Iranian Journal of Forest

Iranian Journal of Forest

Evaluation of genetic diversity and population structure of Juniperus excelsa M. Bieb. in Ardabil using SCoT markers

Document Type : Research Paper

Authors
Y Mohammadi 1
M.R. Mashayekhi 2
Shiva Gheytaranpour Sehrigh 3
1 Assistant Prof., Dept. of biotechnology, Research institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, I. R. Iran
2 Assistant Prof., Molecular Genetics, Tabriz Branch, Islamic Azad University, Tabriz, Iran
3 Ph.D. Plant Breeding and Biotechnology Dept. Faculty of Agriculture, University of Tabriz, Tabriz, Iran
10.22034/ijf.2024.433673.1960
Abstract
Introduction: The Juniper tree is one of the most important tree species in the forests of southern Ardabil and plays a significant role in the province's reforestation programs. Providing standard seeds and seedlings is one of the primary concerns of natural resource managers. Seed orchards, along with seed production areas, are among the most important sustainable sources for supplying seeds and seedlings of forest trees and shrubs. The aim of this study is to assess the genetic diversity and structure of juniper seed production areas in Ardabil province.
Material and Methods: In this study, the intra- and inter-population genetic diversity of five different juniper populations, including 38 individual genotypes, was evaluated using the SCoT molecular marker. Initially, leaf samples were collected from the various genotypes, and after DNA extraction, PCR reactions were performed using six SCoT molecular primers. The polymorphic information content (PIC) of the markers was calculated using Excel, and genetic diversity parameters such as the number of alleles, effective number of alleles, Shannon's index, expected heterozygosity, and unbiased expected heterozygosity were estimated using GenALEx 6.5 software. Nei’s genetic distances between populations were calculated using NTSYS-2.10 software, and cluster analysis was conducted using the UPGMA method. Molecular variance analysis and principal coordinate analysis were also performed using GenALEx 6.5 software.
Results: Based on agarose gel electrophoresis, a total of 125 alleles were detected using these markers, all of which were polymorphic. The number of alleles ranged from 16 to 24. Among the primers, SCoT62 showed the highest number of polymorphic alleles (24), while SCoT41 had the lowest (16). The average PIC for the primers was 0.404. In this study, SCoT9 had the highest PIC value (0.440), indicating its important role in distinguishing different juniper genotypes, while the lowest PIC (0.384) was observed for SCoT41. The mean value for genetic diversity parameters, including number of alleles, effective number of alleles, Shannon's index, expected heterozygosity and unbiased expected heterozygosity were 1.69, 1.45, 0.420, 0.276, and 0.295, respectively.
Conclusion: Molecular variance analysis showed that 92% of the total variance is distributed within populations, and 8% is distributed between populations. Using the UPGMA algorithm, a phylogenetic tree was constructed for the juniper genotypes, placing them into five distinct clades. One of the most important points in the formation of a seed orchard is the use of trees that have less genetic affinity so that the progeny obtained from them has a high genetic diversity and prevents the genetic erosion of the forest in the future. As a result, it is suggested to use trees A1, A3, B4, B6, C2, B2, D3, C7, D1, D2, E2, D7, E4 and A5 to form a juniper seed orchard in Ardabil.
 
