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Omposite map are described (Additional file 8: Table S4). The percentages of SNPs that showed segregation distortion (P < 0.01) were estimated at 14.8 , 6.8 , 5.5 and 4.5 in populations derived from the crosses JI296xDP, ChampagnexTerese, ChinaxCameor and BaccaraxPI180693, respectively. A total of 2070 markerscould be reliably mapped including 1340 SNP from the present study (65 ) and 730 previously mapped markers (Additional file 12: Figure S7), giving a density of 1.65 markers per cM. This map presented only one gap larger than 10 cM between two contiguous markers, and only 12 gaps larger than 10 cM between contiguous newly developed SNPs (Table 2). Marker density was high and similar for all P. sativum Linkage Groups (PsLGs), ranging from 1.6 to 2.1 markers/cM (1.1 to 1.3 for the developed SNP) with the noticeable exception of PsLGII forDuarte et al. BMC Genomics 2014, 15:126 http://www.biomedcentral.com/1471-2164/15/Page 7 ofTable 2 Number of markers and newly developed SNP, map length, distribution of markers and SNPs per linkage group and on the whole genome mapLG1 Number of markers Number of developped SNPs Length (cM) Number of Markers/cM Number of gaps > 10 cM between two contiguous Markers Number of developed SNPs/cM Number of gaps > 10 cM between two contiguous developed SNPs 235 161 147 1.6 0 1.1 0 LG2 260 150 218 1.2 1 0.7 6 LG3 339 214 203 1.7 0 1.1 3 LG4 270 180 169 1.6 0 1.1 2 LG5 265 198 156 1.7 0 1.3 0 LG6 298 166 142 2.1 0 1.2 0 LG7 404 270 220 1.8 0 1.2 1 Whole 2071 1340 1255 1.7 1 1.1which the marker density was 1.2 (0.7 for developed SNPs). Positions of the 730 previously mapped markers on our consensus map were generally collinear with their published positions [32,33,38] [Mohamadi et al. A composite genetic map in pea including new eSSR loci., in preparation]: 14 to 25 markers mapped on each Linkage Group were common with both the Loridon et al. [38] and Bordat et al. [39] consensus maps (Additional file 13: Figure S10). Except for a few local inversions, collinearity of these markers was maintained along the three maps, with the notable exception of the PsLGII for which a block inversion was observed at the distal part LGII with the Loridon et al. [38] consensus map but not with the Bordat et al. [39] consensus map (Figure 3). Map sizes were similar between the present consensus map (1255 cM), the Loridon et al. map (1430 PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/3021955 cM) [38] and the Bordat et al. map (1389 cM) [39] but the number of mapped markers was increased 4-fold in comparison to those previous composite reference maps, respectively comprising 462 [38] and 536 [39] markers.Synteny between a 1252 SNP-based pea genetic map and the M. truncatula physical mapPsLGIII but showed many breaks and reversals blocks. The central part of PsLGVI corresponded to the entire Mtchr6, its upper part to the upper portion of the Mtchr2, and its lower part to the central part of Mtchr2. Finally the lower and middle portions of Mtchr2 corresponded to PsLGVI, and its upper part to the upper part of PsLGIII, with two collinear blocks framing two reversed blocks (Additional file 16: Figure S11).Discussion and conclusions Sequencing of eight cDNA normalized libraries Letrozole from genotypes representative of modern pea breeding material allowed the assembly of a large collection of cDNA contigs, and identification of over 35,000 reliable SNP markers. PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/9547713 A subset of SNPs were genotyped with the Golden Gate assay to generate a high density composite genetic map including 1340 newly develo.