars introduced from foreign countries were present in distinct clusters. The SSR marker analysis generated 66 alleles. The observed heterozygosity values ranged from 0.05 to 0.63, with a mean value of 0.30. Maximum molecular genetic dissimilarity was observed between 'IC-318720' and 'Gul-e-Shah Red' (0.30). The neighbor-joining dendrogram separated wild accessions from cultivated varieties. The combination of morphological, biochemical, and molecular characterization allowed for comprehensively characterizing the pomegranate diversity and provided information on the relationships between the different aspects of the diversity. This work also suggests that the origin of the accessions is an important factor of discrimination and that the level of admixture between local and foreign material is currently limited.
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Affiliation(s)
- Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | - Nripendra Vikram Singh
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | | | - Giandomenico Corrado
- Department of Agricultural Sciences, University of Naples Federico II, 80138 Portici, NA, Italy
| | - P. Roopa Sowjanya
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | - Boris Basile
- Department of Agricultural Sciences, University of Naples Federico II, 80138 Portici, NA, Italy
| | - Nitesh Shirur Devaraja
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture & Technology, Kanpur 208002, Utter Pradesh, India
| | - Ram Chandra
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | | | - Prakash Goudappa Patil
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
| | - Pradeep Kumar
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India
| | - Akath Singh
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India
| | - Rajiv Arvind Marathe
- ICAR-National Research Centre on Pomegranate, Kegaon, Solpaur 413255, Maharashtra, India
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Evaluation of Genetic Diversity in Dog Breeds Using Pedigree and Molecular Analysis: A Review. DIVERSITY 2022. [DOI: 10.3390/d14121054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Domestic dogs are important for many economic and social reasons, and they have become a well-known model species for human disease. According to research, dog breeds exhibit significant levels of inbreeding and genetic diversity loss, decreasing the population’s ability to adapt in certain conditions, and indicating the need of conservation strategies. Before the development of molecular markers, pedigree information was used for genetic diversity management. In recent years, genomic tools are frequently applied for accurate estimation of genetic diversity and improved genetic conservation due to incomplete pedigrees and pedigree errors. The most frequently used molecular markers include PCR-based microsatellite markers (STRs) and DNA sequencing-based single-nucleotide polymorphism markers (SNP). The aim of this review was to highlight genetic diversity studies on dog breeds conducted using pedigree and molecular markers, as well as the importance of genetic diversity conservation in increasing the adaptability and survival of dog breed populations.
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Characterizing wild germplasm of neglected and underutilized crops: A case study of pomegranate (Punica granatum L.) from remote Pir Panjal Himalaya. BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Patil PG, Jamma S, N M, Bohra A, Pokhare S, Dhinesh Babu K, Murkute AA, Marathe RA. Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate. FRONTIERS IN PLANT SCIENCE 2022; 13:943959. [PMID: 36110362 PMCID: PMC9468638 DOI: 10.3389/fpls.2022.943959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Despite the availability of whole genome assemblies, the identification and utilization of gene-based marker systems has been limited in pomegranate. In the present study, we performed a genome-wide survey of intron length (IL) markers in the 36,524 annotated genes of the Tunisia genome. We identified and designed a total of 8,812 potential intron polymorphism (PIP) markers specific to 3,445 (13.40%) gene models that span 8 Tunisia chromosomes. The ePCR validation of all these PIP markers on the Tunisia genome revealed single-locus amplification for 1,233 (14%) markers corresponding to 958 (27.80%) genes. The markers yielding single amplicons were then mapped onto Tunisia chromosomes to develop a saturated linkage map. The functional categorization of 958 genes revealed them to be a part of the nucleus and the cytoplasm having protein binding and catalytic activity, and these genes are mainly involved in the metabolic process, including photosynthesis. Further, through ePCR, 1,233 PIP markers were assayed on multiple genomes, which resulted in the identification of 886 polymorphic markers with an average PIC value of 0.62. In silico comparative mapping based on physically mapped PIP markers indicates a higher synteny of Tunisia with the Dabenzi and Taishanhong genomes (>98%) in comparison with the AG2017 genome (95%). We then performed experimental validation of a subset of 100 PIP primers on eight pomegranate genotypes and identified 76 polymorphic markers, with 15 having PIC values ≥0.50. We demonstrated the potential utility of the developed markers by analyzing the genetic diversity of 31 pomegranate genotypes using 24 PIP markers. This study reports for the first time large-scale development of gene-based and chromosome-specific PIP markers, which would serve as a rich marker resource for genetic variation studies, functional gene discovery, and genomics-assisted breeding of pomegranate.
