Solanum Tuberosum Group Phureja Research Articles

Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii

Key messageA new resistance locus acting against the potato cyst nematode Globodera pallida was mapped to chromosome VI in the diploid wild potato species Solanum spegazzinii CPC 7195.The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato.

Genome Report: Genome sequence of 1S1, a transformable and highly regenerable diploid potato for use as a model for gene editing and genetic engineering.

Availability of readily transformable germplasm, as well as efficient pipelines for gene discovery are notable bottlenecks in the application of genome editing in potato. To study and introduce traits such as resistance against biotic and abiotic factors, tuber quality traits and self-fertility, model germplasm that is amenable to gene editing and regeneration is needed. Cultivated potato is a heterozygous autotetraploid and its genetic redundancy and complexity makes studying gene function challenging. Genome editing is simpler at the diploid level, with fewer allelic variants to consider. A readily transformable diploid potato would be further complemented by genomic resources that could aid in high throughput functional analysis. The heterozygous Solanum tuberosum Group Phureja clone 1S1 has a high regeneration rate, self-fertility, desirable tuber traits and is amenable to Agrobacterium-mediated transformation. We leveraged its amenability to Agrobacterium-mediated transformation to create a Cas9 constitutively expressing line for use in viral vector-based gene editing. To create a contiguous genome assembly, a homozygous doubled monoploid of 1S1 (DM1S1) was sequenced using 44 Gbp of long reads generated from Oxford Nanopore Technologies (ONT), yielding a 736 Mb assembly that encoded 31,145 protein-coding genes. The final assembly for DM1S1 represents a nearly complete genic space, shown by the presence of 99.6% of the genes in the Benchmarking Universal Single Copy Orthologs (BUSCO) set. Variant analysis with Illumina reads from 1S1 was used to deduce its alternate haplotype. These genetic and genomic resources provide a toolkit for applications of genome editing in both basic and applied research of potato.

BLUP (Best Linear Unbiased Predictors) analysis for the selection of superior genotypes in the yellow diploid potato (Solanum tuberosum group Phureja)

Uno de los principales desafíos que enfrentan los mejoradores es la respuesta diferencial de los genotipos de un entorno a otro, conocida como la interacción genotipo × ambiente (GxE). El procedimiento óptimo restringido de máxima verosimilitud/mejor predictor imparcial lineal (REML / BLUP) permite la estimación simultánea de parámetros genéticos y la predicción de valores genotípicos. Los predictores BLUP se presentan como una alternativa al estrechamiento de los valores sesgados. Se basa en las variaciones por genotipo para determinar su valor de respuesta como complemento al índice de selección (SI). El índice de selección (IS) ESIM (Eigenvalue Selection Index) permite seleccionar genotipos basados en dos o más variables o caracteres de selección siempre y cuando la matriz económica posea los valores adecuados para resaltar la variable respuesta deseada. Se evaluaron tres etapas de selección en un programa avanzado de mejoramiento de papa diploide, se obtuvieron los valores BLUP para las variables rendimiento y gravedad específica (GE), y a partir de ellos los parámetros genéticos y el IS. La ganancia genética para rendimiento correspondió a 1.228 kg/planta con una heredabilidad (H2)=0,82, mientras que la GA para GE fue 0,02 con una H2 = 0,935. El IS a partir de los valores BLUP seleccionó en las etapas finales tres nuevos cultivares (Criolla Dorada, Criolla Ocarina y Criolla Sua Pa) que fueron registradas ante el Instituto Colombiano Agropecuario (ICA). Aunque BLUE y BLUP están altamente correlacionadas, el análisis BLUP/ESIM da ventaja al predictor pues reduce las respuestas con efecto ambiental, seleccionando eficientemente genotipos con alto potencial varietal.

