Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand

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ONGKARN VANIJAJIVA
PIMWADEE PORNPONGRUNGRUENG

Abstract

Abstract. Vanijajiva O, Pornpongrungrueng P. 2020. Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand. Biodiversitas 21: 3919-3928. Cissampelopsis is a small climbing tropical Asian genus of Asteraceae-Senecioneae. In Thailand, the genus is represented by two species, C. corifolia and C. Volubilis, distributed through the mountain evergreen forest. Study on the genetic diversity and structure of populations of both Cissampelopsis species provide better understanding of the biology and pattern of species diversification in the genus. To identify the genetic diversity, we used the inter-primer binding site (iPBS) retrotransposon system, in 96 accessions of Cissampelopsis species collected from different regions in Thailand. A total of 120 iPBS bands were scored as presence? absence characters. Results from UPGMA and PCoA analyses indicated that C. corifolia and C. volubilis are different species. Genetic diversity and genetic differentiation among and within populations of C. volubilis is higher than C. corifolia. Molecular Variance (AMOVA) analysis of both species indicated that the genetic variance value within populations is higher than among populations of each species. Bayesian model-based STRUCTURE analysis detected two gene pools for both Cissampelopsis and showed admixture within individuals. Differences among the two Cissampelopsis species, in total diversities and levels of population differentiation, indicated that the genetic structure of Cissampelopsis populations are congruent with long-lived perennial habit with regional distribution, even for congeneric species, may vary considerably. This study suggests the effectiveness of the iPBS marker system to estimate the population genetic diversity and structure of Cissampelopsis genotypes.

