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

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 farmercultivated genotypes collected from SouthWestern 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 (F ST estimate = 0.3037) Electronic supplementary material The online version of this article (

Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria

“…The C. canephora varieties used were ‘Kouillou’, ‘Gold Coast’, ‘Java Robusta’, ‘Niaouli’, ‘Uganda’ and ‘Java Robusta Ex Gamba’. More information about the methods used for this analysis is available [7].…”

“…These genotypes and those within the ‘Kouillou’ and ‘Java Robusta’ groups were used for metabolomics analysis. These varieties (‘Niaouli’, ‘Kouillou’ and ‘Java Robusta’) represented three genetic structures detected by GBS-SNP analysis on C. canephora repository in Nigeria [7]. These genotypes were selected because they were used to establish the pioneer model polyclonal seed garden plot, which will be replicated in farmers’ fields.…”

“…The use of these varieties led to an increase in coffee yields from 800 kg to 1.4 ton per hectare [6]. We recently used Single Nucleotide Polymorphism-Genotype-By-Sequencing analyses to determine the relatedness of some of the conserved and cultivated C. canephora genotypes in Nigeria [7]. The data showed that the genetic diversity of the conserved CRIN germplasm was narrow and comprised of three genetic groups (‘Niaouli’, ‘Kouillou’ and ‘Java Robusta’)—of which, one of the groups (‘Niaouli’) dominated the cultivated accessions [7].…”

Short Communication: Genetic polymorphism of registered and popularly cultivated coffee (Coffea spp.) in the Philippines using inter-simple sequence repeats markers

“…liberica (also known as Liberica) and Coffea liberica var. dewevrei (also known as Excelsa) (Davis et al 2006). The Excelsa (codes 26-29) and Liberica (codes 19-25) coffee as labeled by the farmers were grouped in a separate cluster which may indicate that they are varieties of Coffea liberica.…”

“…Moreover, morphological characters of some coffee individuals have been observed to be overlapping even at the matured stage, when they are already bearing flowers and fruits. As an example, Anagbogu et al (2019) reported that previous morphological characterizations of Coffea canephora in Nigeria were inconclusive. An accession formerly classified as Coffea liberica based on morphology was revealed as a Coffea canephora by using molecular marker.…”