Additional file 1: Figure S1. of Mixed model approach for IBD-based QTL mapping in a complex oil palm pedigree

Pedigree of oil palm heterotic groups A (A) and B (B) individuals related to A×B progenies providing phenotypic data. Palm trees from group A originate from populations Deli (DELI) and Angola (AN), those of group B originate from populations La Mé (LAME), Yangambi (YBI), Nigeria (NI) and Sibiti (SI). Palm trees used as parents of A×B progenies are in white, and for group A pedigree, palm trees surrounded with red were reconstructed using MOLCOANC software. Figure S2. Oil palm consensus genetic map obtained from recombination information in group A and B pedigrees. Linkage groups are numbered according to Billotte et al. (2005, 2010). Map distance is given on the left in centimorgans (cM) and marker names on the right. Figure S3. Null distribution of log-likelihood ratio test in oil palm group A (green) and B (blue) for first (LRT_1,A) and second (LRT_2,B) genome scan for fresh fruit bunch weight (FFB), bunch number (BN) and average bunch weight (ABW) in heterotic group A (green lines) and B (blue lines). Figure S4. Log-likelihood ratio test (LRT) profile obtained in the first genome scan (see Material and Methods) using known (black lines) or reconstructed (green lines) pedigree of oil palm heterotic group A individuals. Figure S5. Example of QTL segregation in oil palm pedigree. Additive effects on bunch number for pedigree term (A,D) and QTLs on linkage group 9 at 69 cM (B,E) and on linkage group 15 at 117 cM (C,F) are projected on two subsets of heterotic group B pedigree, one centered on La Mé LM10T individual (A-C) and one grouping most of Yangambi individuals (D-F) . Red to green scale indicates lowest to highest value of BLUP of bunch number. (PPTX 289 kb)