Genotyping-by-sequencing targets genic regions and improves resolution of genome-wide association studies in autotetraploid potato.

KEY MESSAGE: De novo genotyping in potato using methylation-sensitive GBS discovers SNPs largely confined to genic or gene-associated regions and displays enhanced effectiveness in estimating LD decay rates, population structure and detecting GWAS associations over 'fixed' SNP genotyping platform. Study also reports the genetic architectures including robust sequence-tagged marker-trait associations for sixteen important potato traits potentially carrying higher transferability across a wider range of germplasm. This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a 'fixed' SNP Infinium array platform and a 'flexible and open' genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~ 90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation-sensitive restriction enzyme (PstI) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense de novo genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL 'hotspots' for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and de novo SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.

A combined approach of lauroyl arginine ethyl ester hydrochloride and kojic acid in mitigating fresh-cut potato deterioration.

The combinational effects of kojic acid and lauroyl arginine ethyl ester hydrochloride (ELAH) on fresh-cut potatoes were investigated. Kojic acid of 0.6% (w/w) effectively inhibited the browning of fresh-cut potatoes and displayed antimicrobial capacity. The color difference value of samples was decreased from 175 to 26 by kojic acid. In contrast, ELAH could not effectively bind with the active sites of tyrosinase and catechol oxidase at molecular level. Although 0.5% (w/w) of ELAH prominently inhibited the microbial growth, it promoted the browning of samples. However, combining kojic acid and ELAH effectively inhibited the browning of samples and microbial growth during the storage and the color difference value of samples was decreased to 52. This amount of kojic acid inhibited enzyme activities toward phenolic compounds. The results indicated that combination of kojic acid and ELAH could provide a potential strategy to extend the shelf life of fresh-cut products.

Development of aerial and belowground tubers in potato is governed by photoperiod and epigenetic mechanism.

Plants exhibit diverse developmental plasticity and modulate growth responses under various environmental conditions. Potato (Solanum tuberosum), a modified stem and an important food crop, serves as a substantial portion of the world's subsistence food supply. In the past two decades, crucial molecular signals have been identified that govern the tuberization (potato development) mechanism. Interestingly, microRNA156 overexpression in potato provided the first evidence for induction of profuse aerial stolons and tubers from axillary meristems under short-day (SD) photoperiod. A similar phenotype was noticed for overexpression of epigenetic modifiers-MUTICOPY SUPRESSOR OF IRA1 (StMSI1) or ENAHNCER OF ZESTE 2 (StE[z]2), and knockdown of B-CELL-SPECIFIC MOLONEY MURINE LEUKEMIA VIRUS INTEGRATION SITE 1 (StBMI1). This striking phenotype represents a classic example of modulation of plant architecture and developmental plasticity. Differentiation of a stolon to a tuber or a shoot under in vitro or in vivo conditions symbolizes another example of organ-level plasticity and dual fate acquisition in potato. Stolon-to-tuber transition is governed by SD photoperiod, mobile RNAs/proteins, phytohormones, a plethora of small RNAs and their targets. Recent studies show that polycomb group proteins control microRNA156, phytohormone metabolism/transport/signaling and key tuberization genes through histone modifications to govern tuber development. Our comparative analysis of differentially expressed genes between the overexpression lines of StMSI1, StBEL5 (BEL1-LIKE transcription factor [TF]), and POTATO HOMEOBOX 15 TF revealed more than 1,000 common genes, indicative of a mutual gene regulatory network potentially involved in the formation of aerial and belowground tubers. In this review, in addition to key tuberization factors, we highlight the role of photoperiod and epigenetic mechanism that regulates the development of aerial and belowground tubers in potato.

Using probabilistic genotypes in linkage analysis of polyploids.

