A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size

To breed a new variety of coffee (Coffea arabica) requires approximately 25 years due to the long generation time (5–6 years) of this perennial plant and the fact that it takes at least five generations of selection to obtain superior individuals. One way to reduce the number of generations is to use marker-assisted selection (MAS). To implement MAS, it is necessary to develop a genetic map and to identify markers associated with quantitative trait loci (QTLs) governing traits of interest. The objective of this study was to identify QTLs associated with yield, plant height, and bean size. An F2 mapping population consisting of 278 individuals was developed from a cross between Caturra × CCC1046. A total of 338 SSR were used to construct a framework linkage map. Subsequently, SNP markers were added to construct a more robust genetic map. R/qtl software was used to integrate SSR and SNP markers. The integrated linkage map consists of 22 linkage groups populated by 848 SSR and SNP markers, with a total map length of 3800 cM. F3 progenies of the mapping population were planted in five locations and evaluated for yield, plant height, and bean size. A major yield QTL was significant at two locations and a second was significant at one location. Two QTL were each detected for plant height and bean size.