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Additional file 1: Figure S1 Plots of average linkage disequilibrium values (r2) against physical distances in increments of 10 kb. Gray curves show local polynomial fits obtained using kernel smoothing regression. Dotted lines indicate the genetic distance at which r2 fell below 0.2. Figure S2 Summary of the results of genome-wide association studies using two different models. a Manhattan plots of −log10(p) values based on a MLM for 10 fruit traits. Red lines indicate a false discovery rate of 0.05. Chromosome location information is based on GDDH13 Version 1.1. The fictive chromosome 0 contains all unassigned scaffolds. b Posterior probability of having a QTL based on vBayesB, estimated for 10 fruit traits. Figure S3 Heatmap showing the percentage of the phenotypic variance explained by each QTL in each population. The percentages for the cultivar collection (designated as “Cultivar”) and for all 1218 accessions including the populations and cultivars (designated as “ALL”) are shown on the right. The prefix rrBLUP indicates the SNPs identified in the MLM-based GWAS analysis; BayesB indicates those identified in the vBayesB-based GWAS. A blank indicates that the population showed no segregation for the SNPs. The intensity of the red color corresponds to the percentage of phenotypic variance explained

Figure S1. Pedigree of susceptible apple accessions used in this study. (PDF 50 kb)

Figure S4. Amino acid sequence alignment of predicted candidate genes of Alt, A10, a4, and G16. (PDF 36 kb)

Table S2. Graphical illustration of genotypes showing recombination between Alt and flanking markers. (PDF 38 kb)

Table S1. Mapping of SSR markers used in marker enrichment analysis. (PDF 30 kb)

Figure S3. Amino acid sequence alignment of predicted candidate genes of Alt, A8, a2, and G14. (PDF 37 kb)

Figure S2. Pairwise alignment of A6, a predicted ORF in the Alt region and XP_009379454.1, the gene most similar to A6, as revealed by a database search. (PDF 49 kb)

Table S3. Presence of 12-bp insertion among founders and old cultivars. (PDF 50 kb)

Gametophytic self-incompatibility in Japanese pear (Pyrus pyrifolia Nakai) is controlled by the single, multi-allelic S-locus. Information about the S-genotypes is important for breeding and the selection of pollen donors for fruit production. Rapid and reliable S-genotype identification system is necessary for efficient breeding of new cultivars in Japanese pear. We designed S allele-specific PCR primer pairs for ten previously reported S-RNase alleles (S (1)-S (9) and S (k)) as simple and reliable method. Specific nucleotide sequences were chosen to design the primers to amplify fragments of only the corresponding S alleles. The developed primer pairs were evaluated by using homozygous S-genotypes (S (1)/S (1)-S (9)/S (9) and S (4sm)/S (4sm)) and 14 major Japanese pear cultivars, and found that S allele-specific primer pairs can identify S-genotypes effectively. The S allele-specific primer pairs developed in this study will be useful for efficient S-genotyping and for marker-assisted selection in Japanese pear breeding programs.

Although the potential of marker-assisted selection (MAS) in fruit tree breeding has been reported, bi-parental QTL mapping before MAS has hindered the introduction of MAS to fruit tree breeding programs. Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. Selection based on genomic predictions of breeding values (genomic selection: GS) is another alternative for MAS. This study examined the potential of GWAS and GS in pear breeding with 76 Japanese pear cultivars to detect significant associations of 162 markers with nine agronomic traits. We applied multilocus Bayesian models accounting for ordinal categorical phenotypes for GWAS and GS model training. Significant associations were detected at harvest time, black spot resistance and the number of spurs and two of the associations were closely linked to known loci. Genome-wide predictions for GS were accurate at the highest level (0.75) in harvest time, at medium levels (0.38–0.61) in resistance to black spot, firmness of flesh, fruit shape in longitudinal section, fruit size, acid content and number of spurs and at low levels (