Advertisement

Tropical Plant Biology

, Volume 12, Issue 1, pp 32–43 | Cite as

Development of SSR Markers for Coconut (Cocos nucifera L.) by Selectively Amplified Microsatellite (SAM) and Its Applications

  • Yi Wu
  • Yaodong YangEmail author
  • Rashad Qadri
  • Amjad Iqbal
  • Jing Li
  • Haikuo Fan
  • Yaoting WuEmail author
Article
  • 65 Downloads

Abstract

Coconut is an important tropical fruit and oil crop. Its long generation time, low multiplication rate and recalcitrant seeds make coconut more difficult for breeding and selection. New technologies and extensive resources to evaluate coconut breeding strategies are the demand of today. Molecular markers had the potential to dramatically increase the efficiency and efficacy in the areas of germplasm management, genotype identification and marker-assisted selection of economically important traits of coconut. However, the lack of relevant molecular techniques impedes the development of a new strategy for the genetic improvement of the coconut. In this study, we have successfully developed 84 SSR markers by Selectively Amplified Microsatellite from coconut genome and more than 90% of these SSR showed good transferability to the palm family. The study will enrich the genomic-SSR pool for coconut and also for the other palm tree. Besides, it will provide the scientists with more options for coconut germplasm evaluation, constructing a coconut genetic linkage map and designing the breeding programs for producing superior cultivars of coconut.

Keywords

Coconut Selectively amplified microsatellite (SAM) SSR markers Transferability Palm trees 

Notes

Acknowledgements

Researches were supported by the International Science and Technology Cooperation projects of Hainan Province (#KJHZ2014-24) and the Fundamental Scientific Research Funds for Chinese Academy of Tropical Agricultural Sciences (CATAS-No. 1630032012044 and 1630052014002) and “948” projects for Ministry of Agriculture of China (2015-Z25),Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (No.1630152017019) and Central Public-interest Scientific Institution Basal Research Fund for Innovative Research Team Program of CATAS (NO. 17CXTD-28).

Author’s Contribution

YW, JL and LZ did the DNA extract and subsequently PCR amplification. YW, YY and YaW participated in the design of the study, performed the data analysis and drafted the manuscript. RQ and AI critically revised the manuscript. HF participated in the design of the study. All authors reviewed the manuscript and have given final approval of the version to be published.

Compliance with Ethical Standards

Conflicts of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary material

12042_2018_9215_MOESM1_ESM.doc (285 kb)
ESM 1 (DOC 285 kb)
12042_2018_9215_MOESM2_ESM.pdf (53 kb)
ESM 2 (PDF 53 kb)
12042_2018_9215_MOESM3_ESM.pdf (235 kb)
ESM 3 (PDF 235 kb)
12042_2018_9215_MOESM4_ESM.jpg (87 kb)
ESM 4 (JPG 86 kb)
12042_2018_9215_MOESM5_ESM.jpg (134 kb)
ESM 5 (JPG 134 kb)