Genome-Wide Identification, Expression Profile and Evolution Analysis of Karyopherin β Gene Family in Solanum tuberosum Group Phureja DM1-3 Reveals Its Roles in Abiotic Stresses

In eukaryotic cells, nucleocytoplasmic trafficking of macromolecules is largely mediated by Karyopherin β/Importin (KPNβ or Impβ) nuclear transport factors, and they import and export cargo proteins or RNAs via the nuclear pores across the nuclear envelope, consequently effecting the cellular signal cascades in response to pathogen attack and environmental cues. Although achievements on understanding the roles of several KPNβs have been obtained from model plant Arabidopsis thaliana, comprehensive analysis of potato KPNβ gene family is yet to be elucidated. In our genome-wide identifications, a total of 13 StKPNβ (Solanum tuberosum KPNβ) genes were found in the genome of the doubled monoploid S. tuberosum Group Phureja DM1-3. Sequence alignment and conserved domain analysis suggested the presence of importin-β N-terminal domain (IBN_N, PF08310) or Exporin1-like domain (XpoI, PF08389) at N-terminus and HEAT motif at the C-terminal portion in most StKPNβs. Phylogenetic analysis indicated that members of StKPNβ could be classified into 16 subgroups in accordance with their homology to human KPNβs, which was also supported by exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis and quantitative real-time PCR experiments revealed that, except StKPNβ3d and StKPNβ4, almost all StKPNβs were ubiquitously expressed in all tissues analyzed, whereas transcriptional levels of several StKPNβs were increased upon biotic/abiotic stress or phytohormone treatments, reflecting their potential roles in plant growth, development or stress responses. Furthermore, we demonstrated that silencing of StKPNβ3a, a SA- and H2O2-inducible KPNβ genes led to increased susceptibility to environmental challenges, implying its crucial roles in plant adaption to abiotic stresses. Overall, our results provide molecular insights into StKPNβ gene family, which will serve as a strong foundation for further functional characterization and will facilitate potato breeding programs.

Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja

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.

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans

BackgroundThe increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN). We present a simple yet effective method to estimate transcription factors’ GRNs from transcriptional data.MethodWe defined interactions between pairs of genes (edges in the GRN) as the partial mutual information between these genes that takes into account time and possible lags in time from one gene in relation to another. We call this method Gene Regulatory Networks on Transfer Entropy (GRNTE) and it corresponds to Granger causality for Gaussian variables in an autoregressive model. To evaluate the reconstruction accuracy of our method, we generated several sub-networks from the GRN of the eukaryotic yeast model, Saccharomyces cerevisae. Then, we applied this method using experimental data of the plant pathogen Phytophthora infestans. We evaluated the transcriptional expression levels of 48 transcription factors of P. infestans during its interaction with one moderately resistant and one susceptible cultivar of yellow potato (Solanum tuberosum group Phureja), using RT-qPCR. With these data, we reconstructed the regulatory network of P. infestans during its interaction with these hosts.ResultsWe first evaluated the performance of our method, based on the transfer entropy (GRNTE), on eukaryotic datasets from the GRNs of the yeast S. cerevisae. Results suggest that GRNTE is comparable with the state-of-the-art methods when the parameters for edge detection are properly tuned. In the case of P. infestans, most of the genes considered in this study, showed a significant change in expression from the onset of the interaction (0 h post inoculum - hpi) to the later time-points post inoculation. Hierarchical clustering of the expression data discriminated two distinct periods during the infection: from 12 to 36 hpi and from 48 to 72 hpi for both the moderately resistant and susceptible cultivars. These distinct periods could be associated with two phases of the life cycle of the pathogen when infecting the host plant: the biotrophic and necrotrophic phases.ConclusionsHere we presented an algorithmic solution to the problem of network reconstruction in time series data. This analytical perspective makes use of the dynamic nature of time series data as it relates to intrinsically dynamic processes such as transcription regulation, were multiple elements of the cell (e.g., transcription factors) act simultaneously and change over time. We applied the algorithm to study the regulatory network of P. infestans during its interaction with two hosts which differ in their level of resistance to the pathogen. Although the gene expression analysis did not show differences between the two hosts, the results of the GRN analyses evidenced rewiring of the genes’ interactions according to the resistance level of the host. This suggests that different regulatory processes are activated in response to different environmental cues. Applications of our methodology showed that it could reliably predict where to place edges in the transcriptional networks and sub-networks. The experimental approach used here can help provide insights on the biological role of these interactions on complex processes such as pathogenicity. The code used is available at https://github.com/jccastrog/GRNTE under GNU general public license 3.0.

