Hostname: page-component-78c5997874-t5tsf Total loading time: 0 Render date: 2024-11-19T05:07:10.719Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity of Jatropha curcas collections from different islands in Indonesia

Published online by Cambridge University Press:  05 March 2018

Tantri Dyah Ayu Anggraeni ,
Dani Satyawan ,
Yang Jae Kang ,
Jungmin Ha ,
Moon Young Kim ,
Annapurna Chitikineni ,
Rajeev K. Varshney  and
Suk-Ha Lee
Tantri Dyah Ayu Anggraeni
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Indonesian Sweetener and Fiber Crops Research Institute, IAARD, Malang 65100, Indonesia
Dani Satyawan
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Indonesian Center for Agricultural Biotechnology and Genetic Resources and Development, IAARD, Bogor 16111, Indonesia
Yang Jae Kang
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
Jungmin Ha
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
Moon Young Kim
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
Annapurna Chitikineni
Affiliation:
Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India
Rajeev K. Varshney
Affiliation:
Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Andhra Pradesh, India
Suk-Ha Lee*
Affiliation:
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
*
*Corresponding author. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Jatropha curcas L. is a potential bioenergy crop but has a lack of improved cultivars with high yields and oil content. Therefore, increasing our understanding of J. curcas germplasm is important for designing breeding strategies. This study was performed to investigate the genetic diversity and population structure of Indonesian J. curcas populations from six different islands. To construct a reference, we de novo assembled the scaffolds (N50 = 355.5 kb) using 182 Gb Illumina HiSeq sequencing data from Thai J. curcas variety Chai Nat. Genetic diversity analysis among 52 Indonesian J. curcas accessions was conducted based on yield traits and single nucleotide polymorphism (SNP) markers detected by mapping genotyping-by-sequencing reads from Indonesian population to Chai Nat scaffolds. Strong variation in yield traits was detected among accessions. Using J. integerrima as an outgroup, 13,916 SNPs were detected. Among J. curcas accessions, including accessions from other countries (Thailand, the Philippines and China), 856 SNPs were detected, but only 297 SNPs were detected among Indonesian J. curcas populations, representing low genetic diversity. Through phylogenetic and structural analysis, the populations were clustered into two major groups. Group one consists of populations from Bangka and Sulawesi in the northern part of Indonesia, which are located at a distance of 1572.59 km. Group two contains populations from islands in the southern part: Java, Lombok-Sumbawa, Flores and Timor. These results indicate that introduction of diverse J. curcas germplasms is necessary for the improvement of the genetic variation in the Indonesian collections.