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Affiliation(s)
| | - Shivani Jamma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Manjunatha N
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Somnath Pokhare
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | | | | | - Rajiv A. Marathe
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
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Kumar P, Lokesh V, Doddaraju P, Kumari A, Singh P, Meti BS, Sharma J, Gupta KJ, Manjunatha G. Greenhouse and field experiments revealed that clove oil can effectively reduce bacterial blight and increase yield in pomegranate. Food Energy Secur 2021. [DOI: 10.1002/fes3.305] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Pavan Kumar
- Biocontrol laboratory University of Horticultural Sciences Bagalkot India
- Department of Biotechnology Basaveshwar Engineering College (Autonomous) Bagalkot India
| | - Veeresh Lokesh
- Biocontrol laboratory University of Horticultural Sciences Bagalkot India
| | - Pushpa Doddaraju
- Biocontrol laboratory University of Horticultural Sciences Bagalkot India
| | - Aprajita Kumari
- National Institute for Plant Genome Research New Delhi India
| | - Pooja Singh
- National Institute for Plant Genome Research New Delhi India
| | - Bharati S. Meti
- Department of Biotechnology Basaveshwar Engineering College (Autonomous) Bagalkot India
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Singh NV, Patil PG, Sowjanya RP, Parashuram S, Natarajan P, Babu KD, Pal RK, Sharma J, Reddy UK. Chloroplast Genome Sequencing, Comparative Analysis, and Discovery of Unique Cytoplasmic Variants in Pomegranate ( Punica granatum L.). Front Genet 2021; 12:704075. [PMID: 34394192 PMCID: PMC8356083 DOI: 10.3389/fgene.2021.704075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022] Open
Abstract
Here we report on comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing commercial cultivars, ornamental and wild types, through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild, “1201” and “1181”) to 158,662 bp (cultivar, “Gul-e-Shah Red”) among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and IRs (IR-A and IR-B) were observed across all the cp genomes. Interestingly, high variations were observed in sizes of large single copy (LSC, 88,976 to 89,044 bp) and small single copy (SSC, 18,682 to 18,684 bp) regions. Although, the structural organization of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate (“Helow,” “Tunisia,” and “Bhagawa”), the striking differences were observed with the Lagerstroemia lines, viz., Lagerstroemia intermedia (NC_0346620) and Lagerstroemia speciosa (NC_031414), which clearly confirmed previous findings. Furthermore, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC, and SSC have significantly accounted for the evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted in the identification of a total of 233 to 234 SSRs, with majority of them being mono- (A/T or C/G, 164–165 numbers), followed by di- (AT/AT or AG/CT, 54), tri- (6), tetra- (8), and pentanucleotides (1). Furthermore, the comparative structural variant analyses across cp genomes resulted in the identification of many varietal specific SNP/indel markers. In summary, our study has offered a successful development of large-scale cp genomics resources to leverage future genetic, taxonomical, and phylogenetic studies in pomegranate.
