Mapping QTLs for X-Disease Resistance in Chokecherry Using SSR and RJM Markers

Identifying disease-resistance in plants is a powerful way to overcome production limitations, yet it can be difficult to identify novel resistance traits in cultivars and breeding germplasm. Chokecherry (Prunus virginiana L.) is a native tree species to North America and has the potential to provide X-disease resistance to agriculturally important fruit crops, such as peach, plum, cherry, and almond. In this study, we used 232 simple sequence repeat (SSR) and 344 repeat junction markers (RJMs) to improve an established chokecherry linkage map. A partial chokecherry genome sequence was used for the development of 336 polymerase chain reaction (PCR) primer pairs that amplify across unique repeat junctions created by retrotransposons. A total of 50 RJMs were anchored to the chokecherry map spanning 7 of the 16 linkage groups. A total of 22 newly designed peach SSR primer pairs producing 8 quality markers were mapped to 5 linkage groups. Additional peach SSR markers collected from publications were also used for mapping in chokeberry. To date, 33 peach SSR markers have been anchored to 11 of the 16 linkage groups. Addition of these markers saturated the chromosome region where a previously identified QTL was located. A new QTL was identified from a different linkage group. More markers including 113 peach SSRs, 22 pear SSRs, and 8 pear RJMs will be used. We expect that more markers will be anchored to the chokecherry map, which have the potential to produce stronger QTL signals and/or new QTLs. This research will facilitate marker-assisted breeding and map-based cloning of candidate genes related to X-disease in chokecherry and other Prunus species.