Genetic Diversity, Phylogeography and Population gene flow of Tunisian Pistacia vera L.

Genetic Diversity, Phylogeography and Population gene flow of Tunisian Pistacia vera L.

The aim of this paper was to determine how the pistachio trees evolve, and the evolving factors that influence pistachiopopulation establishment. For that, we investigated pistachio genetic structure from some regions of Tunisia, by sequencing twononcoding chloroplastic regions (trnL (UAA) and trnL-trnF intergenic spacer). We found strong genetic diversity among groups, withthe absence of high differentiation between population pairs. A deep phylogeographical break separated two major clusters: “El-Guetarand “Gafsa/Sidi-Bouzid. This conclusion is proved by the haplotype networks, the phylogenetic trees, and the molecular variance analysis.Different interpretations were proposed to explain this cytoplasm dimorphism, based on the molecular evolution and demographichistory analysis: (1) the domestication events, which are very important to understand the variability between the prospective areas, (2)the gene flow between them, a process that occurs both in time and in space through pollen and seeds, and strongly interacts with thelocal farming systems, (3) the geographical barriers that exist, which limit gene flow transfer and make particular climatic conditions ofthe El-Guetar oasis. Given that, the genetic diversity study within Tunisian pistachio cultivars is very useful to contribute to the nationalmanagement effort for the improvement and conservation of pistachio genetic resources. Moreover, in 2017, Tunisia ranked among thetop 10 countries in global pistachio production. Thus, studying the diversity of Tunisian pistachio can make an important impact onglobal production

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  • Abdedaeim S (2015). Plan d’action de la stratégie de développement durable des oasis en Tunisie. Ministère de l’environnement et de développement durable Direction générale de l’environnement et de la qualité de la vie. p. 47 (in French).
  • Addinsoft (2007). XLSTAT, Analyse de données et statistique avec MS Excel. AddinSoft, New York, USA (in French).
  • Altschul SF, Thomas LM, Alejandro AS, Jinghui Z, Zheng Z et al. (1997). Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
  • Baghizadeh A, Noroozi SH, Jalali-Javaran M (2010). Study on genetic diversity of some Iranian Pistachio (Pistacia vera L.) cultivars using random amplified polymorphic DNA (RAPD), inter sequence repeat (ISSR) and simple sequence repeat (SSR) markers: A comparative study. African Journal of Biotechnology 9(45): 7632-7640.
  • Bakker FT, Culham A, Gomez Martinez R, Carvalho J, Compton J et al. (2000). Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions. Molecular Biology and Evolution 17: 1146-1155.
  • Bandelt HJ, Forster P, Rohl A (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.
  • Baraket G, Olfa S, Chatti K, MarsM, Marrakchi M, Trifi M et al. (2009). Chloroplast DNA analysis in Tunisian fig cultivars (Ficus carica L.): sequence variations of the trnL-trnF intergenic spacer. Biochemical Systematics and Ecology 36(11): 828-835.
  • Batnini MA, Bourguiba H, Trifi-Farah N, Krichen L (2014). Étude de la diversité de l’ADN chloroplastique chez l’abricotier (Prunus armeniaca L.). Revue des Régions Arides - Numéro Spécial - n° 35 (3/2014) - Actes du 4ème Meeting International Aridoculture et Cultures Oasisennes: Gestion des Ressources et Applications Biotechnologiques en Aridoculture et Cultures Sahariennes : perspectives pour un développement durable des zones arides 17- 19/12/2013 (in French).
  • Beck JB, Schmuths H, Schaal BA (2008). Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics. Molecular Ecology 17: 902- 915.
  • Benabid A (2000). Flore et Écosystèmes Du Maroc: Évaluation et préservation de la biodiversité, ed. Paris: Ibis Press (in French). Borsch T, Hilu KW, Quandt D, Wilde V, Neinhuis C et al. (2003). Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. Journal of Evolutionary Biology 16: 558-576.
  • Castric V, Bechsgaard J, Schierup MH, Vekemans X (2008). Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genetics 4(8): e1000168.
  • Chatti K, Choulak S, Guenni K, Salhi-Hannachi A (2017). Genetic diversity analysis using morphological parameters in Tunisian Pistachio (Pistacia vera L.). Journal of Research in Biological Sciences 2: 29-34.
  • Chen J, Tauer CG, Huang Y (2002). Paternal chloroplast inheritance patterns in pine hybrids detected with trnL-trnF intergenic region polymorphism. Theoretical and Applied Genetics 104: 1307-1311.
  • Choulak S, Chatti K, Marzouk Z, Chatti, N (2017). Genetic differentiation and gene flow of some Tunisian pistachio (Pistacia vera L.) varieties using chloroplastic DNA. Journal of Research in Biological Sciences 2: 35-41.
