Wild Potato Germplasm Research Articles

Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii.

Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

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

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

De Novo Domestication Concept for Potato Germplasm Enhancement

Wild potato germplasm serves as a natural pool of agronomically valuable traits for potato breeding, such as resistance to pathogens and abiotic stresses, quality, and consumer-oriented traits. The introgression of these traits into cultivated potato is hampered by the different kinds of incompatibility and linkages between desirable and undesirable features in hybrid progeny. The trait donor improvement via correction of negative characteristics prior to hybridization to domestic potato can be a solution to the linkage drag problem. The de novo domestication concept for developing new crops using gene editing technologies was previously proposed and performed for tomato and physalis. In this review, we collected information about donor properties of different wild potato species and developed a strategy for potato germplasm enhancement using the de novo domestication approach. The possible modifications of several candidate genes responsible for undesirable traits in wild potato, including high steroidal glycoalkaloid content, self-incompatibility, tuberization under short day conditions, and long stolons are proposed. The current challenges and future prospects of implementing the de novo domestication strategy for potato are discussed.

A Core Subset of the ex situ Collection of S. demissum at the US Potato Genebank

Useful genetic diversity found in wild potato germplasm is important for progress in potato breeding and science. An effective way to maximize its utilization is through characterization of ex situ collections. For example, marker-based core subsets from large collections are an effective strategy to accelerate evaluation, utilize germplasm, and enhance cost-effectiveness. This project used AFLP markers to create a core subset for the US Potato Genebank’s collection of S. demissum. This species from Mexico and Guatemala is known for excellent levels of late blight resistance and frost tolerance. A total of 149 accessions with diverse geographic origin were characterized with 1403 AFLP markers; these markers were effective on determining genetic associations among the accessions. For the core subset, the AFLP loci were considered as traits, with the presence of the marker as the required state to include in a core. The results of the analyses identified that 10 of the accessions of S. demissum captured 83% of all the markers detected in the whole collection. The inclusion of 28 additional accessions, which had between 1 to 5 unique markers, resulted in a core set of 38 accessions that captured 96% of all the marker diversity. We expect this can benefit the genebank and the potato community by opening opportunities for research, trait screenings, and marker association studies.

Evaluation of Wild Potato Germplasm for Tuber Starch Content and Nitrogen Utilization Efficiency.

Potato wild relatives provide a considerable source of variation for important traits in cultivated potato (Solanum tuberosum L.) breeding. This study evaluates the variation of tuber starch content and nitrogen utilization efficiency (NutE) in wild potato germplasm. For the experiments regarding starch content, 28 accessions of ten different tuber-bearing wild Solanum-species were chosen, and in vitro plantlets were raised from seeds. Twenty plantlets (= genotypes) per accession were then cultivated in the greenhouse until natural senescence and tuber starch content was determined. The average tuber starch content across all genotypes tested was 21.7% of fresh mass. Contents above 28% of fresh mass were found in 50 genotypes, belonging to the species S. chacoense, S. commersonii, S. jamesii, and S. pinnatisectum. Subsequently, 22 wild genotypes revealing high tuber starch contents and four modern varieties of cultivated potato were studied as in vitro plantlets under optimal and low N supply (30 and 7.5 mmol L−1 N). Low N supply lead to a genotype-dependent reduction of shoot dry mass between 13 and 46%. The majority of the wild types also reduced root dry mass by 26 to 62%, while others maintained root growth and even exceeded the NutE of the varieties under low N supply. Thus, wild potato germplasm appears superior to cultivars in terms of tuber starch contents and N utilization efficiency, which should be investigated in further studies.