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References
Amom T, Tikendra L, Apana N, Goutam M, Sonia P, Koijam AS, Potshangbam AM, Rahaman H and Nongdam P. 2020. Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India. Phytochemistry 174: 112330. Doi:10.1016/j.phytochem.2020.112330
Andeden EE, Baloch FS, Derya M, Kilian B, Özkan H. 2013. iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. Journal of Plant Biochemistry and Biotechnology 22 (4): 453-466. Doi:10.1007/s13562-012-0175-5
Anderson C, Epperson BK, Fortin MJ, Holderegger R, James PMA, Rosenberg MS, Scribner KT, Spear S. 2010. The importance of spatial and temporal scale in landscape genetics. Molecular Ecology 19: 3565–3575. Doi: 10.1111/j.1365-294X.2010.04757.x
Al-Naggar AMM, El-Salam RA, Badran AEE, El-Moghazi MM. 2017. Molecular differentiation of five quinoa (Chenopodium quinoa Willd.) genotypes using inter-simple sequence repeat (ISSR) markers. Biotechnology Journal International 20 (1): 1-12. Doi: 10.9734/BJI/2017/37053
Baloch FS, Alsaleh A, de Miera LES, Hatipo?lu R, Çiftçi V et al.2015. DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey. Biochemical Systematics and Ecology 61: 244-252. Doi: 10.1016/j.bse.2015.06.017
De Riek J, Calsyn E, Everaert I, Van Bockstaele E, De Loose M. 2001. AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theory Apply Genetic 103:1254–1265. https://doi:10.1007/s001220100710
Doyle JJ, Doyle JL. 1990 Isolation ofplant DNA from fresh tissue. Focus 12 (13): 39-40.
Coutinho JP, Carvalho A, Martin A, Lima-Brito J. 2018. Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers. Molecular Biology Reports 45:133–142. Doi:10.1007/s11033-018-4146-3
Cushman SA, McKelvey KS, Hayden J, Schwartz MK. 2006. Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. The American Naturalist 168(4): 486-499. Doi:10.1086/506976
Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14 (8): 2611-2620. Doi:10.1111/j.1365-294x.2005.02553.x
Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: A new series of pro¬grams to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10 (3): 564-567. Doi:10.1111/j.1755-0998.2010.02847.x
Frankham R, Ballou JD, Briscoe DA, McInnes KH. 2010. Introduction to Conservation Genetics. Cambridge University Press: Cambridge, UK.
Freeland JR, Kirk H, Petersen SD. 2011. Molecular Ecology. Wiley-Blackwell: Chichester, UK.
Gallagher RV, Leishman MR. 2012 A global analysis of trait variation and evolution in climbing plants. Journal of Biogeography 39(10): 1757-1771. Doi:10.1111/j.1365-2699.2012.02773.x
Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological statistics soft¬ware package for education and data analysis. Palaeontologia Electronica 4: 1- 9.
Hamrick JL, Godt MJW. 1996. Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 351: 1291–1298.
Hamrick JL, Murawski DA, Nason JD. 1993. The influence of seed dispersal mechanisms on the genetic structure of tropical tree populations. Vegetatio 107: 281–297.
Hedrick PW. 1999. Perspective: highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313–318.
Holsinger KE, Weir BS. 2009. Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics 10: 639–650. Doi:10.1038/nrg2611
Hossein-Pour A, Haliloglu K, Ozkan G, Tan M. 2019. Genetic diversity and population structure of quinoa (Chenopodium quinoa Willd.) using iPBS-retrotransposons markers. Applied Ecology and Environmental Research 17 (2): 1899-1911. Doi:10.15666/aeer/1702_18991911
Hubisz MJ, Falush D, Stephens M, Pritchard JK. 2009. Inferring weak popula¬tion structure with the assistance of sample group information. Molecular Ecology Resources 9 (5): 1322-1332. Doi.org/10.1111/j.1755-0998.2009.02591.x
Jeffrey C, Chen YL. 1984. Taxonomic studies on the tribe Senecioneae (Compositae) of eastern Asia. Kew Bull. 39: 205–446.
Kalendar R, Antonius K, Smýkal P, Schulman AH. 2010 iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics 121 (8): 1419-1430. Doi: 10.1007/s00122-010-1398-2
Kalendar R. 2011. The use of retrotransposon-based molecular markers to analyze genetic diversity. Ratarstvo i Povrtarstvo 48: 261–274. Doi:10.5937/ratpov1102261K
Kalendar R. Schulman AH. 2014. Transposon-based tagging: IRAP, REMAP, and iPBS. In: Molecular Plant Taxonomy. Humana Press, Totowa.
Kalendar R, Amenov A, Daniyarov A. 2019. Use of retrotransposon derived genetic markers to analyze genomic variability in plants. Function Plant Biology. 46(1):15–29. Doi:10.1071/FP18098
Karagoz H, Cakmakci R, Hosseinpour A, Ozkan G, Haliloglu K. 2020). Analysis of genetic variation and population structure among of oregano (Origanum acutidens L.) accessions revealed by agro-morphological traits, oil constituents and retrotransposon-based inter-primer binding sites (iPBS) markers. Genetic Resources and Crop Evolution 1-18. Doi.org/10.1007/s10722-020-00887-7
