Genetic diversity and re-classification of coffee (Coffea canephora Pierre ex A. Froehner) from South Western Nigeria through genotyping-by-sequencing-single nucleotide polymorphism analysis

  • Chinyere F. AnagboguEmail author
  • Ranjana Bhattacharjee
  • Christopher Ilori
  • Pumipat Tongyoo
  • Keji E. Dada
  • Anna A. Muyiwa
  • Paul Gepts
  • Diane M. Beckles
Research Article


Coffea canephora is an important economic crop in Nigeria, however, little is known about the diversity inherent within, and the genetic relationship among coffee grown and conserved in the country. We examined the genetic diversity and relatedness among 48 Coffea genotypes which included: (a) C. arabica, C. abeokutae, C. liberica, and C. stenophylla, (b) 14 C. canephora accessions conserved in the germplasm of Cocoa Research Institute of Nigeria (CRIN), and (c) 30 farmer-cultivated genotypes collected from South-Western Nigeria. By analyzing 433048 single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing we discovered that previous characterizations of C. canephora based on morphological data were inconclusive. Here, we established the correct number of C. canephora varieties present in the CRIN genebank which was four and not six as previously described based on morphological characters. We found three distinct diversity structures within the C. canephora genepool that were dominated by a single genetic group determined from passport descriptors to most likely be of Congolese (Democratic Republic of Congo) origin. High uniformity was also found among the farmer-cultivated accessions with 99% of them representing C. canephora var. Niaouli as their ancestral background. The analysis showed that the genetic base of coffee germplasm in Nigeria is narrow compared to the large genetic diversity of C. canephora. Therefore, broadening this genetic base through future acquisition and hybridization is imperative. However, the relatively high genetic differentiation (FST estimate = 0.3037) identified between Java Robusta and Niaouli will be used as a starting point for our breeding program.


Coffea canephora Genetic diversity Genotyping-by-sequencing Single nucleotide polymorphism 



Support for this research was provided in part by the Norman E. Borlaug Leadership Enhancement in Agriculture Program (Borlaug LEAP) through a grant to the University of California-Davis by the United States Agency for International Development. The opinions expressed herein are those of the authors and do not necessarily reflect the views of USAID. We are grateful to the International Institute of Tropical Agriculture and the University of California Davis, USA for providing free access to their facilities. Funding was also provided by the Federal Ministry of Agriculture in Nigeria through a grant to the Cocoa Research Institute of Nigeria. We are also grateful to Dr. May Thitisaksakul, Ms. Karin Albornoz, Dr. Shaoyun Dong, Ms. Tamara Miller, Dr. Sarah Dohle, and Dr. Jorge Dubcovsky at UC Davis, USA for their advice and technical support.


United States Agency for International Development (USAID) and Federal Ministry of Agriculture, Nigeria.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10722_2019_744_MOESM1_ESM.docx (1.9 mb)
Supplementary material 1 (DOCX 1920 kb)


