With the aim to develop a 20K genotyping chip for the international community, forty-five diverse Vitis vinifera ssp sativa, 4 V. vinifera ssp sylvestris, 3 V. cinerea , 3 V. berlandieri , 4 V. aestivalis , 3 V. labrusca , 5 M. rotundifolia, 1 V. lincecumii genotypes were paired end re-sequenced using either a GAII or a HiSeq Illumina platform. This allowed the detection of an average of 4,3 millions SNP per V. vinifera genotype and of 3,4 millions SNP per genotype from other Vitis species. SNPs were first filtered upon technical criteria: Illumina score >0.9 and class I type. The project was aimed at developing two subsets for the chip; Vitis vinifera specific and Vitis species in general. For the Vitis vinifera subset, SNPs in regions involved in structural variations and repetitions were filtered out and the remaining SNPs were then selected based on their even physical repartition along the genome together with their MAF (90% of the SNP with MAF > 0.1 and 10% with 0.05 < MAF < 0.1). For the Vitis species subset, SNPs in repeated areas were filtered out and the remaining SNPs were chosen based on those being heterozygous in two out of three of the genotypes from a same species and being evenly distributed along the genome. In the end, 14,817 Vitis vinifera SNPs and 4,978 Vitis species SNPs were selected along with 205 control SNPs and were added to design a 20K grapevine genotyping chip (http://urgi.versailles.inra.fr/Species/Vitis/GrapeReSeq_Illumina_20K). Illumina designed an 18,071 SNP chip, which is currently used for genotyping assays. The first results will be presented together with the main characteristics of the chip.

Póster presentado en el IX International Symposium on Grapevine Physiology and Biotechnology, celebrado en La Serena (Chile) del 21 al 26 de abril de 2013.-- Le Paslier, M-C. et al.

Acknowledgements: Grant Plant-KBBE-2008-GrapeReSeq.

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