Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

Pourian, Mohammad Aref; Bakhshi, Davood; Aalami, Ali; Hokmabadi, Hossein

doi:10.2478/johr-2019-0005

Abstract

Iran is one of the main diversity centers and origins of pistachios in the world. Pistachio cultivation spread first within the ancient Persian Empire and then moved gradually westward. Knowledge of the genetic relationships among wild and cultivated varieties of pistachio is important for the efficient utilization of the available germplasm resources. Three molecular marker strategies, namely, inter-simple sequence repeat (ISSR), inter-retrotransposon amplified polymorphism (IRAP), and retrotransposon microsatellite amplified polymorphism (REMAP), were used to study the genetic relationships among 35 pistachio accessions including 15 wild-type genotypes of Pistacia vera and 20 important cultivars from Iran. According to the results, high levels of polymorphism were observed for all three marker systems. REMAP and IRAP techniques had the higher mean values of genetic relationships parameters than ISSR technique. The results from this study showed that the 5′LTR2, Sukkula, Sukkula + UBC855, and 5′LTR2 + UBC811 primers were the most informative and could be used to evaluate the genetic relationships of pistachios accessions. Cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) properly separated the accessions and divided them into four main groups. The presence of most cultivated genotypes in a group indicates genetic erosion of cultivated pistachio in Iran. Wild-type genotypes of P. vera are located in different clusters indicating the high diversity of the genotypes. The results provide useful genetic information about wild pistachios in northeastern of Iran and indicate that the use of wild pistachios in breeding programs could be useful for generating new genotypes with interesting characters.