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Affiliation(s)
| | | | - Roopa P Sowjanya
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | | | - Purushothaman Natarajan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, West Virginia, WV, United States
| | | | - Ram Krishna Pal
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, India
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, West Virginia, WV, United States
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Differential gene responses in different varieties of pomegranate during the pathogenesis of Xanthomonas axonopodis pv. punicae. 3 Biotech 2021; 11:180. [PMID: 33927971 DOI: 10.1007/s13205-021-02721-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/05/2021] [Indexed: 01/15/2023] Open
Abstract
Bacterial blight (BB) caused by Xanthomonas axonopodis pv. punicae (Xap) is the major scourge in pomegranate cultivation leading to an extensive yield loss up to 60-80%. Hence, identifying a novel resistance source for BB is very necessary for developing a suitable management strategy. Host range analysis and cross-inoculation studies revealed that Xap is specific to pomegranate and there are no alternative hosts to the pathogen. Screening of 149 accessions recorded the varied disease resistance levels with mean disease severity of 30.67%. Accession lines IC318735, IC318724, and IC318762 exhibited maximum disease tolerance by exhibiting the lowest disease severity of 4.91, 5.66, and 6.82%, respectively. Comparative expression analysis of defence genes in IC318724 and IC318735 recorded significant upregulation of phenylalanine ammonia-lyase (PAL), callose synthase-3 (CS3), chitinase, pathogenesis-related protein-1 (PR1), and pathogenesis-related protein-10 (PR10), indicating these genes might be actively involved in conferring disease tolerance. Abiotic elicitors were tested to induce systemic resistance in agronomically superior and widely adapted variety Bhagwa for managing BB of pomegranate. Among the various elicitors tested; proline (600 ppm), gamma-aminobutyric acid (600 ppm), chitosan (600 ppm), β-aminobutyric acid (200 ppm), laminarin (600 ppm), and eugenol (200 ppm) recorded maximum disease protection in prophylactic treatment with disease protection of 89.59, 88.59, 87.15, 86.08, 81.05, and 78.72%, respectively. Similar observations were recorded when these were applied as curative treatment. The present study will broaden our understanding of host-pathogen interactions during BB infection in pomegranate, also aid in developing ideal approach for developing effective disease management. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02721-y.
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Patil PG, Singh NV, Bohra A, Raghavendra KP, Mane R, Mundewadikar DM, Babu KD, Sharma J. Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate ( Punica granatum L.) cv. Tunisia Genome. FRONTIERS IN PLANT SCIENCE 2021; 12:645055. [PMID: 33796127 PMCID: PMC8007985 DOI: 10.3389/fpls.2021.645055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/12/2021] [Indexed: 05/05/2023]
Abstract
The simple sequence repeat (SSR) survey of 'Tunisia' genome (296.85 Mb) identified a total of 365,279 perfect SSRs spanning eight chromosomes, with a mean marker density of 1,230.6 SSRs/Mb. We found a positive trend in chromosome length and the SSR abundance as marker density enhanced with a shorter chromosome length. The highest number of SSRs (60,708) was mined from chromosome 1 (55.56 Mb), whereas the highest marker density (1,294.62 SSRs/Mb) was recorded for the shortest chromosome 8 (27.99 Mb). Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. Across the eight chromosomes, the class III had maximum number of SSR motifs (301,684, 82.59%), followed by the class II (31,056, 8.50%) and the class I (5,003, 1.37%). Examination of the distribution of SSR motif types within a chromosome suggested the abundance of hexanucleotide repeats in each chromosome followed by dinucleotides, and these results are consistent with 'Tunisia' genome features as a whole. Concerning major repeat types, AT/AG was the most frequent (14.16%), followed by AAAAAT/AAAAAG (7.89%), A/C (7.54%), AAT/AAG (5.23%), AAAT/AAAG (4.37%), and AAAAT/AAAAG (1.2%) types. We designed and validated a total of 3,839 class I SSRs in the 'Tunisia' genome through electronic polymerase chain reaction (ePCR) and found 1,165 (30.34%) SSRs producing a single amplicon. Then, we selected 906 highly variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across multiple draft genomes of pomegranate, which provided us a subset of 265 highly polymorphic SSRs. Of these, 235 primers were validated on six pomegranate genotypes through wet-lab experiment. We found 221 (94%) polymorphic SSRs on six genotypes, and 187 of these SSRs had ≥ 0.5 PIC values. The utility of the developed SSRs was demonstrated by analyzing genetic diversity of 30 pomegranate genotypes using 16 HvSSRs spanning eight pomegranate chromosomes. In summary, we developed a comprehensive set of highly polymorphic genome-wide SSRs. These chromosome-specific SSRs will serve as a powerful genomic tool to leverage future genetic studies, germplasm management, and genomics-assisted breeding in pomegranate.