Influence of storage conditions on the quality of two varieties of native potato (Solanum Tuberosum group phureja)•

Las variedades nativas presentan la oportunidad para recuperar la biodiversidad y contribuir a la seguridad alimentaria en algunas regiones de bajo desarrollo, sin embargo no han sido estudiadas lo suficiente. Se someten a diferentes temperaturas de almacenamiento las variedades de papa nativa Curiquinga y Ratona Morada cultivadas en el departamento de Nariño para observar el comportamiento de característicascomo humedad, pérdida de peso, contenido de glucosa y ácido ascórbico. La variedad Ratona Morada conserva mejor sus características en refrigeración, deteriorándose más rápido en incubación, la Curiquinga en cambio presenta mayor deterioro en refrigeración que en temperatura ambiente e incubación. Se recomienda profundizar los estudios de almacenamiento pos cosecha en variedades nativas para enlazar la producción con el procesamiento que permita generar cadenas agroindustriales de valor agregado, conservar estos recursos genéticos y brindar alternativas a pequeños productores.

Genome-wide Identification, Expression Profiling and Evolutionary Analysis of Auxin Response Factor Gene Family in Potato (Solanum tuberosum Group Phureja)

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.

Macronutrient contents of potato genotype collections in the Solanum tuberosum Group Phureja

Macronutrient contents of 94 genotypes from the Colombian Central Collection (CCC) and 13 genotypes from the Native Collection (NC) of diploid potatoes (Solanum tuberosum Group Phureja) were evaluated, considering six genotypes, four diploid and two tetraploid potato commercial cultivars, as control. Dry matter, protein, soluble dietary fibre (SDF) and insoluble dietary fibre (IDF), fat, and ash contents were determined in entire boiled tubers. Macronutrient contents varied widely among the 113 genotypes. Protein contents found in CCC and NC (1.8–17.2 g/100 g dry weight, DW) were greater than those in commercial cultivars (3.1–9.5 g/100 g DW). Total dietary fibre (TDF), SDF, and IDF were greater in CCC and NC (9.4–27.1 g/100 g DW, 1.6–6.6 g/100 g DW, and 6.4–20.9 g/100 g DW, respectively) than in the commercial cultivars (9.0–15.3 g/100 g DW, 2.7–4.4 g/100 g DW, and 6.4–12.3 g/100 g DW, respectively). Several genotypes from CCC and NC are good candidates as parental materials for developing new cultivars, with the highest protein content in CCC-76 (17.2 ± 0.3 g/100 g DW) and NC-8 (16.7 ± 0.7 g/100 g DW) and the highest TDF in CCC-110 (27.1 ± 4.0 g/100 g DW).

Breeding Differently: Participatory Selection and Scaling Up Innovations in Colombia

Global challenges like sustainable development, climate change, malnutrition and gender inequality can be tackled from an agricultural perspective. Micronutrient deficiency is a major problem for the health and food security of the population. In Colombia, iron deficiencies affect 32% of the children under the age of five; and 43% of the Colombian population have zinc and vitamin A deficiencies. We designed and implemented a research-for-development programme that links agriculture and nutrition through a two-stage project. In the first stage, we selected three new yellow potato cultivars with better nutritional contents, higher yield and better resistance to late blight than the traditional yellow cultivars. We characterized the Colombian germplasm, Solanum tuberosum Group Phureja, for its nutritional attributes. During this stage, studies of the social and nutritional status of the communities were also conducted. In the second stage, we focused on scaling up new potato cultivars to reach potato producers and consumers by promoting the production and marketing of good quality seed potatoes, by establishing four Rural Entrepreneurs Nuclei. The programme promotes gender equity, good dietary habits, the consumption of more nutritious potatoes and empowers local leadership to strengthen governance. Field work was conducted in southern and central regions of Colombia by employing social strategies such as the Family Farming Community Schools. In 50% of the cultivated area, we are replacing the originally used traditional yellow potatoes by the new, more nutritious, potatoes to reach 6 million consumers. A good quality seed system for small-scale potato growers has been implemented. These achievements have been reached through a comprehensive approach in a period of two years.