  1. Achar D, Awati MG, Udayakumar M, Prasad TG (2015) Identification of putative molecular markers associated with root traits in Coffea canephora Pierre ex Froehner. Mol Biol Int 2015:11. CrossRefGoogle Scholar
  2. Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11:155–165. CrossRefGoogle Scholar
  3. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Cheetham RK, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IMJ, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DMD, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Catenazzi MCE, Chang S, Cooley RN, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang G-D, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O’Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Rodriguez AC, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218):53–59CrossRefGoogle Scholar
  4. Bertrand B, Guyot B, Anthony F, Lashermes P (2003) Impact of the Coffea canephora gene introgression on beverage quality of C. arabica. Theor Appl Genet 107(3):387–394. CrossRefGoogle Scholar
  5. Bolvenkel E, Buckley T, Eijgendaal C (1993) Report on a mission for the International Trade Centre. Dissemination activities for coffee—an exporters guideGoogle Scholar
  6. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19):2633–2635. CrossRefGoogle Scholar
  7. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G et al (2011) The variant call format and VCFtools. Bioinformatics 27(15):2156–2158. CrossRefGoogle Scholar
  8. Davis AP, Govaerts R, Bridson DM, Stoffelen P (2006) An annotated taxonomic conspectus of the genus Coffea (Rubiaceae). Bot J Linn Soc 152(4):465–512. CrossRefGoogle Scholar
  9. Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng CF, Alberti A et al (2014) The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345(6201):1181–1184. CrossRefGoogle Scholar
  10. Dent EA, Bridgett MH (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359–361. CrossRefGoogle Scholar
  11. Dicum G, Luttinger N (2006) The coffee book: anatomy of an industry from the crop to the last drop. The New Press, New York, NYGoogle Scholar
  12. Dussert S, Lashermes P, Anthony F, Montagnon C, Trouslot P, Combes M-C, Berthaud JMN, Hamon S (1999) Le caféier, Coffea canephora. Diversité génétique des plantes tropicales cultivées. CIRAD, MontpellierGoogle Scholar
  13. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379. CrossRefGoogle Scholar
  14. Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA (2011) SNP discovery and genotyping for evolutionary genetics using RAD sequencing. Mol Methods Evolut Genet 772:157–178. CrossRefGoogle Scholar
  15. Garavito A, Montagnon C, Guyot R, Bertrand B (2016) Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico. BMC Plant Biol 16:242. CrossRefGoogle Scholar
  16. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, Sun Q, Buckler ES (2014) TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS ONE 9(2):e90346. CrossRefGoogle Scholar
  17. Gomez C, Dussert S, Hamon P, Hamon S, de Kochko A, Poncet V (2009) Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. BMC Evol Biol 9:167. CrossRefGoogle Scholar
  18. Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P et al (2017) Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 109:351–361. CrossRefGoogle Scholar
  19. He JF, Zhao XQ, Laroche A, Lu ZX, Liu HK, Li ZQ (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484. CrossRefGoogle Scholar
  20. Hendre PS, Aggarwal RK (2007) DNA markers: development and application for genetic improvement of coffee. In: Varshney RK, Tuberosa R (eds) Genomic Assisted Crop Improvement: Genomics Applications in Crops. Springer, Berlin, pp 399–434CrossRefGoogle Scholar
  21. Hendre PS, Phanindranath R, Annapurna V, Lalremruata A, Aggarwal RK (2008) Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies. BMC Plant Biol 8:51. CrossRefGoogle Scholar
  22. Kwok PY (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genom Hum Genet 2:235–258CrossRefGoogle Scholar
  23. Lashermes P, Combes MC, Robert J, Trouslot P, D’Hont A, Anthony F, Charrier A (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 261(2):259–266CrossRefGoogle Scholar
  24. Leroy T, De Bellis F, Legnate H, Musoli P, Kalonji A, Solorzano RGL, Cubry P (2014) Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora. Genetica 142(3):185–199. CrossRefGoogle Scholar