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Affiliation(s)
- Prakash Goudappa Patil
- ICAR-National Research Centre on Pomegranate, Solapur, India
- *Correspondence: Prakash Goudappa Patil,
| | | | | | | | - Rushikesh Mane
- ICAR-National Research Centre on Pomegranate, Solapur, India
| | | | | | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate, Solapur, India
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Poudel K, Luo X, Chen L, Jing D, Xia X, Tang L, Li H, Cao S. Identification of the SUT Gene Family in Pomegranate ( Punica granatum L.) and Functional Analysis of PgL0145810.1. Int J Mol Sci 2020; 21:ijms21186608. [PMID: 32927615 PMCID: PMC7554910 DOI: 10.3390/ijms21186608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 11/20/2022] Open
Abstract
Sucrose, an important sugar, is transported from source to sink tissues through the phloem, and plays important role in the development of important traits in plants. However, the SUT gene family is still not well characterized in pomegranate. In this study, we first identified the pomegranate sucrose transporter (SUT) gene family from the whole genome. Then, the phylogenetic relationship of SUT genes, gene structure and their promoters were analyzed. Additionally, their expression patterns were detected during the development of the seed. Lastly, genetic transformation and cytological observation were used to study the function of PgL0145810.1. A total of ten pomegranate SUT genes were identified from the whole genome of pomegranate ‘Tunisia’. The promoter region of all the pomegranate SUT genes contained myeloblastosis (MYB) elements. Four of the SUT genes, PgL0328370.1, PgL0099690.1, PgL0145810.1 and PgL0145770.1, were differentially expressed during seed development. We further noticed that PgL0145810.1 was expressed most prominently in the stem parts in transgenic plants compared to other tissue parts (leaves, flowers and silique). The cells in the xylem vessels were small and lignin content was lower in the transgenic plants as compared to wild Arabidopsis plants. In general, our result suggests that the MYB cis-elements in the promoter region might regulate PgL0145810.1 expression to control the structure of xylem, thereby affecting seed hardness in pomegranate.
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Singh NV, Parashuram S, Sharma J, Potlannagari RS, Karuppannan DB, Pal RK, Patil P, Mundewadikar DM, Sangnure VR, Parvati Sai Arun PV, Mutha NVR, Kumar B, Tripathi A, Peddamma SK, Kothandaraman H, Yellaboina S, Baghel DS, Reddy UK. Comparative transcriptome profiling of pomegranate genotypes having resistance and susceptible reaction to Xanthomonas axonopodis pv. punicae. Saudi J Biol Sci 2020; 27:3514-3528. [PMID: 33304163 PMCID: PMC7714969 DOI: 10.1016/j.sjbs.2020.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 01/14/2023] Open
Abstract
Pomegranate (Punica granatum L.) is an important fruit crop, rich in fiber, vitamins, antioxidants, minerals and source of different biologically active compounds. The bacterial blight caused by Xanthomonas axonopodispv. punicae is a serious threat to the crop leading to 60–80% yield loss under epiphytotic conditions. In this work, we have generated comparative transcriptome profile to mark the gene expression signatures during resistance and susceptible interactions. We analyzed leaf and fruits samples of moderately resistant genotype (IC 524207) and susceptible variety (Bhagawa) of pomegranate at three progressive infection stages upon inoculation with the pathogen. RNA-Seq with the Illumina HiSeq 2500 platform revealed 1,88,337 non-redundant (nr) transcript sequences from raw sequencing data, for a total of 34,626 unigenes with size >2 kb. Moreover, 85.3% unigenes were annotated in at least one of the seven databases examined. Comparative analysis of gene-expression signatures in resistant and susceptible varieties showed that the genes known to be involved in defense mechanism in plants were up-regulated in resistant variety. Gene Ontology (GO) analysis successfully annotated 90,485 pomegranate unigenes, of which 68,464 were assigned to biological, 78,107 unigenes molecular function and 44,414 to cellular components. Significantly enriched GO terms in DEGs were related to oxidations reduction biological process, protein binding and oxidoreductase activity. This transcriptome data on pomegranate could help in understanding resistance and susceptibility nature of cultivars and further detailed fine mapping and functional validation of identified candidate gene would provide scope for resistance breeding programme in pomegranate.
