Examination of the hybrid origin of the wild potato Solanum ruiz-lealii Brücher

The common potato, tetraploid Solanum tuberosum spp. tuberosum L. (tbr), has a narrow genetic base but a large number of related tuber-bearing species that harbor genetic diversity for agronomic characters. The taxonomic status of Solanum ruiz-lealii Brücher (rzl), a diploid species endemic to Mendoza province, Argentina, is controversial. It has been described as a new species of non-hybrid origin and as a natural hybrid between S. kurtzianum Bitt. & Wittm. (ktz) and S. chacoense Bitt. (chc). The hypothesis of the hybrid origin of rzl is examined systematically for the first time by phenetic analyses of morphological and molecular (SSR markers) data, and cytological analyses of interspecific hybrids. The morphological, cytological and molecular data are congruent, and suggest that rzl is not a recent natural hybrid between the ktz and the chc populations studied but has probably originated by divergence of chc, or by hybridization between chc and another taxon.     

Hybridization and polyploidization effects on LTR-retrotransposon activation in potato genome

Hybridization and polyploidization are major forces in plant evolution and potatoes are not an exception. It is proposed that the proliferation of Long Terminal Repeat-retrotransposons (LTR-RT) is related to genome reorganization caused by hybridization and/or polyploidization. The main purpose of the present work was to evaluate the effect of interspecific hybridization and polyploidization on the activation of LTR-RT. We evaluated the proliferation of putative active LTR-RT in a diploid hybrid between the cultivated potato Solanum tuberosum and the wild diploid potato species S. kurtzianum, allotetraploid lines derived from this interspecific hybrid and S. kurtzianum autotetraploid lines (ktz-autotetraploid) using the S-SAP (sequence-specific amplified polymorphism) technique and normalized copy number determination by qPCR. Twenty-nine LTR-RT copies were activated in the hybrid and present in the allotetraploid lines. Major LTR-RT activity was detected in Copia-27, Copia-12, Copia-14 and, Gypsy-22. According to our results, LTR-RT copies were activated principally in the hybrid, there was no activation in allotetraploid lines and only one copy was activated in the autotetraploid.

     

Marker-assisted selection of diploid and tetraploid potatoes carryingRpi-phu1, a major gene for resistance toPhytophthora infestans

TheRpi-phu1 gene originates from an interspecific hybrid betweenSolanum stenotomum andS. phureja, and confers a high level of resistance toPhytophthora infestans (late blight) in potato. TheRpi-phu1 was introduced by crossing at the diploid level into theS. tuberosum gene pool and then transferred to the tetraploid level by means of2n gametes. Tetraploid lines carrying theRpi-phu1 were selected for further crosses. A molecular marker GP94, linked in mapping population 97-30 with theRpi-phu1 (6.4 cM), was applied to other unselected populations (2 diploid and 1 tetraploid), and was shown to be useful in marker-assisted selection (MAS) of the resistant individuals. GP94 was applied also in commercial breeding in 2 tetraploid populations. Although the marker allele of GP94, characteristic for theRpi-phu1 presence, was rare in theS. tuberosum gene pool, it seemed to be common in 2 other sources of resistance to late blight:S. ruizceballosii andS. kurtzianum.     

Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei

A population of diploid potato (Solanum tuberosum) was used for the genetic analysis and mapping of a locus for resistance to the potato cyst nematode Globodera rostochiensis, introgressed from the wild potato species Solanum vernei. Resistance tests of 108 genotypes of a F₁ population revealed the presence of a single locus with a dominant allele for resistance to G. rostochiensis pathotype Ro1. This locus, designated GroV1, was located on chromosome 5 with RFLP markers. Fine-mapping was performed with RAPD and SCAR markers. The GroV1 locus was found in the same region of the potato genome as the S. tuberosum ssp. andigena H1 nematode resistance locus. Both resistance loci could not excluded to be allelic. The identification of markers flanking the GroV1 locus offers a valuable strategy for marker-assisted selection for introgression of this nematode resistance.Abbreviations BSA bulked segregant analysis - RAPD random-amplified polymorphic DNA - RFLP restriction fragment length polymorphism - SCAR sequence-characterized amplified region     

GENETIC VARIATION IN PLANT-INSECT ASSOCIATIONS: SURVIVAL OF LEPTINOTARSA DECEMLINEATA POPULATIONS ON SOLANUM CAROLINENSE

Populations of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae), from the east coast of the United States differ in their ability to survive on a wild host, Solanum carolinense (Solanaceae), but not on their most important cultivated host, Solanum tuberosum. On the wild host, the North Carolina population survived best, while populations from Virginia, New Jersey, and Connecticut exhibited uniformly low survival. Formal genetic studies of populations from Connecticut and North Carolina demonstrated heritable variation in the ability to survive on S. carolinense both between and within populations; the North Carolina population had the higher heritability for this trait. Overall, there was no genetic variation between populations or within the North Carolina population for survival on S. tuberosum, but such variation existed within the Connecticut population. Hybrids and backcrosses between these two lines all survived at intermediate levels, although survivorship did not appear to be inherited additively. Differences in survival were greater than differences in adult weight at emergence and development time of the survivors. Leptinotarsa decemlineata was first reported from North Carolina less than 100 years ago. The rapid expansion of L. decemlineata's host range in North Carolina is attributed to the poor synchrony between the insect and S. tuberosum compared to more northerly locations. In contrast to the prediction of a strong negative correlation in fitness on different host species, the ability of L. decemlineata to survive on S. carolinense was not correlated with that on S. tuberosum. Adult weight and female development time were significantly positively correlated across hosts. Our results are in accord with most previous studies in which strong negative correlations in fitness of specialized phytophagous insects feeding on different hosts were expected, sought, but not found.     

