Genetic linkage maps of Citrus sunki Hort. ex Tan. and Poncirus trifoliata (L.) Raf. and mapping of citrus tristeza virus resistance gene

A linkage map for Citrus sunki Hort. ex. Tan. and Poncirus trifoliate (L.) Raf cv. Rubidoux has been developed exploiting the pseudo-testcross mapping strategy and RAPD markers. From controlled crosses 314 F1 zygotic progeny individuals were obtained. Two separate data sets were generated, one for each parent. Preliminary linkage analysis was carried out with a phase-unknown backcross model at a LOD > 4.0 and max. Theta = 0.30. A total of 203 arbitrary 10-mer primers and 5 arbitrary 8-mer primers were screened for segregating RAPD markers. Pseudo-testcrosss mating configurations were displayed by 78 primers where the marker was present in one parent, absent in the other and segregating in the progeny. These 78 primers were run on 80 individuals of the progeny amplifying a total of 169 RAPD markers. Linkage analysis revealed that 125 of these RAPD loci fell into 18 linkage groups (10 groups for ‘Sunki’ and 8 groups for ‘Rubidoux’) while 44 loci remained unassigned to any linkage group. The total length of the maps was 732.32 cM for ‘Sunki’ and 866.88 cM for ‘Rubidoux’ with the distance between markers ranging from 0 to 43.8 cM. Bulked segregant analysis (BSA) was used to identify potential resistance-associated RAPD fragment markers. Two RAPD fragments were found flanking the CTV gene (OPAV12_470 - 17.8 cM and OPN15_1630 - 23.1 cM).