References

  1. Acquadro A, Portis E, Albertini E, Lanteri S (2005) M-AFLP-based protocol for microsatellite loci isolation in Cynara cardunculus L.(Asteraceae). Mol Ecol Notes 5(2):272–274CrossRefGoogle Scholar
  2. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J, Arondel V, Ohlrogge J, Saie IJ, Suliman-Elmeer KM, Bennetzen JL, Kruegger RR, Malek JA (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29(6):521–527.  https://doi.org/10.1038/nbt.1860 CrossRefGoogle Scholar
  3. Al-Mssallem IS et al (2013) Genome sequence of the date palm Phoenix dactylifera L. Nat Commun 4:2274–2274.  https://doi.org/10.1038/ncomms3274 CrossRefGoogle Scholar
  4. Ashburner G (1995) Genetic markers for coconut palms. In: Lethal yellowing: Research and practical aspects. Springer, pp 173–186Google Scholar
  5. Ashburner GR, Thompson WK, Halloran GM (1997) RAPD Analysis of South Pacific Coconut Palm Populations. Crop Sci 37(3):992–997.  https://doi.org/10.2135/cropsci1997.0011183X003700030048x CrossRefGoogle Scholar
  6. Cavagnaro PF, Senalik DA, Yang L, Simon PW, Harkins TT, Kodira CD, Huang S, Weng Y (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11(1):569.  https://doi.org/10.1186/1471-2164-11-569 CrossRefGoogle Scholar
  7. Cifarelli RA, Gallitelli M, Cellini F (1995) Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones. Nucleic Acids Res 23(18):3802–3803CrossRefGoogle Scholar
  8. Dumhai R, Wanchana S, Saensuk C, Choowongkomon K, Mahatheeranont S, Kraithong T, Toojinda T, Vanavichit A, Arikit S (2019) Discovery of a novel CnAMADH2 allele associated with higher levels of 2-acetyl-1-pyrroline (2AP) in yellow dwarf coconut (Cocos nucifera L.). Sci Hortic 243:490–497.  https://doi.org/10.1016/j.scienta.2018.09.005 CrossRefGoogle Scholar
  9. Fan H, Xiao Y, Yang Y, Xia W, Mason AS, Xia Z, Qiao F, Zhao S, Tang H (2013) RNA-Seq Analysis of Cocos nucifera: Transcriptome Sequencing and De Novo Assembly for Subsequent Functional Genomics Approaches. PLoS One 8(3):e59997.  https://doi.org/10.1371/journal.pone.0059997 CrossRefGoogle Scholar
  10. Hamarsheh O, Amro A (2011) Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs). Parasit Vectors 4:189–189.  https://doi.org/10.1186/1756-3305-4-189 CrossRefGoogle Scholar
  11. Hayden MJ, Sharp PJ (2001) Targeted development of informative microsatellite (SSR) markers. Nucleic Acids Res 29(8):e44–e44CrossRefGoogle Scholar
  12. Hendre PS, Aggarwal RK (2014) Development of Genic and Genomic SSR Markers of Robusta Coffee (Coffea canephora Pierre Ex A. Froehner). PLoS One 9(12):e113661.  https://doi.org/10.1371/journal.pone.0113661 CrossRefGoogle Scholar
  13. Holmen J, Vøllestad LA, Jakobsen KS, Primmer CR (2009) Cross-species amplification of 36 cyprinid microsatellite loci in Phoxinus phoxinus (L.) and Scardinius erythrophthalmus (L.). BMC Research Notes 2:248–248.  https://doi.org/10.1186/1756-0500-2-248 CrossRefGoogle Scholar
  14. Hu J, Wang L, Li J (2011) Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol Plant 55(3):577–580.  https://doi.org/10.1007/s10535-011-0129-0 CrossRefGoogle Scholar
  15. Joy N, Prasanth VP, Soniya EV (2011) Microsatellite based analysis of genetic diversity of popular black pepper genotypes in South India. Genetica 139(8):1033–1043.  https://doi.org/10.1007/s10709-011-9605-x CrossRefGoogle Scholar
  16. Kanno M, Li Q, Kijima A (2005) Isolation and characterization of twenty microsatellite loci in Japanese sea cucumber (Stichopus japonicus). Marine biotechnology (New York, NY) 7(3):179–183.  https://doi.org/10.1007/s10126-004-0006-3 CrossRefGoogle Scholar
  17. Kuleung C, Baenziger PS, Dweikat I (2004) Transferability of SSR markers among wheat, rye, and triticale. Theor Appl Genet 108(6):1147–1150.  https://doi.org/10.1007/s00122-003-1532-5 CrossRefGoogle Scholar
