A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping

Flowering time genes branching out

Plants are sessile by nature, and as such they have evolved to sense changes in seasonality and their surrounding environment, and adapt to these changes. One prime example of this is the regulation of flowering time in angiosperms, which is precisely timed by the coordinated action of two proteins: FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). Both of these regulators are members of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family of proteins. These regulatory proteins do not interact with DNA themselves, but instead interact with transcriptional regulators, such as FLOWERING LOCUS D (FD). FT and TFL1 were initially identified as key regulators of flowering time, acting through binding with FD; however, PEBP family members are also involved in shaping plant architecture and development. In addition, PEBPs can interact with TCP transcriptional regulators, such as TEOSINTE BRANCHED 1 (TB1), a well-known regulator of plant architecture, and key domestication-related genes in many crops. Here, we review the role of PEBPs in flowering time, plant architecture, and development. As these are also key yield-related traits, we highlight examples from the model plant Arabidopsis as well as important food and feed crops such as, rice, barley, wheat, tomato, and potato.

Genome-wide identification and drought stress-induced expression analysis of the NHX gene family in potato

NHX proteins are transmembrane antiporters belonging to the cation/proton antiporter gene family, with a conserved Na+ (K+)/H+ exchange (PF00999) protein domain. NHXs play a prominent role in plant growth, development, and defense. However, the role of NHX gene family in potato (Solanum tuberosum L.) is yet to be known. In this study, we conducted a genome-wide analysis of the potato NHX gene family. A total of 25 StNHX family members were identified to be unevenly distributed on 10 chromosomes. The proteins ranged in length from 252 to 1,153 amino acids, with molecular masses ranging from 27516.32 to 127860.87 kD, and isoelectric points (pI) ranging from 4.96 to 9.3. Analyses of gene structures and conserved motifs indicated that StNHX genes in the same phylogenetic cluster are conserved. Phylogenetic analysis divided the StNHX genes into three subfamilies (Classes I, II, and III). Synteny analysis indicated that StNHX gene family Class III of NHX and all Arabidopsis thaliana NHXs shared a close evolutionary relationship. Analysis of cis-acting elements in the upstream 1,500 bp promoter region of potato NHX genes showed that these genes could be regulated by light, stress, and hormones such as abscisic acid and gibberellic acid. Protein-protein interaction network analysis indicated that StNHX proteins may participate in the regulation of potato growth and stress response. Besides, To determine a potential role of these genes in tissue development and drought response, we analyzed the RNA-seq data of different DM potato tissues. The results showed that NHX genes exhibited distinct tissue-specific expression patterns. We further examined the expression patterns of StNHX in different tissues (leaves, roots, shoots, tubers, stolons, and flowers) during the flowering stage in 'Jizhangshu NO.8.' potato. The qRT-PCR results further confirmed the importance of StNHX genes in potato plant growth and development. We further analyzed the RNA-seq data (DM potato) under different abiotic stresses (salt, drought, and heat), and found that the expression of StNHX genes was induced under abiotic stress. qRT-PCR analysis of shoots and roots of 'Jizhangshu NO.8.' potato treated for 0, 6, 12, and 24 h with 15% PEG6000 confirmed that the 25 StNHX genes are involved in the response to drought stress in potato. The results of this study may be useful for selecting appropriate candidate genes for the breeding of new drought-tolerant potato varieties. Furthermore, this study lays a foundation for prospective analysis of StNHX gene functions.

A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes

Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E-genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.

A Walk on the Wild Side: Genome Editing of Tuber-Bearing Solanum bulbocastanum

Solanum bulbocastanum is a wild diploid tuber-bearing plant. We here demonstrate transgene-free genome editing of S. bulbocastanum protoplasts and regeneration of gene-edited plants. We use ribonucleoproteins, consisting of Cas9 and sgRNA, assembled in vitro, to target a gene belonging to the nitrate and peptide transporter family. Four different sgRNAs were designed and we observed efficiency in gene-editing in the protoplast pool between 8.5% and 12.4%. Twenty-one plants were re-generated from microcalli developed from individual protoplasts. In three of the plants we found that the target gene had been edited. Two of the edited plants had deletion mutations introduced into both alleles, whereas one only had a mutation in one of the alleles. Our work demonstrates that protocols for the transformation of Solanum tuberosum can be optimized to be applied to a wild Solanum species.

Fatty Acids and Starch Identification within Minute Archaeological Fragments: Qualitative Investigation for Assessing Feasibility

Within the realm of archaeology, the analysis of biomolecules assumes significant importance in elucidating historical dietary patterns and their implications for contemporary contexts. To achieve this, knowledge and tools of both chemistry and archaeology are essential to yield objective outcomes and conduct analyses of archaeological materials for the detection of biomolecules. Usually, only minuscule remnants of ceramic fragments are retrieved from excavations, which limits the feasibility of comprehensive laboratory analysis. This study aimed to establish a protocol for analyzing fatty acids and starch from archaeological food utensils with minimal sample quantities. Various experiments were conducted to replicate preparations that might have occurred in archaeological vessels, aiming to establish the optimal protocol. The analyses were performed using clay griddles, subjecting vegetable oil to varying temperatures for fatty acid assessment. For starch analysis, a series of experiments encompassed diverse forms of potato preparations (pulp, chuño, tortilla, carbonization, and freeze-drying) and maize (flour, tortilla, and carbonization). The verification of the experiments was confirmed by conducting identical analyses, as developed in the current study, on authentic archaeological fragments. The principal outcomes of this investigation include the successful extraction of both types of biomolecules using only 0.25 g of the sample, obtained through direct scraping from the vessel. Soxhlet extraction was identified as the most efficient strategy to recover fatty acids. Additionally, a comprehensive protocol for the identification of starch extraction was developed. This study has, for the first time, elucidated two detailed methodologies for the extraction of fatty acids and starch in scenarios in which researchers can obtain limited quantities of archaeological food utensil fragments.

