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Conserved DNA-derived polymorphism as a useful molecular marker to explore genetic diversity and relationships of wild and cultivated Tunisian figs (Ficus carica L.)

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Abstract

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The first insight into the genome of Ficus carica L. with a gene target marker (conserved DNA-derived polymorphism (CDDP)) and assessment of genetic diversity mostly related to functional domains of plant genes.

Abstract

To improve the molecular database of Ficus carica L. species, we report for the first time the use of conserved DNA-derived polymorphism (CDDP) as a gene-targeted marker to assess molecular diversity, and establish relationships among 62 Tunisian cultivated and wild fig trees. The mapping process for the in silico analysis of CDDP primers against the whole F. carica genome cv Dottato verified the specificity of the CDDPs and the stringency of PCR conditions. Overall, a set of twelve CDDP primers were tested revealing 200 markers. Based on the polymorphic information content (PIC = 0.90), resolving power (Rp = 8.13) and the level of polymorphisms (98.04%) CDDP markers were found to highly discriminant and informative compared to other non-targeted methods. The UPGMA dendrogram revealed that Tunisian figs could be differentiated into three main groups, which was also supported by the principal coordinate analysis. The analysis of molecular variance (AMOVA) suggested that the maximum genetic variation was within groups (86.10%) with less variation among groups (19%) indicating that there is a limited diversity that distinguishes fig groups. Here, we present the first report in which a targeted DNA region molecular marker successfully clustered the Tunisian fig germplasm depending on the sex, the botanical classification of figs and consistently in agreement, with their geographic origin). The results highlight that the CDDP markers are able to characterize wild and cultivated Ficus carica L. species and provide a new valuable tool for further genome investigation and will guide the development of conservation and management strategies for existing fig tree germplasm.

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References

  • Achtak H, Ater M, Oukabli A, Santoni S, Kjellberg F, Khadari B (2010) Traditional agroecosystems as conservatories and incubators of cultivated plant varietal diversity: the case of fig (Ficus carica L.) in Morocco. BMC Plant Biol 10:28

    Article  PubMed  PubMed Central  Google Scholar 

  • Aljane F, Ferchichi A (2009) Postharvest chemical properties and mineral contents of some fig (Ficus carica L.) cultivars in Tunisia. J Food Agric Environ 7(2):209–212

    CAS  Google Scholar 

  • Aljane F, Ferchichi A (2010) Assessment of genetic diversity of Tunisian fig (F. carica L.) cultivars using morphological and chemical characters. Acta Bot Gall 157(1):171–182

    Article  CAS  Google Scholar 

  • Aljane F, Ferchichi A, Boukhris M (2008) Pomological characteristics of local fig (Ficus carica) cultivars in southern Tunisia. Acta Hort (ISHS) 798:123–128

    Article  Google Scholar 

  • Aouadi M, Guenni K, Abdallah D, Louati M, Chatti K, Baraket G, Hannachi AS (2019) Conserved DNA-derived polymorphism, new markers for genetic diversity analysis of Tunisian Pistacia vera L. Physiol Mol Biol Plants 25:1211–1223. https://doi.org/10.1007/s12298-019-00690-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aradhya MK, Stover E, Velasco D, Koehmstedt A (2010) Genetic structure and differentiation in cultivated fig (Ficus carica L.). Genetica 138:681–694. https://doi.org/10.1007/s10709-010-9442-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Atia MAM, Sakr MM, Adawy SS (2017) Assessing date palm genetic diversity using different molecular markers. Methods Mol Biol 1638:125–142. https://doi.org/10.1007/978-1-4939-7159-6_12

    Article  CAS  PubMed  Google Scholar 

  • Baraket G, Chatti K, Saddoud O, Mars M, Marrakchi M, Trifi M, Salhi Hannachi A (2009) Genetic analysis of Tunisian fig (Ficus carica L.) cultivars using amplified fragment length polymorphism (AFLP) markers. Sci Hortic 120:487–492

    Article  CAS  Google Scholar 

  • Baraket G, Chatti K, Saddoud O, Ben Abdelkrim A, Mars M, Marrakchi M, Trifi M, Salhi Hannachi A (2011) Comparative assessment of SSR and AFLP markers for evaluation of genetic diversity and conservation of fig, Ficus carica L., genetic resources in Tunisia. Plant Mol Biol Rep 29:171–184