  18. Lalitha S (2004). Primer Premier 5. Biotech. Softw. Inter. Rep. 1, 270–272.  https://doi.org/10.1089/152791600459894
  19. Lebrun P, Baudouin L, Myrie W, Berger A, Dollet M (2008) Recent lethal yellowing outbreak: why is the Malayan Yellow Dwarf Coconut no longer resistant in Jamaica? Tree Genet Genomes 4(1):125–131.  https://doi.org/10.1007/s11295-007-0093-1 CrossRefGoogle Scholar
  20. Lebrun P, N'cho YP, Seguin M, Grivet L, Baudouin L (1998) Genetic diversity in coconut (Cocos nucifera L.) revealed by restriction fragment length polymorphism (RFLP) markers. Euphytica 101(1):103–108.  https://doi.org/10.1023/a:1018323721803 CrossRefGoogle Scholar
  21. Lin Y, Guoqian X, Zhang H, Lu Y, Sun X (2000) The ecological characteristics of coconut and the choice of production base. Journal of Hainan University (Natural Science Edition) (in Chinese) 18 (2)Google Scholar
  22. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics (Oxford, England) 21(9):2128–2129.  https://doi.org/10.1093/bioinformatics/bti282 CrossRefGoogle Scholar
  23. Lunt DH, Hutchinson WF, Carvalho GR (1999) An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Mol Ecol 8(5):891–894CrossRefGoogle Scholar
  24. Manimekalai R, Nagarajan P (2006) Assessing genetic relationships among coconut (Cocos nucifera L.) accessions using inter simple sequence repeat markers. Sci Hortic 108(1):49–54.  https://doi.org/10.1016/j.scienta.2006.01.006 CrossRefGoogle Scholar
  25. Paliwal R, Kumar R, Choudhury DR, Singh AK, Kumar S, Kumar A, Bhatt KC, Singh R, Mahato AK, Singh NK, Singh R (2016) Development of genomic simple sequence repeats (g-SSR) markers in Tinospora cordifolia and their application in diversity analyses. Plant Gene 5:118–125.  https://doi.org/10.1016/j.plgene.2016.02.001 CrossRefGoogle Scholar
  26. Perera L, Baudouin L, Mackay I (2016) SSR markers indicate a common origin of self-pollinating dwarf coconut in South-East Asia under domestication. Sci Hortic 211:255–262.  https://doi.org/10.1016/j.scienta.2016.08.028 CrossRefGoogle Scholar
  27. Perera L, Russell RJ, Provan J, McNicol WJ, Powell W (1998) Evaluating genetic relationships between indigenous coconut (Cocos nucifera L.) accessions from Sri Lanka by means of AFLP profiling. Theor Appl Genet 96(3):545–550.  https://doi.org/10.1007/s001220050772 CrossRefGoogle Scholar
  28. Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Report 15(1):8–15CrossRefGoogle Scholar
  29. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1(7):215–222.  https://doi.org/10.1016/1360-1385(96)86898-1 CrossRefGoogle Scholar
  30. Qiu D et al (2006) A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. TAG Theoretical and Applied Genetics Theoretische und Angewandte Genetik 114(1):67–80.  https://doi.org/10.1007/s00122-006-0411-2 CrossRefGoogle Scholar
  31. Rajesh MK, Jerard BA, Preethi P, Thomas RJ, Fayas TP, Rachana KE, Karun A (2013) Development of a RAPD-derived SCAR marker associated with tall-type palm trait in coconut. Sci Hortic 150:312–316.  https://doi.org/10.1016/j.scienta.2012.11.023 CrossRefGoogle Scholar
  32. Rassmann K, Schlotterer C, Tautz D (1991) Isolation of simple-sequence loci for use in polymerase chain reaction-based DNA fingerprinting. Electrophoresis 12(2–3):113–118.  https://doi.org/10.1002/elps.1150120205 CrossRefGoogle Scholar
  33. Saensuk C, Wanchana S, Choowongkomon K, Wongpornchai S, Kraithong T, Imsabai W, Chaichoompu E, Ruanjaichon V, Toojinda T, Vanavichit A, Arikit S (2016) De novo transcriptome assembly and identification of the gene conferring a “pandan-like” aroma in coconut (Cocos nucifera L.). Plant Sci 252:324–334.  https://doi.org/10.1016/j.plantsci.2016.08.014 CrossRefGoogle Scholar
  34. Santana Q, Coetzee M, Steenkamp E, Mlonyeni O, Hammond G, Wingfield M, Wingfield B (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. BioTechniques 46(3):217–223.  https://doi.org/10.2144/000113085 CrossRefGoogle Scholar