Gibberellin 2-Oxidases in Potato (Solanum tuberosum L.): Cloning, Characterization, In Silico Analysis and Molecular Docking

Gibberellins (GAs; tetracyclic di-terpenoid carboxylic acids) are endogenous plant growth regulators responsible for stimulating plant growth and development from seed germination to plant maturity. In potato (Solanum tuberosum L.), GA levels are known to be crucial in the complex process of tuberization. Gibberellin 2-oxidases (GA2oxs) inactivate bioactive GAs during stolon swelling and early stages of tuberization as evident from the predominant expression of a member of this gene family namely GA2ox1. We isolated and characterized a 1105-bp cDNA clone encoding a 340-aa GA2ox1 form, designated St-GA2ox1, using total RNA from growing tuber of a potato (Solanum tuberosum L.) cultivar, Kufri Chipsona-1 (KC-1) based on RT-PCR approach. A total of 26 GA2ox sequences were also retrieved from potato genome database and analysed. Multiple sequence alignment revealed sequence relatedness between the GA2oxs. Crucial protein motifs were identified. Phylogenetic analysis revealed the evolutionary relationships between the GA2oxs. Three-dimensional structure of St-GA2ox1 was predicted by using AlphaFold tool, validated by the predicted local-distance difference test and Ramachandran Plot. Structural analysis and molecular docking were carried out to identify domains, binding sites and affinity for the ligand. The STRING database and hydropathy analysis revealed the presence of a putative interaction site for other enzymes. Expression Atlas database and semi-quantitative RT-PCR revealed the expression patterns of various GA2ox forms in different potato organs. This comprehensive report would be useful in providing new insights into possible underlying mechanisms involved in tuber development, and could facilitate the targeted alteration of genes responsible to combat the stress and enhance tuber production.

The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato

Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

Stable isotope chemistry reveals plant-dominant diet among early foragers on the Andean Altiplano, 9.0-6.5 cal. ka

Current models of early human subsistence economies suggest a focus on large mammal hunting. To evaluate this hypothesis, we examine human bone stable isotope chemistry of 24 individuals from the early Holocene sites of Wilamaya Patjxa (9.0-8.7 cal. ka) and Soro Mik'aya Patjxa (8.0-6.5 cal. ka) located at 3800 meters above sea level on the Andean Altiplano, Peru. Contrary to expectation, Bayesian mixing models based on the isotope chemistry reveal that plants dominated the diet, comprising 70-95% of the average diet. Paleoethnobotanical data further show that tubers may have been the most prominent subsistence resource. These findings update our understanding of earliest forager economies and the pathway to agricultural economies in the Andean highlands. The findings furthermore suggest that the initial subsistence economies of early human populations adapting to new landscapes may have been more plant oriented than current models suggest.

Genome-wide analysis of the U-box E3 ligases gene family in potato (Solanum tuberosum L.) and overexpress StPUB25 enhance drought tolerance in transgenic Arabidopsis

BACKGROUND

Plant U-box (PUB) E3 ubiquitin ligases have vital effects on various biological processes. Therefore, a comprehensive and systematic identification of the members of the U-box gene family in potato will help to understand the evolution and function of U-box E3 ubiquitin ligases in plants.

RESULTS

This work identified altogether 74 PUBs in the potato (StPUBs) and examined their gene structures, chromosomal distributions, and conserved motifs. There were seventy-four StPUB genes on ten chromosomes with diverse densities. As revealed by phylogenetic analysis on PUBs within potato, Arabidopsis, tomato (Solanum lycopersicum), cabbage (Brassica oleracea), rice (Oryza sativa), and corn (Zea mays), were clustered into eight subclasses (C1-C8). According to synteny analysis, there were 40 orthologous StPUB genes to Arabidopsis, 58 to tomato, 28 to cabbage, 7 to rice, and 8 to corn. In addition, RNA-seq data downloaded from PGSC were utilized to reveal StPUBs' abiotic stress responses and tissue-specific expression in the doubled-monoploid potato (DM). Inaddition, we performed RNA-seq on the 'Atlantic' (drought-sensitive cultivar, DS) and the 'Qingshu NO.9' (drought-tolerant cultivar, DT) in early flowering, full-blooming, along with flower-falling stages to detect genes that might be involved in response to drought stress. Finally, quantitative real-time PCR (qPCR) was carried out to analyze three candidate genes for their expression levels within 100 mM NaCl- and 10% PEG 6000 (w/v)-treated potato plantlets for a 24-h period. Furthermore, we analyzed the drought tolerance of StPUB25 transgenic plants and found that overexpression of StPUB25 significantly increased peroxidase (POD) activity, reduced ROS (reactive oxygen species) and MDA (malondialdehyde) accumulation compared with wild-type (WT) plants, and enhancing drought tolerance of the transgenic plants.

CONCLUSION

In this study, three candidate genes related to drought tolerance in potato were excavated, and the function of StPUB25 under drought stress was verified. These results should provide valuable information to understand the potato StPUB gene family and investigate the molecular mechanisms of StPUBs regulating potato drought tolerance.

