Genetic analysis of potato tuber quality traits

In this thesis the results of the four year project P5 within the Centre for BioSystems Genomics (www.cbsg.nl) are described. The intention of this project was to gain understanding of the genetic principles underlying a series of different potato tuber quality traits and the development of molecular markers linked to the traits of interest. Molecular markers that can be used in breeding programs with the aim of producing potato varieties with improved quality. To provide a window in which the research of this thesis can be placed, a review of the current status of quality genetics in potato is given in chapter 1. Here the different quality traits applicable for potato are described and different breeding methodologies discussed. Enzymatic discoloration (ED) of potato tubers was investigated in chapter 2. QTL analysis of the trait itself an it’s potential substrates was performed in combination with an allele specificity study (including expression analysis) on the candidate genes PPO. In chapter 3, potato starch related traits and the underlying starch biosynthesis and degradation are investigated by a QTL analysis in combination with a candidate gene approach. Furthermore, in chapter 4 we analyzed potato tuber metabolic content through liquid chromatography-time of flight mass spectrometry (LC-QTOF MS). This resulted in a large set of mass peaks. Clustering of the signals through a multivariate mass spectra reconstruction strategy revealed reconstructed metabolites (ea centrotypes). Quantitative Trait Locus (QTL) analysis of the centrotypes revealed over 800 metabolite QTLs (mQTLs), distributed over all 12 chromosomes. To investigate the contribution of the metabolome to phenotypic traits, the mQTL results were compared with the QTL results for tuber flesh colour (raw and after-cooking) and total tuber protein content. Finally in chapter 5, the general discussion, the results obtained in the preceding chapters are discussed and placed in the bigger perspective of finding tools for breeding for quality traits in potato. Prospects on the basis of these results and an outlook for breeding for quality are presented as well. </p

A limited set of starch related genes explain several interrelated traits in potato

To understand the molecular basis of potato starch related traits and the underlying starch biosynthesis and degradation, a Quantitative Trait Locus (QTL) analysis in combination with a candidate gene approach was performed. The diploid mapping population C × E, consisting of 249 individuals, was assayed over two consecutive years, for chipping colour, cold induced sweetening, starch content, starch granule size, starch gelling temperature, starch enthalpy, amylose content and degree of starch phosphorylation. QTLs were observed for all traits, except enthalpy on eight out of the twelve potato chromosomes. Several QTLs were found to be consistent over 2 years. Clustering of co-localizing QTLs was observed on some chromosomes, indicating common genetic factors for the different traits. On chromosome 2, Soluble Starch Synthase 2 mapped on the same position as QTLs for starch phosphorylation, starch gelling temperature and amylose content. a-glucan, water dikinase co-localizes on chromosome 5 together with QTLs for starch phosphorylation and cold induced sweetening. Furthermore, the genes coding for two phosphorylases (StPho1a and StPho2) coincide with QTLs for starch gelling temperature, chipping colour and starch granule size on chromosome 2 and a QTL for starch phosphorylation on chromosome 9, respectively. The results suggest allelic variation acting on the genetics of the different trait

Data integration and network reconstruction with ~omics data using Random Forest regression in potato

In the post-genomic era, high-throughput technologies have led to data collection in fields like transcriptomics, metabolomics and proteomics and, as a result, large amounts of data have become available. However, the integration of these ~omics data sets in relation to phenotypic traits is still problematic in order to advance crop breeding. We have obtained population-wide gene expression and metabolite (LC–MS) data from tubers of a diploid potato population and present a novel approach to study the various ~omics datasets to allow the construction of networks integrating gene expression, metabolites and phenotypic traits. We used Random Forest regression to select subsets of the metabolites and transcripts which show association with potato tuber flesh color and enzymatic discoloration. Network reconstruction has led to the integration of known and uncharacterized metabolites with genes associated with the carotenoid biosynthesis pathway. We show that this approach enables the construction of meaningful networks with regard to known and unknown components and metabolite pathways

The R3 resistance to Phytophthora infestans in potato is conferred by two closely linked R genes with distinct specificities

The R3 locus of potato (Solanum tuberosum L.) confers full resistance to avirulent isolates of Phytophthora infestans, the causal agent of late blight. R3 resides in the distal part of chromosome 11 and segregates in a potato mapping population, from which a well-saturated amplified fragment length polymorphism map is available. Using a population of 1,748 plants, we constructed a high-resolution genetic map at the R3 locus. Using the combination of fine mapping and accurate disease testing with specific P infestans isolates, we detected that the R3 locus is composed of two genes with distinct specificities. The two genes R3a and R3b are 0.4 cM apart and have both been introgressed from S. demissum, the 'donor' species of most characterized race-specific R genes to P infestans. A natural recombinant between R3a and R3b was discovered in one accession of S. demissum. The synteny between the R3 locus and the tomato 12 locus is discussed