    Article  Google Scholar 

  • Ben Abdelkrim A, Baraket G, Essalouh L, Achtak H, Khadari B, Salhi Hannachi A (2015) Use of morphological traits and microsatellite markers to characterize the Tunisian cultivated and wild figs (Ficus carica L.). Biochem Syst Ecol 59:209–219

    Article  Google Scholar 

  • Boudchicha RH, Hormaza JI, Benbouza H (2018) Diversity analysis and genetic relationships among local Algerian fig cultivars (Ficus carica l.) using SSR markers. S Afr J Bot 116:207–215. https://doi.org/10.1016/j.sajb.2018.03.015

    Article  CAS  Google Scholar 

  • Caliskan O, Polat AA (2012) Morphological diversity among fig (Ficus carica L.) accessions sampled from the eastern Mediterranean region of Turkey. Turk J Agric for 36:179–193

    Google Scholar 

  • Caliskan O, Polat AA, Celikkol P, Bakir M (2012) Molecular characterization of autochthonous Turkish fig accessions. Span J Agric Res 10:130–140. https://doi.org/10.5424/sjar/2012101-094-11

    Article  Google Scholar 

  • Caliskan O, Bayazit S, Ilgin M, Karatas N, Ergul A (2018) Genetic diversity and population structure in caprifigs (Ficus carica var caprificus) using SSR markers. Span J Agric Res 16(3):703. https://doi.org/10.5424/sjar/2018163-11662

    Article  Google Scholar 

  • Chai L, Wang Z, Chai P, Chen S, Ma H (2017) Transcriptome analysis of San Pedro type fig (Ficus carica L.) parthenocarpic breba and non-parthenocarpic main crop reveals divergent phytohormone- related gene expression. TrEe Genet Genomes 13:83. https://doi.org/10.1007/s11295-017-1166-4

    Article  Google Scholar 

  • Chatti K, Saddoud O, Salhi Hannachi A, Mars M, Marrakchi M, Trifi M (2007) Analysis of genetic diversity and relationships in a Tunisian fig (Ficus carica) germplasm collection by random amplified microsatellite polymorphisms. J Integr Plant Biol 49(3):386–391

    Article  CAS  Google Scholar 

  • Chatti K, Baraket G, Abdelkrim AB, Saddoud O, Mars M, Trifi M, Hannachi AS (2010) Development of molecular tools for characterization and genetic diversity analysis in Tunisian fig (Ficus carica) cultivars. Biochem Genet 48(9–10):789–806

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Li W, Hong T (2018) System optimization and genetic diversity of different color Paeonia rockii by CDDP markers. Acta Botan Boreali-Occiden Sin 38(10):1823–1831

    Google Scholar 

  • Collard BC, Mackill DJ (2009) Conserved DNA-derived polymorphism (CDDP): a simple and novel method for generating DNA markers in plants. Plant Mol Biol Report 27(4):558–562

    Article  CAS  Google Scholar 

  • Condit IJ (1947) The Fig. The Chronica Botanica Company Waltham

  • Condit I (1955) Fig varieties: a monograph. Hilgardia 23:323–511

    Article  Google Scholar 

  • Cui Y, Wang Z, Chen S et al (2019) Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.). BMC Plant Biol 19:146. https://doi.org/10.1186/s12870-019-1742-x

    Article  PubMed  PubMed Central  Google Scholar 

  • Dalkilic Z, Mestav HO, Gunver-Dalkilic G, Kocatas H (2011) Genetic diversity of male fig (Ficus carica caprificus L.) genotypes with random amplified polymorphic DNA (RAPD) markers. Afr J Biotec 10:519–526

    CAS  Google Scholar 

  • Dellapor SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21

    Article  Google Scholar 

  • Esquinas-Alcázar J (2005) Protecting crop genetic diversity for food security: political, ethical and technical challenges. Nat Rev Genet 6:946–953. https://doi.org/10.1038/nrg1729