Kar?k Ü, Nadeem MA, Habyarimana E, Erci?li S, Yildiz M et al. 2019. Exploring the genetic diversity and population structure of Turkish Laurel germplasm by the iPBS-Retrotransposon Marker System. Agronomy 9 (10): 647. Doi: 10.3390/agronomy9100647
Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. 2015. CLUMPAK: a program for identifying clustering modes and packaging pop¬ulation structure inferences across K. Molecular Ecology Resources 15 (5): 1179-1191. Doi:10.1111/1755-0998.12387
Koyama H, Bunwong S, Pornpongrungrueng P, Nicholas Hind DJ. 2016 Compositae (Asteraceae). In: T Santisuk and H Balslev (eds) Flora of Thailand Vol 13 part 2. Bangkok: Royal Forest Herbarium.
Lau CP, Saunders RM, Ramsden L. 2009. Floral biology, breeding systems and population genetic structure of three climbing Bauhinia species (Leguminosae: Caesalpinioideae) in Hong Kong, China. Journal of tropical ecology 25(2): 147-159.
Li HM, Ren C. 2018. Cissampelopsis quinquesquamata (Asteraceae–Senecioneae), a new species from western Myanmar and northeastern India. Nordic journal of botany. 36(10): e01977. Doi: 10.1111/njb.01977
Li W. 1976. Effect of migration on genetic distance. American Naturalist. 110: 841–847.
Loveless MD. Hamrick JL. 1984. Ecological determinants of genetic structure in plant populations. Annual Review of Ecology and Systematics 15: 60–90.
Mehmood A, Luo S, Ahmad NM, Dong C, Mahmood T, Sajjad Y, Sharp P. 2016. Molecular variability and phylogenetic relationships of guava (Psidium guajava L.) cultivars using inter-primer binding site (iPBS) and microsatellite (SSR) markers. Genetic Resources and Crop Evolution 63: 1345-1361. Doi:10.1007/s10722-015-0322-7
Nemli S, Kianoosh T, Tanyolac MB. 2015. Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turkish Journal of Agriculture and Forestry 39 (6): 940-948. Doi:10.3906/tar-1505-59
Nei M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70 (12): 3321-3323.
Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
Nybom H, Bartish I. 2000. Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspectives in Plant Ecology, Evolution and Systematics 3(2): 93–114.
Nybom H. 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology. 13: 1143–1155.
Petit RJ, El Mousadik A, Pons O. 2008. Identifying populations for conserva¬tion on the basis of genetic markers. Conservation Biology 12 (4): 844–855. Doi:10.1111/j.1523-1739.1998.96489.x
Phillips OL, Martínez RV, Arroyo L, Baker TR, Killeen T, Lewis SL, Malhi Y, Mendoza AM, Neill D, Vargas PN, Alexiades M. 2002. Increasing dominance of large lianas in Amazonian forests. Nature 418(6899): 770–774. Doi:10.1038/nature00926
Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. 2000 Association map¬ping in structured populations. The American Journal of Human Genetics 67: 170-181. Doi:10.1086/302959
Reis MS. 1996. Dinâmica da movimentação dos alelos: subsídios para conservação e manejo de populações naturais em plantas. Brazilian Journal of Genetics 19: 37–47.
Roldán-Ruiz I, Calsyn E, Gilliland TJ, Coll R, van Eijk MJT, De Loose M. 2000. Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Molecular Breeding 6: 593-602.
Sennikov A. 2010. Proposal to conserve the name Cissampelopsis (DC.) Lem. ex Lindl. (Asteraceae) with a conserved type. Taxon 59: 1285–1286. Doi:10.1111/njb.01977
Tong Y, Durka W, Zhou W, Zhou L, Yu D, Dai, L. 2020. Ex situ conservation of Pinus koraiensis can preserve genetic diversity but homogenizes population structure. Forest Ecology and Management 465: 117820. Doi:10.1016/j.foreco.2019.117820
Vanijajiva O and Kadereit JW. 2008. A revision of Cissampelop¬sis (Asteraceae: Senecioneae). Kew Bull. 63: 213–226.
Vanijajiva O. 2020. Start codon targeted (SCoT) polymorphism reveals genetic diversity of Manilkara in Thailand. Biodiversitas 21(2): 666-673. DOI: 10.13057/biodiv/d210232

Vasilyeva YS, Zhulanov AA, Boronnikova SV. Yanbaev YA. 2020. Genetic structure of ural populations of Larix sibirica Ledeb. on the base of analysis of nucleotide polymorphism. Silvae Genetica 69(1): 20-28. Doi:10.2478/sg-2020-0004
Vos P, Hogers R, Bleeker M et al. 1995 AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23: 4407–4414.
Weising K, Nybom H, Wolff K, Meyer W. 1995. DNA Fingerprinting in Plants and Fungi. CRC Press, Boca Raton, Florida.
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18: 6531– 6535.
Yeh F, Yang R, Boyle T.1999. POPGENE Version 1.32. Microsoft Window-based Freeware for Population Genetic Analysis. Molecular Biology and Biotech¬nology Center, University of Alberta, Edmonton.
Zietkiewicz E, Rafalski A, Labuda D. 1994. Genome fingerprinting by simple sequence repeats (SSR)-anchored PCR amplification. Genomics 20: 176 –183.

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