  • Choulak S, Rhouma-Chatti S, Marzouk Z, Said K, Chatti N, Chatti K (2015). Chloroplast DNA analysis of Tunisian pistachio (Pistacia vera L.): Sequence variations of the intron trnL (UAA). Scientia Horticulturae191: 57-64.
  • Ennos R (1994). Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72: 250-259.
  • Evreinoff VA (1955). Le Pistachier. Étude pomologique. Journal d’agriculture tropicale et de botanique appliquée 2(7): 387-415 (in French).
  • Excoffier L, Smouse P, Quattro J (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
  • Excoffier L, Lischer HEL (2010). Arlequin suite version 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564-567.
  • Faostat (2017). http://www.fao.org/faostat/en/data/QC. Farès K, Guasmi L, Touil T, Ferchichi A (2009). Genetic diversity of pistachio tree using inter-simple sequence repeat markers ISSR supported by morphological and chemical marker. Biotechnology 8(1): 24-34.
  • Fu YX (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
  • Fu YX, Li WH (1993). Statistical tests of neutrality of mutations. Genetics 133: 693-709.
  • Ghrab M, Zribi F, Ben Mimoun M, Rhouma A (2012). Morphological investigation of genetic diversity of pistachio (Pistacia vera L.) germplasm in arid land of Tunisia. Plant Ecology and Evolution 145(3): 363-372.
  • Golan-Goldhirsh A, Barazani O, Wang ZS, Khadkal DK, Saunders JA et al. Genetic relationships among Mediterranean Pistacia species evaluated by RAPD and AFLP markers. Plant Systematics and Evolution 246: 9-18.
  • Guenni K, Aouadi M, Chatti K, Salhi-Hannachi A (2016). Analysis of genetic diversity of Tunisian pistachio (Pistacia vera L.) using sequence-related amplified polymorphism (SRAP) markers. Genetics and Molecular Research 15: 166-175.
  • Hachicha M, Ben Aissa I (2014). Managing salinity in Tunisian oases. Life Science Journal 8(9): 775-782.
  • Hall TA (1999). Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symposium Series 41: 95-98.
  • Hamrick JL, Murawski DA, Nason JD (1993). The influence of seed dispersal mechanisms on the genetic structure of tropical tree populations. In: Fleming TH, Estrada A. (eds) Frugivory and seed dispersal: ecological and evolutionary aspects. Advances in vegetation science, vol 15. Springer, Dordrecht.
  • Heredia SM, Ellstrand NC (2014). Novel seed protection in the recently evolved invasive, California wild radish, a hybrid Raphanus sp. (Brassicaceae). American journal of botany 101(12): 2043-2051.
  • Hey J (2010). Isolation with migration models for more than two populations. Molecular Biology and Evolution 27: 905.
  • Hormaza JI, Dollo L, Polito VS (1994). Determination of relatedness and geographical movements of Pistacia vera (Pistachio; Anacardiaceae) germplasm by RAPD analysis. Economic Botany 48(4): 349-358.
  • IPGRI (1997). Descriptors for Pistachio (Pistacia vera L.). International Plant Genetic Resources Institute, Rome, Italy.
  • Jansen RK, Saski C, Lee SB, Hansen AK, Daniell H (2011). Complete Plastid Genome Sequences of three Rosids (Castanea, Prunus, Theobroma): Evidence for at least two independent transfers of rpl22 to the Nucleus. Molecular Biology and Evolution 28(1): 835-847.
  • Job JO (1992). Les sols salés de l’oasis d’El Guettar. Thèse de doctorat. Université de Montpellier II, 150 p (in French).
  • Katsiotis A, Hagidimitriou M, Drossoul A, Pontikis C, Loukas M (2003). Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs. Euphytica 132: 279-286.
  • Kimura M (1968). Evolutionary rate at the molecular level. Nature 217 (5129): 624-626.
  • Librado P, Rozas J (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451- 1452.
  • Maggs DH (1973). Genetic resources in pistachio. Plant Genetic Resources Newsletter 29: 7-15.
  • McKey D, Elias M, Pujol B, Duputie A (2010). The evolutionary ecology of clonally propagated domesticated plants. New Phytologist 186: 318-332.
  • Mlika M (1980). Contribution à l’étude du pistachier en Tunisie : Choix de variétés mâles et femelles à floraison synchroneAnatomie des fleurs. Mémoire de fin d’études du cycle de spécialisation INAT, Tunisie (in French).
  • Morton BR, Clegg MT (1993). A chloroplast DNA mutational hotspots and gene conversion in a non-coding region near rbcl in the grass family (Poaceae). Current Genetics 24: 357-365.