References

Ahmad R., Ferguson L., Southwick S.M. 2003. Identification of pistachio (Pistacia vera L.) nuts with microsatellite markers. Journal of the American Society for Horticultural Science 128(6): 898–903. DOI: 10.21273/jashs.128.6.0898.10.21273/JASHS.128.6.0898
Search in Google Scholar Back to article
Arabnezhad H., Bahar M., Tajabadi Pour A. 2011. Evaluation of genetic relationships among Iranian pistachios using microsatellite markers developed from Pistacia khinjuk Stocks. Scientia Horticulturae 128(3): 249–254. DOI: 10.1016/j.scienta.2011.01.028.10.1016/j.scienta.2011.01.028
Open DOI Search in Google Scholar Back to article
Barazani O., Atayev A., Yakubov B., Kostiukovsky V., Popov K., Golan-Goldhirsh A. 2003. Genetic variability in Turkmen populations of Pistacia vera L. Genetic Resources and Crop Evolution 50(4): 383–389. DOI: 10.1023/a:1023928017410.10.1023/a:1023928017410
Open DOI Search in Google Scholar Back to article
Crane J.C. 1979. Pistachio nuts. In: Woodroof J.G. (Ed.), Tree nuts: production, processing, products, 2^nd ed. USA, AVI Publishing, 731 p.
Search in Google Scholar Back to article
Dempewolf H., Baute G., Anderson J., Kilian B., Smith C., Guarino L. 2017. Past and future use of wild relatives in crop breeding. Crop Science 57(3): 1070–1082. DOI: 10.2135/cropsci2016.10.0885.10.2135/cropsci2016.10.0885
Open DOI Search in Google Scholar Back to article
Ghaemmaghami L., Attar F., Rahiminejad M.R. 2013. Distinctness and inter relationships of Pistacia L. species in Iran as evidenced by retroelement insertional polymorphisms (IRAP method). Iranian Journal of Botany 19(1): 78–85. DOI: 10.22092/ijb.2013.2998.
Search in Google Scholar Back to article
He S.-A., Yi T.-S., Pei S.-J., Huang H.-W. 2015. Crop plants and their wild relatives. In: Hong D.-Y., Blackmore S. (Eds.), Plants of China: A companion to the flora of China. Cambridge University Press, UK, p. 283–308.
Search in Google Scholar Back to article
Hormaza J.I., Pinney K., Polito V.S. 1998. Genetic diversity of pistachio (Pistacia vera, Anacardiaceae) germplasm based on randomly amplified polymorphic DNA (RAPD) markers. Economic Botany 52(1): 78–87. DOI: 10.1007/bf02861298.10.1007/bf02861298
Open DOI Search in Google Scholar Back to article
Kalendar R., Flavell A.J., Ellis T., Sjakste T.H.N., Moisy C., Schulman A.H. 2011. Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106(4): 520–530. DOI: 10.1038/hdy.2010.93.10.1038/hdy.2010.93318391120683483
Open DOI Search in Google Scholar Back to article
Kalendar R., Grob T., Regina M., Suoniemi A., Schulman A. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics 98(5): 704–711. DOI: 10.1007/s001220051124.10.1007/s001220051124
Open DOI Search in Google Scholar Back to article
Kar P.K., Vijayan K., Mohandas T.P., Nair C.V., Saratchandra B., Thangavelu K. 2005. Genetic variability and genetic structure of wild and semi-domestic populations of tasar silkworm (Antheraea mylitta) ecorace Daba as revealed through ISSR markers. Genetica 125(2–3): 173–183. DOI: 10.1007/s10709-005-7002-z.10.1007/s10709-005-7002-z16247690
Open DOI Search in Google Scholar Back to article
Kırdök E., Çiftçi Y.Ö. 2016. Retrotransposon marker systems as a tool to analyze molecular diversity of Mediterranean Pistacia species. International Journal of Agriculture and Biology 18(3): 601–606. DOI: 10.17957/ijab/15.0132.10.17957/IJAB/15.0132
Search in Google Scholar Back to article
Michel D. 2017. Iran’s Impending Water Crisis. In: Reed D. (Ed.), Water, Security and U.S. Foreign Policy. Routledge, USA, pp. 168–188. DOI: 10.4324/9781315168272-10.10.4324/9781315168272-10
Open DOI Search in Google Scholar Back to article
Mohammadi S.A., Prasanna B.M. 2003. Analysis of genetic diversity in crop plants – salient statistical tools and considerations. Crop Science 43(4): 1235–1248. DOI: 10.2135/cropsci2003.1235.10.2135/cropsci2003.1235
Open DOI Search in Google Scholar Back to article
Parfitt D.E., Badenes M.L. 1997. Phylogeny of the genus Pistacia as determined from analysis of the chloroplast genome. Proceedings of the National Academy of Sciences of the USA 94(15): 7987–7992. DOI: 10.1073/pnas.94.15.7987.10.1073/pnas.94.15.7987215429223300
Open DOI Search in Google Scholar Back to article
Pazouki L., Mardi M., Shanjani P.S., Hagidimitriou M., Pirseyedi S.M., Naghavi M.R. et al. 2010. Genetic diversity and relationships among Pistacia species and cultivars. Conservation Genetics 11(1): 311–318. DOI: 10.1007/s10592-009-9812-5.10.1007/s10592-009-9812-5
Open DOI Search in Google Scholar Back to article
