Genetic diversity of rosewood (Dalbergia latifolia) in Yogyakarta, Indonesia for plus trees selection

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INDIRA RIASTIWI
WITJAKSONO
DIAH RATNADEWI
https://orcid.org/0000-0003-1638-4742
ULFAH JUNIARTI SIREGAR

Abstract


Abstract. Riastiwi I, Witjaksono, Ratnadewi D, Siregar UJ. 2022. Genetic diversity of rosewood (Dalbergia latifolia) in Yogyakarta, Indonesia for plus trees selectionBiodiversitas 23: 2630-2639Rosewood (Dalbergia latifolia Roxb.) or sonokeling is an important woody plant species with a high selling value. However, due to overexploitation, this species has been listed in Appendix II of CITES and its trade is strictly regulated. Therefore, the cultivation of this plant needs encouragement, and superior planting materials from selected plus trees are needed. This study aimed to examine the genetic diversity of the rosewood population and select plus trees in Yogyakarta Province, Indonesia. The plus tree selection was performed by comparing plus tree candidates with five other trees nearby in four districts, i.e. Bantul, Gunungkidul, Kulon Progo, and Sleman. As many as 61 plus tree candidates have been identified. Genetic diversity was assessed using 10 selected ISSR primers, resulting in 101 ISSR loci with average Polymorphic Loci values ??of 64.71% and Nei Heterozygosity of 0.23. The highest gene diversity (He=0.29) was found in the Kulon Progo population, and the lowest He=0.17 was in the Bantul population. The dendogram and PCA analysis put Gunungkidul and Bantul populations into one group, separated from the Sleman and Kulon Progo populations. Based on morphological and molecular analysis, six superior plus trees were obtained.