  • Palmer JD, Stein DB (1986). Conservation of chloroplast genome structure among vascular plants. Current Genetics 10: 823-833.
  • Pazouki L, Mardi M, Salehi-Shanjani P, Hagidimitriou M, Pirseyedi SM et al. (2010). Genetic diversity and relationships among Pistacia species and cultivars. Conservation Genetics 11: 311- 318.
  • Posada D (2008). jModel Test: phylogenetic model averaging. Molecular Biology and Evolution 25(7): 1253-1256.
  • Purvis A, Bromham L (1997). Estimating the transition / transversion ratio from independent pairwise comparison with an assumed phylogeny. Journal of Molecular Evolution 44: 112-119.
  • Ramanatha-Rao V, Hodgkin T (2002). Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell, Tissue and Organ Culture 68: 1-19.
  • Ramos-Onsins SE, Rozas J (2002). Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution 19: 2092-2100.
  • Ray N, Currat M, Excoffier L (2003). Intra-Deme molecular diversity in Spatially expanding populations. Molecular Biololgy and Evolution 20: 76-86.
  • Reales A, Sargent DJ, Tobutt KR, Rivera D (2010). Phylogenetics of Eurasian plums, Prunus L. section Prunus (Rosaceae), according to coding and non-coding chloroplast DNA sequences. Tree Genetics and Genomes 6: 37-45.
  • Risterucci AM, Grivet L, N’goran J, Pieretti I, Flament MH, Lanaud C (2000). A high-density linkage map of Theobroma cacao L. Theoretical and Applied Genetics 101(5): 948-955.
  • Rogers AR, Harpending H (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552-569.
  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A et al. (2012). MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61(3): 539-542.
  • Saitou N, Nei M (1987). The Neighbor-Joining method: A new method for reconstructing phylogenetic Trees. Molecular Biology and Evolution 4(4): 406-425
  • Sambrook J, Frithsch EF, Maniatis T (1989). Molecular Cloning: A Laboratory Manual. 2nd ed. New York, NY, USA: Cold Spring Harbor Laboratory.
  • Saski C, Lee SB, Fjellheim S, Guda C, Jansen RK et al. (2007). Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera and comparative analyses with other grass genomes. Theoretical and Applied Genetics 115: 571-590.
  • Tajima F (1989). Statistical testing for the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
  • Talebi M, Kazemi M, Sayed-Tabatabaei BE (2012). Molecular diversity and phylogenetic relationships of Pistacia vera, Pistacia atlantica subsp. mutica and Pistacia khinjuk using SRAP markers. Biochemical Systematics and Ecology 44: 179- 185.
  • Talebi M, Akbari M, Zamani M, Sayed-Tabatabaei BE (2016). Molecular polymorphism in Pistacia vera L. using non-coding regions of chloroplast DNA. Journal of Genetic Engineering and Biotechnology 14: 31-37.
  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729.
  • Wade MJ, McCauley DE (1988). Extinction and recolonization: Their effects on the genetic differentiation of local populations. Evolution 42: 995-1005.
  • Weeks A, Zapata F, Pell SK, Daly DC, Mitchell JD et al. (2014). To move or to evolve contrasting patterns of intercontinental connectivity and climatic niche evolution in “Terebinthaceae” (Anacardiaceae and Burseraceae). Frontiers in Genetics 5: 409. Wright S (1931). Evolution in mendelian populations. Genetics 16: 97-159.
  • Xie L, Yang ZY, Wen J, Li DZ, Yi TS (2014). Biogeographic history of Pistacia (Anacardiaceae), emphasizing the evolution of the Madrean-Tethyan and the eastern Asian-Tethyan disjunctions. Molecular Phylogenetics and Evolution 77: 136-146.
  • Yi T, Wen J, Golan-Goldhirsh A, Parfitt DE (2008). Phylogenetics and reticulate evolution inPistacia (Anacardiaceae). American Journal of Botany 95: 241-251.
  • Ziya-Motalebipour E, Kafkas S, Khodaeiaminjan M, Çoban N, Gözel H (2016). Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species. BMC Genomics 17(1): 998.
  • Zohary D (1996). The genus Pistacia L. In Taxonomy, distribution, conservation and uses of Pistacia genetic resources, Padulosi S, Caruso T, Barone E (eds) (IPGRI, Palermo), pp. 1-11.
  • Zohary D, Hopf M (2000). Domestication of Plants in the Old World. 3rd ed. Oxford, UK : Oxford University Press.
  • Zuang H, Barret P, Beau C (1988). Nouvelles espèces fruitières. CTIFL, Paris, p. 182 (in French).