Screening of wild potato genetic resources for combined resistance to late blight on tubers and pale potato cyst nematodes

The Leibniz Institute of Plant Genetics and Crop Plant Research maintains a diverse collection of wild potato germplasm with more than 2800 accessions from 139 botanical species, 19 Solanum series and 14 countries of origin. During the past two decades, almost half of the collection has been screened for resistance to late blight (Phytophthora infestans) and pale cyst nematode (Globodera pallida (Pa2/3)) infection under laboratory conditions. In particular, resistance to tuber blight was considered, which is an important component of P. infestans resistance and has not been investigated that detailed yet. Out of the 1055 accessions tested, 68 were very resistant and 311 were classified as partially resistant against tuber blight. Besides in accessions of species well-known for foliage resistance, resistance to tuber blight was also observed in previously less reported species such as S. acaule, S. fendleri, S. megistacrolobum, S. polytrichon, S. jamesii, S. trifidum, and S. tarnii. In regard to G. pallida infection, 78 out of 749 tested accessions were classified as resistant, belonging to the species S. acaule, S. circaeifolium, S. gourlayi, S. kurtzianum, S. oplocense, S. sparsipilum, S. spegazzini and S. vernei. New or previously less reported sources of G. pallida resistance were identified in accessions of S. brevicaule, S. demissum and S. microdontum. In various accessions of different species, combined resistance was observed and the relationship to their country of origin is discussed.

Comparison of Two Strategies to Introgress Genes for Resistance to Common Scab from Diploid Solanum chacoense into Tetraploid Cultivated Potato

Wild potato relatives are important sources of novel genes useful for potato improvement. Since most wild potato species are diploid and most cultivars are tetraploid, it is typically necessary to employ ploidy manipulations to access wild potato germplasm. A common strategy is unilateral sexual polyploidization (USP), in which a tetraploid cultivated clone is crossed with a diploid that produces 2n gametes. The diploid parent may be a wild plant selected for a trait of interest. Alternatively, the wild plant may be crossed to a cultivated diploid and, after selection, the diploid hybrid is then crossed to the tetraploid parent. This study was designed to compare these two strategies for the introgression of common scab resistance from wild diploid Solanum chacoense (chc) into cultivated potato. Progeny were evaluated in naturally scab-infested soil in Maine and Michigan. There were no differences between introgression methods for tuber surface area covered by scab. Scab lesions were significantly more severe when a hybrid was used as the diploid parent, but this difference is likely not large enough to be important in a breeding program. Reciprocal cross differences were not significant. However, location x clone interactions were detected for both surface area and lesion type. This study revealed that, while hybridization strategy did not play a major role in developing this scab resistant germplasm, it is critical to consider production environment when screening for resistance.

Considerations for selecting disease resistant wild germplasm (Solanum spp.): lessons from a case study of resistance to bacterial soft rot and Colorado potato beetle

Predictions of distributions of resistance phenotypes have been attempted for major diseases in wild potato germplasm. Interestingly, no consistent taxonomic or biogeographic predictors have been identified. However, an important lesson learned was that there are interactions among host plants, environmental factors, and characters of the pathogens. A logical extension of the predictivity project is to examine the dynamics of resistances when multiple biotic stresses are involved. In this study, we found that populations susceptible to a foliar feeding pest [Colorado potato beetle, Leptinotarsa decemlineata (Say)] are resistant to a bacterial pathogen [Pectobacterium carotovorum subsp. carotovorum (Jones, 1901; Hauben et al. 1999)]. We propose that wounds caused by the insect pest allow the bacterial pathogen to gain entry and cause disease. This would lead to strong selection pressure for resistance to the bacterial pathogen. Consequently, when searching for traits of interest in germplasm collections, it is important to consider the complex biotic and abiotic environments in which the source populations evolved.

Gametic Embryogenic Response in Wild Diploid Solanum Species and its Implications for Genome Sequencing Projects and Breeding

The anther culture response in Solanum commersonii (2n = 2x = 24, 1EBN) and S. chacoense (2n = 2x = 24, 2EBN), two wild potato germplasm resources was studied to obtain haploid plants. Three accessions from each of the two species and 3200 anthers from each genotype were cultured. Authors assessed different culture media; ascorbic acid, L?cysteine and silver nitrate (AgNO3) were included to prevent browning of anther cultures. Addition of AgNO3, was effective to induce embryogenesis. The clones from S. commersonii showed different embryogenic response to androgenesis. However, the three accessions from S. chacoense did not induce any embryo in the same conditions. Ploidy level of the regenerated clones was estimated by flow cytometry and confirmed by chromosome counts. This is the first report of haploid plants obtained from anther culture in S. commersonii, with important implications in sequencing efforts and potato breeding.Plant Tissue Cult. & Biotech. 26(2): 159-173, 2016 (December)

