|Title||Genetic dissection of drought tolerance in potato|
|Source||University. Promotor(en): Richard Visser, co-promotor(en): Gerard van der Linden. - [S.l.] : S.n. - ISBN 9789085858379 - 152|
Laboratory of Plant Breeding
WUR Plant Breeding
|Publication type||Dissertation, internally prepared|
|Keyword(s)||solanum tuberosum - aardappelen - droogteresistentie - genetische analyse - diploïdie - single nucleotide polymorphism - genetische merkers - kwantitatieve kenmerken - loci voor kwantitatief kenmerk - genetische kartering - plantenveredeling - potatoes - drought resistance - genetic analysis - diploidy - genetic markers - quantitative traits - quantitative trait loci - genetic mapping - plant breeding|
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
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.