Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller Bridge) in Coffea arabica L. variety Rume Sudan

Coffee Berry Disease (CBD) is a major constraint that limits Coffea arabica production, whose resistance is governed by three genes, T, R that are dominant and recessive k in varieties Hibrido de Timor (HDT), Rume Sudan (RS) and K7 respectively. This study identified the genomic region occupied by R-gene using F2 genotypes from varieties RS and SL28; and Single Nucleotide Polymorphic (SNP) markers obtained through Genotyping by Sequencing. Redundant markers were removed and 699 markers obtained for linkage mapping and quantitative trait loci (QTL) analysis. The Linkage map spread over 5525.39 cM across eleven coffee chromosomes (Chr). The QTL was analyzed by both Interval Mapping (IM) and Inclusive Composite Interval Mapping (ICIM) using SNP markers and CBD resistance mean scores of the F2 genotypes and their parents. Three QTLs, qCBD 1-1 in Chr 1, qCBD 2-1 and qCBD 2-2 in Chr 2 were significantly associated with CBD resistance, detected by both IM and ICIM at LOD ≥ 2.5 (P≤0.05).  Two flanking markers that were closer to the three QTLs; 100025973|F|0-59:T\u003eC-59:T\u003eC at a distance of 3 centi Morgans (cM) from qCBD 1-1 and 100034991|F|0-44:C\u003eT-44:C\u003eT, that was flanking in both qCBD 2-1 and qCBD 2-2  at 12.5 cM, whose SNPs were significant (P≤0.05), are recommended for validation and use in marker-assisted breeding.\r\n\r\n\tKey words: Coffee berry disease, linkage map, quantitative trait loci, genotyping by sequencing, single nucleotide polymorphism, SL 28, R-gene.