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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

Genetic Resources and Crop Evolution volume 66, pages 685–696 (2019)Cite this article

Abstract

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.

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Acknowledgements

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.

Funding

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

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Authors and Affiliations

  1. Crop Improvement Division, Cocoa Research Institute of Nigeria, Ibadan, Nigeria

    Chinyere F. Anagbogu, Keji E. Dada & Anna A. Muyiwa

  2. Crop Protection and Environmental Biology Department, University of Ibadan, Ibadan, Nigeria

    Chinyere F. Anagbogu & Christopher Ilori

  3. Department of Plant Sciences, University of California, Davis, CA, USA

    Chinyere F. Anagbogu, Paul Gepts & Diane M. Beckles

  4. Bioscience Laboratory, International Institute of Tropical Agriculture, Ibadan, Nigeria

    Ranjana Bhattacharjee

  5. Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand

    Pumipat Tongyoo

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  1. Chinyere F. Anagbogu
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Anagbogu, C.F., Bhattacharjee, R., Ilori, C. et al. 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. Genet Resour Crop Evol 66, 685–696 (2019). https://doi.org/10.1007/s10722-019-00744-2

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Keywords

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