Large Scale SNP Genotyping in Various Plant Species

With the identification of many SNPs in crop plants, the genotyping with large numbers of SNP markers on arrays is now possible in many different species. TraitGenetics has been involved in the development of genotyping arrays for a number of crop and vegetable species including maize, tomato, barley, wheat, oilseed rape and other Brassica species. During that process, we have accumulated a wealth of know-how on the array generation and data analysis. This includes the selection of suitable SNP markers for genotyping that later have a high success rate in array-based genotyping. We also have accumulated considerable experience in the scoring of allotetraploid and allohexaploid species which is not easy due to the different patterns that are obtained with markers from such species. Finally, we have made the experience that the efficient data analysis from genotyping with large arrays requires a number of downstream information including the alignment of available genome sequences and/or large scale mapping data. Taking all information together we show on selected examples, how it is possible to generate very precise and reproducible results regarding whole genome SNP and haplotype data.