Keywords
Ardabil
Genetic diversity
Juniper
SCoT marker

Subjects

 
Adams, R.P., & Schwarzbach, A.E. (2013). Phylogeny of Juniperus using nrDNA and four cpDNA regions. Phytologia, 95(2), 179-187.
Bruschi, P., Vendramin, G.G., Bussotti, F., & Grossoni, P. (2003). Morphological and molecular diversity among Italian populations of Quercus petraea (Fagaceae). Annals of Botany, 91(6), 707-716. doi: 10.1093/aob/mcg075
Buer, H., Rula, S., Wang, Z.Y., Fang, S., & Bai, Y.E. (2022). Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers. Genetic Resources and Crop Evolution, 69(3), 1057-1068. doi: 10.1007/s10722-021-01284-4
Collard, B.C., & Mackill, D.J. (2009). Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant molecular biology reporter, 27, 86-93. doi: 10.1007/s11105-008-0060-5
Douaihy, B., Vendramin, G.G., Boratyński, A., Machon, N., & Bou Dagher-Kharrat, M. (2011). High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region. AoB plants, 2011, 1-14. doi: 10.1093/aobpla/plr003
Dzialuk, A., Mazur, M., Boratyńska, K., Montserrat, J. M., Romo, A., & Boratyński, A. (2011). Population genetic structure of Juniperus phoenicea (Cupressaceae) in the western Mediterranean Basin: gradient of diversity on a broad geographical scale. Annals of Forest Science, 68(8), 1341-1350. doi: 10.1007/s13595-011-0150-7
Evren, Ö.H., & Kaya, N. (2021). High genetic diversity within and low differentiation among Juniperus excelsa M. Bieb. populations: Molecular markers reveal their genetic structure patterns. Turkish Journal of Botany, 45(3), 192-202. doi: 10.3906/bot-2006-22
Fallah, A., Nadi, M., Imani, M., & Hamidi, S.K. (2022). Reconstruction of precipitation using the chronology of juniper trees (Juniperus polycarpus) in North Khorasan Province, Iran. Iranian Journal of Forest and Poplar Research, 31(1), 1-13. doi: 10.22092/IJFPR.2023.361515.2089 (In Persian)
Hao, J., Jiao, K., Yu, C., Guo, H., Zhu, Y., Yang, X., & Shen, C. (2018). Development of SCoT-based SCAR marker for rapid authentication of Taxus media. Biochemical genetics, 56, 255-266. doi: 10.1007/s10528-018-9842-0
Jime´nez, J.F., Werner, O., Sa´nchez-Go´mez, P., Ferna´ndez, S., Guerra, J. (2003). Genetic variations and migration pathway of Juniperus thurifera L. (Cupressaceae) in the western Mediterranean region. Israel Journal of Plant Sciences, 51, 11–22. doi: 10.1560/ABR5-A6MP-5XEG-V0WF
Ju, T., Han, Z.T., Ruhsam, M., Li, J.L., Tao, W.J., Tso, S., & Mao, K.S. (2022). Reproduction and genetic diversity of Juniperus squamata along an elevational gradient in the Hengduan Mountains. Plant Diversity, 44(4), 369-376. doi: 10.1016/j.pld.2021.12.002
Kartoolinejad, D., Ravanbakhsh, H., Fadaei, Z., Moshki, A.R., & Nikouee, E. (2024). Infection of juniper trees (Juniperus excelsa M. Bieb.) to juniper dwarf mistletoe (Arceuthobium oxycedri (D.C.) M. Bieb) in forests of Miankouh Tash protected area, Shahroud. Iranian Journal of Forest, 15(4), 497-514. doi: 10.22034/IJF.2023.363540.1894 (In Persian)
Kasaian, J., Behravan, J., Hassany, M., Emami, S.A., Shahriari, F., & Khayyat, M.H. (2011). Molecular characterization and RAPD analysis of Juniperus species from Iran. Genetics and Molecular Research, 10(2), 1069-1074. doi: 10.4238/vol10-2gmr1021
Kermani, M., Maraashi, S.H., & Melati, F. (2010). Study of genetic variation of Juniperus polycarpus from Tandure National Park of Iran using RAPD markers. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research, 18(1), 115-124. (In Persian)
Kim, E.H., Shin, J.K., Jeong, K.S., Lee, C.S., & Chung, J.M. (2018). Genetic variation and structure of Juniperus chinensis L. (Cupressaceae) in Korea. Journal of Ecology and Environment, 42(1), 1-9. doi: 10.1186/s41610-018-0073-4
Khoshal Sarmast, M., Mosavizadeh, S.J., & Sharifani, M. (2018). Evaluation of Junipers spp. Genetic Diversity in Northern Iran using ISSR Markers. Ecology of Iranian Forests, 6(11), 14-20. doi: 10.29252/ifej.6.11.14. (In Persian)