KEY MESSAGE: In polyploids, linkage mapping is carried out using genotyping with discrete dosage scores. Here, we use probabilistic genotypes and we validate it for the construction of polyploid linkage maps. Marker genotypes are generally called as discrete values: homozygous versus heterozygous in the case of diploids, or an integer allele dosage in the case of polyploids. Software for linkage map construction and/or QTL analysis usually relies on such discrete genotypes. However, it may not always be possible, or desirable, to assign definite values to genotype observations in the presence of uncertainty in the genotype calling. Here, we present an approach that uses probabilistic marker dosages for linkage map construction in polyploids. We compare our method to an approach based on discrete dosages, using simulated SNP array and sequence reads data with varying levels of data quality. We validate our approach using experimental data from a potato (Solanum tuberosum L.) SNP array applied to an F1 mapping population. In comparison to the approach based on discrete dosages, we mapped an additional 562 markers. All but three of these were mapped to the expected chromosome and marker position. For the remaining three markers, no physical position was known. The use of dosage probabilities is of particular relevance for map construction in polyploids using sequencing data, as these often result in a higher level of uncertainty regarding allele dosage.

Targeting of anti-microbial proteins to the hyphal surface amplifies protection of crop plants against Phytophthora pathogens.

Phytophthora pathogens are a persistent threat to the world's commercially important agricultural crops, including potato and soybean. Current strategies aim at reducing crop losses rely mostly on disease-resistance breeding and chemical pesticides, which can be frequently overcome by the rapid adaptive evolution of pathogens. Transgenic crops with intrinsic disease resistance offer a promising alternative and continue to be developed. Here, we explored Phytophthora-derived PI3P (phosphatidylinositol 3-phosphate) as a novel control target, using proteins that bind this lipid to direct secreted anti-microbial peptides and proteins (AMPs) to the surface of Phytophthora pathogens. In transgenic Nicotiana benthamiana, soybean, and potato plants, significantly enhanced resistance to different pathogen isolates was achieved by expression of two AMPs (GAFP1 or GAFP3 from the Chinese medicinal herb Gastrodia elata) fused with a PI3P-specific binding domain (FYVE). Using the soybean pathogen P. sojae as an example, we demonstrated that the FYVE domain could boost the activities of GAFPs in multiple independent assays, including those performed in vitro, in vivo, and in planta. Mutational analysis of P. sojae PI3K1 and PI3K2 genes of this pathogen confirmed that the enhanced activities of the targeted GAFPs were correlated with PI3P levels in the pathogen. Collectively, our study provides a new strategy that could be used to confer resistance not only to Phytophthora pathogens in many plants but also potentially to many other kinds of plant pathogens with unique targets.

Plastid Transformation in Potato: An Important Source of Nutrition and Industrial Materials.

For a long time, plastid transformation has been a routine technology only in tobacco due to lack of effective selection and regeneration protocols, and, for some species, due to inefficient recombination using heterologous flanking regions in transformation vectors. Nevertheless, the availability of this technology to economically important crops offers new possibilities in plant breeding to manage pathogen resistance or improve nutritional value. Herein we describe an efficient plastid transformation protocol for potato (Solanum tuberosum subsp. tuberosum), achieved by the optimization of the tissue culture procedures and using transformation vectors carrying homologous potato flanking sequences. This protocol allowed to obtain up to one shoot per shot, an efficiency comparable to that usually accomplished in tobacco. Further, the method described in this chapter has been successfully used to regenerate potato transplastomic plants expressing recombinant GFP protein in chloroplasts and amyloplasts or long double-stranded RNAs for insect pest control.

Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise.

Water limitation represents the main environmental constraint affecting crop yield worldwide. Photosynthesis is a primary drought target, resulting in over-reduction of the photosynthetic electron transport chain and increased production of reactive oxygen species in plastids. Manipulation of chloroplast electron distribution by introducing alternative electron transport sinks has been shown to increase plant tolerance to multiple environmental challenges including hydric stress, suggesting that a similar strategy could be used to improve drought tolerance in crops. We show herein that the expression of the cyanobacterial electron shuttle flavodoxin in potato chloroplasts protected photosynthetic activities even at a pre-symptomatic stage of drought. Transcriptional and metabolic profiling revealed an attenuated response to the adverse condition in flavodoxin-expressing plants, correlating with their increased stress tolerance. Interestingly, 5-6% of leaf-expressed genes were affected by flavodoxin in the absence of drought, representing pathways modulated by chloroplast redox status during normal growth. About 300 of these genes potentially contribute to stress acclimation as their modulation by flavodoxin proceeds in the same direction as their drought response in wild-type plants. Tuber yield losses under chronic water limitation were mitigated in flavodoxin-expressing plants, indicating that the flavoprotein has the potential to improve major agronomic traits in potato.