  25. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25(14):1754–1760. CrossRefGoogle Scholar
  26. Mishra MK, Nishani S, Jayarama (2011) Genetic relationship among indigenous coffee species from India using RAPD, ISSR and SRAP markers. Biharean Biol 5:17–24Google Scholar
  27. Montagnon C, Leroy T, Eskes AB (1998) Coffea canephora I. Amélioration variétale de Critères et méthodes de selection. Plant Rech Dév 5:18–33Google Scholar
  28. Musoli P, Cubry P, Aluka P, Billot C, Dufour M, De Bellis F, Pot D, Bieysse D, Charrier A, Leroy T (2009) Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda. Genome 52(7):634–646. CrossRefGoogle Scholar
  29. Omolaja SS, Fawole I (2004) Characterization of Nigerian robusta coffee (Coffea Canephora Pierra ex. Froehner) germplasm. In: Proceedings of 20th International Conference on coffee science, Bangalore, India. 11-15 October, 2004.Google Scholar
  30. Omolaja SS, Williams JA, Obatolu CR (1997) Germplasm collection of Coffea abekutae and C. liberica. CRIN Annual ReportGoogle Scholar
  31. Omolaja SS, Obatolu CR, Williams JA (2000) Collection of Coffea abeokutae Cramer and Coffea liberica. Bull in South Western Nigeria. Plant Genet Resour 122:26–31Google Scholar
  32. Oxfam (2001) The coffee market: a background study. Oxfam, LondonGoogle Scholar
  33. Pearl HM, Nagai C, Moore PH, Steiger DL, Osgood RV, Ming R (2004) Construction of a genetic map for arabica coffee. Theor Appl Genet 108(5):829–835. CrossRefGoogle Scholar
  34. Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7(2):e32253. CrossRefGoogle Scholar
  35. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, Bakker PIW, Daly MJ, Sham PCS (2007) PLINK: a tool set for whole-genome association and population-based linkage analysis. Am J Hum Genet 81:559–575CrossRefGoogle Scholar
  36. Rabbi IY, Kulakow PA, Manu-Aduening JA, Dankyi AA, Asibuo JY, Parkes EY, Abdoulaye T, Girma G et al (2015) Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz). BMC Genet 16:115. CrossRefGoogle Scholar
  37. Razafinarivo NJ, Guyot R, Davis AP, Couturon E, Hamon S, Crouzillat D, Rigoreau M, Dubreuil-Tranchant C et al (2013) Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites. Ann Bot London 111(2):229–248. CrossRefGoogle Scholar
  38. Santa Ram A, Sreenath HL (2000) Genetic fingerprinting of coffee leaf rust differentials with RAPD markers. In: Sera T, Soccol CR, Pandey A, Roussos S (eds) Proceedings of the 3rd international seminar on biotechnology in the coffee agro-industry. Springer Science, Dordrecht. Google Scholar
  39. Silvestrini M, Maluf MP, Silvarolla MB, Guerreiro O, Medina HP, Vanini MMT, Oliveira AS, de Gaspari-Pezzopane C, Fazuoli LC (2008) Genetic diversity of a Coffea Germplasm Collection assessed by RAPD markers. Genet Resour Crop Evol 55(6):901–910. CrossRefGoogle Scholar
  40. Souza FD, Caixeta ET, Ferrao LFV, Pena GF, Sakiyama NS, Zambolim EM, Zambolim L, Cruz CD (2013) Molecular diversity in Coffea canephora germplasm conserved and cultivated in Brazil. Crop Breed Appl Biotechnol 13(4):221–227CrossRefGoogle Scholar
  41. Steiger DL, Nagai C, Moore PH, Morden CW, Osgood RV, Ming R (2002) AFLP analysis of genetic diversity within and among Coffea arabica cultivars. Theor Appl Genet 105(2–3):209–215. CrossRefGoogle Scholar
  42. Williams JA (1989) Coffee breeding in Nigeria. In: Progress in tree crop research, 2nd edn. Cocoa Research Institute of Nigeria (CRIN) Ibadan, pp 127–140Google Scholar
  43. Zamir D (2014) A wake-up call with coffee. Science 345(6201):1124–1124. CrossRefGoogle Scholar
  44. Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012) A high-performance computing toolset for relatedness and principal component analysis on SNP data. Bioinformatics 28:3326–3328CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Crop Improvement DivisionCocoa Research Institute of NigeriaIbadanNigeria
  2. 2.Crop Protection and Environmental Biology DepartmentUniversity of IbadanIbadanNigeria
  3. 3.Department of Plant SciencesUniversity of CaliforniaDavisUSA
  4. 4.Bioscience LaboratoryInternational Institute of Tropical AgricultureIbadanNigeria
  5. 5.Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE)BangkokThailand

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