    Article  PubMed  Google Scholar 

  • Essid A, Aljane F, Ferchichi A, Hormaza JI (2015) Analysis of genetic diversity of Tunisian caprifig (Ficus carica L.) accessions using simple sequence repeat (SSR) markers. Hereditas 152:1–7. https://doi.org/10.1186/s41065-015-0002-9

    Article  PubMed  PubMed Central  Google Scholar 

  • Falistocco E (2009) Presence of triploid cytotypes in the common fig (Ficus carica L.). Genome 52:919–925

    Article  CAS  PubMed  Google Scholar 

  • Falistocco E (2016) Recurrent events of polyploidy in Ficus carica L. (Moraceae). Int J Plant Sci 177:319–325

    Article  Google Scholar 

  • Falistocco E (2020) The millenary history of the fig tree (Ficus carica L.). Adv Agric Hortic Entomol 2020(5):130

    Google Scholar 

  • FAOSTAT (2019) Food and agriculture organization, FAO STAT database. http://www.fao.org/faostat/en/#data/QC. Accessed 27 Dec 2020

  • Flaishman MA, Rodov V, Stover E (2008) The fig: botany, horticulture, and breeding. Hortic Rev 34:113–196

    Article  CAS  Google Scholar 

  • Freiman ZE, Doronfaigenboim A, Dasmohapatra R, Yablovitz Z, Flaishman MA (2014) High-throughput sequencing analysis of common fig (Ficus carica L.) transcriptome during fruit ripening. Tree Genet Genomes 10(4):923–935. https://doi.org/10.1007/s11295-014-0732-2

    Article  Google Scholar 

  • Freiman ZE, Rosianskey Y, Dasmohapatra R, Kamara I, Flaishman MA (2015) The ambiguous ripening nature of the fig (Ficus carica L.) fruit: a gene expression study of potential ripening regulators and ethylene-related genes. J Exp Bot 66(11):3309. https://doi.org/10.1093/jxb/erv140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ganopoulos I, Xanthopoulou A, Molassiotis A, Karagiannis E, Moysiadis T, Katsaris P, Aravanopoulos F, Tsaftaris A, Kalivas A, Madesis P (2015) Mediterranean basin Ficus carica L.: from genetic diversity and structure to authentication of a Protected Designation of Origin cultivar using microsatellite markers. Trees 29(6):1959–1971

    Article  CAS  Google Scholar 

  • Giraldo E, Viruel MA, Lopez-Corrales M, Hormaza JI (2005) Characterisation and cross-species transferability of microsatellites in common fig (Ficus carica L.). J Hortic Sci Biotechnol 80:217–224

    Article  CAS  Google Scholar 

  • Giraldo E, Lopez-Corrales M, Hormaza JI (2008) Optimization of the management of an ex-situ germplasm bank in common fig with SSRs. J Am Soc Hortic Sci 133(1):69–77

    Article  CAS  Google Scholar 

  • Groupement Interprofessionnel des fruits (GIFruits) (2019) http://gifruits.com/?p=2268&lang=fr. Accessed 4 Mar 2019

  • Guillonchon L (1927) La culture du figuier en Tunisie. Revue De Botanique Appliquée Et D’agriculture Coloniale 7:18–28

    Article  Google Scholar 

  • Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9. http://palaeo-electronica.org/2001_1/past/issue1_01.htm. Accessed 20 Oct 2021

  • Hamrick JL, Godt MJW (1996) Conservation genetics of endemic plant species. In: Avise JC, Hamrick JL (eds) Conservation genetics. Chapman and Hall, pp 281–304

    Chapter  Google Scholar 

  • Ikegami H, Habu T, Mori K (2013) De novo sequencing and comparative analysis of expressed sequence tags from gynodioecious fig (Ficus carica L.) fruits: caprifig and common fig. Tree Genet Genomes 9(4):1075–1088

    Article  Google Scholar 

  • Jiang L, Zang D (2018) Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism markers. Biotechnol Biotechnol Equip 32(1):88–94

    Article  Google Scholar 

  • Khadari B, Lashermes PH, Kjellberg F (1995) RAPD Fingerprints for identification and genetic characterization of fig (Ficus carica L.) genotypes. J Genet Breed 49:77–86

    CAS  Google Scholar 

  • Khadari B, Hochu I, Santoni S, Kjellberg F (2001) Identification and characterization of microsatellite loci in the common fig (Ficus carica L.) and representative species of the genus Ficus. Mol Ecol 1:191–193