Potential Molecular Markers Associated with Tuber Calcium Content in Wild Potato Germplasm

High tuber Ca is associated with a reduced incidence of disease and physiological disorders in potato (Solanum tuberosum L.). However, genetic variation for tuber Ca content in cultivated potato is low, limiting opportunities to study the genetic basis of this trait. We used wild germplasm to develop a population segregating for tuber Ca concentration. The high‐Ca‐accumulating potato wild relative S. microdontum Bitter (clone M15) was crossed to low‐Ca‐accumulating S. kurtzianum Bitter & Wittm. (clone K12) and 12 F1 individuals were intercrossed to create a segregating population. Significant variation in tuber Ca content was found in this population, and simple sequence repeats (SSRs) were tested for association with tuber Ca content. Twelve of 42 SSRs tested were associated with tuber Ca content. SSR4743 on chromosome 7 was found to be linked to a cation exchanger‐like (CAX3‐like) gene known to be involved with Ca uptake in plants. This SSR may be used to develop a molecular marker to identify tubers with high Ca levels.

Genetic diversity of Bolivian wild potato germplasm: changes during ex situ conservation management and comparisons with resampled in situ populations

Potato wild relatives are important sources of novel variation for the genetic improvement of the cultivated potato. Consequently, many natural populations have been sampled and were deposited as accessions in gene banks around the world. Here we investigate to what extent the genetic variation of Bolivian wild potato species is maintained under gene bank conditions and how this diversity relates to that of current in situ populations. For this purpose, materials from seven potato species were screened for microsatellite variation. Genetic changes between different generations of ex situ germplasm were not observed for Solanum leptophyes and S. megistacrolobum, but were detected for S. neocardenasii and S. okadae, while each of the species S. acaule, S. avilesii and S. berthaultii showed stability in some cases and genetic change in others. The observed changes were ascribed to genetic drift and contamination resulting from human error during regeneration. Re-collected populations of six of the studied species showed highly significant genetic differences with the ex situ accessions that, apart from changes during ex situ maintenance, are most likely to be attributed to sampling effects during collecting and in situ genetic changes over time. The implications of the results for ex situ and in situ conservation strategies of wild potato species are discussed.

Current situation of wild Solanum spp. L. sect. Petota (Solanum, Solanaceae) in some Colombian regions

Potatoes are grown as a staple food in a number of countries around the world. Potatoes production is fourth at the worldwide level and provides carbohydrates and other nutrients in several developing countries. In South America a large diversity of wild and cultivated potato genotypes have been identified, from which several species have been described in Colombia. The last known collections of wild potato germplasm in Colombia were performed up to 1992, and we know little of wild potato distribution since that time. Several factors may threaten these populations, and we performed field surveys of the Colombian populations, as well as a literature review, studies of herbarium specimens from eight Colombian herbaria and databases from reference collections available on the internet. Based in these data we performed field trips in several Colombian regions where wild and cultivated species were reported previously. We identified Solanum andreanum Baker, S. colombianum Dunal and S. flahaultii Bitter, populations according to the taxonomic concepts of Spooner and Fajardo; or S. andreanum, S. colombianum, S. flahaultii, S. moscopanum Hawkes and S. tuquerrense Hawkes, according to the taxonomy of Hawkes. We observed habitat loss or disturbance that may partially explain the apparent decrease or eventual disappearance of some species at specific sites.

Variation in Bactericera cockerelli (Hemiptera: Triozidae) Oviposition, Survival, and Development on Solanum bulbocastanum Germplasm

The potato psyllid, Bactericera cockerelli, is a key pest of potato and important vector of the pathogen that causes zebra chip disease. Control of zebra chip relies entirely on the use of insecticides to reduce populations of this vector. The development of potato varieties resistant to B. cockerelli would contribute to cost-effective control of this insect. Wild potato germplasm are key sources for desirable traits including pest resistance to develop new potato cultivars. Our objective was to screen Solanum bulbocastanum germplasm for resistance to B. cockerelli. The combined use of choice and no-choice assays demonstrated considerable variability among S. bulbocastanum populations in their susceptibility to psyllids. At least six S. bulbocastanum populations exhibited resistance to B. cockerelli: PI 243512, PI 243513, PI 255518, PI 275194, PI 275197, and PI 283096. The documentation of the variability among S. bulbocastanum germplasm populations in their susceptibility to B. cockerelli can aid the development of potato cultivars that are naturally resistant to the potato psyllid.