Potato Snakin-1: an antimicrobial player of the trade-off between host defense and development.

Snakin-1 (SN1) from potato is a cysteine-rich antimicrobial peptide with high evolutionary conservation. It has 63 amino acid residues, 12 of which are cysteines capable of forming six disulfide bonds. SN1 localizes in the plasma membrane, and it is present mainly in tissues associated with active growth and cell division. SN1 is active in vitro against bacteria, fungus, yeasts, and even animal/human pathogens. It was demonstrated that it also confers in vivo protection against commercially relevant pathogens in overexpressing potato, wheat, and lettuce plants. Although researchers have demonstrated SN1 can disrupt the membranes of E. coli, its integral antimicrobial mechanism remains unknown. It is likely that broad-spectrum antimicrobial activity is a combined outcome of membrane disruption and inhibition of intracellular functions. Besides, in potato, partial SN1 silencing affects cell division, leaf metabolism, and cell wall composition, thus revealing additional roles in growth and development. Its silencing also affects reactive oxygen species (ROS) and ROS scavenger levels. This finding indicates its participation in redox balance. Moreover, SN1 alters hormone levels, suggesting its involvement in the complex hormonal crosstalk. Altogether, SN1 has the potential to integrate development and defense signals directly and/or indirectly by modulating protein activity, modifying hormone balance and/or participating in redox regulation. Evidence supports a paramount role to SN1 in the mechanism underlying growth and immunity balance. Furthermore, SN1 may be a promising candidate in preservation, and pharmaceutical or agricultural biotechnology applications.

Agronomical traits, phenolic compounds and antioxidant activity in raw and cooked potato tubers growing under saline conditions.

BACKGROUND: Potato yields and tuber compositions are linked to mechanisms adopted by plants to cope with salinity and often can change after cooking. The current study aimed to evaluate the effects of salinity, variety and cooking method in the composition of potato tubers. Three potato varieties (Spunta, Bellini and Alaska) grown under distinct salt levels (T1: 2.2 ms cm-1 EC, T2: 8.5 ms cm-1 EC before electromagnetic treatment and 6.3 ms cm-1 EC after electromagnetic treatment, T3: 8.5 ms cm-1 EC) were studied. Yield and tuber quality attributes (starch, dry matter, specific density and tuber size) were evaluated. Carotenoids, total and individual phenolics determined by high-performance liquid chromatography (HPLC), relative antioxidant capacity (RAC) and ions content were analyzed, in both raw and water boiled tubers. RESULTS: Tuber yield, starch, dry matter, ions and antioxidants were significantly influenced by the salinity level and variety. The least production and the highest antioxidants were obtained under T3. Antioxidants were influenced by cooking method, the interactions treatment × cooking method and variety × cooking method. Individual phenolic compounds exhibited different response to cooking as quercetin, caffeic acid and catechin decreased significantly after boiling. However, coumaric acid increased in Alaska tubers. CONCLUSION: Salinity level, variety and cooking method are important determinants of tuber yield and composition. Electromagnetic water may be useful to enhance potato production and tuber quality in areas suffering from water salinization. © 2020 Society of Chemical Industry.

Trypsin inhibitor, antioxidant and antimicrobial activities as well as chemical composition of potato sprouts originating from yellow- and colored-fleshed varieties.

Potato sprouts could be a valuable resource of phytochemicals such as secondary plant metabolites, potential antioxidants and nutritive compounds. In this work, potato sprout extracts of five varieties were examined; they differed in major glycoalkaloid content, trypsin inhibitor activity, total polyphenol content and antioxidant activity, as well as in antimicrobial activity against Gram + and G - bacteria, and yeast. Sprouts of colored-fleshed tubers were characterized by higher trypsin inhibitor activity than sprouts of yellow potatoes. The strongest microorganism growth inhibition effect was observed for macerate with sprouts from the purple-fleshed Blaue Annelise variety against B. subtilis, whereas C. albicans yeasts were sensitive to macerates with sprouts from purple-fleshed Blue Congo and yellow-fleshed Vineta potato varieties.

