Abstract
The dwarf coconut is widely used in the coconut hybrids production (tall × dwarf) because it presents higher precocity and higher productivity of the number of fruits in relation to the other varieties. However, these hybrids originated from Intervarietal crossing, produce fruits with low market acceptance for water quality. Intravarietal crosses (dwarf × dwarf) could act as an alternative, but little is known about the diversity within and between the dwarf sub-varieties, which can lead to a misdirection to breeding programs. In this study, we report the level of genetic variability between dwarf coconut accessions belonging to three sub-varieties (green, yellow and red), as well as the analysis of population structure. We used the RAD-sequencing methodology for analyzing 39 genotypes belonging to dwarf coconut populations collected in different producing regions of Brazil. Our results show that the SNP markers increased the power of detection of genetic variability, facilitating the decision making regarding future crosses in order to explore the heterosis in dwarf coconut breeding programs. Inter-sub-varietal crosses of dwarf coconut are highly promising to reduce the time and optimize the process of obtaining new cultivars for water production requiring field assessments to confirm its agronomic potential.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Azevedo AON, Azevedo CDO, Santos PHAD et al (2018) Selection of legitimate dwarf coconut hybrid seedlings using DNA fingerprinting. Crop Breed Appl Biotechnol. https://doi.org/10.1590/1984-70332018v18n4a60
Bondar G (1955) A Cultura do Coqueiro no Brasil. Tipografia Naval, Salvador
Bourdeix R (1988) Genetic determinism in dwarf coconut germ colour. Oleagineux (France) 43:371–374
Cambuí E (2007) Diversidade genética entre cultivares de coqueiro anão (Cocos nucifera L., Var. Nana). Universidade Federal de Sergipe, São Cristóvão
Castro CP, Passos EEM, Aragão WM (2009) Fenologia de cultivares de coqueiro-anão nos tabuleiros costeiros de sergipe. Revista Brasileira de Fruticultura 31:13–19. https://doi.org/10.1590/S0100-29452009000100004
Catchen JM, Amores A, Hohenlohe P et al (2011) Stacks: building and genotyping Loci de novo from short-read sequences. G3. https://doi.org/10.1534/g3.111.000240
Craig DW, Pearson JV, Szelinger S et al (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887–893. https://doi.org/10.1038/nmeth.1251
Davey JW, Hohenlohe PA, Etter PD et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510
Desalegne BA, Dagne K, Melaku G et al (2017) Efficiency of SNP and SSR-based analysis of genetic diversity, population structure, and relationships among cowpea (Vigna unguiculata (L.) Walp.) germplasm from East Africa and IITA inbred lines. J Crop Sci Biotechnol 20:107–128. https://doi.org/10.1007/s12892-016-0051-0
Duran C, Appleby N, Clark T et al (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 37:D951–D953. https://doi.org/10.1093/nar/gkn650
Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8:2–9. https://doi.org/10.1111/j.1467-7652.2009.00459.x
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Futuyma DJ (2006) Ernst Mayr, genetics and speciation. Trends Ecol Evol 21:7–8. https://doi.org/10.1016/j.tree.2005.10.001
Geethanjali S, Anitha Rukmani J, Rajakumar D et al (2018) Genetic diversity, population structure and association analysis in coconut (Cocos nucifera L.) germplasm using SSR markers. Plant Genet Resour Charact Util 16:156–168. https://doi.org/10.1017/S1479262117000119
Gunn BF, Baudouin L, Olsen KM (2011) Independent origins of cultivated coconut (Cocos nucifera L.) in the old world tropics. PLoS ONE 6:e21143. https://doi.org/10.1371/journal.pone.0021143
HexaResearch (2019) Coconut water market size and forecast, by form (liquid, powder), by packaging (tetra pack, plastic bottle, others), by distribution channel (offline, online), by region, and trend analysis, 2015–2025. https://www.hexaresearch.com/research-report/coconut-water-market. Accessed 9 May 2019
Kwiatkowski A, Clemente E, Scarcelli A, Vida JB (2008) Quality of coconut water “in natura” belonging to Green Dwarf fruit variety in different stages of development, in plantation on the northwest area of Paraná, Brazil. J Food Agric Environ 6:102–105