M6: A Diploid Potato Inbred Line for Use in Breeding and Genetics Research

M6 (Reg. No. GP-1, BS 228) is a diploid self-compatible inbred line of the potato wild relative Solanum chacoense. It is a vigorous, homozygous breeding line derived by self-pollinating the diploid wild potato relative S. chacoense for seven generations. While most wild Solanum species are self-incompatible, this clone is homozygous for the dominant self-incompatibility inhibitor gene Sli. In addition, it is homozygous for 90% of single-nucleotide polymorphism markers in the Infinium Array developed by the SolCAP consortium. M6 is vigorous and both male and female fertile, producing seeds in crosses to diploid cultivated and wild potato germplasm. These traits enable us to systematically develop diploid inbred lines, which was not possible in potato breeding until the discovery of Sli. M6 produces tubers under both short and long photoperiods, unlike other wild potato relatives. In addition, M6 has several desirable traits, including high dry matter content, good chip processing quality, and resistance to soft rot and Verticillium wilt. M6 is being used to develop recombinant inbred line populations.

Pollen-mediated gene flow from a commercial potato cultivar to the wild relativeS. chacoenseBitter under experimental field conditions in Argentina

The common potato, Solanum tuberosum ssp. tuberosum (tbr, 2n = 4x = 48; 4EBN), has many closely related wild tuber-bearing species. Around 28 to 35 of them spontaneously grow in Argentina overlapping, in some areas, with the crop and/or experimental transgenic potatoes. Although it is well proven that hybridization barriers in potatoes can be incomplete, information on gene flow between cultivated and wild germplasm is scarce. Thus, a gene flow field experiment with a circular array was set up in Balcarce, Argentina, in 2009, and evaluated over two seasons. The tetraploid tbr cultivar Huinkul MAG and one compatible cloned genotype of the related wild potato S. chacoense Bitter (chc, 2n = 2x = 24; 2EBN), which produced 2n eggs, were used, respectively, as pollen donor and receptor. Berries with hybrid seeds - as revealed by ploidy and RAPD profiles - were obtained in one season, at 30 m from the pollen donor. These results reinforce others previously obtained with the same pollen donor and a male sterile tbr cultivar in a similar array, pointing out to the need of increasing isolation distances in areas of overlap between cultivated and wild potato germplasm to prevent or minimize undesirable pollen-mediated gene flow.

Hybridization barriers between diploid Solanum tuberosum and wild Solanum raphanifolium

Wild potato germplasm represents a unique, diverse and accessible resource for disease and pest resistance, along with useful agronomic traits that may be introgressed into the cultivated potato (Solanum tuberosum L.). Hybridization of diploid wild Solanum species with haploids (2×) of cultivated potato (4×) is generally an effective technique for introducing genetic diversity and desirable traits into potato. However, in this study, hybridization barriers were found in crosses between S. tuberosum haploids and the wild species S. raphanifolium. Male sterility, likely due to nuclear-cytoplasmic interactions, was observed in some haploid tbr × S. raphanifolium hybrids. In addition, pollen-pistil incompatibilities were observed in backcross, F2, and reciprocal cross hybridization attempts that failed to produce seed. More crosses were successful when F1 clones were crossed as females to wild clones than to cultivated clones. When crosses were made in the other direction, with F1 hybrids used as male parents, seeds were almost never produced.

Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato.

Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to prevent sprouting, minimize disease losses, and supply consumers and the processing industry with high-quality tubers throughout the year. Unfortunately, cold storage triggers an accumulation of reducing sugars in tubers. High-temperature processing of these tubers results in dark-colored, bitter-tasting products. Such products also have elevated amounts of acrylamide, a neurotoxin and potential carcinogen. We demonstrate that silencing the potato vacuolar acid invertase gene VInv prevents reducing sugar accumulation in cold-stored tubers. Potato chips processed from VInv silencing lines showed a 15-fold acrylamide reduction and were light in color even when tubers were stored at 4°C. Comparable, low levels of VInv gene expression were observed in cold-stored tubers from wild potato germplasm stocks that are resistant to cold-induced sweetening. Thus, both processing quality and acrylamide problems in potato can be controlled effectively by suppression of the VInv gene through biotechnology or targeted breeding.