Agronomic and Economic Interactions between Sidedressed Nitrogen and Potassium Fertilizations on Atlantic Potato

Abstract Nitrogen (N) and potassium (K) in potato crop planting synergistically increase tuber yield, but there are no studies on this interaction in sidedressing. In two experiments with 'Atlantic' potato combinations of four N rates (0, 50, 100, and 150 kg ha-1) with four K2O rates (0, 100, 200, and 300 kg ha-1) were applied in sidedressing in a 4×4 factorial scheme with three replications in a completely randomized design. Adjacent commercial fields were sampled to economic comparisons with experimental results. Significant interaction between N and K sidedressing rates with tuber yields increase also was confirmed and classified as Liebig-synergism. Compared to the isolated N and K applications in sidedressing, joint N and K fertilizations, respectively, increases by 11% and 48% marketable tuber yields in the summer-fall experiment, and 12% and 7% in the spring experiment. Joint N and K applications as sidedressing was more profitable than planting fertilization, mainly at higher N and K rates. The response of specific gravity of 'Atlantic' potato tubers to the N and K sidedressing rates was mediated by interactions between edaphoclimatic conditions and inputs of N and K. The combined application of N and K sidedressing rates increased specific gravity in the summer-fall experiment, but had a negative effect in the spring experiment. Therefore, our results provide strong evidence that the fertilization management for potato crop in Brazil can be modified by applying higher amounts of N and K in sidedressing to match nutritional needs of the crop.

Transgenic RXLR Effector PITG_15718.2 Suppresses Immunity and Reduces Vegetative Growth in Potato.

Phytophthora infestans causes the severe late blight disease of potato. During its infection process, P. infestans delivers hundreds of RXLR (Arg-x-Leu-Arg, x behalf of any one amino acid) effectors to manipulate processes in its hosts, creating a suitable environment for invasion and proliferation. Several effectors interact with host proteins to suppress host immunity and inhibit plant growth. However, little is known about how P. infestans regulates the host transcriptome. Here, we identified an RXLR effector, PITG_15718.2, which is upregulated and maintains a high expression level throughout the infection. Stable transgenic potato (Solanum tuberosum) lines expressing PITG_15718.2 show enhanced leaf colonization by P. infestans and reduced vegetative growth. We further investigated the transcriptional changes between three PITG_15718.2 transgenic lines and the wild type Désirée by using RNA sequencing (RNA-Seq). Compared with Désirée, 190 differentially expressed genes (DEGs) were identified, including 158 upregulated genes and 32 downregulated genes in PITG_15718.2 transgenic lines. Eight upregulated and nine downregulated DEGs were validated by real-time RT-PCR, which showed a high correlation with the expression level identified by RNA-Seq. These DEGs will help to explore the mechanism of PITG_15718.2-mediated immunity and growth inhibition in the future.

Gas chromatography-mass spectrometry metabolomics-based prediction of potato tuber sprouting during long-term storage.

In order to supply potato (Solanum tuberosum L.) tubers for the processed food industry throughout the year, suppliers should provide consistent quality potatoes even after long-term storage. Despite being one of the most important foods, there is no simple way to control tuber quality and, in particular, controlling sprouting. Chemical suppression such as chlorpropham is used to inhibit sprouting, however, the regulatory status of such chemical inhibition differs in each country. Gas chromatography-mass spectrometry-based metabolomics was applied to identify the applicable biomarkers for prediction of potato sprouting during long-term storage. Sprouting was measured in chipping potatoes, and these were also subjected to metabolite profiling to develop a predictive model. The model was based on projections to latent structures (PLS) regression calculated from a metabolome data set obtained before storage and was consistent with actual measured sprouting values. Sucrose, phosphate, and amino acids were selected as valid contributing biomarkers for prediction in a validation field experiment. These biomarkers will contribute to the development of a successful novel method for prediction and control of potato tuber quality during long-term storage.

Gamma radiation degradation of chitosan for application in growth promotion and induction of stress tolerance in potato (Solanum tuberosum L.).