    Article  CAS  Google Scholar 

  • Kislev ME, Hartmann A, Bar-Yosef O (2006) Early domesticated fig in the Jordan Valley. Science 312:1372–1374

    Article  CAS  PubMed  Google Scholar 

  • Knap T, Jakše J, Cregeen S, Javornik B, Hladnik M, Bandelj D (2016) Characterization and defining of a core set of novel microsatellite markers for use in genotyping and diversity study of Adriatic fig (Ficus carica L.) germplasm. Braz J Bot 39:1095–1102. https://doi.org/10.1007/s40415-016-0299-2

    Article  Google Scholar 

  • Li T, Guo JE, Li YY, Ning H, Sun X, Zheng CS (2013) Genetic diversity assessment of chrysanthemum germplasm using conserved DNA-derived polymorphism markers. Sci Hortic 162:271–277. https://doi.org/10.1016/j.scienta.2013.08.027

    Article  CAS  Google Scholar 

  • Liu H, Zang F, Wu Q, Ma Y, Zheng Y, Zang D (2020) Genetic diversity and population structure of the endangered plant Salix taishanensis based on CDDP markers. Glob Ecol Conserv 24:e01242. https://doi.org/10.1016/j.gecco.2020.e01242

    Article  Google Scholar 

  • Marcotuli I, Mazzeo A, Colasuonno P, Terzano R, Nigro D, Porfido C, Tarantino A, Aiese Cigliano R, Sanseverino W, Gadaleta A, Ferrara G (2020) Fruit development in Ficus carica L.: morphological and genetic approaches to fig buds for an evolution from monoecy toward dioecy. Front Plant Sci 11:1208

    Article  PubMed  PubMed Central  Google Scholar 

  • Mars M (2003) Fig (Ficus carica L.) genetic resources and breeding. Acta Hortic 605:19–27

    Article  Google Scholar 

  • Mori K, Shirasawa K, Nogata H, Hirata C, Tashiro K, Habu T, Kim S, Himeno S, Kuhara S, Ikegami H (2017) Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.). Sci Rep 7:46784. https://doi.org/10.1038/srep46784

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nabli M (1991) Ressources végétales en Tunisie : evaluation, valorisation et conservation. In: Rejdali M, Heywood VH (eds) Conservation des ressources végétales. Actes Editions. Institut Agronomique et Vétérinaire Hassan II, Rabat, Maroc, pp 53–58

    Google Scholar 

  • Ochiai A (1957) Zoogeographic studies on the soleoid fishes found in Japan and its neighbouring regions. Bull Jpn Soc Sci Fish 22:526–530

    Article  Google Scholar 

  • Okeh Igwe D, Ihearahu Onyinye C, Adhiambo Osano A, Acquaah G, Nkem Ude G (2021) Genetic diversity and population assessment of Musa L. (Musaceae) employing CDDP markers. Plant Mol Biol Rep. https://doi.org/10.1007/s11105-021-01290-x

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel Population genetic software for teaching and research—an update. Bioinformatics 28(19):2537–2539. https://doi.org/10.1093/bioinformatics/bts460

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Poczai P, Varga I, Laos M, Cseh A, Bell N, Valkonen JP, Hyvönen J (2013) Advances in plant gene-targeted and functional markers: a review. Plant Methods 9(1):6. https://doi.org/10.1186/1746-4811-9-6

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98(1):107–112

    Article  CAS  Google Scholar 

  • Rosianski Y, Doron-Faigenboim A, Freiman ZE, Lama K, Milo-Cochavi S, Dahan Y, Kerem Z, Flaishman MA (2016) Tissue-specific transcriptome and hormonal regulation of pollinated and parthenocarpic fig (Ficus carica L.) fruit suggest that fruit ripening is coordinated by the reproductive part of the syconium. Front Plant Sci 7:1696. https://doi.org/10.3389/fpls.2016.01696

    Article  PubMed  PubMed Central  Google Scholar 

  • Saidi A, Daneshvar Z, Hajibarat Z (2018) Comparison of genetic variation of Anthurium (Anthurium andraeanum) cultivars using SCoT, CDDP and RAPD markers. Plant Tissue Cult Biotechnol 28(2):171–182. https://doi.org/10.3329/ptcb.v28i2.39676