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Affiliation(s)
| | - Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | | | | | - Ram Krishna Pal
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | - Prakash Patil
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | | | - Vipul R Sangnure
- ICAR-National Research Centre on Pomegranate, Solapur, Maharashtra 413255, India
| | | | - Naresh V R Mutha
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | - Bipin Kumar
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | - Abhishek Tripathi
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | | | | | - Sailu Yellaboina
- Nucleome Informatics Private Limited., Hyderabad, Telangana State 500049, India
| | | | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA
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Patil PG, Jamma SM, Singh NV, Bohra A, Parashuram S, Injal AS, Gargade VA, Chakranarayan MG, Salutgi UD, Dhinesh Babu K, Sharma J. Assessment of genetic diversity and population structure in pomegranate ( Punica granatum L.) using hypervariable SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1249-1261. [PMID: 32549687 PMCID: PMC7266888 DOI: 10.1007/s12298-020-00825-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 05/21/2023]
Abstract
The present study investigates the genetic diversity and population structure among 42 diverse pomegranate genotypes using a set of twenty one class I hypervariable SSR markers (> 24 bp), which were reported earlier from the analysis of cv. Dabenzi genome. The study material comprised 16 indigenous and 13 exotic cultivars, and 13 wild accessions. A total of 66 alleles (Na) were detected with an average of 3.14 alleles per marker. The average values of polymorphic information content (PIC), observed heterozygosity (Ho) and Shannon's gene diversity index (I) were 0.44, 0.21 and 0.95, respectively suggesting moderate genetic diversity. The pairwise genetic distance ranged from 0.07 to 0.80 with a mean value of 0.53. Population structure analysis divided all the genotypes into four subpopulations (SP1, SP2, SP3 and SP4). Interestingly, the results of phylogenetic and principal component analyses coincided with the results of structure analysis and the grouping of genotypes followed the geographical origins. AMOVA revealed that 25% of the variation was attributed to differences among populations, whereas 75% within the subpopulations with significant F ST value 0.25 (p < 0.001), indicating a high level of genetic differentiations or low level of gene flow. Based on the F ST values, pomegranate genotypes belonging to SP4 (indigenous cultivars) followed by SP1 (exotic lines) exhibited higher gene diversity and genetic differentiations within and among populations. These genetic relationships based on SSR markers could be harnessed in future genetic improvement of pomegranate through informed hybridization programs.
