SNPs Based Molecular Diversity of Coffea canephora

Abstract

Coffee offers one of the most widely drunk beverages in the world, and is a very important source of foreign currency income for many countries. Coffea canephora Pierre presents a great genetic variability, with one of the widest natural geographical distribution within the subgenus. Newly developed single nucleotide Polymorphism (SNP) markers are effective in genetic diversity detection. The objective of this study was to analyze the genetic diversity and group C. canephora accessions, which were genotyped with SNPs molecular markers. In the present study, C. canephora germplasm consisting of 50 clones (24 Conilon and 26 Robusta) were used. Genetic diversity was investigated using 46074 polymorphic SNP markers covering the entire genome of C. canephora. The estimation of genetic similarity between each pair of individuals was calculated by the Jaccard coefficient using the program NTSYS pc2.1. A simplified representation of the similarity was obtained by constructing the dendrogram using UPGMA method (Unweighted Pair-Group Method using Arithmetic Mean). The optimal number of groups in the dendrogram was determined by the relative size of distances in the dendrogram. Thus, the first group was composed of clones 1, 5, 24, 6, 9, 14, 23, 22, 10, 17, 19, 18, 20, 2, 13, 11, 15, 7, 4 , 3 and 21; the second group 8, the third group 12, the fourth 16, the fifth group 26, 31, 33, 34, 37, 38, 28, 45, 46, 41 25, 29, 36, 43, 48, 49, 47, 50, 35, 39, 44, 40, 32, 30, and the sixth composed by 27 and 42. Generally, the analysis showed that the C. canephora clones were clearly divided into diversity groups that can be used for further breeding programs;