Marina AM, Che Man YB, Nazimah SAH, Amin I (2009) Antioxidant capacity and phenolic acids of virgin coconut oil. Int J Food Sci Nutr. https://doi.org/10.1080/09637480802549127
Marshall D, Brown A (1975) Optimum sampling strategies in genetic resources conservation. In: Frankel O, Hawkes J (eds) Crop genetic resources for today and tomorrow. Cambridge University Press, Cambridge, pp 55–80
Mayr E (1940) Speciation phenomena in birds. Am Nat 74:249–278. https://doi.org/10.1086/280892
Meerow AW, Wisser RJ, Steven Brown J et al (2003) Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar. Theor Appl Genet. https://doi.org/10.1007/s00122-002-1121-z
Monteiro CM, Caron ES, da Silveira SF et al (2013) Control of foliar diseases by the axillary application of systemic fungicides in Brazilian coconut palms. Crop Prot 52:78–83. https://doi.org/10.1016/j.cropro.2013.05.013
Ninan CA, Satyabalan K (1964) A study of natural, self and cross (dwarf × tall) progenies of dwarf coconuts of the West Coast of India and its bearing on the genetics of dwarfs and the putative hybridity of their off-type progenies. Caryologia 17:77–91. https://doi.org/10.1080/00087114.1964.10796118
Noël KKJ (2011) Microsatellite gene diversity within Philippines dwarf coconut palm (Cocos nucifera L.) resources at Port-Bouët, Côte d’Ivoire. Sci Res Essays. https://doi.org/10.5897/sre11.877
Perera L, Russell JR, Provan J, Powell W (2000) Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.). Genome 43:15–21
Perera L, Russell JR, Provan J, Powell W (2003) Studying genetic relationships among coconut varieties/populations using microsatellite markers. Euphytica 132:121–128. https://doi.org/10.1023/A:1024696303261
Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol 53:793–808. https://doi.org/10.1080/10635150490522304
Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics. https://doi.org/10.1093/bioinformatics/14.9.817
Pritchard JK (2010) Documentation for structure software: version 2.3. In: Practice. https://doi.org/10.1002/spe.4380060305
Purcell S, Neale B, Todd-Brown K et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. https://doi.org/10.1086/519795
R Development Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. ISBN 3-900051-07-0
Rambaut A, Drummond AJ, Xie D et al (2018) Posterior summarization in Bayesian phylogenetics using tracer 1.7. Syst Biol. https://doi.org/10.1093/sysbio/syy032
Rannala B, Yang Z (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311. https://doi.org/10.1007/BF02338839
Ribeiro FE, Baudouin L, Lebrun P et al (2013) Genetic diversity in Brazilian tall coconut populations by microsatellite markers. Crop Breed Appl Biotechnol 13:356–362. https://doi.org/10.1590/S1984-70332013000400006
Rivera R, Edwards KJ, Barker JH et al (1999) Isolation and characterization of polymorphic microsatellites in Cocos nucifera L. Genome 42:668–675
Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574. https://doi.org/10.1093/bioinformatics/btg180
Rowe HC, Renaut S, Guggisberg A (2011) RAD in the realm of next-generation sequencing technologies. Mol Ecol. https://doi.org/10.1111/j.1365-294x.2011.05197.x
Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5:16–18. https://doi.org/10.1038/nmeth1156
Siqueira LA, Aragão WM, Tupinambá EA (2002) A introdução do coqueiro no Brasil, importância histórica e agronômica. Documentos. Embrapa Tabuleiros Costeiros, Aracaju
Swofford DL (2001) Phylogenetic analysis using parsimony. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland. https://doi.org/10.1007/bf02198856
Acknowledgements
The authors kindly thank the North Fluminense State University (UENF), Commercial Regon and FAPERJ for the financial support and infrastructure to carry out this work. This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brasil (CAPES).
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Santos, P.H.A.D., Venâncio, T.M., dos Santos, P.H.D. et al. Genotyping-by-sequencing technology reveals directions for coconut (Cocos nucifera L.) breeding strategies for water production. Euphytica 216, 45 (2020). https://doi.org/10.1007/s10681-020-02582-1
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10681-020-02582-1