Keywords

genetic diversitygenotyping-by-sequencingIndonesiaislandsJatropha curcasmigratory rout
Type
Research Article
Information
Plant Genetic Resources , Volume 16 , Issue 4 , August 2018 , pp. 334 - 342
Copyright
Copyright © NIAB 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Achten, WMJ, Nielsen, LR, Aerts, R, Lengkeek, AG, Kjaer, ED, Trabucco, A, Hansen, JK, Maes, WH, Graudal, L, Akinnifesi, FK and Muys, B (2010) Towards domestication of Jatropha curcas. Biofuels 1: 91–107.Google Scholar
Amalia Kartika, I, Yani, M, Ariono, D, Evon, P and Rigal, L (2013) Biodiesel production from jatropha seeds: solvent extraction and in situ transesterification in a single step. Fuel 106: 111–117. doi: 10.1016/j.fuel.2013.01.02.Google Scholar
Amkul, K, Panngam, M, Tanya, P, Srinives, P and Laosatit, K (2016) Pollen viability and seed set of interspecific hybrids between Jatropha curcas x Jatropha integerrima. Genomics and Genetics 9: 50–55.Google Scholar
Ammarel, G (1999) Bugis Navigation, vol. 2. New Haven: Yale University Southeast Asia Studies.Google Scholar
Brittaine, R and Lutaladio, NB (2010) Jatropha curcas L. In: Brittaine, R and Lutaladio, NB (eds) Jatropha: A Smallholder Bioenergy Crop, the Potential for Pro-poor Development. Rome: FAO, pp. 13–26.Google Scholar
de Oliveira, JS, Leite, PM, de Souza, LB, Mello, VM, Silva, EC, Rubima, JC, Meneghetti, SMP and Suarez, PAZ (2009) Characteristics and composition of Jatropha gossypiifolia and Jatropha curcas L. oils and application for biodiesel production. Biomass and Bioenergy 3: 449–453. doi: 10.1016/j.biombioe.2008.08.006.Google Scholar
Earl, DA and vonHoldt, BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361. doi: 10.1007/s12686-011-9548-7.Google Scholar
Elshire, J, Glaubitz, JC, Sun, Q, Poland, JA, Kawamoto, K, Buckler, E and Mitchell, SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379. doi: 10.1371/journal.pone.0019379.Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14: 2611–2620. doi: 10.1111/j.1365-294X.2005.02553.Google Scholar
Fearless, D (2007) Biofuel: the little shrub that could – maybe. Nature 449: 652–655.Google Scholar
Gnerre, S, Maccallum, I, Przybylski, D, Ribeiro, FJ, Burton, JN, Walker, BJ, Sharpe, T, Hall, G, Shea, TP, Sykes, S, Berlin, AM, Aird, D, Costello, M, Daza, R, Williams, L, Nicol, R, Gnirke, A, Nusbaum, C, Lander, ES and Jaffe, DB (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proceedings of the National Academy of Sciences of the United States of America 108: 1513–1518.Google Scholar
Gupta, P, Idris, A, Mantri, S, Asif, MH, Yadav, HK, Roy, JK, Tuli, R and Mohanty, CS (2012) Discovery and use of single nucleotide polymorphic (SNP) markers in Jatropha curcas L.. Molecular Breeding 30: 1325–1335. doi: 10.1007/s11032-012-9719-6.Google Scholar
Heller, J (1996) Origin and centre of of diversity. In: Heller, J (ed.) Promoting the Conservation and use of Underutilized and Neglected Crops. 1. Physic Nut. Jatropha curcas L. Rome: International Plant Genetic Resources Institute, pp. 13–15.Google Scholar
Heyne, K (1927) De Nuttige Planten Van Nederlansch-Indie II (in Dutch). Buitenzorg (Bogor), Indonesia: Departement van Landbouw, Nijverheid en Handel.Google Scholar
Kassa, MT, Penmetsa, RV, Carrasquilla-Garcia, N, Sarma, BK, Datta, S, Upadhyaya, HD, Varshney, RK, von Wettberg, EJB and Cook, DR (2012) Genetic patterns of domestication in pigeon pea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives. PLoS ONE 7: e39563. doi: 10.1371/journal.pone.0039563.Google Scholar
Lampe, M (2012) Bugis-Makassar seamanship and reproduction of maritime cultural values in Indonesia. Humaniora 24: 121–132.Google Scholar
Langmead, B and Salzberg, S (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357–359. doi: 10.1038/nmeth.1923.Google Scholar
Letunic, I and Bork, P (2011) Interactive tree of life v2. Online annotation and display of phylogenetic trees made easy. Nucleic Acids Research 39: 475–478. doi: 10.1093/nar/gkr201 PMID:21470960.Google Scholar
Liu, K and Muse, SV (2005) Powermarker: integrated analysis environment for genetic diversity in core collection accessions of wild barley, Hordeum vulgare ssp. Spontaneum. Hereditas 136: 67–73.Google Scholar
Machua, J, Muturi, G, Omondi, SF and Gicheru, J (2011) Genetic diversity of Jatropha curcas L. Populations in Kenya using RAPD molecular markers: implication to plantation establishment. African Journal of Biotechnology 10: 3062–3069. doi: 10.5897/AJB10.1990.Google Scholar
Maghuly, F, Jankowicz-Cieslak, J, Pabinger, S, Till, BJ and Laimer, M (2015) Geographic origin is not supported by the genetic variability found in a large living collection of Jatropha curcas with accessions from three continents. Biotechnology Journal 10: 536–551. doi: 10.1002/biot.201400196.Google Scholar
Na-ek, Y, Wongkaew, A, Phumichai, T, Kongsiri, N, Kaveeta, R, Reewongchai, T and Phumicai, C (2011) Genetic diversity of physic nut (Jatropha curcas L.) revealed by SSR markers. Journal of Crop Science and Biotechnology 14: 105–110. doi: 10.1007/s12892-011-0008-4.Google Scholar