Rooting Characteristics of Solanum chacoense and Solanum tuberosum in Vitro

The precise level of environmental control in vitro may aid in identifying genetically superior plant germplasm for rooting characteristics (RC) linked to increased foraging for plant nitrogen (N). The objectives of this research were to determine the phenotypic variation in root morphological responses of 49 Solanum chacoense (chc), 30 Solanum tuberosum Group Phureja – Solanum tuberosum Group Stenotomum (phu-stn), and three Solanum tuberosum (tbr) genotypes to 1.0 and 0.5 N rate in vitro for 28 d, and identify genotypes with superior RC. The 0.5 N significantly increased density of root length, surface area, and tips. All RC were significantly greater in chc than in either phu-stn or tbr. Based upon clustering on root length, surface area, and volume, the cluster with the greatest rooting values consisted of eight chc genotypes that may be utilized to initiate a breeding program to improve RC in potato.

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja.

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.

Pairing analysis and in situ Hybridisation reveal autopolyploid-like behaviour in Solanum commersonii\xa0\xd7\xa0S. tuberosum (potato) interspecific hybrids

Wild potato relatives are rich sources of desirable traits for introgressive hybridisation into cultivated potato. One of them, Solanum commersonii (2n = 2x = 24, 1EBN, endosperm balance number), is an important species belonging to the potato tertiary genepool. It can be used in potato breeding through bridge crosses and 2n gamete production. Triploid F1 hybrids between S. commersonii (through spontaneous 2n egg formation) and diploid 2EBN Solanum tuberosum Group Phureja were crossed with S. tuberosum Group Tuberosum, resulting in successive backcross 1, 2 and 3 progenies. The main aim of this study was to determine if there are any barriers to homoeologous pairing and recombination in the allotriploid (S. commersonii × potato) hybrids and their backcrosses, and so to predict if S. commersonii chromosomes can be transmitted to the next generation and introgressed into their recipient potato chromosomes. Microscopic observations of spread pollen mother cells suggested no preferential pairing in the triploid hybrids, while chromosome transmission and segregation in further meiotic stages were fairly balanced. Fluorescent in situ hybridisation with BAC probes (BAC FISH) was used to obtain markers to trace the meiotic behaviour of specific chromosome pairs. Moreover, genomic in situ hybridisation (GISH) demonstrated no obvious differences in fluorescence signals between the homoeologues suggesting that repetitive sequences did not diverge much between the parental species. As a consequence, we were not able to trace the course of the S. commersonii chromosomes in the successive introgressive hybridisation backcross generations. Our results strongly point at a high genomic similarity between the homoeologous chromosomes promising high suitability of S. commersonii in introgressive hybridisation breeding of potato.

Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja

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-C45711901T and InvGE-C2475454T were associated with sucrose content and frying color, respectively, and were not found previously in tetraploid genotypes. The rare haplotype InvGE-A2475187C2475295A2475344 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.

Allelic diversity of S-RNase alleles in diploid potato species.