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Affiliation(s)
- Prakash G. Patil
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | | | - N. V. Singh
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Shilpa Parashuram
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | | | | | | | | | - K. Dhinesh Babu
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Jyotsana Sharma
- ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
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Doddaraju P, Kumar P, Gunnaiah R, Gowda AA, Lokesh V, Pujer P, Manjunatha G. Reliable and early diagnosis of bacterial blight in pomegranate caused by Xanthomonas axonopodis pv. punicae using sensitive PCR techniques. Sci Rep 2019; 9:10097. [PMID: 31300709 PMCID: PMC6625978 DOI: 10.1038/s41598-019-46588-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/27/2019] [Indexed: 11/09/2022] Open
Abstract
Bacterial blight caused by Xanthomonas axonopodis pv. punicae is a major disease of pomegranate. Bacterial blight drastically reduces the yield and quality of fruits, which are critical for pomegranate production. Precise and early diagnosis of bacterial blight is crucial for active surveillance and effective management of the disease. Symptoms based disease diagnostic methods are labor-intensive, time-consuming and may not detect disease on asymptomatic plants. DNA-based disease diagnostics using polymerase chain reaction (PCR) are reliable, precise, accurate and quick. PCR coupled with agarose gel electrophoresis (PCR-AGE), PCR coupled with capillary electrophoresis (PCR-CE) and real-time PCR (qPCR) were applied for the early and accurate diagnosis of bacterial blight in pomegranate. PCR-CE and qPCR were capable of diagnosing bacterial blight 6 to 10 days before symptom appearance, with detection limits of 100 fg and 10 fg of bacterial DNA respectively. However, conventional PCR-AGE detected pathogen at the onset of disease symptoms with a detection limit of 10 pg of bacterial DNA. qPCR detected bacterial blight in orchards that did not show any disease symptoms. Our data demonstrate that qPCR is more sensitive than other PCR methods along with being reliable for early diagnosis.
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Affiliation(s)
- Pushpa Doddaraju
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Pavan Kumar
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Raghavendra Gunnaiah
- Department of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Abhishek A Gowda
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Veeresh Lokesh
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Parvati Pujer
- Department of Biotechnology and Crop Improvement, University of Horticultural Sciences, Bagalkot, Karnataka, India
| | - Girigowda Manjunatha
- Bio-control Lab, Directorate of Research, University of Horticultural Sciences, Bagalkot, Karnataka, India.
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Zhang M, Zhou C, Song Z, Weng Q, Li M, Ji H, Mo X, Huang H, Lu W, Luo J, Li F, Gan S. The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae). Sci Rep 2018; 8:2319. [PMID: 29396525 DOI: 10.1038/s41598-41018-20780-41599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 01/24/2018] [Indexed: 05/28/2023] Open
Abstract
Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Changpin Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- Baoshan University, Yuanzheng Road, Baoshan, 678000, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Hongxia Ji
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Wanhong Lu
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Jianzhong Luo
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Fagen Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
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16
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Zhang M, Zhou C, Song Z, Weng Q, Li M, Ji H, Mo X, Huang H, Lu W, Luo J, Li F, Gan S. The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae). Sci Rep 2018; 8:2319. [PMID: 29396525 PMCID: PMC5797152 DOI: 10.1038/s41598-018-20780-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 01/24/2018] [Indexed: 01/30/2023] Open
Abstract
Genomic loci related with resistance to gall-inducing insects have not been identified in any plants. Here, association mapping was used to identify molecular markers for resistance to the gall wasp Leptocybe invasa in two Eucalyptus species. A total of 86 simple sequence repeats (SSR) markers were screened out from 839 SSRs and used for association mapping in E. grandis. By applying the mixed linear model, seven markers were identified to be associated significantly (P ≤ 0.05) with the gall wasp resistance in E. grandis, including two validated with a correction of permutation test (P ≤ 0.008). The proportion of the variance in resistance explained by a significant marker ranged from 3.3% to 37.8%. Four out of the seven significant associations in E. grandis were verified and also validated (P ≤ 0.073 in a permutation test) in E. tereticornis, with the variation explained ranging from 24.3% to 48.5%. Favourable alleles with positive effect were also mined from the significant markers in both species. These results provide insight into the genetic control of gall wasp resistance in plants and have great potential for marker-assisted selection for resistance to L. invasa in the important tree genus Eucalyptus.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Changpin Zhou
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- Baoshan University, Yuanzheng Road, Baoshan, 678000, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Hongxia Ji
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou, 510642, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Wanhong Lu
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Jianzhong Luo
- China Eucalypt Research Centre, Zhanjiang, 524022, China
| | - Fagen Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China.
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China.
