Haplotype Analysis in Tomato - Data From Array Genotyping and Genome Resequencing

Genotyping of tomato varieties (inbreds and hybrids) has been performed with the 10K SOLCap Infinium array containing approximately 7700 scorable SNP markers. Analysis of the data has been performed after ordering the marker data along the tomato genome reference sequence. The results indicate that the extent of linkage disequilibrium varies greatly in different regions of the genome and haplotypes are extending over significantly longer distances in the centromeric regions. The introgression of novel haplotypes into the tomato genome can be observed for disease resistance genes and the reduction of linkage drag for these introgressions through specific recombination events monitored. For an even more detailed look at the tomato genome, we have resequenced 8 tomato inbreds and compared the resequencing data to the array data. The results show that beside specific introgressions from disease resistance genes, there are also large introgressions in some other regions of the tomato genome. The genetic variation in introgressed regions of the tomato genome can be ten to fifty times higher as in other parts of the tomato genome.