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.
This is a preview of subscription content, access via your institution.
References
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):272–274
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
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
Ashburner G (1995) Genetic markers for coconut palms. In: Lethal yellowing: Research and practical aspects. Springer, pp 173–186
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
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
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):3802–3803
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
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
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
Hayden MJ, Sharp PJ (2001) Targeted development of informative microsatellite (SSR) markers. Nucleic Acids Res 29(8):e44–e44
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
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
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
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
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
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
Lalitha S (2004). Primer Premier 5. Biotech. Softw. Inter. Rep. 1, 270–272. https://doi.org/10.1089/152791600459894
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
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
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)
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
Lunt DH, Hutchinson WF, Carvalho GR (1999) An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Mol Ecol 8(5):891–894
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
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
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
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
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):8–15
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
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
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
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
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
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
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
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
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
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
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):980–985
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
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
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
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
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
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):923–936
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):525–535
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):193
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
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
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
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 information
Authors and Affiliations
Contributions
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.
Corresponding authors
Ethics declarations
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.
Additional information
Communicated by: Ray Ming
Rights and permissions
About this article
Cite this article
Wu, Y., Yang, Y., Qadri, R. et al. Development of SSR Markers for Coconut (Cocos nucifera L.) by Selectively Amplified Microsatellite (SAM) and Its Applications. Tropical Plant Biol. 12, 32–43 (2019). https://doi.org/10.1007/s12042-018-9215-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12042-018-9215-1
Keywords
- Coconut
- Selectively amplified microsatellite (SAM)
- SSR markers
- Transferability
- Palm trees