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References
REFERENCE
Adema F, Ohashi H, Sunarno B. 2016. Notes on Malesian Fabaceae (Leguminosae-Papilioideae) 17. The Genus Dalbergia. Blumea 61(3): 186-206.
Anonymous. 2017. Peraturan Terbaru Peredaran Kayu Sonokeling (Dalbergia latifolia) Dalam Negeri dan Luar Negeri. [access 2020 Nov 16]. http://ksdae.menlhk.go.id/. [Indonesian]
Araujo FS, Pacheco MV, Vieira FA, Ferrari CS, Felix FC, Chagas KPT. 2016. ISSR molecular markers for the study of the genetic diversity of Mimosa caesalpiniaefolia Benth. Idesia 34: 47-52.
Bakshi M, Sharma A. 2011. Assessment of genetic diversity in Dalbergia sissoo clones through RAPD profiling. J. For. Res. 22(3): 393-397.
Bal P, Panda PC. 2018. Molecular characterization and phylogenetic relationships of Dalbergia species of Eastern India Based on RAPD and ISSR analysis. Int. J. Innov. Sci. Res. Tech. 3(7): 417-425.
Ballesta P, Mora F, Soto RIC, Ruiz E, Perret S. 2015. Analysis of the genetic diversity of Eucalyptus cladocalyx (sugar gum) using ISSR markers. Acta Scient. Agro. 37(2): 133-140.
Barber PA. 2004. Forest Pathology: The threat of disease to plantation forests in Indonesia. Plant Path. J. 3(2): 97-104.
Blair MW, McCouch SR, Panaud O. 1999. Inter simple sequence repeat (ISSR) amplifcation for analysis of microsatellite motif frequency and fngerprinting in rice (Oryza sativa L.). Theo. App. Gen. 98: 780-792.
Cai M, Wen Y, Uchiyama K, Onuma Y, Tsumura Y. 2021. Genetic Diversity and Population Structure of Chinese Cryptomeria (Cryptomeria japonica var. sinensis) for Conservation Strategies. Forests 11: 1192.
Chhajer S, Jukanti AK, Bhatt RK, Kalia RK. 2018. Genetic diversity studies in endangered desert teak Tecomella undulata (Sm) Seem] using arbitrary (RAPD), semi-arbitrary (ISSR) and sequence based (nuclear rDNA) markers. Trees 32(4): 1083-1101.
Crowther J, Zimmer H, Le Thi H, Quang TL, Nichols JD. 2020. Forestry in Vietnam: The potential role for native timber species. For. Policy Econ. 116:102182.
Devi SV, Singh AV, Handa K, Datta A, Uthappa AR. 2015. Genetic variability in candidate plus trees of Acacia nilotica an important fodder tree under agroforestry system. The XXIII International Grassland Congress (Sustainable use of Grassland Resources for Forage Production, Biodiversity and Environmental Protection) took place in New Delhi, India from November 20 through November 24.
Dickinson L, Noble H, Gardner E, Puad ASA, Zakaria WNFW, Zerega NJC. 2020. Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus). PeerJ 8(e9897): 1-21.
Dwianto W, Bahanawan A, Kusumah SS, Darmawan T, Amin Y, Pramasari DA, Lestari E, Akbar F, Sudarmanto. 2019. Study on the existence and characteristics of Sonokeling (Dalbergia latifolia Roxb) as an Appendix II CITES Wood. IOP Conf. Series: Earth and Env. Sci. 374 (012063): 1-6.
Fatima T, Srivastava A, Hanur VS, Rao MS. 2018a. An effective wood dna extraction protocol for three economic important timber species of India. American. J. Plant. Sci. 9(2): 139-149.
Fatima T, Srivastava A, Somashekar PV, Hanur VS. 2018b. Optimization of genomic dna extraction routine from Rosewood (Dalbergia Latifolia) and Ben Teak (Lagerstroemia Lanceolata). Int. J. Gen. 10(6): 446-451.
Frankham R, Ballou JD, Briscoe DA. 2002. Introduction to Conservation Genetics. Cambridge University Press, Melbourne.
Godwin ID, Aitken EAB, Smith LW. 1997. Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18(9): 1524-1528.
Goncharenko GG, Padutov VE, Silin AE. 1992. Population structure, gene diversity, and differentiation in natural populations of cedar pine (Pinus subsect. Cembrae, Pinaceae) in the USSR. Plant Syst. and Evol. 182: 121-134.
Goncharenko GG, Padutov VE, Silin AE. 1993. Allozyme variation in natural populations of Eurasian pines. I. Population structure, genetic variation, and differentiation in Pinus pumila (Pall.) Regel from Chukotsk and Sakhalin. Silv. Gen. 42: 237-246.
Hammami R, Jouve N, Soler C, Frieiro E, Gonzalez JM. 2014. Genetic diversity of SSR and ISSR markers in wild populations of Brachypodium distachyon and its close relatives B. stacei and B. hybridum (Poaceae). Plant Syst. Evol. 300(9): 2029-2040.
Hidayat Y. 2010. Morphological Variation of Surian (Toona sinensis Roem) Candidate Plus Trees Collected from Communty Forest Populations in West Java and Central Java. Conference: Promoting Biodiversity, Rainforest Protection, and Economic Development in Indonesia.
Hiremath SC, Nagasampige MH. 2004. Genome size variation and evolution in some species of Dalbergia Linn.f. (Fabaceae). Caryologia 57(4): 367-372.
Hong YP, Cho KJ, Kim YY, Shin EM, Pyo SK. 2000. Diversity of ISSR variants in the population of Torreya nucifera. Jour. Korean For. Soc. 89(2): 167-172.