Evidence that an Unnamed Isometric Virus Associated with Potato Rugose Disease in Peru Is a New Species of Genus Torradovirus

A previously uncharacterized torradovirus species infecting potatoes was detected by high-throughput sequencing from field samples from Peru and in customs intercepts in potato tubers that originated from South America in the United States of America and the Netherlands. This new potato torradovirus showed high nucleotide sequence identity to an unidentified isometric virus (SB26/29), which was associated with a disease named potato rugose stunting in southern Peru characterized over two decades ago. Thus, this virus is tentatively named potato rugose stunting virus (PotRSV). The genome of PotRSV isolates sequenced in this study were composed of two polyadenylated RNA segments. RNA1 ranges from 7,086 to 7,089 nt and RNA2 from 5,228 to 5,230 nt. RNA1 encodes a polyprotein containing the replication block (helicase-protease-polymerase), whereas RNA2 encodes a polyprotein cleaved into a movement protein and the three capsid proteins (CPs). Pairwise comparison among PotRSV isolates revealed amino acid identity values greater than 86% in the protease-polymerase (Pro-Pol) region and greater than 82% for the combined CPs. The closest torradovirus species, squash chlorotic leaf spot virus, shares amino acid identities of ∼58 and ∼41% in the Pro-Pol and the combined CPs, respectively. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Genome sequence analysis provides insights into the mode of 2n egg formation in Solanum malmeanum

KEY MESSAGE

Our genomic investigation confirms the mechanism of 2n eggs formation in S. malmeanum and aid in optimizing the use of wild germplasm. Wild potatoes are a valuable source of agronomic traits. However, substantial reproductive barriers limit gene flow into cultivated species. 2n gametes are instrumental in preventing endosperm abortion caused by genetic imbalances in the endosperm. However, little is known about the molecular mechanisms underlying the formation of 2n gametes. Here, the wild species Solanum malmeanum Bitter (2x, 1EBN, endosperm balance number) was used in inter- and intrapoloid crosses with other Solanum species, with viable seeds being produced only when S. malmeanum was used as the female parent to cross the 2EBN Solanum genus and with the likely involvement of 2n gametes. Subsequently, we substantiated the formation of 2n eggs in S. malmeanum using fluorescence in situ hybridization (FISH) and genomic sequencing technology. Additionally, the transmission rate of maternal heterozygous polymorphism sites was assessed from a genomic perspective to analyze the mode of 2n egg formation in S. malmeanum × S. tuberosum and S. malmeanum × S. chacoense crosses; each cross acquired an average of 31.12% and 22.79% maternal sites, respectively. This confirmed that 2n egg formation in S. malmeanum attributed to second-division restitution (SDR) coupled with the occurrence of exchange events. The high-throughput sequencing technology used in this study has strong advantages over traditional cytological analyses. Furthermore, S. malmeanum, which has a variety of excellent traits not available from present cultivated potato genepool, has received little research attention and has successfully achieved gene flow in cultivated species in the current study. These findings will facilitate the understanding and optimization of wild germplasm utilization in potatoes.

Prehistoric Plant Exploitation and Domestication: An Inspiration for the Science of De Novo Domestication in Present Times

De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the past. We suggest here that in this process of de novo domestication, the study of Late Paleolithic/Late Archaic and Early Neolithic/Early Formative exploration of wild plants and identification of neglected species can help identify the barriers towards domestication. Modern breeding technologies may then assist us to break these barriers in order to perform de novo domestication to increase the crop species diversity of modern agriculture.

Identification of a Comprehensive Gene Co-Expression Network Associated with Autotetraploid Potato (Solanum tuberosum L.) Development Using WGCNA Analysis

The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. The regulatory mechanisms underlying the growth and development are still unclear. In this work, we aimed to explore the changes in gene expression patterns and genetic characteristics of potato tissues throughout different developmental stages. To achieve this, we used autotetraploid potato JC14 as an experimental subject to analyze the transcriptome of the root, stem, and leaf at the seedling, tuber formation, and tuber expansion stages. The results revealed thousands of differentially expressed genes, predominantly involved in defense response and carbohydrate metabolism according to KEGG pathway enrichment analysis. Weighted gene co-expression network analysis (WGCNA) revealed a total of 12 co-expressed gene modules, with 4 modules showing the highest correlation with potato stem development. By calculating the connectivity of genes within the module, hub genes were identified, and functional annotations were subsequently performed. A total of 40 hub genes from the four modules were identified, and their functions were found to be related to carbohydrate metabolism, defense response, and transcription factors. These findings provide important insights for further understanding of the molecular regulation and genetic mechanisms involved in potato tissue development.

A Compendium for Novel Marker-Based Breeding Strategies in Eggplant

The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.

Global transcriptome and targeted metabolite analyses of roots reveal different defence mechanisms against Ralstonia solanacearum infection in two resistant potato cultivars

Ralstonia solanacearum (Rs), the causal agent of bacterial wilt disease in an unusually wide range of host plants, including potato (Solanum tuberosum), is one of the most destructive phytopathogens that seriously reduces crop yields worldwide. Identification of defence mechanisms underlying bacterial wilt resistance is a prerequisite for biotechnological approaches to resistance breeding. Resistance to Rs has been reported only in a few potato landraces and cultivars. Our in vitro inoculation bioassays confirmed that the cultivars 'Calalo Gaspar' (CG) and 'Cruza 148' (CR) are resistant to Rs infection. Comparative transcriptome analyses of CG and CR roots, as well as of the roots of an Rs-susceptible cultivar, 'Désirée' (DES), were carried out two days after Rs infection, in parallel with their respective noninfected controls. In CR and DES, the upregulation of chitin interactions and cell wall-related genes was detected. The phenylpropanoid biosynthesis and glutathione metabolism pathways were induced only in CR, as confirmed by high levels of lignification over the whole stele in CR roots six days after Rs infection. At the same time, Rs infection greatly increased the concentrations of chlorogenic acid and quercetin derivatives in CG roots as it was detected using ultra-performance liquid chromatography - tandem mass spectrometry. Characteristic increases in the expression of MAP kinase signalling pathway genes and in the concentrations of jasmonic, salicylic, abscisic and indoleacetic acid were measured in DES roots. These results indicate different Rs defence mechanisms in the two resistant potato cultivars and a different response to Rs infection in the susceptible cultivar.

