Additional file 10 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

Additional file 10: Table S4. Marker haplotype analysis of the association mapping collection. For each linkage group (LG), the list of markers significantly detected by GWAS and markers in linkage disequilibrium (LD; r2 > 0.8) with the former ones is shown. The third line shows genetic positions from the consensus map of Tayeh et al. [36]. The fourth line indicates the LD blocks composed and named as mentioned in the legend of Additional file 9. The following lines show the allelic composition of haplotypes defined by LD blocks and individual associated markers at each of the 6 frost tolerance loci on linkage groups (LGs) I, II, III, V, VI and VII. For each frost damage (FD)-associated marker, the favorable allele is in red font and the unfavorable allele in blue font. Haplotypes are named in consecutive numerical order following their linkage group name; only haplotypes without missing values or heterozygous markers and carried by more than 3% of the lines from the association mapping collection are listed. For each haplotype, accessions and their mean phenotypic values ± standard error of the variables significantly associated with marker(s) in the linkage group are shown. Significant differences between haplotypes were assayed by a SNK means comparison test; favorable haplotypes are shown by a red background and unfavorable haplotypes by a blue background, regarding the SNK test. Haplotypes with a white background are classified in intermediate groups.