Correction to: Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja.
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ABSTRACT:
SUBMITTER: Duarte-Delgado D
PROVIDER: S-EPMC5649525 | biostudies-literature | 2017 Oct
REPOSITORIES: biostudies-literature
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Correction to: Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja.
Duarte-Delgado D D Juyó D D Gebhardt C C Sarmiento F F Mosquera-Vásquez T T
BMC genetics 20171020 1
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Project description:BackgroundPotato frying color is an agronomic trait influenced by the sugar content of tubers. The candidate gene approach was employed to elucidate the molecular basis of this trait in Solanum tuberosum Group Phureja, which is mainly diploid and represents an important genetic resource for potato breeding. The objective of this research was to identify novel genetic variants related with frying quality in loci with key functions in carbohydrate metabolism, with the purpose of discovering genetic variability useful in breeding programs. Therefore, an association analysis was implemented with 109 SNP markers identified in ten candidate genes.ResultsThe analyses revealed four associations in the locus InvGE coding for an apoplastic invertase and one association in the locus SssI coding for a soluble starch synthase. The SNPs SssI-C 45711901 T and InvGE-C 2475454 T were associated with sucrose content and frying color, respectively, and were not found previously in tetraploid genotypes. The rare haplotype InvGE-A 2475187 C 2475295 A 2475344 was associated with higher fructose contents. Our study allowed a more detailed analysis of the sequence variation of exon 3 from InvGE, which was not possible in previous studies because of the high frequency of insertion-deletion polymorphisms in tetraploid potatoes.ConclusionThe association mapping strategy using a candidate gene approach in Group Phureja allowed the identification of novel SNP markers in InvGE and SssI associated with frying color and the tuber sugar content measured by High Performance Liquid Chromatography (HPLC). These novel associations might be useful in potato breeding programs for improving quality traits and to increase crop genetic variability. The results suggest that some genes involved in the natural variation of tuber sugar content and frying color are conserved in both Phureja and tetraploid germplasm. Nevertheless, the associated variants in both types of germplasm were present in different regions of these genes. This study contributes to the understanding of the genetic architecture of tuber sugar contents and frying color at harvest in Group Phureja.
| S-EPMC5345157 | biostudies-literature
Project description:BackgroundPotato frying quality is a complex trait influenced by sugar content in tubers. Good frying quality requires low content of reducing sugars to avoid the formation of dark pigments. Solanum tuberosum Group Phureja is a valuable genetic resource for breeding and for genetic studies. The sugar content after harvest was analyzed in a germplasm collection of Group Phureja to contribute to the understanding of the natural variation of this trait.ResultsSucrose, glucose and fructose genotypic mean values ranged from 6.39 to 29.48 g kg(-1) tuber dry weight (DW), from 0.46 to 28.04 g kg(-1) tuber DW and from 0.29 to 27.23 g kg(-1) tuber DW, respectively. Glucose/fructose and sucrose/reducing sugars ratios ranged from 1.01 to 6.67 mol mol(-1) and from 0.15 to 7.78 mol mol(-1) , respectively. Five clusters of genotypes were recognized, three of them with few genotypes and extreme phenotypic values.ConclusionSugar content showed a wide variation, representing the available variability useful for potato breeding. The results provide a quantitative approach to analyze the frying quality trait and are consistent with frying color. The analyzed germplasm presents extreme phenotypes, which will contribute to the understanding of the genetic basis of this trait. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
| S-EPMC5094549 | biostudies-literature
Project description:Key messageNovel major gene resistance against Potato virus Y in diploid populations of Solanum tuberosum Groups Phureja and Tuberosum was biologically and genetically characterised. Named Ry(o)phu, it mapped to chromosome 9. A new source of genetic resistance derived from Solanum tuberosum Group Phureja against Potato virus Y (PVY) was identified and genetically characterised in three diploid biparental potato populations. Segregation data for two populations (05H1 and 08H1) suggested the presence of a single dominant gene for resistance to PVY which, following DaRT analysis of the 08H1 cross, was mapped to chromosome 9. More detailed genetic analysis of resistance utilised a well-characterised SNP-linkage map for the 06H1 population, together with newly generated marker data. In these plants, which have both S. tuberosum Group Phureja and S. tuberosum Group Tuberosum in their pedigree, the resistance was shown to map to chromosome 9 at a locus not previously associated with PVY resistance, although there is evidence for at least one other genetic factor controlling PVY infection. The resistance factor location on chromosome 9 (named as Ry(o)phu) suggests a potential role of NB-LRR genes in this resistance. Phenotypic analysis using a GUS-tagged virus revealed that a small amount of PVY replication occurred in occasional groups of epidermal cells in inoculated leaves of resistant plants, without inducing any visible hypersensitive response. However, the virus did not enter the vascular system and systemic spread was completely prevented.
| S-EPMC7021755 | biostudies-literature
Project description:Potato (Solanum tuberosum L.) is the third largest source of antioxidants in the human diet, after maize and tomato. Potato landraces have particularly diverse contents of antioxidant compounds such as anthocyanins. We used this diversity to study the evolutionary and genetic basis of anthocyanin pigmentation. Specifically, we analyzed the transcriptomes and anthocyanin content of tubers from 37 landraces with different colorations. We conducted analyses of differential expression between potatoes with different colorations and used weighted correlation network analysis to identify genes whose expression is correlated to anthocyanin content across landraces. A very significant fraction of the genes identified in these two analyses had annotations related to the flavonoid-anthocyanin biosynthetic pathway, including 18 enzymes and 5 transcription factors. Importantly, the causal genes at the D, P and R loci governing anthocyanin accumulation in potato cultivars also showed correlations to anthocyanin production in the landraces studied here. Furthermore, we found that 60% of the genes identified in our study were located within anthocyanin QTLs. Finally, we identified new candidate enzymes and transcription factors that could have driven the diversification of anthocyanins. Our results indicate that many anthocyanins biosynthetic genes were manipulated in ancestral potato breeding and can be used in future breeding programs.