A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes

The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.

Regenerative plantlets with improved agronomic characteristics caused by anther culture of tetraploid potato (Solanum tuberosum L.)

Objective

As the primary means of plant-induced haploid, anther culture is of great significance in quickly obtaining pure lines and significantly shortening the potato breeding cycle. Nevertheless, the methods of anther culture of tetraploid potato were still not well established.

Methods

In this study, 16 potato cultivars (lines) were used for anther culture in vitro. The corresponding relation between the different development stages of microspores and the external morphology of buds was investigated. A highly-efficient anther culture system of tetraploid potatoes was established.

Results

It was shown in the results that the combined use of 0.5 mg/L 1-Naphthylacetic acid (NAA), 1.0 mg/L 2,4-Dichlorophenoxyacetic acid (2,4-D), and 1.0 mg/L Kinetin (KT) was the ideal choice of hormone pairing for anther callus. Ten of the 16 potato cultivars examined could be induced callus with their respective anthers, and the induction rate ranged from 4.44% to 22.67% using this hormone combination. According to the outcome from the orthogonal design experiments of four kinds of appendages, we found that the medium with sucrose (40 g/L), AgNO₃ (30 mg/L), activated carbon (3 g/L), potato extract (200 g/L) had a promotive induction effect on the anther callus. In contrast, adding 1 mg/L Zeatin (ZT) effectively facilitated callus differentiation.

Conclusion

Finally, 201 anther culture plantlets were differentiated from 10 potato cultivars. Among these, Qingshu 168 and Ningshu 15 had higher efficiency than anther culture. After identification by flow cytometry and fluorescence in situ hybridization, 10 haploid plantlets (5%), 177 tetraploids (88%), and 14 octoploids (7%) were obtained. Some premium anther-cultured plantlets were further selected by morphological and agronomic comparison. Our findings provide important guidance for potato ploidy breeding.

Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions

At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity-the Peru-Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern-central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.

Comprehensive Analysis of StSRO Gene Family and Its Expression in Response to Different Abiotic Stresses in Potato

As a highly conserved family of plant-specific proteins, SIMILAR-TO-RCD-ONE (SROs) play an essential role in plant growth, development and response to abiotic stresses. In this study, six StSRO genes were identified by searching the PARP, RST and WWE domains based on the genome-wide data of potato database DM v6.1, and they were named StSRO1–6 according to their locations on chromosomes. StSRO genes were comprehensively analyzed using bioinformatics methods. The results showed that six StSRO genes were irregularly distributed on five chromosomes. Phylogenetic analysis showed that 30 SRO genes of four species were distributed in three groups, while StSRO genes were distributed in groups II and III. The promoter sequence of StSRO genes contained many cis-acting elements related to hormones and stress responses. In addition, the expression level of StSRO genes in different tissues of doubled monoploid (DM) potato, as well as under salt, drought stresses and hormone treatments, was analyzed by RNA-seq data from the online database and quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Furthermore, the expression level of StSRO genes was analyzed by transcriptome analysis under mild, moderate and severe salt stress. It was concluded that StSRO genes could respond to different abiotic conditions, but their expression level was significantly different. This study lays a foundation for further studies on the biological functions of the StSRO gene family.

Biofungicides for Improvement of Potato (Solanum tuberosum L) Production

Potato (Solanum tuberosum L) cultivation originated from Peru in Latin America. The cultivation has spread fast across the globe due to its ability to cope in the warm tropical and temperate climate. It is spotted by the United Nations as the only tuberous crop that can compete with the cereals in productivity. Fungal disease infestation has been identified as a major challenge confronting the farmers during the cultivation and marketing processes. Farmers' reliance on Chemical fungicides has lost its credibility to the adoption of the use of biofungicides due to its toxic, high cost, and environmental hazard effects. The trend of the adoption of biofungicides by potato farmers is gaining ground at a fast rate. Various national governments are devising means of collaborating with the United Nations stakeholders through encouraging research funding and by organizing conferences that will enhance potato production. This could be achieved by minimizing losses through farmer's complete adoption of biofungicides. This review, therefore, examines the various botanicals with antimicrobial properties as potential biofungicide against fungi diseases of potato.

Genomic regions associated with tuber traits in tetraploid potatoes and identification of superior clones for breeding purposes

In potato breeding, morphological tuber traits are important selection targets to meet the demands of the fresh and processing markets. Understanding the genetic basis of tuber traits should guide selection and improve breeding efficiencies. However, this is challenging in potato due to the complexity of the traits and the polyploid nature of the potato genome. High-throughput affordable molecular markers and new software specific for polyploid species have the potential to unlock previously unattainable levels of understanding of the genetic basis of tuber traits in tetraploid potato. In this study, we genotyped a diversity panel of 214 advanced clones with the 22 K SNP potato array and phenotyped it in three field environments in Texas. We conducted a genome-wide association study using the GWASpoly software package to identify genomic regions associated with tuber morphological traits. Some of the QTLs discovered confirmed prior studies, whereas others were discovered for the first time. The main QTL for tuber shape was detected on chromosome 10 and explained 5.8% of the phenotypic variance. GWAS analysis of eye depth detected a significant QTL on chromosome 10 and explained 3.9% of the phenotypic variance. Another QTL peak for eye depth on chromosome 5 was located near the CDF1 gene, an important regulator of maturity in potato. Our study found that multiple QTLs govern russeting in potato. A major QTL for flesh color on chromosome 3 that explained 26% of the phenotypic variance likely represents the Y locus responsible for yellow flesh in potato tubers. Several QTLs were detected for purple skin color on chromosome 11. Furthermore, genomic estimated breeding values were obtained, which will aid in the early identification of superior parental clones that should increase the chances of producing progenies with higher frequencies of the desired tuber traits. These findings will contribute to a better understanding of the genetic basis of morphological traits in potato, as well as to identifying parents with the best breeding values to improve selection efficiency in our potato breeding program.

