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.
Highlights
Coffee belongs to the family Rubiaceae and the genus Coffea with over 124 species that have been characterized (Davis et al, 2011)
The main objective of this study was to evaluate the genetic relationship within selected C. arabica cultivars R11, Batian and their resistance donor parent Hibrido De Timor (HDT), Rume Sudan (RS) and the recurrent parent SL28 using Diversity Arrays Technology sequencing (DArTseq) based single nucleotide polymorphism (SNP) markers and identify genotypes within R11 and Batian with multiple gene resistance to Coffee Berry Disease (CBD) conferred by the T and R genes
The DArTseq generated 2280 good quality SNP markers (MAF>5% and Ho
Summary
Coffee belongs to the family Rubiaceae and the genus Coffea with over 124 species that have been characterized (Davis et al, 2011). Despite the diversity of this genus, only two species, Coffea arabica L. and Coffea canephora. C. arabica is the only tetraploid species of the Coffea genus while the rest of the species are diploid (Spiniso-Castillo et al, 2020). The C. arabica is believed to have been formed as a result of spontaneous hybridization between two diploid species, C. canephora and Coffea eugenioides (Lashermes et al, 1999, 2011). C. canephora is diploid (2n = 2x = 22), highly diverse (Bertrand et al, 2003), with resistance to common disease and a good source of genes for disease resistance (Ky et al, 2001)
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