Nitrate Reductase Phylogeny of Potato (Solanum sect. Petota) Genomes with Emphasis on the Origins of the Polyploid Species

Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. There is much disagreement regarding species boundaries and affiliation of species to series. Elucidating the phylogenetic relationships within the polyploids is crucial for an effective taxonomic treatment of the section and for the utilization of wild potato germplasm in breeding programs. We here infer relationships among the potato diploids and polyploids using nitrate reductase (NIA) sequence data in comparison to prior plastid phylogenies and: 1) examine genome types within section Petota, 2) show species in the polyploid series Conicibaccata, Longipedicellata, and in the Iopetalum group to be derived from allopolyploidization, 3) support an earlier hypothesis by confirming S. verrucosum as the maternal genome donor for the polyploid species S. demissum as well as species in the Iopetalum Group, 4) demonstrate that S. verrucosum is the closest relative to the maternal genome donor for species in ser. Longipedicellata, 5) support the close relationship between S. acaule and diploid species from series Megistacroloba and Tuberosa, and 6) show the North and Central American B genome species to be well distinguished from the A genome species of South America.

The potential for genomics in potato improvement.

Abstract Demand for the potato, the fourth most consumed food crop in the world, is steadily increasing. In order to meet the rising demands on the industry, researchers and breeders have been working to better all aspects of potato production, including improvements to the tuber itself. This review will highlight the potential for genomics-assisted advancements, paying particular attention to the genomics tools and resources that are available, and the translation of this information into potato improvements. Immense amounts of genomic data have been generated from expressed sequence tag library construction, molecular linkage maps and microarray expression analyses. This information is helping to clarify the genetic components underlying many of the traits that are important for the continued success of the potato, including increased yields, processing quality traits and disease/pest resistance. Natural genetic resources, such as wild potato varieties and germplasm collections contain valuable genetic variation that, when combined with genomics-assisted breeding techniques such as marker-assisted selection and polymorphism identification, hold great potential for future improvements. With the continued integration of genomics tools and information with rapidly developing technologies such as proteomics and metabolomics, improvements to potato health and quality characteristics will be achieved in an expedited manner with full knowledge and understanding of the genetics involved. Moreover, as the technology advances, the potential exists for the production of potatoes with improved environmental and economic impacts, thus ensuring the sustainability of the industry for future generations.

Genetic heterogeneity estimated by RAPD polymorphism of four tuber-bearing potato species differing by breeding system

Most wild potato germplasm in genebanks is collected, preserved, and evaluated as botanical seed populations that may be highly heterozygous and heterogeneous. However, some species are selfers so potentially very homozygous, perhaps also homogeneous. Intrapopulation heterogeneity increases sampling error that can undermine consistency in seed regeneration in the genebank, screening results, germplasm collecting, and estimates of taxonomic relationships. Thus, knowledge of genetic heterogeneity (GH) can predict the need to commit more resources for larger sample sizes or replication when populations of a given species are being regenerated, evaluated, collected, and classified. This study investigated withinpopulation GH in 32 potato populations comprising four different breeding systems observed inSolatium species:S. fendleri (2n=4x=48, disomic selfer),S. jamesii (2n=2x=24, outcrosser),S. sucrense (2n=4x=48, tetrasomic outcrosser), andS. verrucosum (2n=2x=24, selfer). RAPD markers were used to estimate heterogeneity among 24 individuals per population. Populations ofS. verrucosum were quite homogeneous with an average GH of 6.0%. Similarly low heterogeneity was detected among the eight populations ofS. fendleri (average GH=7.1%). In contrast,S. jamesii andS. sucrense had a much higher GH of 29.4% and 44.1%, respectively. These results demonstrate and quantify the great difference in intrapopulation heterogeneity among wild potato species. Calculations based on intrapopulation heterogeneity indicate that samples should be composed of 25 to 30 random plants for low sample variation that is uniform for all species.