Korshikov, I.I., & Nikolaeva, A.V. (2013). Genetic variability of tall junipers (Juniperus excelsa Bieb.) on the northern and southern boundaries of their natural distribution. Cytology and Genetics, 47(3), 156-163. doi: 10.3103/S0095452713030043
Lu, D., Huang, H., Wang, A., & Zhang, G. (2022). Genetic Evaluation of Juniperus sabina L. (Cupressaceae) in Arid and Semi-Arid Regions of China Based on SSR Markers. Forests, 13(2), 231. doi: 10.3390/f13020231
Luo, C., He, X.H., Chen, H., Ou, S.J., & Gao, M.P. (2010). Analysis of diversity and relationships among mango cultivars using Start Codon Targeted (SCoT) markers. Biochemical Systematics and Ecology, 38(6), 1176-1184. doi: 10.1016/j.bse.2010.11.004
Meloni, M., Perini, D., Filigheddu, R., & Binelli, G. (2006). Genetic variation in five Mediterranean populations of Juniperus phoenicea as revealed by inter-simple sequence repeat (ISSR) markers. Annals of Botany, 97(2), 299-304. doi: 10.1093/aob/mcj024
Mohammadi, Y. (2023). Preliminary assessment of juniper (Juniperus excelsa) seed production area of Ardabil. Sustainable management of Hyrcanian forests, 4(2), 39-43. (In Persian)
Motahari, B., Shabanian, N., Rahmani, M.S., & Mohammad-Hasani, F. (2021). Genetic diversity and genetic structure of Acer monspessulanum L. across Zagros forests of Iran using molecular markers. Gene, 769, 145245. doi: 10.1016/j.gene.2020.145245
Nagy, S., Poczai, P., Cernák, I., Gorji, A.M., Hegedűs, G., & Taller, J. (2012). PICcalc: an online program to calculate polymorphic information content for molecular genetic studies. Biochemical genetics, 50, 670-672. doi: 10.1007/s10528-012-9509-1
Nybom, H. (2004). Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular ecology, 13(5), 1143–1155. doi: 10.1111/j.1365-294X.2004.02141.x
Peakall, R., & Smouse, P.E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics, 28, 2537–2539. doi: 10.1093/ bioinformatics/bts460.
Rahimian Boogar, A., & Salehi, H. (2021). ISSR-based genetic diversity assessment of five populations of Juniperus polycarpos K. Koch in southern habitats of Iran. Flower and Ornamental Plants, 6(1), 1-12. doi: 10.52547/flowerjournal.6.1.1. (In Persian)
Renau‐Morata, B., Nebauer, S.G., Sales, E., Allainguillaume, J., Caligari, P., & Segura, J. (2005). Genetic diversity and structure of natural and managed populations of Cedrus atlantica (Pinaceae) assessed using random amplified polymorphic DNA. American Journal of Botany, 92(5), 875-884. doi: 10.3732/ajb.92.5.875
Rohlf, F.J. (2000). NTSYS 2.1: numerical taxonomic and multivariate analysis system. New York, Exeter Software.
Saghai-Maroof, M.A., Soliman, K.M., Jorgensen, R.A., Allard, R., (2007). Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences, 1984, 81 (24), 8014-8018. doi: 10.1073/pnas.81.24.8014
Teixeira, H., Rodriguez-Echeverria, S., & Nabais, C. (2014). Genetic diversity and differentiation of Juniperus thurifera in Spain and Morocco as determined by SSR. PLoS One, 9(2), e88996. doi: 10.1371/journal.pone.0088996
Terrab, A., Schönswetter, P., Talavera, S., Vela, E., & Stuessy, T.F. (2008). Range-wide phylogeography of Juniperus thurifera L., a presumptive keystone species of western Mediterranean vegetation during cold stages of the Pleistocene. Molecular Phylogenetics and Evolution, 48(1), 94-102. doi: 10.1016/j.ympev.2008.03.018
Vivodík, M., Balážová, Ž., Gálová, Z., & Petrovičová, L. (2019). Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated castor (Ricinus communis L.) genotypes. Genetika, 51(1), 137-146. doi: 10.2298/GENSR1901137V
Yermagambetova, M., Almerekova, S., Turginov, O., Sultangaziev, O., Abugalieva, S., & Turuspekov, Y. (2023). Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia. Plants, 12(16), 2961. doi: 10.3390/plants12162961
Yücedağ, C., & Gailing, O. (2013). Genetic variation and differentiation in Juniperus excelsa M. Bieb. populations in Turkey. Trees, 27, 547-554. doi: 10.1007/s00468-012-0807-3

  • Receive Date 22 December 2023
  • Revise Date 02 May 2024
  • Accept Date 25 May 2024