Negussie, AM, Achten, WMJ, Verboven, H, Hermy, M and Muys, B (2014) Floral display and effects of natural and artificial pollination on fruiting and seed yield of the tropical biofuel crop Jatropha curcas L. Global Change Biology Bioenergy 6: 210–218. doi: 10.1111/gcbb.12072.Google Scholar
Nei, M, Tajima, F and Tateno, Y (1983) Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. Journal of Molecular Evolution 19: 153–170.Google Scholar
Osorio, LRM, Salvador, AFT, Jongschaap, REE, Perez, CAA, Sandoval, JEB, Trindade, LM, Visser, RGF and van Loo, EN (2014) High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America. BMC Plant Biology 14: 77. doi: 10.1186/1471-2229-14-77.Google Scholar
Ouattara, B, Ndir, KN, Gueye, MC, Diedhiou, I, Adeline, B, Fonceka, D, Cisse, N, Akpo, EL and Diouf, D (2014) Genetic diversity of Jatropha curcas L. in Senegal compared with exotic accessions based on microsatellite markers. Genetic Resources and Crop Evolution 61: 1039–1045. doi: 10.1007/s10722-014-1006-5.Google Scholar
Pamidimarri, DVNS and Reddy, MP (2014) Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis. Molecular Biology Reports 41: 3225–3234. doi: 10.1007/s11033-014-3185-7.Google Scholar
Peakall, R and Smouse, PE (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.Google Scholar
Poesponegoro, MD and Notosusanto, N (1984) Sejarah Nasional Indonesia IV (in Indonesian). Jakarta: Balai Pustaka.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Raju, AJS and Ezradanam, V (2002) Pollination ecology and fruiting behaviour in a monoecious species Jatropha curcas L. (Euphorbiaceae). Current Science 83: 1395–1398.Google Scholar
Saadaoui, E, Martin, JJ, Bouazizi, R, Romdhane, CB, Grira, M, Abdelkabir, S, Khouja, ML and Cervantes, E (2015) Phenotypic variability and seed yield of Jatropha curcas L. introduced to Tunisia. Acta Botánica Mexicana 110: 119–134.Google Scholar
Sanou, H, Angulo-Escalante, MA, Martinez-Herrera, J, Kone, S, Nikiema, A, Kalinganire, A, Hansen, JK, Kjaer, ED, Graudal, L and Nielsen, LR (2015) Loss of genetic diversity of Jatropha curcas L. through domestication: implications for its genetic improvement. Crop Science 55: 749–759.Google Scholar
Sato, S, Hirakawa, H, Isobe, S, Fukai, E, Watanabe, A, Kato, M, Kawashima, K, Minami, C, Muraki, A, Nakazaki, N, Takahashi, C, Nakayama, S, Kishida, Y, Kohara, M, Yamada, M, Tsuruoka, H, Sasamoto, S, Tabata, S, Aizu, T, Toyoda, A, Shin-i, T, Minakuchi, Y, Kohara, Y, Fujiyama, A, Tsuchimoto, S, Kajiyama, S, Makigano, E, Ohmido, N, Shibagaki, N, Cartagena, JA, Wada, N, Kohinata, T, Atefeh, A, Yuasa, S, Matsunaga, S and Fukui, K (2011) Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Research 18: 65–76. doi: 10.1093/dnares/dsq030.Google Scholar
Satyawan, D and Tasma, M (2011) Genetic diversity analysis of Jatropha curcas provenances using randomly amplified polymorphic DNA markers. Journal Agrobiogen 7: 47–55.Google Scholar
Silitonga, AS, Atabania, AE, Mahlia, TMI, Masjukia, HH, Badruddina, IA and Mekhilefe, S (2011) A review on prospect of Jatropha curcas for biodiesel in Indonesia. Renewable & Sustainable Energy Reviews 15: 3733–3756. doi: 10.1016/j.rser.2011.07.011.Google Scholar
Tamura, K, Stecher, G, Peterson, D, Filipski, A and Kumar, S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725–2729.Google Scholar
Tanya, P, Taeprayoon, P, Hadkan, Y and Srinives, P (2011) Genetic diversity among Jatropha and Jatropha-related species based on ISSR markers. Plant Molecular Biology Reporter 29: 252–264. doi: 10.1007/s11105-010-0220-2.Google Scholar
Wang, J, Chu, S, Zhang, H, Zhu, Y, Cheng, H and Yu, D (2016) Development and application of a novel genome-wide SNP array revelas domestication history in soybean. Scientific Reports 6: 20728. doi: 10.1038/srep20128.Google Scholar
Wen, M, Wang, H, Xia, Z, Zou, M, Lu, C and Wang, W (2010) Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Research Notes 3: 42. doi: 10.1186/1756-0500-3-42.Google Scholar
Wright, S (1978) Evolution and the Genetics of Populations: Variability within and among Natural Populations. Chicago: University of Chicago Press.Google Scholar
Wu, P, Zhou, C, Cheng, S, Wu, Z, Lu, W, Han, J, Chen, Y, Chen, Y, Ni, P, Wang, Y, Xu, X, Huang, Y, Song, C, Wang, Z, Shi, N, Zhang, X, Fang, X, Yang, Q, Jiang, H, Chen, Y, Li, M, Wang, Y, Chen, F, Wang, J and Wu, G (2015) Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant. Plant Journal 81: 810–821. doi: 10.1111/tpj.12761.Google Scholar
Yi, C, Zhang, S, Liu, X, Bui, HTN and Hong, Y (2010) Does epigenetic polymorphism contribute to phenotypic variances in Jatropha curcas L.? BMC Plant Biology 10: 259. doi: 10.1186/1471-2229-10-259.Google Scholar
Supplementary material: File

Anggraeni et al. supplementary material

Anggraeni et al. supplementary material 1

Download Anggraeni et al. supplementary material(File)
File 830.5 KB