Alternative modes of introgression-mediated selection shaped crop adaptation to novel climates

Recent plant genomic studies provide fine-grained details on the evolutionary consequences of adaptive introgression during crop domestication. Modern genomic approaches and analytical methods now make it possible to better separate the introgression signal from the demographic signal thus providing a more comprehensive and complex picture of the role of introgression in local adaptation. Adaptive introgression has been fundamental for crop expansion and has involved complex patterns of gene flow. In addition to providing new and more favorable alleles of large effect, introgression during the early stages of domestication also increased allelic diversity at adaptive loci. Previous studies have largely underestimated the effect of such increased diversity following introgression. Recent genomic studies in wheat, potato, maize, grapevine, and ryegrass show that introgression of multiple genes, of as yet unknown effect, increased the effectiveness of purifying selection, and promoted disruptive or fluctuating selection in early cultivars and landraces. Historical selection processes associated with introgression from crop wild relatives provide an instructive analog for adaptation to current climate change and offer new avenues for crop breeding research that are expected to be instrumental for strengthening food security in the coming years.

Diversity and population structure of Nordic potato cultivars and breeding clones

BACKGROUND

The genetic diversity and population structure of breeding germplasm is central knowledge for crop improvement. To gain insight into the genetic potential of the germplasm used for potato breeding in a Nordic breeding program as well as all available accessions from the Nordic genebank (NordGen), 133 potato genotypes were genotyped using the Infinium Illumina 20 K SNP array. After SNP filtering, 11 610 polymorphic SNPs were included in the analysis. In addition, data from three important breeding traits - percent dry matter and uniformity of tuber shape and eye - were scored to measure the variation potato cultivars and breeding clones.

RESULTS

The genetic diversity among the genotypes was estimated using principal coordinate analysis based on the genetic distance between individuals, as well as by using the software STRUCTURE. Both methods suggest that the collected breeding material and the germplasm from the gene-bank are closely related, with a low degree of population structure between the groups. The phenotypic distribution among the genotypes revealed significant differences, especially between farmer's cultivars and released cultivars and breeding clones. The percent heterozygosity was similar between the groups, with a mean average of 58-60%. Overall, the breeding germplasm and the accessions from the Nordic genebank seems to be closely related with similar genetic background.

CONCLUSION

The genetic potential of available Nordic potato breeding germplasm is low, and for genetic hybridization purposes, genotypes from outside the Nordic region should be employed.

Genome architecture and tetrasomic inheritance of autotetraploid potato

Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging the state-of-the-art sequencing technologies and polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting a distinct evolutionary trajectory of potato homologous centromeres. Furthermore, we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny, a feature of autopolyploid inheritance. By distinguishing maternal and paternal haplotype sets in C88, we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations, which were masked in the heterozygous condition by two parents. This study provides insights into the genomic architecture of autopolyploids and will guide their breeding.

Breeding Diploid F1 Hybrid Potatoes for Propagation from Botanical Seed (TPS): Comparisons with Theory and Other Crops

This paper reviews the progress and the way ahead in diploid F1 hybrid potato breeding by comparisons with expectations from the theory of inbreeding and crossbreeding, and experiences from other diploid outbreeding crops. Diploid potatoes can be converted from an outbreeding species, in which self-pollination is prevented by a gametophytic self-incompatibility system, into one where self-pollination is possible, either through a dominant self-incompatibility inhibitor gene (Sli) or knockout mutations in the incompatibility locus. As a result, diploid F1 hybrid breeding can be used to produce genetically uniform potato cultivars for propagation from true potato seeds by crossing two near-homozygous inbred lines, derived from a number of generations of self-pollination despite inbreeding depression. Molecular markers can be used to detect and remove deleterious recessive mutations of large effect, including those in tight repulsion linkage. Improvements to the inbred lines can be made by introducing and stacking genes and chromosome segments of large desirable effect from wild relatives by backcrossing. Improvements in quantitative traits require a number of cycles of inbreeding and crossbreeding. Seed production can be achieved by hand pollinations. F1 hybrid planting material can be delivered to farmers as true seeds or young plants, and mini-tubers derived from true seeds.

5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy

The Solanum genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as Solanum tuberosum (potato), Solanum lycopersicum (tomato), and Solanum melongena (eggplant) as well as medical and ornamental plants. The huge Solanum genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the Solanum genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the Solanum genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the Solanum genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (S. cochoae, S. clivorum, S. macrocarpon, and S. spirale) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the Solanum genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. Petota. The origin of several polyploid species should be reconsidered.