  35. Senan S, Kizhakayil D, Sasikumar B, Sheeja TE (2014) (2014) Methods for Development of Microsatellite Markers. An Overview 6(1):13.  https://doi.org/10.15835/nsb.6.1.9199 Google Scholar
  36. Singh R et al (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500(7462):335–339.  https://doi.org/10.1038/nature12309 CrossRefGoogle Scholar
  37. Sorkheh K, Prudencio AS, Ghebinejad A, Dehkordi MK, Erogul D, Rubio M, Martínez-Gómez P (2016) In silico search, characterization and validation of new EST-SSR markers in the genus Prunus. BMC Research Notes 9(1):336.  https://doi.org/10.1186/s13104-016-2143-y CrossRefGoogle Scholar
  38. Stępień Ł, Mohler V, Bocianowski J, Koczyk G (2007) Assessing genetic diversity of Polish wheat (Triticum aestivum) varieties using microsatellite markers. Genet Resour Crop Evol 54(7):1499–1506.  https://doi.org/10.1007/s10722-006-9140-2 CrossRefGoogle Scholar
  39. Tabkhkar N, Rabiei B, Sabouri A (2012) Genetic diversity of rice cultivars by microsatellite markers tightly linked to cooking and eating quality. Aust J Crop Sci 6(6):980–985Google Scholar
  40. Techen N, Arias RS, Glynn NC, Pan Z, Khan IA, Scheffler BE (2010) Optimized construction of microsatellite-enriched libraries. Mol Ecol Resour 10(3):508–515.  https://doi.org/10.1111/j.1755-0998.2009.02802.x CrossRefGoogle Scholar
  41. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106(3):411–422.  https://doi.org/10.1007/s00122-002-1031-0
  42. Ujino T, Kawahara T, Tsumura Y, Nagamitsu T, Yoshimaru H, Ratnam W (1998) Development and polymorphism of simple sequence repeat DNA markers for Shorea curtisii and other Dipterocarpaceae species. Heredity 81:422.  https://doi.org/10.1046/j.1365-2540.1998.00423.x CrossRefGoogle Scholar
  43. Upadhyay A, Jayadev K, Manimekalai R, Parthasarathy VA (2004) Genetic relationship and diversity in Indian coconut accessions based on RAPD markers. Sci Hortic 99(3–4):353–362.  https://doi.org/10.1016/S0304-4238(03)00103-1 CrossRefGoogle Scholar
  44. Viruel MA, Hormaza JI (2004) Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae). TAG Theoretical and Applied Genetics Theoretische und Angewandte Genetik 108(5):896–902.  https://doi.org/10.1007/s00122-003-1497-4 CrossRefGoogle Scholar
  45. Witsenboer H, Michelmore RW, Vogel J (1997) Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.). Genome 40(6):923–936CrossRefGoogle Scholar
  46. Xia W, Xiao Y, Liu Z, Luo Y, Mason AS, Fan H, Yang Y, Zhao S, Peng M (2014) Development of gene-based simple sequence repeat markers for association analysis in Cocos nucifera. Mol Breed 34(2):525–535CrossRefGoogle Scholar
  47. Xiao Y, Luo Y, Yang Y, Fan H, Xia W, Mason AS, Zhao S, Sager R, Qiao F (2013) Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera. Plant Omics 6(3):193Google Scholar
  48. Xiao Y, Xu P, Fan H, Baudouin L, Xia W, Bocs S, Xu J, Li Q, Guo A, Zhou L, Li J, Wu Y, Ma Z, Armero A, Issali AE, Liu N, Peng M, Yang Y (2017) The genome draft of coconut (Cocos nucifera). Gigascience 6(11):1–11.  https://doi.org/10.1093/gigascience/gix095 CrossRefGoogle Scholar
  49. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11(1):1–16.  https://doi.org/10.1046/j.0962-1083.2001.01418.x CrossRefGoogle Scholar
  50. Zhu H, Senalik D, McCown BH, Zeldin EL, Speers J, Hyman J, Bassil N, Hummer K, Simon PW, Zalapa JE (2012) Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). TAG Theoretical and Applied Genetics Theoretische und Angewandte Genetik 124(1):87–96.  https://doi.org/10.1007/s00122-011-1689-2 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research InstituteChinese Academy of Tropical Agricultural SciencesWenchangPeople’s Republic of China
  2. 2.Hainan UniversityHaikouPeople’s Republic of China

Personalised recommendations