Development of EST-SSR Markers from Jatropha curcas (Euphorbiaceae) and Their Application in Genetic Diversity Analysis among Germplasms

doi:10.3724/SP.J.1143.2011.11064

Abstract

Abstract:

Jatropha curcas (Euphorbiaceae) has created tremendous interest all over the world for the use of its seed oil as a commercial source of biodiesel. Based on 9843 ESTs available from the developing seeds of Jatropha curcas, we identified 1009 SSRs in 4640 unigenes and developed 11 polymorphic EST-SSR markers which exhibited a low level of genetic diversity among germplasms, i.e. allele number varied from 2 to 3, with a average of 2.45; Heterozygosity (He) ranged from 0.0887-0.5128, with a average of 0.2736; Polymorphic Information Content (PIC) ranged from 0.0847-0.4031, with a average of 0.2313. Further, we analyzed the genetic relationships among 24 germplasms collected from different areas in southern China, northern Vietnam, and India using the 11 EST-SSR markers. The results showed that there was no a geographic pattern of genotypes across the collection areas of Jatropha curcas. The EST-SSR markers developed in current study is useful for both genetic diversity analysis and identification of genetic relationships among germplasms in Jatropha curcas.

Key words: Biodiesel plant, EST-SSR, Genetic diversity, Jatropha curcas

CLC Number:

Q 78

YANG Chun-, LIU Ai-Zhong. Development of EST-SSR Markers from Jatropha curcas (Euphorbiaceae) and Their Application in Genetic Diversity Analysis among Germplasms[J]. Plant Diversity, 2011, 33(5): 529-534.

References

丘华兴, 1996. 中国植物志，第44卷第2分册［M］. 北京: 科学出版社, 148
陈冀胜, 郑硕, 1987. 中国有毒植物［M］. 北京: 科学出版社, 258
Basha SD, Sujatha EM, 2007. Inter and intra-population variability of Jatropha curcas (L.) characterized by RAPD and ISSR markers and development of population specific SCAR markers［J］. Euphoria, 156: 375—386
Cai Y, Sun DK, Wu GJ et al., 2010. ISSR-based genetic diversity of Jatropha curcas germplasm in China［J］. Biomass & Bioenergy, 34: 1739—1750
Cardle L, Ramsay L, Milbourne D et al., 2000. Computational and experimental characterization of physically clustered simple sequence repeats in plants［J］. Genetics, 156: 847—854
Carvalho CR, Clarindo WR, Prac MM et al., 2008. Genome size, base composition and karyotype of Jatropha curcas L.: an important biofuel plant［J］. Plant Science, 174: 613—617
Doyle J, Doyle J, 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue［J］. Phytochemistry, 19: 11—15
Ellis JR, Burke JM, 2007. EST-SSRs as a resource for population genetics analysis［J］. Heredity, 99: 125—132
Fairless D, 2007. Biofuel: The little shrub that could-maybe［J］. Nature, 449: 652—655
Foidl N, Foidl G, Sanchez M et al., 1996. Jatropha curcas L. as a source for the production of biofuel in Nicaragua［J］. Bioresource Technology, 58: 77—82
Gübitz GM, Mittelbach M, Trabi M, 1999. Exploitation of the tropical oil seed plant Jatropha curcas L［J］. Bioresource Technology, 67: 73—82
Li WZ, Godzik A, 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences［J］. Bioinformatics, 22: 1658—1659
Morgante M, Hanafey M, Powell W, 2002. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes［J］. Nature Genetics, 30: 194—200
Nicot N, Chiquet V, Gandon B et al., 2004. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)［J］. Theoretical and Applied Genetics, 109: 800—805
Qiu L, Yang C, Tian B et al., 2010. Exploiting EST databases for the development and characterization of EST-SSR marker in castor (Ricinus communis L.)［J］. BMC Plant Biology, 10: 278
Ranade SA, Srivastava AP, Rana TS et al., 2008. Easy assessment of diversity in Jatropha curcas L. plants using two single-primer amplification reaction (SPAR) methods［J］. Biomass & Bioenergy, 32: 533—540
Sun QB, Li LF, Li Y et al., 2008. SSR and AFLP markers reveal low genetic diversity in the biofuel plant Jatropha curcas in China［J］. Crop Science, 48: 1865—1871
Tatikonda L, Wani SP, Kannan S et al., 2009. AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant［J］. Plant Science, 176: 505—513
Tóth G, Gáspári Z, Jurka J, 2000. Microsatellites in different eukaryotic genomes: Survey and analysis［J］. Genome Research, 10: 967—981
Varshney RK, Thiel T, Stein N et al., 2002. In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species［J］. Cellular & Molecular Biology Letters, 7: 537—546
Wen M, Wang H, Xia Z et al., 2010. Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L.［J］. BMC Research Notes, 3:42
Yadav HK, Ranjan A, Asif M et al., 2010. EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera［J］. Tree Genetics & Genomes, 7: 207—219

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