Oligo-chitosan (82.20 kDa) was prepared from chitosan (337.73 kDa) by application of 100 kGy γ-irradiation. UV-vis spectroscopy, FTIR, XRD, DSC and TGA analyses showed typical properties of chitosan with slight variations after γ-irradiation. Degree of deacetylation of chitosan and oligo-chitosan was 82%, while 1,1-diphenyl-2-picrylhydrzyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging activity were 10.01 ± 0.18 and 43.30 ± 3.75 µMTE/mL and 13.64 ± 0.16 and 79.93 ± 4.44 µMTE/mL, respectively. Chitosan and oligo-chitosan was applied as foliar spray on potato plants to analyze growth promoting and stress tolerance inducing effects. Improvement in shoot height and number of nodes was observed after foliar spray of chitosan and oligo-chitosan at 50-75 mg/L. Furthermore, membrane stability index and malondialdehyde reduced while chlorophyll, carotenoids, proline, reducing and total sugars, enhanced considerably. The antioxidant and defense enzymes CAT, POD, SOD, chitinase and chitosanase showed prominent increment. Overall results indicated that chitosan (75 mg/L) and oligo-chitosan (50 mg/L) can augment plant growth and induce defense mechanism for drought stress tolerance in potato.

Antiviral Activity of Curcumin Loaded Milk Proteins Nanoparticles on Potato Virus Y.

BACKGROUND AND OBJECTIVE: Potato is one of the world's leading vegetable crops. Potato viral diseases cause adversely effects on the agricultural sector. Recently there is a growing interest to control plant viruses using spices and herbs (including curcumin). Poor solubility of curcumin in water limited its applications. Therefore, the main objective of the present study was to evaluate the effect of antiviral activity of curcumin-milk proteins nanoparticles against potato virus Y (PVY). MATERIALS AND METHODS: Curcumin-milk proteins nanoparticles were prepared via ionic gelation method. The antiviral activity of the resultant nanoparticles against PVY was evaluated at different concentrations (500, 1000 and 1500 mg/100 mL). Chlorophyll content as well as the activity of peroxidase (POX) and polyphenol oxidase (PPO) was examined. RESULTS: Curcumin-milk proteins nanoparticles showed inhibitory effect on PVY in a concentration dependent manner. CONCLUSION: Curcumin-milk proteins nanoparticles displayed a successful tool to control the PVY under green house conditions.

Investigation of the response to salinity of transgenic potato plants overexpressing the transcription factor StERF94.

Salinity is one of the most important constraints threatening the cultivation of potato plants (Solanum tuberosum L.). It affects plant growth and leads to significant yield loss. Consequently, it is important to improve the tolerance of potato plants to salinity. In this context, we investigated the involvement of a potato ethylene responsive factor (StERF94) in plant response to salinity, since our previous genome-wide analysis showed that it may be related to biotic and abiotic stress response. ERF proteins belong to a large family of transcription factors that participate in plant response to abiotic stresses. We have previously identified the StERF94 gene which shows increased expression in potato plants submitted to salt treatment. In this study, transgenic potato plants overexpressing StERF94 were produced and submitted to salt treatment (100 mM NaCl) in vitro and under greenhouse culture conditions. StERF94 transgenic lines showed lower decrease of stem elongation under salt treatment in comparison to non-transgenic wild-type plants. Moreover, these plants showed a low level of H2O2 and Malondialdehyde content, and an increase in catalase and GPX (Gluthation peroxidase) activities compared to non-transgenic plants. In a second step, enhanced expression of some target genes for example CuZn-SOD, DHN25 (Dehydrin) and ERD (Early Responsive to Dehydration) was noted in the StERF94 transgenic plants, submitted to salt treatment. The StERF94 factor was also involved in the activation of osmoprotectant synthesis. Taken together, all these data suggest that overexpression of the StERF94 transcription factor increases the tolerance of potato plants to salinity by improving plant growth, osmoprotectant synthesis and antioxidant activityleading to low oxidative stress damage.

Establishment of a modified CRISPR/Cas9 system with increased mutagenesis frequency using the translational enhancer dMac3 and multiple guide RNAs in potato.

CRISPR/Cas9 is a programmable nuclease composed of the Cas9 protein and a guide RNA (gRNA) molecule. To create a mutant potato, a powerful genome-editing system was required because potato has a tetraploid genome. The translational enhancer dMac3, consisting of a portion of the OsMac3 mRNA 5'-untranslated region, greatly enhanced the production of the protein encoded in the downstream ORF. To enrich the amount of Cas9, we applied the dMac3 translational enhancer to the Cas9 expression system with multiple gRNA genes. CRISPR/Cas9 systems targeting the potato granule-bound starch synthase I (GBSSI) gene examined the frequency of mutant alleles in transgenic potato plants. The efficiency of the targeted mutagenesis strongly increased when the dMac3-installed Cas9 was used. In this case, the ratio of transformants containing four mutant alleles reached approximately 25% when estimated by CAPS analysis. The mutants that exhibited targeted mutagenesis in the GBSSI gene showed characteristics of low amylose starch in their tubers. This result suggests that our system may facilitate genome-editing events in polyploid plants.

