Natural diversity of potato (Solanum tuberosum) invertases

<p>Abstract</p> <p>Background</p> <p>Invertases are ubiquitous enzymes that irreversibly cleave sucrose into fructose and glucose. Plant invertases play important roles in carbohydrate metabolism, plant development, and biotic and abiotic stress responses. In potato (<it>Solanum tuberosum</it>), invertases are involved in 'cold-induced sweetening' of tubers, an adaptive response to cold stress, which negatively affects the quality of potato chips and French fries. Linkage and association studies have identified quantitative trait loci (QTL) for tuber sugar content and chip quality that colocalize with three independent potato invertase loci, which together encode five invertase genes. The role of natural allelic variation of these genes in controlling the variation of tuber sugar content in different genotypes is unknown.</p> <p>Results</p> <p>For functional studies on natural variants of five potato invertase genes we cloned and sequenced 193 full-length cDNAs from six heterozygous individuals (three tetraploid and three diploid). Eleven, thirteen, ten, twelve and nine different cDNA alleles were obtained for the genes <it>Pain-1</it>, <it>InvGE</it>, <it>InvGF</it>, <it>InvCD141 </it>and <it>InvCD111</it>, respectively. Allelic cDNA sequences differed from each other by 4 to 9%, and most were genotype specific. Additional variation was identified by single nucleotide polymorphism (SNP) analysis in an association-mapping population of 219 tetraploid individuals. Haplotype modeling revealed two to three major haplotypes besides a larger number of minor frequency haplotypes. cDNA alleles associated with chip quality, tuber starch content and starch yield were identified.</p> <p>Conclusions</p> <p>Very high natural allelic variation was uncovered in a set of five potato invertase genes. This variability is a consequence of the cultivated potato's reproductive biology. Some of the structural variation found might underlie functional variation that influences important agronomic traits such as tuber sugar content. The associations found between specific invertase alleles and chip quality, tuber starch content and starch yield will facilitate the selection of superior potato genotypes in breeding programs.</p

Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity.

Resistance to pathogens is essential for survival of wild and cultivated plants. Pathogen susceptibility causes major losses of crop yield and quality. Durable field resistance combined with high yield and other superior agronomic characters are therefore important objectives in every crop breeding program. Precision and efficacy of resistance breeding can be enhanced by molecular diagnostic tools, which result from knowledge of the molecular basis of resistance and susceptibility. Breeding uses resistance conferred by single R genes and polygenic quantitative resistance. The latter is partial but considered more durable. Molecular mechanisms of plant pathogen interactions are elucidated mainly in experimental systems involving single R genes, whereas most genes important for quantitative resistance in crops like potato are unknown. Quantitative resistance of potato to Phytophthora infestans causing late blight is often compromised by late plant maturity, a negative agronomic character. Our objective was to identify candidate genes for quantitative resistance to late blight not compromised by late plant maturity. We used diagnostic DNA-markers to select plants with different field levels of maturity corrected resistance (MCR) to late blight and compared their leaf transcriptomes before and after infection with P. infestans using SuperSAGE (serial analysis of gene expression) technology and next generation sequencing. We identified 2034 transcripts up or down regulated upon infection, including a homolog of the kiwi fruit allergen kiwellin. 806 transcripts showed differential expression between groups of genotypes with contrasting MCR levels. The observed expression patterns suggest that MCR is in part controlled by differential transcript levels in uninfected plants. Functional annotation suggests that, besides biotic and abiotic stress responses, general cellular processes such as photosynthesis, protein biosynthesis and degradation play a role in MCR

Genes with functions in the jasmonate pathway that were tested for association with MCR, rAUDPC and PM.

<p>Genes with functions in the jasmonate pathway that were tested for association with MCR, rAUDPC and PM.</p

Number of genes containing from 1 to 60 SNPs with different allele frequency in the R8 and S8 genotype pools.

<p>Number of genes containing from 1 to 60 SNPs with different allele frequency in the R8 and S8 genotype pools.</p

Number of SolCAP SNPs and corresponding loci showing putative associations with MCR, rAUDPC and PM based on different ranking criteria.

<p>Number of SolCAP SNPs and corresponding loci showing putative associations with MCR, rAUDPC and PM based on different ranking criteria.</p

Genomic segments harboring QTL for MCR, rAUDPC and PM based on GWAS.

<p>Genomic segments harboring QTL for MCR, rAUDPC and PM based on GWAS.</p

Frequency distribution of the <i>tbr</i> (<i>S</i>. <i>tuberosum</i>) SNP alleles with different allele frequencies (q < 0.01) in the R8 and S8 genotype pools (significant SNPs) and without significant differences (q > 0.01, non-significant SNPs).

<p>Frequency distribution of the <i>tbr</i> (<i>S</i>. <i>tuberosum</i>) SNP alleles with different allele frequencies (q < 0.01) in the R8 and S8 genotype pools (significant SNPs) and without significant differences (q > 0.01, non-significant SNPs).</p