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Martinez-Nicolas JJ, Melgarejo P, Legua P, Garcia-Sanchez F, Hernández F. Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics. PeerJ 2016; 4:e2214. [PMID: 27547535 PMCID: PMC4957998 DOI: 10.7717/peerj.2214] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/14/2016] [Indexed: 11/20/2022] Open
Abstract
Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the juice’s acidity and pH had the highest power of discrimination, and were, therefore, the most useful for genetic characterization of this pomegranate germplasm banks. This is opposed to leaf and flower characteristics, which had a low power of discrimination. This germplasm bank, more specifically, was characterized by its considerable phenotypic (and presumably genetic) diversity among pomegranate accessions, with a greater proximity existing among the varieties from the same geographical area, suggesting that over time, there had not been an exchange of plant material among the different cultivation areas. In summary, knowledge on the extent of the genetic diversity of the collection is essential for germplasm management. In this study, these data may help in developing strategies for pomegranate germplasm management and may allow for more efficient use of this germplasm in future breeding programs for this species.
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Affiliation(s)
- Juan J Martinez-Nicolas
- Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche , Orihuela , Spain
| | - Pablo Melgarejo
- Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche , Orihuela , Spain
| | - Pilar Legua
- Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche , Orihuela , Spain
| | | | - Francisca Hernández
- Producción Vegetal y Microbiología, Universidad Miguel Hernández de Elche , Orihuela , Spain
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Saminathan T, Bodunrin A, Singh NV, Devarajan R, Nimmakayala P, Jeff M, Aradhya M, Reddy UK. Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high-throughput sequencing. BMC PLANT BIOLOGY 2016; 16:122. [PMID: 27230657 PMCID: PMC4880961 DOI: 10.1186/s12870-016-0807-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 05/17/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response. Knowledge and roles of miRNAs in pomegranate fruit development have not been explored. RESULTS Pomegranate, which accumulates a large amount of anthocyanins in skin and arils, is valuable to human health, mainly because of its antioxidant properties. In this study, we developed a small RNA library from pooled RNA samples from young seedlings to mature fruits and identified both conserved and pomegranate-specific miRNA from 29,948,480 high-quality reads. For the pool of 15- to 30-nt small RNAs, ~50 % were 24 nt. The miR157 family was the most abundant, followed by miR156, miR166, and miR168, with variants within each family. The base bias at the first position from the 5' end had a strong preference for U for most 18- to 26-nt sRNAs but a preference for A for 18-nt sRNAs. In addition, for all 24-nt sRNAs, the nucleotide U was preferred (97 %) in the first position. Stem-loop RT-qPCR was used to validate the expression of the predominant miRNAs and novel miRNAs in leaves, male and female flowers, and multiple fruit developmental stages; miR156, miR156a, miR159a, miR159b, and miR319b were upregulated during the later stages of fruit development. Higher expression of miR156 in later fruit developmental may positively regulate anthocyanin biosynthesis by reducing SPL transcription factor. Novel miRNAs showed variation in expression among different tissues. These novel miRNAs targeted different transcription factors and hormone related regulators. Gene ontology and KEGG pathway analyses revealed predominant metabolic processes and catalytic activities, important for fruit development. In addition, KEGG pathway analyses revealed the involvement of miRNAs in ascorbate and linolenic acid, starch and sucrose metabolism; RNA transport; plant hormone signaling pathways; and circadian clock. CONCLUSION Our first and preliminary report of miRNAs will provide information on the synthesis of biochemical compounds of pomegranate for future research. The functions of the targets of the novel miRNAs need further investigation.
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Affiliation(s)
- Thangasamy Saminathan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Abiodun Bodunrin
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Nripendra V Singh
- ICAR-National Research Center on Pomegranate, Kegaon, Solapur, Maharashtra, 413255, India
| | - Ramajayam Devarajan
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari, Andhra Pradesh, 534450, India
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA
| | - Moersfelder Jeff
- National Clonal Germplasm Repository, USDA-ARS, University of California, Davis, CA, 95616, USA
| | - Mallikarjuna Aradhya
- National Clonal Germplasm Repository, USDA-ARS, University of California, Davis, CA, 95616, USA
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, 25112-1000, USA.
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