Key messageThe S-ribonuclease sequences of 16 S-alleles derived from diploid types of Solanum are presented. A phylogenetic analysis and partial phenotypic analysis support the conclusion that these are functional S-alleles.S-Ribonucleases (S-RNases) control the pistil specificity of the self-incompatibility (SI) response in the genus Solanum and several other members of the Solanaceae. The nucleotide sequences of S-RNases corresponding to a large number of S-alleles or S-haplotypes have been characterised. However, surprisingly, few S-RNase sequences are available for potato species. The identification of new S-alleles in diploid potato species is desirable as these stocks are important sources of traits such as biotic and abiotic resistance. S-RNase sequences are reported here from three distinct diploid types of potato: cultivated Solanum tuberosum Group Phureja, S. tuberosum Group Stenotomum, and the wild species Solanum okadae. Partial S-RNase sequences were obtained from pistil RNA by RT-PCR or 3′RACE (Rapid Amplification of cDNA Ends) using a degenerate primer. Full-length sequences were obtained for two alleles by 5′RACE. Database searches with these sequences identified 16 S-RNases in total, all of which are novel. The sequence analysis revealed all the expected features of functional S-RNases. Phylogenetic analysis with selected published S-RNase and S-like-RNase sequences from the Solanaceae revealed extensive trans-generic evolution of the S-RNases and a clear distinction from S-like-RNases. Pollination tests were used to confirm the self-incompatibility status and cross-compatibility relationships of the S. okadae accessions. All the S. okadae accessions were found to be self-incompatible as expected with crosses amongst them exhibiting both cross-compatibility and semi-compatibility consistent with the S-genotypes determined from the S-RNase sequence data. The progeny analysis of four semi-compatible crosses examined by allele-specific PCR provided further confirmation that these are functional S-RNases.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2754-7) contains supplementary material, which is available to authorized users.

Natural variation of sucrose, glucose and fructose contents in Colombian genotypes of Solanum tuberosum Group Phureja at harvest.

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.

Carotenoids Extracted from Promising Clones of Criolla Potato (Solanum tuberosum Group Phureja) for Food Industry

The carotenoids are natural pigments that contribute to the replacement of the synthetic colorants which are still used in food industry. With this aim, the carotenoids from 15 promising clones and one commercial variety, named Yema de Huevo, of Criolla potato (Solanum tuberosum Group Phureja) supplied by Corpoica were extracted and evaluated. The tubers lyophilized for 72 h by triplicate, and their carotenoids extracted with acetone and hexane. Absorbance of the supernatants obtained after centrifuging measured using spectrophotometry at intervals of 3 nm. Presence of carotenoids was also confirmed by thin layer chromatography. Absorbance values showed a presence of lutein-5, 6-epoxide in clones 2, 4, 5, 6, 7, 8, 15, and α-carotene in clones 3, 10, 11, 12, 13, 14, 16, 17, and commercial variety. The promising clones 11, 12 and 14 were selected due to their higher carotenoid concentration. Their carotenoids extracted were evaluated their stability under different pH, temperature, and light conditions. A decrease in the color intensity was observed at 13.5 and 1.0 pH. There were not significant changes of color intensity at 50 and 70 °C temperatures. This carotenoids exposure to the light displayed a decrease in the absorbance. After, a commercial colorless yogurt was dyed with the selectedcarotenoids. Carotenoids from promising clone 14 showed higher pigmentation according to the spatial coordinates CIELAB of L*48.66 a*-1.65 b*5.63.Accepted for publication: August 15, 2013.

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii.

