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We assess if the mapping of genomic DNA reads on a transcriptome reference could impact SNP calling in our special case. Table S1. Summary of mapping and SNP calling using simulated data. (DOCX 15 kb)

The fast development of new sequencing technologies allows unlocking diversity of tropical crops. The French institutes CIRAD, IRD and INRA have worked together the last 7 years to improve the yam's genomics toolkit. Using RNASeq from leaves and flower tissues, we have assembled the transcriptomes of three yam cultivated species: Dioscorea rotundata, D. alata and D. trifida. Genotyping by sequencing approaches are currently used to develop a genetic map from four half-sibling families of D. alata. Such tools will allow refining genome assembly and identifying QTL related to anthracnose resistance. The study of genomics diversity of D. alata using sampling covering the four continents Asia, Pacific, Africa and America is currently underway. Using similar approaches, we obtained 600K SNPs in D. rotundata, D. abyssinica and D. praehensilis. We will present result of this study documenting both the relationship and diversity in these three African species and the detection of genes under selection, genes that may be of importance for yam improvement. We further investigated the important role of wild to cultivated gene flow between D. nummularia/D. alata and D. abyssinica/D. praehensilis/D. rotundata could play in yam improvement. (Texte intégral)