GENOME-WIDE VARIATION AND OCCURRENCE OF BROAD-BASED RESISTANCE TO COFFEE BERRY DISEASE (Colletotrichum kahawae, Waller&Brige) WITHIN Coffea arabica CULTIVAR, BATIAN

Abstract

Coffea arabica varieties are characterized by a narrow genetic base, leading to their susceptibility to disease including Coffee Berry Disease (CBD) and hindered development of molecular tools for improvement. CBD epidemics destroys up to 100% of the crop on a susceptible variety when no control measure is applied. Resistance to CBD is conferred by the dominant T and R genes in Hibrido De Timor (HDT) and Rume Sudan (RS) respectively. The cultivar Batian has three phenotypically uniform crosses that may carry T, R or both genes. 27 families from the three crosses were evaluated for genome-wide variation and occurrence of Tand R genes. Genomic DNA was extracted using standard protocols. Genome-wide single nucleotide polymorphism (SNP) markers were obtained through genotyping by sequencing (GBS), which were used in the analysis of variation and occurrence of the R gene. The variation was analyzed by Principal Component Analysis and hierarchical clustering. The occurrence of the T gene was confirmed through agarose gel electrophoresis using Microsatellite primer, Sat 235 while the R gene was by marker sequence search within the GBS result files. The first two PCs accounted for 37% of the total variation. Both the PCA and hierarchical clustering revealed that majority of the genotypes were closely related to SL 28, while two genotypes, CR30EX809 and CR8EX155 were closely related to RS and HDT. All the genotypes were confirmed to carry the T gene, where 17 were homozygous while 12 were heterozygous. Three genotypes were confirmed to carry both T and R genes, therefore with broad-based resistance to CBD and with relatively high diversity. The genotypes with broadbased resistance to CBD are recommended for multiplication, use in breeding of varieties with multiple gene resistance and improvement of diversity in Arabica varieties.