BackgroundSolanum commersonii is a wild potato species that exhibits high tolerance to both biotic and abiotic stresses and has been used as a source of genes for introgression into cultivated potato. Among the interesting features of S. commersonii is resistance to the bacterial wilt caused by Ralstonia solanacearum, one of the most devastating bacterial diseases of crops.ResultsIn this study, we used deep sequencing of S. commersonii RNA (RNA-seq) to analyze the below-ground plant transcriptional responses to R. solanacearum. While a majority of S. commersonii RNA-seq reads could be aligned to the Solanum tuberosum Group Phureja DM reference genome sequence, we identified 2,978 S. commersonii novel transcripts through assembly of unaligned S. commersonii RNA-seq reads. We also used RNA-seq to study gene expression in pathogen-challenged roots of S. commersonii accessions resistant (F118) and susceptible (F97) to the pathogen. Expression profiles obtained from read mapping to the S. tuberosum reference genome and the S. commersonii novel transcripts revealed a differential response to the pathogen in the two accessions, with 221 (F118) and 644 (F97) differentially expressed genes including S. commersonii novel transcripts in the resistant and susceptible genotypes. Interestingly, 22.6% of the F118 and 12.8% of the F97 differentially expressed genes had been previously identified as responsive to biotic stresses and half of those up-regulated in both accessions had been involved in plant pathogen responses. Finally, we compared two different methods to eliminate ribosomal RNA from the plant RNA samples in order to allow dual mapping of RNAseq reads to the host and pathogen genomes and provide insights on the advantages and limitations of each technique.ConclusionsOur work catalogues the S. commersonii transcriptome and strengthens the notion that this species encodes specific genes that are differentially expressed to respond to bacterial wilt. In addition, a high proportion of S. commersonii-specific transcripts were altered by R. solanacearum only in F118 accession, while phythormone-related genes were highly induced in F97, suggesting a markedly different response to the pathogen in the two plant accessions studied.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1460-1) contains supplementary material, which is available to authorized users.

Nutritional contents of advanced breeding clones of Solanum tuberosum group Phureja

Nutritional contents of seven advanced breeding clones (AC) of potato (Solanum tuberosum group Phureja) and two commercial cultivars, Criolla Colombia and Criolla Galeras, of S. tuberosum group Phureja as control were evaluated. Fat, protein, ash, dietary fibre, and mineral contents were determined in whole boiled tubers. The AC-04 had the highest levels of protein (9.7 g/100 g dried weight, DW) and magnesium (107.0 mg/100 g DW) as compared to Criolla Colombia (4.0 g of protein/100 g DW and 99.5 mg of magnesium/100 g DW) and Criolla Galeras (3.1 g of protein/100 g DW and 95.0 mg of magnesium/100 g DW). The highest contents of fat (0.7 g/100 g DW), soluble dietary fibre (4.9 g/100 g DW), and manganese (0.8 mg/100 g DW) were found in AC-09, values that represented 3.9, 1.7, and 1.2 fold increase as compared to Criolla Colombia, respectively, and 3.9, 1.8, and 1.1 fold increase as compared to Criolla Galeras. The AC-51 had the highest content of insoluble dietary fibre (13.8 g/100 g DW). Among all genotypes the AC-52 had the highest contents of iron (1.3 fold increase), zinc (1.2 fold increase), and calcium (1.3 fold increase) as compared to Criolla Colombia.

Natural co-infection of Solanum tuberosum crops by the Potato yellow vein virus and potyvirus in Colombia

The Potato yellow vein virus (PYVV), a Crinivirus with an RNA tripartite genome, is the causal agent of the potato yellow vein disease, reported in Colombian since 1950, with yield reductions of up to 50%. Co-infection of two or more viruses is common in nature and can be associated with differences in virus accumulation and symptom expression. No evidence of mixed infection between PYVV and other viruses has been reported. In this study, eight plants showing yellowing PYVV symptoms: four Solanum tuberosum Group Phureja (P) and four Group Andigena (A), were collected in Cundinamarca, Colombia to detect mixed infection in the isolates using next generation sequencing (NGS). The Potato virus Y (PVY) complete genome (similar to N strain) and the Potato virus V (PVV) partial genomes were detected using NGS and re-confirmed by RT-PCR. Preliminary field screening in a large sample showed that PYVV and PVY co-infect potato plants with a prevalence of 21% within the P group and 23% within the A group. This is the first report of co-infection of PYVV and potyvirus in Colombia and with the use of NGS. Considering that potyviruses enhance symptom severity and/or yield reductions in mixed infections, our results may be relevant for disease diagnosis, breeding programs and tuber certification.