    Article  Google Scholar 

  • Salhi Hannachi A, Trifi M, Zehdi S, Mars M, Rhouma A, Marrakchi M (2004) Inter simple sequence repeat finger printings to assess genetic diversity in Tunisian fig (Ficus carica L.). Genet Res Crop Evol 51(3):269–275

    Article  CAS  Google Scholar 

  • Salhi Hannachi A, Chatti K, Mars M, Marrakchi M, Trifi M (2005) Comparative analysis of genetic diversity in two collections figs cultivars based on random amplified polymorphic DNA and inter Simple Sequence repeats fingerprints. Genet Res Crop Evol 52(5):563–573

    Article  Google Scholar 

  • Salhi-Hannachi A, Chatti K, Saddoud O, Mars M, Rhouma A, Marrakchi M, Trifi M (2006) Genetic diversity of different Tunisian fig (Ficus carica L.) collections revealed by RAPD fingerprints. Hereditas 143:15–22

    Article  PubMed  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning, a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, NY, p 1659

    Google Scholar 

  • Seyedimoradi H, Talebi R, Fayaz F (2016) Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers. Environ Exp Biol 14:63–68

    Article  Google Scholar 

  • Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95(1–2):163–173

    Article  CAS  Google Scholar 

  • Talebi R, Nosrati S, Etminan A, Mohammad Naji A (2018) Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers. Biotechnol Biotechnol Equip 32(5):1183–1194

    Article  CAS  Google Scholar 

  • Usai G, Mascagni F, Giordani T, Vangelisti A, Bosi E, Zuccolo A, Ceccarelli M, King R, Hassani-Pak K, Zambrano LS, Cavallini A (2020) Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. Plant J 102(3):600–614

    Article  CAS  PubMed  Google Scholar 

  • Vangelisti A, Zambrano LS, Caruso G et al (2019) How an ancient, salt-tolerant fruit crop, Ficus carica L., copes with salinity: a transcriptome analysis. Sci Rep 9:2561. https://doi.org/10.1038/s41598-019-39114-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Z, Song M, Li Y, Chen S, Ma H (2019) Differential color development and response to light deprivation of fig (Ficus carica L.) syconia peel and female flower tissues: transcriptome elucidation. BMC Plant Biol 19:217. https://doi.org/10.1186/s12870-019-1816-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Ma Y, Jia B, Wu Q, Zang D, Yu X (2020) Analysis of the genetic diversity of the coastaland island endangered plant species Elaeagnus macrophylla via conserved DNA-derived polymorphism marker. PeerJ 8:8498. https://doi.org/10.7717/peerj.8498

    Article  Google Scholar 

  • Zambrano LS, Usai G, Vangelisti A, Mascagni F, Giordani T, Bernardi R, Cavallini A, Gucci R, Caruso G, D’Onofrio C, Quartacci MF, Picciarelli P, Conti B, Lucchi A, Natali L (2017) Cultivar-specific transcriptome prediction and annotation in Ficus carica L. Genom Data 13:64–66. https://doi.org/10.1016/j.gdata.2017.07.005

    Article  Google Scholar 

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Acknowledgements

This research was supported by grants from the Tunisian Ministry of Higher Education, Scientific Research. Thanks are due to "FIGGEN/PRIMA19_00197 project, part of the PRIMA Programme supported by the European Union".

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Authors and Affiliations

  1. Department of Biology, Faculty of Sciences of Tunis, University Tunis El Manar, 2092 El Manar, Tunis, Tunisia

    Sahar Haffar, Ghada Baraket, Aymen Aounallah, Sana Ben Mustapha, Ahmed Ben Abdelkrim & Amel Salhi Hannachi

  2. Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy

    Gabriele Usai

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  1. Sahar Haffar
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Haffar, S., Baraket, G., Usai, G. et al. Conserved DNA-derived polymorphism as a useful molecular marker to explore genetic diversity and relationships of wild and cultivated Tunisian figs (Ficus carica L.). Trees 36, 723–735 (2022). https://doi.org/10.1007/s00468-021-02244-2

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