Solanum tuberosum Transcriptome or Gene expression

Late blight caused by the oomycete Phytophthora infestans can completely destroy the potato crop. Since 150 years it is the most important potato disease worldwide. The selection of cultivars with high and durable resistance in the field is therefore objective of most potato breeding programs. This type of resistance is polygenic and therefore quantitative, its evaluation requiring multi-year and location trials. Furthermore, quantitative late blight resistance correlates with late plant maturity, a negative agricultural attribute. Knowledge of the genetic basis of quantitative resistance not compromised by late maturity is essential for developing diagnostic DNA markers that facilitate the efficient combination of superior resistance alleles. We used association genetics in a population of 184 tetraploid potato cultivars to identify single nucleotide polymorphisms (SNPs) associated with maturity corrected resistance (MCR) to late blight. The population was genotyped for nearly 9000 SNPs from three different sources. The first source was candidate genes specifically selected for function in the jasmonate signaling pathway. The second source was novel candidate genes selected based on comparative transcript profiling (RNAseq) between groups of genotypes with contrasting levels of quantitative resistance to P. infestans. The third source was the first 8.3k SolCAP SNP genotyping array available in potato for genome wide association mapping (GWAS). Fourty SNPs from all three sources showed robust association with resistance and some of those were located in genes that are strong candidates for directly controlling quantitative resistance, based on functional annotation. The candidate gene approach and GWAS were complementary. The results of this study provide new insight in the genetic basis of quantitative resistance in potato and a toolbox of SNP markers for breeding applications.

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