Pell S.K. 2004. Molecular systematics of the cashew family (Anacardiaceae). LSU Doctoral Dissertations, 193 p.
Search in Google Scholar Back to article
Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S., Rafalski A. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2(3): 225–238. DOI: 10.1007/bf00564200.10.1007/bf00564200
Open DOI Search in Google Scholar Back to article
Reddy M.P., Sarla N., Siddiq E.A. 2002. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128(1): 9–17. DOI: 10.1023/a:1020691618797.10.1023/a:1020691618797
Open DOI Search in Google Scholar Back to article
Rohlf F. 2009. NTSYSpc. Numerical taxonomy and multivariate analysis system, version 2.2. Exeter Software, Applied Biostatistics, USA.
Search in Google Scholar Back to article
Scariot V., De Keyser E., Handa T., De Riek J. 2007. Comparative study of the discriminating capacity and effectiveness of AFLP, STMS and EST markers in assessing genetic relationships among evergreen azaleas. Plant Breeding 126(2): 207–212. DOI: 10.1111/j.1439-0523.2007.01326.x.10.1111/j.1439-0523.2007.01326.x
Open DOI Search in Google Scholar Back to article
Shahi-Gharahlar A., Zamani Z., Fatahi R., Bouzari N. 2011. Estimation of genetic diversity in some Iranian wild Prunus subgenus Cerasus accessions using inter-simple sequence repeat (ISSR) markers. Biochemical Systematics and Ecology 39(4): 826–833. DOI: 10.1016/j.bse.2011.07.018.10.1016/j.bse.2011.07.018
Open DOI Search in Google Scholar Back to article
Shanjani P.S., Mardi M., Pazouki L., Hagidimitriou M., Avanzato D., Pirseyedi S.M. et al. 2009. Analysis of the molecular variation between and within cultivated and wild Pistacia species using AFLPs. Tree Genetics and Genomes 5(3): 447–458. DOI: 10.1007/s11295-008-0198-1.10.1007/s11295-008-0198-1
Open DOI Search in Google Scholar Back to article
Smith J.S.C., Chin E.C.L., Shu H., Smith O.S., Wall S.J., Senior M.L. et al. 1997. An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree. Theoretical and Applied Genetics 95(1): 163–173. DOI: 10.1007/s001220050544.10.1007/s001220050544
Open DOI Search in Google Scholar Back to article
Soleimani M.H., Talebi M., Sayed-Tabatabaei B.E. 2012. Use of SRAP markers to assess genetic diversity and population structure of wild, cultivated, and ornamental pomegranates (Punica granatum L.) in different regions of Iran. Plant Systematics and Evolution 298(6): 1141–1149. DOI: 10.1007/s00606-012-0626-4.10.1007/s00606-012-0626-4
Open DOI Search in Google Scholar Back to article
Sorkheh K., Amirbakhtiar N., Ercisli S. 2017. Retraction note to: Potential start codon targeted (SCoT) and interretrotransposon amplified polymorphism (IRAP) markers for evaluation of genetic diversity and conservation of wild Pistacia species population. Biochemical Genetics 55(5): 421–422. DOI: 10.1007/s10528-017-9830-9.10.1007/s10528-017-9830-929124522
Open DOI Search in Google Scholar Back to article
Tajima F., Tokunaga T., Miyashita N.T. 1994. Statistical methods for estimating the effective number of alleles, expected heterozygosity and genetic distance in self-incompatibility locus. Japanese Journal of Genetics 69(3): 287–295. DOI: 10.1266/jjg.69.287.10.1266/jjg.69.2878080659
Open DOI Search in Google Scholar Back to article
Xie W.-G., Zhang X.-Q., Cai H.-W., Liu W., Peng Y. 2010. Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass (Dactylis glomerata L.). Biochemical Systematics and Ecology 38(4): 740–749. DOI: 10.1016/j.bse.2010.06.009.10.1016/j.bse.2010.06.009
Open DOI Search in Google Scholar Back to article
Yang H.-B., Kang W.-H., Nahm S.-H., Kang B.-C. 2015. Methods for developing molecular markers. In: Koh H.-J., Kwon S.-Y., Thomson M. (Eds.), Current Technologies in Plant Molecular Breeding. Springer, p. 15–50. DOI: 10.1007/978-94-017-9996-6_2.10.1007/978-94-017-9996-6_2
Open DOI Search in Google Scholar Back to article
Yeh F.C., Boyle T., Rongcai Y., Ye Z., Xiyan J.M. 1999. POPGENE version 1.31: Microsoft Window-based Freeware for Population Genetic Analysis. Quick User Guide, 28 p.
Search in Google Scholar Back to article
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; 998; 14 p. DOI: 10.1186/s12864-016-3359-x.10.1186/s12864-016-3359-x514217427923352
Open DOI Search in Google Scholar Back to article
Zohary M. 1952. A monographical study of the genus Pistacia. Palestine Journal of Botany (Jerusalem Series) 5(4): 187–228.
Search in Google Scholar Back to article

Assessment of Genetic Relationships among Cultivated and Wild Pistachios (Pistacia vera L.) using Molecular Markers

Abstract

Paradigm

My account