Houcque D. 2005. Introduction to Matlab for Engineering Students. USA: Northwestern University.
Javaid A, Akram W, Shoaib A, Haider AS, Ahmed A. 2014. Issr Analysis of Genetic Diversity in Dalbergia Sissoo In Punjab, Pakistan. Pak. J. Bot. 46(5): 1573-1576.
Joker D. 2004. Seed Leaflet: Dalbergia latifolia Roxb. Forest & Landscape Denmark. [access 2020 Nov 16]. http://dfsc.dk/pdf/Seedleaflets/Dalbergia_latifolia_90.pdf. [Indonesian]
Josiah CC, George DO, Eleazar OM, Nyamu WF. 2008. Genetic diversity in Kenyan populations of Acacia senegal (L.) willd revealed by combined RAPD and ISSR markers. African J. Biotech. 7(14): 2333-2340.
Korshikov II, Demkovich AE. 2010. Genetic Polymorphism of Plus Tree Clones and Their Seed Progeny in the Scotch Pine Clone Plantation. Cyt Gen. 44(1): 28-36.
Krutovskii KV, Politov DV, Altukhov YP. 1995. Population Genetics and Genetic Conservation of Forest Trees. Amsterdam. SPB Academic. 279-304.
Lewontin RC. 1972. The apportionment of human diversity. J. Evol. Biol. 6: 381-398.
Louppe D, Oteng Amoaka AA, Brink M. 2008. Plant Resources of Tropical Africa 7 (1). Timbers 1 PROTA Foundation. ISBN 978-90-5782-209-4.
Medrano M, Herrera CM. 2008. Geographical Structuring of Genetic Diversity Across the Whole Distribution Range of Narcissus longispathus, a Habitat specialist, Mediterranean Narrow Endemic. Ann. Bot. 102(2): 183-94.
Mulawarman, James MR, Singgih MS, Djoko I. 2002. Management of tree seeds. Field guidelines for field officers and farmers (ICRAF and Winrock Internasional).
Nair KSS, Sumardi. 2000. Insect Pest and Diseases in Indonesian Forest. CIFOR. Bogor
Nei M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA. 70(12): 3321-3323.
Nei M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York.
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.
Phong DT, Hien VTT, Thanh TVV, Van NT, Binh NQ. 2011. Genetic diversity on the tropical rare wood species of Dalbergia in Vietnam revealed by inter simple sequence repeat (ISSR) markers. Afr. J. Biotech. 10(55): 11397-11408.
Poerba YS dan Ahmad F. 2010. Genetic Variation of Diploid Banana Cultivars (AA) from Collection of Cibinong Science Center Based on RAPDand ISSR Markers. Biota 15(3): 308-315.
Prasetyo E, Widiyatno, Indrioko S, Na’iem M, Matsui T, Matsuo A, Suyama Y, Tsumura Y. 2020. Genetic diversity and the origin of commercial plantation of Indonesian teak on Java Island. Tree. Gen. Genom. 16(34): 1-14.
Prawirohatmodjo S, Suranto J, Martawijaya A, den Outer RW, Sosef MSM. 1994. Plant Resources of South-East Asia. 5(1) Timber trees: Major commercial timbers. PROSEA. Bogor.
Rout GR, Bhatacharya D, Nanda RM, Nayak S, Das P. 2003. Evaluation of genetic relationships in Dalbergia species using RAPD markers. Biodiv. Conserv. 12: 197-206.
Sharma SK, Kumar S, Rawat D, Kumaria S, Kumar A, Rama Rao S. 2011. Genetic diversity and gene flow estimation in Prosopiscineraria (L.) Druce: a key stone tree species of Indian Thar Desert. Biochem. Syst. Ecol. 39(1): 9-13.
Siburian RHS, Siregar UJ, Siregar IZ. 2017. Genetic variation of Gyrinops versteegii originated from Papua based on RAPD. Asian J. Microbiol. Biotechnol. Env. Sci. 19(3): 1-9.
Silva AVC, Muniz EN, Almeida CS, Vitória MF. 2015. Genetic diversity and sex identification in genipa americana. Trop. Subtrop. Agroecosyst. 18: 81-6.
Soares ANR, Vitoria MF, Nascimento ALS, Ledo AS. 2016. Genetic diversity in natural populations of mangaba in Sergipe, the largest producer State in Brazil. Genet. Mol. Res. 15(3): 1-12.
Swofford, DL. 2002. PAUP*. phylogenetic analysis using parsimony (*and other methods) version 4. Sunderland, Massachusetts: Sinauer Associates.
Tsumura Y, Ohba K, Strauss SH. 1996. Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglas-fir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). Theoret. Appl. Gen. 92(1): 40-45.
Vakkari P, Rusanen M, Karkkainen K. 2009. High Genetic Differentiation in Marginal Populations of European White Elm (Ulmus laevis). Silv. Fenn 43(2): 185-96.
Wolfe AD, Liston, A. 1998. Contributions of PCR-based methods to plant systematics and evolutionary biology. pp. 43-86, In: Soltis DE, Soltis PS, Doyle JJ. (Ed.). Plant Molecular Systematics II, Kluwer.
Xia J, Wishart DS. 2016. Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis Curr. Protoc. BioinForm. 55:14.10.1-14.10.91.
Yulita SK, Atikah TD, Wardani W, Susila. 2020. Unraveling genetic variations of Dalbergia latifolia (Fabaceae) from Yogyakarta and Lombok Island, Indonesia. Biodiversitas 21(2): 833-841.
Zakiyah R, Siregar UJ, Hartati N. 2017. Morphological Characterization of Sengon (Paraserianthes falcataria L. Nielsen) Gamma Radiation Mutation Results. J. Silv. Trop. 8(1): 41-47. [Indonesian]

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