Additional file 13: of Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea

Description of linkage disequilibrium (LD) block haplotypes in the pea-Aphanomyces collection. (a) LD blocks are named as described in Additional file 11; (b) Each LD block is subdivided into marker haplotypes according to its allelic composition. Marker haplotypes are named with the LD block name followed by an Arabic numeral. Only haplotypes without missing values or heterozygous markers are shown; For each LD block: (c) list of markers significantly detected by genome-wide association in the LD block; (d) the first line is a list of the markers included in the LD block (detected markers in bold font and their markers in (LD) in plain font); (e) the second line is the genetic positions of the listed markers on the genetic map described in Additional file 11; (f) following lines are the pairwise LD r 2 values between each marker defined in the LD block and the marker detected by GWA; (g) For SNP markers, ‘AA’ and ‘BB’ are allele codes of Genome Studio analysis while for SSR markers, amplicon lengths are indicated. For each Aphanomyces resistance associated marker, enhancing allele(s) is in bold dark green font and unfavourable allele(s) in bold dark red font; (h) the first line is the list of the variables significantly associated with a marker in the LD block, variables are described as in Additional file 4; (i) next lines are p-values of the marker-trait associations; (j) grey or coloured lines are mean phenotypic values ± standard error for marker haplotypes carried by more than 5 % of the lines from the pea-Aphanomyces collection, letters indicate significantly different means (Tukey-HSD, α < 0.05); dark green and red haplotypes: favourable and unfavourable haplotypes of the LD block, respectively, as defined in the Materiel and Methods section of the manuscript. (XLSX 73 kb)