| S-EPMC9498938 | biostudies-literature
Project description:The majority of disease resistance (R) genes identified to date in plants encode a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain containing protein. Additional domains such as coiled-coil (CC) and TOLL/interleukin-1 receptor (TIR) domains can also be present. In the recently sequenced Solanum tuberosum group phureja genome we used HMM models and manual curation to annotate 435 NBS-encoding R gene homologs and 142 NBS-derived genes that lack the NBS domain. Highly similar homologs for most previously documented Solanaceae R genes were identified. A surprising ∼41% (179) of the 435 NBS-encoding genes are pseudogenes primarily caused by premature stop codons or frameshift mutations. Alignment of 81.80% of the 577 homologs to S. tuberosum group phureja pseudomolecules revealed non-random distribution of the R-genes; 362 of 470 genes were found in high density clusters on 11 chromosomes.
| S-EPMC3321028 | biostudies-literature
Project description:Advances in molecular breeding in potato have been limited by its complex biological system, which includes vegetative propagation, autotetraploidy, and extreme heterozygosity. The availability of the potato genome and accompanying gene complement with corresponding gene structure, location, and functional annotation are powerful resources for understanding this complex plant and advancing molecular breeding efforts. Here, we report a reference for the potato transcriptome using 32 tissues and growth conditions from the doubled monoploid Solanum tuberosum Group Phureja clone DM1-3 516R44 for which a genome sequence is available. Analysis of greater than 550 million RNA-Seq reads permitted the detection and quantification of expression levels of over 22,000 genes. Hierarchical clustering and principal component analyses captured the biological variability that accounts for gene expression differences among tissues suggesting tissue-specific gene expression, and genes with tissue or condition restricted expression. Using gene co-expression network analysis, we identified 18 gene modules that represent tissue-specific transcriptional networks of major potato organs and developmental stages. This information provides a powerful resource for potato research as well as studies on other members of the Solanaceae family.
| S-EPMC3203163 | biostudies-literature
Project description:Water deficits are the major constraint in some potato-growing areas of the world. The effect is most severe at the tuberization stage, resulting in lower yield. Therefore, an assessment of genetic and phenotypic variations resulting from water deficits in Colombia germplasm is required to accelerate breeding efforts. Phenotypic variations in response to a water deficit were studied in a collection of Solanum tuberosum Group Phureja. A progressive water deficit experiment on the tuberization stage was undertaken using 104 genotypes belonging to the Working Collection of the Potato Breeding Program at the Universidad Nacional de Colombia. The response to water deficit conditions was assessed with the relative chlorophyll content (CC), maximum quantum efficiency of PSII (Fv/Fm), relative water content (RWC), leaf sugar content, tuber number per plant (TN) and tuber fresh weight per plant (TW). Principal Component Analysis (PCA) and cluster analysis were used, and the Drought Tolerance Index (DTI) was calculated for the variables and genotypes. The soluble sugar contents increased significantly under the deficit conditions in the leaves, with a weak correlation with yield under both water treatments. The PCA results revealed that the physiological, biochemical and yield-component variables had broad variation, while the yield-component variables more powerfully distinguished between the tolerant and susceptible genotypes than the physiological and biochemical variables. The PCA and cluster analysis based on the DTI revealed different levels of water deficit tolerance for the 104 genotypes. These results provide a foundation for future research directed at understanding the molecular mechanisms underlying potato tolerance to water deficits.
| S-EPMC8065493 | biostudies-literature
Project description:The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein (StTL15A) and a stem 28 kDa glycoprotein (StGP28). Key message: A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight.
| S-EPMC5475386 | biostudies-literature
Project description:Auxin response factors (ARFs) play central roles in conferring auxin-mediated responses through selection of target genes in plants. Despite their physiological importance, systematic analysis of ARF genes in potato have not been investigated yet. Our genome-wide analysis identified 20 StARF (Solanum tuberosum ARF) genes from potato and found that they are unevenly distributed in all the potato chromosomes except chromosome X. Sequence alignment and conserved motif analysis suggested the presence of all typical domains in all but StARF18c that lacks B3 DNA-binding domain. Phylogenetic analysis indicated that potato ARF could be clustered into 3 distinct subgroups, a result supported by exon-intron structure, consensus motifs, and domain architecture. In silico expression analysis and quantitative real-time PCR experiments revealed that several StARFs were expressed in tissue-specific, biotic/abiotic stress-responsive or hormone-inducible manners, which reflected their potential roles in plant growth, development or under various stress adaptions. Strikingly, most StARFs were identified as highly abiotic stress responsive, indicating that auxin signaling might be implicated in mediating environmental stress-adaptation responses. Taken together, this analysis provides molecular insights into StARF gene family, which paves the way to functional analysis of StARF members and will facilitate potato breeding programs.
| S-EPMC6370904 | biostudies-literature
Project description:Solanum phureja Transcriptome or Gene expression
| PRJNA96087 | ENA