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

Resequencing and genome-wide association studies of autotetraploid potato

Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

Importance of Potato as a Crop and Practical Approaches to Potato Breeding

Potatoes (Solanum tuberosum L. subsp. tuberosum and andigena) and seven other related species, which are cultivated today, have become the most important non-cereal crop in the world. It is grown on a significant scale in 130 countries, with a gross production value of 63.6 billion US dollars in 2016, with the yearly potato production of 368 million tons in 2018. Today potato is grown for food, animal feed, industrial uses, and seed tuber production, depending on the region, country development, and historical reasons. The food production is both for fresh ware markets and for processing into crisps, french fries, canned potatoes, flakes, etc. More than 10,000 potato varieties have been grown worldwide to date, many of which are still grown. Despite such a large number of varieties, there is still a need for new varieties. Classical breeding of new potato varieties in many programs around the world has changed little in decades and differs mainly in terms of scope and technologies used. Until the turn of the millennium, it was based primarily on empirical experience and selection of individual phenotypic traits. The great genetic diversity that exists in potato and its wild relatives is both an opportunity and a challenge to introduce traits that do not currently exist in the potato gene pool into modern potato varieties. Molecular marker technology development has reached the point where published markers for use in commercial breeding are available. Markers can be used during the whole selection process, with an even more important role of molecular breeding in pre-breeding programs and creation of the most appropriate parental lines.

The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato

Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T₁) which had not undergone any selection, or individuals selected at least once in the field (T₂). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T₁) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.

Evaluation of By-Products of Potato Peel as Food Additive

Abstract:

The potato plant is an important food source produced all over the world and it provides a significant portion of daily energy intake in nourishment. In addition, a significant rate of vitamins, fibre, mineral matters, protein, and fat can be obtained by consuming potato. In this study, the production, consumption, and usage areas of potato, a crucial source of our diet, and the possibilities of using it as food additives with the nutritional properties of its peel have been investigated. Generally, potato is consumed after its peel is removed in the homes and industrial areas and many of these peels are disposed off as wastes. Studies show that potato peel has a high content of dietary fibre, protein, carbohydrate, mineral matters, vitamin, phenolic, and antioxidant. The use of potato peel as food additives have also been discussed in this study.

Sequence coverage required for accurate genotyping by sequencing in polyploid species

Polyploidy plays an important role in the evolution of eukaryotes, especially for flowering plants. Many of ecologically or agronomically important plant or crop species are polyploids, including sycamore maple (tetraploid), the world second and third largest food crops wheat (hexaploid) and potato (tetraploid) as well as economically important aquaculture animals such as Atlantic salmon and trout. The next generation sequencing data enables to allocate genotype at a sequence variant site, known as genotyping by sequencing (GBS). GBS has stimulated enormous interests in population based genomics studies in almost all diploid and many polyploid organisms. DNA sequence polymorphisms are codominant and thus fully informative about the underlying genotype at the polymorphic site, making GBS a straightforward task in diploids. However, sequence data may usually be uninformative in polyploid species, making GBS a far more challenging task in polyploids. This paper presents novel and rigorous statistical methods for predicting the number of sequence reads needed to ensure accurate GBS at a polymorphic site bared by the reads in polyploids and shows that a dozen of reads can ensure a probability of 95% to recover all constituent alleles of any tetraploid genotype but several hundreds of reads are needed to accurately uncover the genotype with probability confidence of 90%, subverting the proposition of GBS using low coverage sequence data in the literature. The theoretical prediction was tested by use of RAD-seq data from tetraploid potato cultivars. The paper provides polyploid experimentalists with theoretical guides and methods for designing and conducting their sequence-based studies.

Genome-Wide Identification and Analysis of the NF-Y Gene Family in Potato (Solanum tuberosum L.)

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor in eukaryotes, which is composed of three subunits (NF-YA, NF-YB, and NF-YC). NF-Y has been identified as a key regulator of multiple pathways in plants. Although the NF-Y gene family has been identified in many plants, it has not been reported in potato (Solanum tuberosum). In the present study, a total of 41 NF-Y proteins in potato (StNF-Ys) were identified, including 10 StNF-YA, 22 StNF-YB, and nine StNF-YC subunits, and their distribution on chromosomes, gene structure, and conserved motif was analyzed. A synteny analysis indicated that 14 and 38 pairs of StNF-Y genes were orthologous to Arabidopsis and tomato (Solanum lycopersicum), respectively, and these gene pairs evolved under strong purifying selection. In addition, we analyzed the expression profiles of NF-Y genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the Potato Genome Sequencing Consortium (PGSC) database. Furthermore, we performed RNA-seq on white, red, and purple tuber skin and flesh of three potato cultivars at the tuber maturation stage to identify genes that might be involved in anthocyanin biosynthesis. These results provide valuable information for improved understanding of StNF-Y gene family and further functional analysis of StNF-Y genes in fruit development, abiotic stress tolerance, and anthocyanin biosynthesis in potato.

A chemical window into the impact of RNAi silencing of the StNAC103 gene in potato tuber periderms: Soluble metabolites, suberized cell walls, and antibacterial defense

