Genetic relationship and the occurrence of multiple gene resistance to coffee berry disease (Colletotrichum kahawae, Waller Bridge) within selected Coffea arabica varieties in Kenya

Abstract

The Coffee Berry Disease (CBD) epidemics destroy up to 100% of the crop on a susceptible variety. Resistance to CBD is conferred by the T-gene in Hibrido De Timor  (HDT), R-gene in Rume Sudan (RS), and k-gene in K7, which were assembled in resistance varieties Ruiru 11(R11) and Batian. This study aimed to evaluate the genetic relationship between R11 and Batian with their parents' HDT, RS,  SL8 and confirm the occurrence of T and R genes using DNA markers. Genome-wide single nucleotide polymorphism (SNP) markers were obtained through Diversity Arrays Technology sequencing (DArTseq). The genetic relationship was analyzed by Principal Component Analysis and hierarchical clustering. The Tgene was confirmed using Microsatellite primer, Sat 235 while the R gene was by marker sequence search within the DArTseq result files. The PC1 accounted for 42% of the total variation. Hierarchical clustering revealed less than 10% dissimilarity index apart from HDT that recorded above 20%. All the R11 and Batian genotypes carry the T gene. Eleven genotypes carry both T and R genes, therefore, with broad-based resistance to CBD. The study confirmed the narrow genetic relations within the Coffea arabica coffee varieties and further confirmed the occurrence of multiple gene resistance in R11 and Batian that will not break easily to new pathogen races.   Key words: Coffee berry disease, diversity arrays technology sequencing, T gene, R gene, Ruiru 11, Batian, SL 28, codominant.