European pear (Pyrus communis) ‘Aihuali’ carrying the dwarf character originating from ‘Nain Vert’ was crossed with ‘Chili’ (Pyrus bretschneideri). A total of 352 F1 progenies was produced to investigate the inheritance of the dwarf trait, and 111 of these were used to develop molecular markers. Chi-square analysis showed that the character fitted a 1:1 ratio indicative of a single dominant gene, which we have named PcDw. Using a bulked segregant analysis approach with 500 random amplified polymorphic DNA (RAPD) and 51 simple sequence repeat (SSR) markers from pear (Pyrus pyrifolia and P. communis) and apple (Malus ×domestica), four markers were identified as cosegregating with the dwarf character. Two of these were fragments produced by the S1212 and S1172 RAPD primers, and the other two were the pear SSR markers KA14 and TsuENH022. The RAPD markers were converted into sequence-characterized amplified regions (SCARs) and designated S1212-SCAR318 and S1172-SCAR930 and, with the SSR markers KA14 and TsuENH022, were positioned 5.9, 9.5, 8.2, and 0.9 cM from the PcDw gene, respectively. Mapping of the KA14 and TsuENH022 markers enabled the location of the PcDw gene on LG 16 of the pear genetic linkage map.
Caihong Wang, Yike Tian, Emily J. Buck, Susan E. Gardiner, Hongyi Dai, and Yanli Jia
Lidia Lozano, Ignasi Iglesias, Diego Micheletti, Michela Troggio, Satish Kumar, Richard K. Volz, Andrew C. Allan, David Chagné, and Susan E. Gardiner
Single-nucleotide polymorphisms (SNPs) have been used for a range of genetic studies and are now starting to be applied for marker-assisted selection in plant breeding programs. To identify SNP markers associated with red fruit skin color, we conducted a genome-wide association (GWA) analysis in an apple (Malus ×domestica Borkh.) breeding population comprising 94 phenotyped individuals using a 384-plex SNP assay. Linkage disequilibrium (LD) analysis indicated that LD extends over a long physical distance in the population (17 Mbp), indicating that a small number of generations separates the individuals. No significant association of anthocyanin content, overcolor, and colorimetric measures (a*, b*, L*, a/b*, and hue angle) with a marker was identified, although the apple fruit skin color locus has been previously located on apple linkage group 9. Our trial of a small SNP panel for GWA in apple breeding material has demonstrated the limitation of this approach for marker trait association.