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

Abstract

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 F 2 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 F 2 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>C-59:T>C at a distance of 3 centi Morgans (cM) from qCBD 1-1 and 100034991|F|0-44:C>T-44:C>T, 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.

Improving Pathogen Resistance by Exploiting Plant Susceptibility Genes in Coffee (Coffea spp.)

“…Molecular markers associated with Ck-1 are located on chromosome 1, which have been used in breeding programs to speed up the introgression efficiency ( Figure 1) [44][45][46][47]. Three quantitative trait loci (QTL), qCBD 1-1 on chromosome 1, qCBD 2-1, and qCBD 2-2 on chromosome 2 were identified as responsible for CBD resistance in the C. arabica cultivar Rume Sudan [48]. SNP (single nucleotide polymorphism) markers for these genomic loci are located on coffee Chromosomes 1 (SNP_100025973) and 2 (SNP_100034991) ( Figure 1) [41,42].…”

“…QTL for resistance are displayed as bars and the names given by the authors are maintained [44]. Molecular markers are depicted as associated disease and original names given by the authors [41,43,[45][46][47][48][49]. MCBD, MCLR, and MRKN denote molecular markers (M) associated with resistance to coffee berry disease, coffee leaf rust, and root-knot nematodes.…”

“…A cucumber Mlo gene, CsaMlo8, was found to co-localize with a known QTL for resistance to powdery mildew [76]. At present, there are relatively few QTL reports for disease resistance in coffee [44,48]. Among them, several QTLs were inherited in a dominant manner [48].…”

“…At present, there are relatively few QTL reports for disease resistance in coffee [44,48]. Among them, several QTLs were inherited in a dominant manner [48]. For many of the other QTLs, it is not clear from the studies whether the resistances inherited dominantly or recessively.…”

Marker-Assisted Pyramiding of Multiple Disease Resistance Genes in Coffee Genotypes (Coffea arabica)

“…Genetic mapping is an effective tool for the identification of such markers as well as for understanding inheritance and isolating disease resistance loci in plants [4,[19][20][21]. Such maps with different types of molecular markers have been developed for C. arabica, and genes and quantitative trait loci (QTLs) associated with resistance to CLR [22][23][24][25][26] and coffee berry disease (CBD) [27,28] have been mapped.…”