Uncovering anthocyanin diversity in potato landraces (Solanum tuberosum L. Phureja) using RNA-seq.

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.

Differential elements of a successful agricultural innovation scaling-up model.

Worldwide, there is currently an increasing demand for an active connection between the generation of innovations and the achievement of their escalation. Between 2015 and 2018 the scaling up of three varieties of yellow potatoes was carried out in Colombia within the framework of the "More Nutritious Potatoes" project, which had results beyond the objectives and goals proposed in a period of 28 months. One of the results of the project was the design of a Scaling-up model of innovations that linked agriculture with nutrition. This article answers the question: Which were the elements of the scaling-up model that allowed the results obtained in the More Nutritious Potatoes Project? To respond, a set of reference criteria was constructed from the literature. These criteria were contrasted with the theoretical project scaling-up model and its subsequent implementation in the field, using focus groups as a methodology and the model design analysis and its execution by the leaders and the evaluator of the project. The project's Scaling-up Model (SM) was found to include all benchmarks, in addition to identify three key elements that made the results possible: (i) the characteristics of the innovation, (ii) the trans-disciplinary work and (iii) facilitating elements of the process. The results of this exercise complement the evaluated scaling-up model and become benchmarks in the design of innovation scaling-up processes.

Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS.

Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

Physiological, Biochemical and Yield-Component Responses of Solanum tuberosum L. Group Phureja Genotypes to a Water Deficit.

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.

Pathway-based analysis of anthocyanin diversity in diploid potato.

Anthocyanin biosynthesis is one of the most studied pathways in plants due to the important ecological role played by these compounds and the potential health benefits of anthocyanin consumption. Given the interest in identifying new genetic factors underlying anthocyanin content we studied a diverse collection of diploid potatoes by combining a genome-wide association study and pathway-based analyses. By using an expanded SNP dataset, we identified candidate genes that had not been associated with anthocyanin variation in potatoes, namely a Myb transcription factor, a Leucoanthocyanidin dioxygenase gene and a vacuolar membrane protein. Importantly, a genomic region in chromosome 10 harbored the SNPs with strongest associations with anthocyanin content in GWAS. Some of these SNPs were associated with multiple anthocyanin compounds and therefore could underline the existence of pleiotropic genes or anthocyanin biosynthetic clusters. We identified multiple anthocyanin homologs in this genomic region, including four transcription factors and five enzymes that could be governing anthocyanin variation. For instance, a SNP linked to the phenylalanine ammonia-lyase gene, encoding the first enzyme in the phenylpropanoid biosynthetic pathway, was associated with all of the five anthocyanins measured. Finally, we combined a pathway analysis and GWAS of other agronomic traits to identify pathways related to anthocyanin biosynthesis in potatoes. We found that methionine metabolism and the production of sugars and hydroxycinnamic acids are genetically correlated to anthocyanin biosynthesis. The results contribute to the understanding of anthocyanins regulation in potatoes and can be used in future breeding programs focused on nutraceutical food.

Vitamin C, protein, and dietary fibre contents as affected by genotype, agro-climatic conditions, and cooking method on tubers of Solanum tuberosum Group Phureja.

The simultaneous effect of genotype, agro-climatic conditions, and cooking method was evaluated towards the contents of vitamin C, protein, and soluble, insoluble, and total dietary fibre in potato tubers from the Group Phureja. Within the tested treatments, vitamin C was affected the most (9.4-85.1 mg/100 g DW), followed by insoluble dietary fibre (3.9-16.6 g/100 DW), soluble dietary fibre (1.0-3.9 g/100 g DW), total dietary fibre (3.6-fold change), and protein (1.7-4.3 g/100 g DW). The cooking method had a high effect on the variability of the contents of vitamin C, protein, insoluble dietary fibre, and total dietary fibre (74.2-92.8% of the total variance). In contrast, not only the cooking method, but also the agro-climatic conditions had a high effect on the content of soluble dietary fibre (32.6 and 34.8% of the total variance, respectively). Total dietary fibre had a protective effect on vitamin C upon cooking.

Novel organ-specific genetic factors for quantitative resistance to late blight in potato.

Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site-associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.

Influence of genotype, agro-climatic conditions, cooking method, and their interactions on individual carotenoids and hydroxycinnamic acids contents in tubers of diploid potatoes.

The effects of genotype, agro-climatic conditions (ACC), and cooking method as well as their interactions on the content of individual carotenoids and hydroxycinnamic acids in different potato tubers were evaluated. While zeaxanthin content was highly influenced by the ACC (up to 631-fold change), chlorogenic acid was similarly influenced by the cooking method (up to 3.1-fold increase after cooking), by the interactions ACC × cooking method (up to 2.1-fold increase) and genotype × cooking method (up to 1.7-fold increase). Stability/extractability of compounds after cooking was found to be genotype and ACC dependent, which suggest that genotype and ACC induces differential expression of genes for the biosynthesis pathways of carotenoids and hydroxycinnamic acids is different among, as well as components of the cellular matrix. These results are promising to apply in potato breeding programs with the perspective to develop new potato cultivars selected by their nutritional attributes.

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

BACKGROUND: Potato 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. RESULTS: The 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. CONCLUSION: The 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.

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

BACKGROUND: Potato 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. RESULTS: Sucrose, 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. CONCLUSION: Sugar 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.

Development and validation of a liquid chromatographic method to quantify sucrose, glucose, and fructose in tubers of Solanum tuberosum Group Phureja.

A High Performance Liquid Chromatography (HPLC) method was developed and validated to quantify sucrose (non-reducing sugar), glucose, and fructose (reducing sugars) in raw tubers of Solanum tuberosum Group Phureja. Chromatographic analysis was performed using an AMINEX HPX 87H column, at 18 °C, linked to a refraction index detector, at 35 °C. The eluent was 10mM sulfuric acid. The conditions established for the method provided an optimum separation of sugars, citric acid, and malic acid, with resolution values higher or equal to one. Among the four sugar extraction methods tested, the double 50% (v/v) aqueous methanol extraction gave the highest level of analytes. Recovery of this extraction method ranged between 94.14 and 99.77%. The HPLC method was validated for repeatability, reproducibility, linearity, and limits of detection, and quantification. Relative standard deviation was found to be lower than five, when testing repeatability and reproducibility, which is suitable considering a range of acceptability from 5.3 to 7.3. Additionally, the regression analyses supported the method linearity in a range of quantification from 3 to 100 mg/L with regression coefficients values greater than 0.998 for the three analytes. Limits of detection were 3.0 mg/L for the three sugars and limits of quantification were 2.0 mg/L for sucrose and 3.0 mg/L for glucose and fructose. Four Colombian commercial cultivars (Criolla Guaneña, Criolla Paisa, Criolla Galeras, and Criolla Colombia) and five landrace accessions from the Colombian Core Collection of Group Phureja were grown in the district of Usme (Bogotá) fields to analyze their sugar contents. Sucrose, glucose, and fructose contents were found ranging from 0.93 to 3.11 g/100 g tuber dried weight (DW), from 0.25 to 4.53 g/100 g tuber DW, and from 0.10 to 1.49 g/100 g tuber DW, respectively. Therefore, a high range in the variability of sugar contents was found among genotypes. However, the variability was low among technical replicates of the same genotype, revealing an accurate quantification of sugars in Group Phureja. This method can be used to assess the amount of reducing and non-reducing sugars accumulation in potato germplasm.