Genetic dissection of drought tolerance in potato

Drought is the most important cause of crop and yield loss around the world. Breeding for drought tolerance is not straightforward, as drought is a complex trait. A better understanding of the expression of drought traits, the genes underlying the traits and the way these genes interact will significantly increase the success of breeding for drought tolerance. Potato is an important food crop, yet it is relatively susceptible to drought. As a first step towards identifying the genetic basis for drought tolerance in potato, we make use of diploid potato populations that have been genetically well characterized (CxE, SHxRH). The CxE population was extensively evaluated for drought tolerance in vitro and for two successive years (2008, 2009) under greenhouse conditions and the data were used for QTL mapping. For optimal QTL mapping, we expanded the CxE and SHxRH genetic maps with 499 SNP markers (two arrays 384 and 768SNP arrays respectively, enriched for putative stress tolerance candidate genes). The SNPs were discovered in public EST databases using QualitySNP software and detected with the Illumina GoldenGate assay. About 300 SNPs served as bridge markers between the CxE and SHxRH maps. This will enable us to make use of the extensive genetic and sequence information of the SHxRH population and the RH genome sequence. With the availability of the potato genome sequence of the doubled monoploid DM1-3 516R44 (DM) (www.potatogenome.net), it was possible to further examine the SNP marker loci for paralogs and intron spanning sequences. In total 732 SNP marker loci were found to be unique in the potato genome sequence. Many of these SNP markers not only served as landmarks on the genetic map but may also as putative genes underlying quantitative traits. In addition the validated SNP markers are now utilized as anchors in the potato physical map. We investigated the possibility of screening potato for relevant drought traits in in vitro cultures and evaluated the CxE population for the response to PEG-induced water deficit stress and recovery potential after stress. Significant genetic variation was observed for the response to drought and for recovery potential. Several shoot and root growth traits were measured. In this study the genetic variation and heritability estimates were high to very high for the measured traits under control and recovery condition. In total 23 QTLs were detected in plants under control, stress and recovery treatments. Interesting putative candidate genes that may underly stress response QTLs were identified. The drought tolerance evaluation of the CxE population in pots in the greenhouse included traits like leaf Relative Water Content, δ13C as a measure of Water Use Efficiency, Chlorophyll Fluorescence, Chlorophyll Content, shoot and root biomass and tuber yield. The progeny displayed a wide contrast for drought tolerance, with individuals surviving and recovering completely after 3 weeks of drought, and others completely wilted beyond recovery. Most of the traits had high heritabilities. QTLs effective in multiple treatments and years were detected for tuber number, tuber weight, plant height, shoot fresh and dry weight. Other QTLs were found to be dependent on the environment: QTL x Environment interaction was found for leaf d13C under drought conditions and we speculate that the function of δ13C was genetically split into a stomatal and non-stomatal component. Many of the QTLs for growth traits measured both in the greenhouse and in in vitro cultures were specific to either of the growth conditions. Yet significant QTLs that were detected for plant height, shoot dry weight, fresh biomass for plants grown in the greenhouse were also found when the population was grown in vitro. These QTLs may be less affected by environmental influences, and we may therefore expect that some of these QTLs will be relevant under field conditions as well. This also suggests that the in vitro system may be used for preliminary selection in breeding programmes for specific performance-related traits. The genetic architecture of transcript-level variation for drought response was captured in the potato population CxE and mapped as expression QTLs (eQTLs). We anchored the differentially expressed genes to the genome sequence of potato, and this enabled us to determine whether the transcription of these genes (the eQTLs) is in cis or in trans regulated. The combined use of genome-wide detection of eQTLs in combination with genome sequence information for gene location has enables us to detect regulatory hot spots for drought response in the CxE population. Based on gene ontology annotation, a number of eQTLs were detected for genes known to be involved in drought signal transduction and drought-induced transcriptional regulation, and for redox genes. Examination of co-localization of eQTLs and phenotypic QTLs identified several interesting eQTLs for genes that may be involved in specifying the phenotypic QTL, for instance, the eQTL for a gene that was annotated with a putative function in the photosystem II light reaction colocalized with trait QTL of chlorophyll florescence (Fv/Fm) on chromosome 1, along with other genes involved in 139 drought response such as heat shock proteins and signaling proteins with known induced expression under stress conditions. On chromosome 10, eQTLs for genes involved in carbon partitioning, signaling receptor kinases, transcription factors and hormone and lipid metabolism were colocalized with phenotypic QTLs for chlorophyll content and stomatal component of δ13C. As we have only touched the surface of the information contained in the transcriptome dataset combined with the phenotyping data, continued efforts on mining the dataset and in depth analysis will most likely reveal more putative candidate genes for QTL effects. This thesis constitutes the first knowledge of in vitro and greenhouse screening for drought tolerance in potato and has led to the description of important traits for screening and selection in breeding for drought tolerance. The QTLs identified in this thesis may be interesting targets for potato breeding to improve drought tolerance of the potato crop. Furthermore, our results illustrate the power of application of integrated genetic and genomics approaches to unravel the molecular components underlying abiotic stress tolerance traits.