Development and validation of molecular marker for Hemileia vastatrix resistance in Coffea arabica

Coffee leaf rust (CLR) is caused by the fungus Hemileia vastatrix and is the primary disease affecting Coffea arabica. Infected plants exhibit productivity and lower coffee quality. Chemical control represents the most common method of immediate management of this disease. However, in addition to increasing production costs, this approach has a significant environmental and social impact. In this context, the most viable and sustainable alternative is the development of resistant cultivars through breeding. Utilizing molecular markers through marker-assisted selection (MAS) is an effective strategy for selecting resistant genotypes and developing such cultivars, thus reducing reliance on chemical control methods. The objective of this study was to develop and validate a marker associated with resistance quantitative trait loci (QTL) of C. arabica against races I, II, and 001 pathotype of H. vastatrix. To achieve this, a cleaved amplified polymorphic sequence marker (CAPS marker) named CaRHv10-CAPS, previously identified as associated with the resistance QTL of C. arabica against H. vastatrix, was converted into an allele-specific polymerase chain reaction (AS-PCR) named CaRHv10-AS. CaRHv10-AS does not necessitate the restriction endonuclease digestion step required for CAPS-type markers. The pair of CaRHv10 primers was designed using the software Primer 3. The forward primer was designed to match the DNA sequence of the genic region of Híbrido de Timor 443-03 (resistant to CLR) and to mismatch with the genic region of Catuaí UFV 2148-57 (susceptible to CLR). These regions correspond to the fragments amplified by the CaRHv10-CAPS marker. The efficiency of genotype selection was evaluated in 247 F2 genotypes from segregating genetic mapping population, with DNA samples from the parents of the F2 population, Híbrido de Timor UFV 443-03 and Catuaí UFV 2148-57, used as positive and negative controls, respectively. CaRHv10-AS functioned as a dominant marker, and the amplified genomic fragments were visualized in an agarose gel. These results demonstrated that the CaRHv10-AS marker can be easily, quickly, and inexpensively applied to MAS. Furthermore, since it is associated with a QTL for resistance against three races of H.vastatrix, it can enable gene pyramiding and thus, promote durable resistance to CLR.