Inhibition of plastid PPase and NTT leads to major changes in starch and tuber formation in potato.

The importance of a plastidial soluble inorganic pyrophosphatase (psPPase) and an ATP/ADP translocator (NTT) for starch composition and tuber formation in potato (Solanum tuberosum) was evaluated by individual and simultaneous down-regulation of the corresponding endogenous genes. Starch and amylose content of the transgenic lines were considerably lower, and granule size substantially smaller, with down-regulation of StpsPPase generating the most pronounced effects. Single-gene down-regulation of either StpsPPase or StNTT resulted in increased tuber numbers per plant and higher fresh weight yield. In contrast, when both genes were inhibited simultaneously, some lines developed only a few, small and distorted tubers. Analysis of metabolites revealed altered amounts of sugar intermediates, and a substantial increase in ADP-glucose content of the StpsPPase lines. Increased amounts of intermediates of vitamin C biosynthesis were also observed. This study suggests that hydrolysis of pyrophosphate (PPi) by action of a psPPase is vital for functional starch accumulation in potato tubers and that no additional mechanism for consuming, hydrolysing, or exporting PPi exists in the studied tissue. Additionally, it demonstrates that functional PPi hydrolysis in combination with efficient ATP import is essential for tuber formation and development.

Combined Amendments of Nano-hydroxyapatite Immobilized Cadmium in Contaminated Soil-Potato (Solanum tuberosum L.) System.

The toxicity of cadmium (Cd) has posed major public health concern in crops grown in the Cd-contaminated soils. The effects of five amendments, nano-hydroxyapatite (n-HA) and it combined with lime, zeolite, bone mill and fly ash on Cd immobilization in soils and uptake in potatoes, were investigated in a contaminated soil by pot experiments. The result showed that the applications of combined amendments significantly decreased the bioavailable Cd concentrations extracted by TCLP, DTPA-TEA and MgCl2 in the contaminated soils, and changed the soluble and exchangeable and specifically sorbed fractions to oxide-bound and organic-bound fractions. Compared to the control group, the concentrations of Cd in the potato tubers grown in n-HA, n-HA + Fly ash, n-HA + Lime, n-HA + Bone mill and n-HA + Zeolite soil were reduced 17.4%, 20.7%, 15.2%, 32.6% and 39.1%, respectively. Nano-hydroxyapatite combined amendments was more effective in reducing bioavailable Cd concentrations and Cd accumulations in potatoes, especially for n-HA + Z.

Comparative epigenomics reveals evolution of duplicated genes in potato and tomato.

The evolution of duplicated genes after polyploidization has been the subject of many evolutionary biology studies. Potato (Solanum tuberosum) and tomato (Solanum lycopersicum) are the first two sequenced genomes of asterids, and share a common polyploidization event. However, the epigenetic role of DNA methylation on the evolution of duplicated genes derived from polyploidization is not fully understood. Here, we explore the role of the DNA methylation in the evolution of duplicated genes in potato and tomato. The overall levels of DNA methylation are different, although patterns of DNA methylation are similar in potato and tomato. Different types of duplicated genes can display different methylation patterns in potato and tomato. In addition, we found that differences in the methylation levels between duplicated genes were associated with gene expression divergence. In particular, for the majority of duplicated gene pairs, one copy is always hyper- or hypo-methylated compared with the other copy across different tomato fruit ripening stages, and these genes are enriched for specific function related to transcription factor (TF) activity. Furthermore, transcription of hundreds of duplicated TFs was shown to be regulated by DNA methylation during fruit ripening stages in tomato, some of which are well-known fruit ripening TFs. Taken together, our results support the notion that DNA methylation may facilitate divergent evolution of duplicated genes and play roles in important biological processes such as tomato fruit ripening.