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Late blight of potato (Solanum tuberosum L.) caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most important bottlenecks of potato production worldwide. The disease could be better managed by using cultivars with high levels of quantitative or field resistance, which is mostly race non-specific and more durable than single R-gene mediated resistance. Breeding for quantitative resistance is however, a complex and challenging process and requires multiple year and location trials. In addition, it is hampered by a correlation between resistance and late maturity. This problem can be tackled by using diagnostic DNA markers, which enhance efficiency and precision of resistance breeding. The aim of this project was the identification of genes for quantitative resistance to P. infestans not compromised by late maturity and the discovery of diagnostic single nucleotide polymorphism (SNP) markers. To meet the objectives, the analysis of candidate genes and genome wide association (GWA) mapping of SNP markers were used. In the first approach, novel candidate genes that were differentially expressed in quantitative resistant versus susceptible potato genotype pools, were selected from transcriptome data generated using SuperSAGE (serial analysis of gene expression) analysis of nine samples comprising three genotype groups with different resistance levels and three infection time points. Twenty-two selected novel candidate genes were subjected to validation of differential expression by quantitative real time PCR (qRT-PCR) and allele specific pyrosequencing. Candidates showing reproducible transcriptional regulation in three independent infection experiments were tested for association with maturity corrected resistance (MCR) to late blight in a population of 184 tetraploid genotypes (CONQUEST2 population). Using mixed linear model (MLM) analysis including kinship and population structure, six novel candidate genes associated with late blight resistance not compromised by late maturity were identified. In the second approach, GWA mapping was conducted by scanning 8303 SNP markers distributed across the 12 potato chromosomes. The genotyping of the CONQUEST2 population was performed with the Illumina SolCAP SNP potato genotyping array and produced a total of 6286 informative bi-allelic SNPs. Approximately 5600 SNP markers could be used for association analysis. No or very weak relatedness and sub populations were detected in CONQUEST2 population. The proportion of pair wise r2 values > 0.1 (loci are in linkage disequilibrium: LD) and > 0.8 (loci are in strong LD) was only 1.57 % and 0.01%, respectively. The trendline of the nonlinear regression curve reached the threshold level for LD, r2 = 0.1, between 270 and 280 bps, showing a rapid LD decay in the potato genome. This fast LD decay implies that a large number of genome wide markers are required for detecting all quantitative trait loci (QTLs) in potato by GWA mapping. Nevertheless, genome wide marker-trait association analysis, with correction for kinship and population structure in a mixed linear model (MLM), identified few novel SNP markers associated with late blight resistance not compromised by late maturity. In conclusion, comparative transcript profiling combined with association mapping can be used for the detection of novel late blight QTLs and diagnostic SNP markers that can be used in marker-assisted resistance breeding. The SolCAP potato genotyping array is a useful but limited tool in identification of diagnostic SNP markers for agronomic traits in potato. |
