Genetic Resources and Crop Evolution

, Volume 66, Issue 7, pp 1371–1377 | Cite as

Microsatellite markers in Spanish lime (Melicoccus bijugatus Jacq., Sapindaceae), a neglected Neotropical fruit crop

  • Jaime Martínez-CastilloEmail author
  • Renée S. Arias
  • Rubén H. Andueza-Noh
  • Matilde M. Ortiz-García
  • Brian M. Irish
  • Brian E. Scheffler
Short Communication


Spanish lime (Melicoccus bijugatus Jacq.) is a Neotropical fruit tree cultivated, mainly, in orchards for self-consumption or local sale. The genus Melicoccus includes other nine species with edible fruits, some of these species are at risk of extinction. Like for the vast majority of tropical fruit trees, there is no information on the genetic diversity of Spanish lime and its related species, and this is mostly due to the lack of molecular markers. The objectives of this study were to present the first microsatellite markers developed for Spanish lime, testing its usefulness on a sample of cultivated accessions, as well as its transferability to Huaya India (M. oliviformis). To do this, we performed high-throughput sequencing of microsatellite-enriched libraries of Spanish lime using Roche 454, assembled 9567 DNA contig sequences and identified 10,117 microsatellites. After screening 384 of those microsatellites on four DNA samples, 31 polymorphic markers were used to screen 25 accessions of Spanish lime and five of Huaya India collected in Yucatan, Mexico. Genetic diversity was low in Spanish lime (A = 20.61, HE = 0.38) and similar for both sexes of this species. Neighbor-Joining and PCoA analyses clearly discriminated between the two Melicoccus species studied. Nine of the markers showed unique alleles for Huaya India. The set of microsatellite markers developed has a great potential to generate information in relation to conservation genetics, improvement of elite cultivars and breeding programs for Spanish lime and related species.


Huaya India Melicoccus oliviformis Mexico Yucatan state SSR markers 



This work was supported by USDA-ARS Project 6044-21000-004-00D. The authors would like to thank Mary V. Duke, Linda L. Ballard, Sheron A. Simpson, and Xiaofen F. Liu, for DNA sequencing, sequence assembly and screening microsatellite markers.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10722_2019_815_MOESM1_ESM.docx (41 kb)
Supplementary material 1 (DOCX 40 kb)
10722_2019_815_MOESM2_ESM.docx (45 kb)
Supplementary material 2 (DOCX 45 kb)


  1. Acevedo-Rodríguez P (2003) Meliococceae (Sapindaceae): Melicoccus and Talisia. Flora Neotropical monograph. Botanical Garden Bronx, New YorkGoogle Scholar
  2. Altschul SF, Gish W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. CrossRefGoogle Scholar
  3. Arias RS, Martínez-Castillo J, Sobolev VS, Blancarte-Jasso NH, Simpson SA, Ballard LL, Duke MV, Liu XF, Irish BM, Scheffler BE (2015) Development of a large set of microsatellite markers in zapote mamey (Pouteria sapota (Jacq.) H.E. Moore & Stearn) and their potential use in the study of the species. Molecules 20:11400–11417. CrossRefGoogle Scholar
  4. Bystrom LM (2012) The potential health effects of Melicoccus bijugatus Jacq. fruits: Phytochemical, chemotaxonomic and ethnobotanical investigations. Fitoterapia 83(2):266–271. CrossRefGoogle Scholar
  5. Davies MR, Marshall RD (1972) Partial purification of l-asparaginyl-tRNA synthetase from rabbit liver. Biochem Biophys Res Commun 47:1386–1395. CrossRefGoogle Scholar
  6. Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biom Trust 53:325–338. CrossRefGoogle Scholar
  7. Jiménez-Rojas MI, Martínez-Castillo J, Potter D, Dzib GR, Ballina-Gómez HS, Latournerie-Moreno L, Andueza-Noh RH (2019) Morphological diversity of Huaya India fruits (Melicoccus oliviformis Kunth) in the Maya lowlands. Genet Res Crop Evol 66:513–522. CrossRefGoogle Scholar
  8. Madhou M, Normand F, Bahorun T, Hormaza JI (2013) Fingerprinting and analysis of genetic diversity of litchi (Litchi chinensis Sonn.) accessions from different germplasm collections using microsatellite markers. Tree Genet Genomes 9:387–396. CrossRefGoogle Scholar
  9. Martin FW, Campbell CW, Ruberté RM (1987) Perennial edible fruits of the tropics: an inventory. Agriculture handbook no. 642. Department of Agriculture, Washington, D.C.Google Scholar
  10. Morton JF (1987) Mamoncillo. In: Morton JF (ed) Fruits of warm climates. Florida, MiamiGoogle Scholar
  11. Nei M (1972) Genetic distance between populations. Am Nat 106:283–292. CrossRefGoogle Scholar
  12. Normah MN, Malik SK, Chaudhury R, Salma I, Makeen MA (2013) Conservation of tropical fruit genetic resources. In: Normah M, Chin H, Reed B (eds) Conservation of tropical plant species. Springer, New YorkCrossRefGoogle Scholar
  13. Paull RE, Duarte O (2012) Tropical fruits. CAB International, LondonCrossRefGoogle Scholar
  14. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539. CrossRefGoogle Scholar
  15. Rohlf FJ (2008) NTSYS-pc. Numerical taxonomy system version 2.2. Exeter Publishing, Ltd., SetauketGoogle Scholar
  16. Rozen S, Skaletsky H (2000) Bioinformatics methods and protocols in the series methods in molecular biology. Humana Press, TotowaGoogle Scholar
  17. Sharapova N, McMullen MD, Schultz L, Schoroeder S, Sánchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481. CrossRefGoogle Scholar
  18. Techen NR, Arias RS, Glynn NC, Pan Z, Khan I, Scheffler BE (2010) Optimized construction of microsatellite-enriched libraries. Mol Ecol Resour 10:508–515. CrossRefGoogle Scholar
  19. Vieira ML, Santini L, Diniz AL, Munhoz C (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39:312–328. CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Unidad de Recursos NaturalesCentro de Investigación Científica de Yucatán A.C.MéridaMexico
  2. 2.National Peanut Research LaboratoryUSDA-ARSDawsonUSA
  3. 3.CONACYT-Instituto Tecnológico de ConkalConkalMexico
  4. 4.Plant Germplasm Introduction and Testing Research UnitUSDA-ARSProsserUSA
  5. 5.Genomics and Bioinformatics Research UnitUSDA-ARSStonevilleUSA

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