The growth and survival of terrestrial plants require control of their interactions with the environment, e.g., to defend against desiccation and microbial invasion. For major food crops, the protection conferred by the outer skins (periderm in potato) is essential to cultivation, storage, and marketing of the edible tubers and fruits. Potatoes are particularly vulnerable to bacterial infections due to their high content of water and susceptibility to mechanical wounding. Recently, both specific and conserved gene silencing (StNAC103-RNAi and StNAC103-RNAi-c, respectively) were found to increase the load of wax and aliphatic suberin depolymerization products in tuber periderm, implicating this NAC gene as a repressor of the wax and suberin biosynthetic pathways. However, an important gap in our understanding of StNAC103 silencing concerns the metabolites produced in periderm cells as antimicrobial defense agents and potential building blocks of the deposited suberin biopolymer. In the current work, we have expanded prior studies on StNAC103 silenced lines by conducting comprehensive parallel analyses to profile changes in chemical constituents and antibacterial activity. Compositional analysis of the intact suberized cell walls using solid-state ¹³C NMR (ssNMR) showed that NAC silencing produced an increase in the long-chain aliphatic groups deposited within the periderm cell walls. LC-MS of polar extracts revealed up-regulation of glycoalkaloids in both StNAC103-RNAi and StNAC103-RNAi-c native periderms but down-regulation of a phenolic amine in StNAC103-RNAi-c and a phenolic acid in StNAC103-RNAi native periderms. The nonpolar soluble metabolites identified using GC-MS included notably abundant long-chain alkane metabolites in both silenced samples. By coordinating the differentially accumulated soluble metabolites and the suberin depolymerization products with the ssNMR-based profiles for the periderm polymers, it was possible to obtain a holistic view of the chemical changes that result from StNAC103 gene silencing. Correspondingly, the chemical composition trends served as a backdrop to interpret trends in the chemical barrier defense function of native tuber periderms, which was found to be more robust for the nonpolar extracts.

Genome assembly of primitive cultivated potato Solanum stenotomum provides insights into potato evolution

Genetic diversity is the raw material for germplasm enhancement. Landraces and wild species relatives of potato, which contain a rich gene pool of valuable agronomic traits, can provide insights into the genetic diversity behind the adaptability of the common potato. The diploid plant, Solanum stenotomum (Sst), is believed to have an ancestral relationship with modern potato cultivars and be a potential source of resistance against disease. Sequencing of the Sst genome generated an assembly of 852.85 Mb (N50 scaffold size, 3.7 Mb). Pseudomolecule construction anchored 788.75 Mb of the assembly onto 12 pseudochromosomes, with an anchor rate of 92.4%. Genome annotation yielded 41,914 high-confidence protein-coding gene models and comparative analyses with closely related Solanaceae species identified 358 Sst-specific gene families, 885 gene families with expansion along the Sst lineage, and 149 genes experiencing accelerated rates of protein sequence evolution in Sst, the functions of which were mainly associated with defense responses, particularly against bacterial and fungal infection. Insights into the Sst genome and the genomic variation of cultivated potato taxa are valuable in elaborating the impact of potato evolution in early landrace diploid and facilitate modern potato breeding.

Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly’s usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

DNA methylation affects photoperiodic tuberization in potato (Solanum tuberosum L.) by mediating the expression of genes related to the photoperiod and GA pathways

Overcoming short-day-dependent tuberization to adapt to long-day conditions is critical for the widespread geographical success of potato. The genetic pathways of photoperiodic tuberization are similar to those of photoperiodic flowering. DNA methylation plays an important role in photoperiodic flowering. However, little is known about how DNA methylation affects photoperiodic tuberization in potato. Here, we verified the effect of a DNA methylation inhibitor on photoperiodic tuberization and compared the DNA methylation levels and differentially methylated genes (DMGs) in the photoperiodic tuberization process between photoperiod-sensitive and photoperiod-insensitive genotypes, aiming to dissect the role of DNA methylation in the photoperiodic tuberization of potato. We found that a DNA methylation inhibitor could promote tuber initiation in strict short-day genotypes. Whole-genome DNA methylation sequencing showed that the photoperiod-sensitive and photoperiod-insensitive genotypes had distinct DNA methylation modes in which few differentially methylated genes were shared. Transcriptome analysis confirmed that the DNA methylation inhibitor regulated the expression of the key genes involved in the photoperiod and GA pathways to promote tuber initiation in the photoperiod-sensitive genotype. Comparison of the DNA methylation levels and transcriptome levels identified 52 candidate genes regulated by DNA methylation that were predicted to be involved in photoperiodic tuberization. Our findings provide a new perspective for understanding the relationship between photoperiod-dependent and GA-regulated tuberization. Uncovering the epigenomic signatures of these pathways will greatly enhance potato breeding for adaptation to a wide range of environments.

Mass Spectrometric Monitoring of Plant Hormone Cross Talk During Biotic Stress Responses in Potato (Solanum tuberosum L.)

The potato is among the most important food crops in the world and of incalculable value for global food security. In 2012, the crop area for potato in Northern and Western Europe reached almost 1 million ha and a production of over 37 million tons with an average yield between 18 and 45 tons/ha. However, current potato production is put in jeopardy by a number of important biotic stress factors including late blight (Phytophthora infestans), which was responsible for the disastrous Irish potato famine during 1843-1845. P. infestans shows a remarkable capacity for adaptation with respect to host genotype and applied fungicides. This has made disease management to become more and more difficult and put substantial emphasis on gaining more detailed insight into the molecular bases of plant pathogen interactions, in order to find more sophisticated ways for biological pest control. The plant hormones jasmonic acid (JA) and salicylic acid (SA) play central roles in the regulation of plant responses to biotic foes. In addition, other phytohormones including auxins and abscisic acid (ABA) have also been associated with plant defense responses. For this reason, the parallel analysis of multiple plant hormones in small tissue amounts represents an important field of research in contemporary plant sciences. Here, we describe a highly sensitive and accurate method for the quantitative analysis of ABA, JA, SA, and indole-3-acetic acid in potato plants by gas chromatography-coupled tandem mass spectrometry (GC-MS/MS).

Genetic Diversity and Population Structure of Potato Germplasm in RDA-Genebank: Utilization for Breeding and Conservation

Potato (Solanum tuberosum L.) is an important staple food and economic crop in many countries. It is of critical importance to understand the genetic diversity and population structure for effective collection, conservation, and utilization of potato germplasm. Thus, the objective of the present study was to investigate the genetic diversity and population structure of potato germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea to provide basic data for future preservation and breeding of potato genetic resources. A total of 24 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 482 potato accessions. A total of 257 alleles were detected, with an average of 10.71 alleles per locus. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual accessions within the population, while only 3% was distributed among populations. Results of genetic structure analysis based on STRUCTURE and discriminant analysis of principal components revealed that 482 potato accessions could be divided into two main subpopulations. Accessions of subpopulation 1 mainly belonged to cultivars and breeding lines. Accessions of subpopulations 2 basically corresponded to wild relatives of potatoes. Results of this study provide useful information for potato improvement and conservation programs, although further studies are needed for a more accurate evaluation of genetic diversity and phenotypic traits of potatoes.

Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits

We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon's information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00978-4.

Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato (Solanum tuberosum L.)

Tuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software "WinRHIZO" (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r 2 = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases "StPP1"), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02727-6.

Amplified Fragment Length Polymorphism: Applications and Recent Developments

AFLP or amplified fragment length polymorphism is a PCR-based molecular technique that uses selective amplification of a subset of digested DNA fragments from any source to generate and compare unique fingerprints of genomes. It is more efficient in terms of time, economy, reproducibility, informativeness, resolution, and sensitivity, compared to other popular DNA markers. Besides, it requires very small quantities of DNA and no prior genome information. This technique is widely used in plants for taxonomy, genetic diversity, phylogenetic analysis, construction of high-resolution genetic maps, and positional cloning of genes, to determine relatedness among cultivars and varietal identity, etc. The review encompasses in detail the various applications of AFLP in plants and the major advantages and disadvantages. The review also considers various modifications of this technique and novel developments in detection of polymorphism. A wet-lab protocol is also provided.

Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering

Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.

The evolutionary history and global spatio-temporal dynamics of potato virus Y

Potato virus Y (PVY) is a destructive plant pathogen that causes considerable losses to global potato and tobacco production. Although the molecular structure of PVY is well characterized, the evolutionary and global transmission dynamics of this virus remain poorly understood. We investigated the phylodynamics of the virus by analysing 253 nucleotide sequences of the genes encoding the third protein (P3), cylindrical inclusion protein (CI), and the nuclear inclusion protein (NIb). Our Bayesian phylogenetic analyses showed that the mean substitution rates of different regions of the genome ranged from 8.50 × 10^-5 to 1.34 × 10^-4 substitutions/site/year, whereas the time to the most recent common ancestor of PVY varied with the length of the genomic regions and with the number of viral isolates being analysed. Our phylogeographic analysis showed that the PVY population originated in South America and was introduced into Europe in the 19th century, from where it spread around the globe. The migration pathways of PVY correlate well with the trade routes of potato tubers, suggesting that the global spread of PVY is associated with human activities.

Investigation of Streptomyces scabies Causing Potato Scab by Various Detection Techniques, Its Pathogenicity and Determination of Host-Disease Resistance in Potato Germplasm

Streptomyces scabies is a Gram-positive bacterial pathogen that causes common scab disease to several crops, particularly in the potato. It is a soil borne pathogen, a very devastating scab pathogen and difficult to manage in the field. Streptomyces has several species that cause common scab such as S. scabiei, S. acidiscabies, S. europaeiscabiei, S. luridiscabiei, S. niveiscabiei, S. puniciscabiei, S. reticuliscabiei, S. stelliscabiei, S. turgidiscabies, S. ipomoeae. Common scab disease harmfully affects potato economic and market value due to the presence of black spots on the tuber. Owing to its genetic diversity and pathogenicity, the determination of pathogen presence in potato fields is still challenging. In this study, S. scabies genetic diversity was measured by surveying five potato-growing areas of Pakistan during the growing season 2019. A total of 50 Streptomyces isolates, including S. scabies, S. acidiscabies, S. griseoflavus were isolated and identified based on morphologic, biochemical and molecular analysis. Virulent confirmation assays confirmed ten virulent strains of Streptomyces spp. On the potato cultivars Cardinal and Santee. Among the Streptomyces species, S. scabies showed the highest scab index, followed by S. acidiscabies and S. griseoflavus by exhibiting the scab-like lesions on potato tubers. Ten potato cultivars were screened against these virulent isolates of Streptomyces. The Faisalabad white variety showed the highest scab index followed By Cardinal, Tourag, Kuroda, Santee, Lady Rosetta, Asterix, Diamant, Faisalabad red and Sadaf. Moreover, genetic diversity and pathogenicity of Streptomyces spp. on potato tubers were also likely diverse in different geographical regions and also potato cultivars. This study represents a contribution to understanding the local interaction between potatoes and Streptomyces spp. in Pakistan. It will aid in supporting a solution for the management of this pathogen around the world.

Adaptation to novel environments during crop diversification

In the context of the global challenge of climate change, mitigation strategies are needed to adapt crops to novel environments. The main goal to address this is an understanding of the genetic basis of crop adaptation to different agro-ecological conditions. The movement of crops during the Colombian Exchange that started with the travels of Columbus in 1492 is an example of rapid adaptation to novel environments. Many diversification-related traits have been characterised in multiple crop species, and association-mapping analyses have identified loci involved in these. Here, we present an overview of current knowledge regarding the molecular basis related to the complex patterns of crop adaptation and dissemination, particularly outside their centres of origin. Investigation of the genomic basis of crop expansion offers a powerful contribution to the development of tools to identify and exploit valuable genetic diversity and to improve and design novel resilient crop varieties.