Environmentally induced phenotypic plasticity and DNA methylation changes in a wild potato growing in two contrasting Andean experimental gardens

DNA methylation can be environmentally modulated and plays a role in phenotypic plasticity. To understand the role of environmentally induced epigenetic variation and its dynamics in natural populations and ecosystems, it is relevant to place studies in a real-world context. Our experimental model is the wild potato Solanum kurtzianum, a close relative of the cultivated potato S. tuberosum. It was evaluated in its natural habitat, an arid Andean region in Argentina characterised by spatial and temporal environmental fluctuations. The dynamics of phenotypic and epigenetic variability (with Methyl Sensitive Amplified Polymorphism markers, MSAP) were assayed in three genotypes across three growing seasons. These genotypes were cultivated permanently and also reciprocally transplanted between experimental gardens (EG) differing in ca. 1000 m of altitude. In two seasons, the genotypes presented differential methylation patterns associated to the EG. In the reciprocal transplants, a rapid epigenomic remodelling occurred according to the growing season. Phenotypic plasticity, both spatial (between EGs within season) and temporal (between seasons), was detected. The epigenetic and phenotypic variability was positively correlated. The lack of an evident mitotic epigenetic memory would be a common response to short-term environmental fluctuations. Thus, the environmentally induced phenotypic and epigenetic variation could contribute to populations persistence through time. These results have implications for understanding the great ecological diversity of wild potatoes.     

The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence

The complete nucleotide sequence of the chloroplast genome of potato Solanum tuberosum L. cv. Desiree was determined. The circular double-stranded DNA, which consists of 155,312 bp, contains a pair of inverted repeat regions (IRa, IRb) of 25,595 bp each. The inverted repeat regions are separated by small and large single copy regions of 18,373 and 85,749 bp, respectively. The genome contains 79 proteins, 30 tRNAs, 4 rRNAs, and unidentified genes. A comparison of chloroplast genomes of seven Solanaceae species revealed that the gene content and their relative positions of S. tuberosum are similar to the other six Solanaceae species. However, undefined open reading frames (ORFs) in LSC region were highly diverged in Solanaceae species except N. sylvestris. Detailed comparison was identified by numerous indels in the intergenic regions that were mostly located in the LSC region. Among them, a single large 241-bp deletion, was not associated with direct repeats and found in only S. tuberosum, clearly discriminates a cultivated potato from wild potato species Solanum bulbocastanum. The extent of sequence divergence may provide the basis for evaluating genetic diversity within the Solanaceae species, and will be useful to examine the evolutionary processes in potato landraces.     

Characterization of the expression and inheritance of potato leafroll virus (PLRV) and potato virus Y (PVY) resistance in three generations of germplasm derived from Solanum etuberosum

Potato virus Y (PVY) and potato leafroll virus (PLRV) are two of the most important viral pathogens of potato. Infection of potato by these viruses results in losses of yield and quality in commercial production and in the rejection of seed in certification programs. Host plant resistance to these two viruses was identified in the backcross progeny of a Solanum etuberosum Lindl. somatic hybrid. Multiple years of field evaluations with high-virus inoculum and aphid populations have shown the PVY and PLRV resistances of S. etuberosum to be stably expressed in two generations of progeny. However, while PLRV resistance was transmitted and expressed in the third generation of backcrossing to cultivated potato (Solanum tuberosum L. subsp. tuberosum), PVY resistance was lost. PLRV resistance appears to be monogenic based on the inheritance of resistance in a BC₃ population. Data from a previous evaluation of the BC₂ progeny used in this study provides evidence that PLRV resistance was partly conferred by reduced PLRV accumulation in foliage. The field and grafting data presented in this study suggests that resistance to the systemic spread of PLRV from infected foliage to tubers also contributes to the observed resistance from S. etuberosum. The PLRV resistance contributed by S. etuberosum is stably transmitted and expressed through sexual generations and therefore would be useful to potato breeders for the development of PLRV resistant potato cultivars.     

Effect of Plant Oligoadenylates on Viral Infection and Antistress and Growth-Regulating Properties in Potato Plants Grown in vitro

Biological properties of plant oligoadenylates (POA) were studied in in vitro grown potato (Solanum tuberosum L.) plants. POA were synthesized by ATP polymerization in the presence of an enzyme preparation isolated from leaves of wild potato Solanum chacoense Bitt. treated with resistance inducers. The concentration of viral antigen was determined by the method of immunoenzyme analysis. In the course of virus elimination by the apical meristem method, pretreatment of potato tuber sprouts with POA increased the survival rate of meristem explants and, in several cultivars, enhanced morphogenesis and increased the yield of virus-free regenerants. Prolonged application of POA in the nutrient medium for microcutting of potato tube plants infected in vitro with X-, S-, and M-viruses increased their height due to internode lengthening. The effect of this treatment on virus reproduction was ambiguous: various combinations of virus species, the duration of growth on POA-containing media, and POA concentration resulted in either statistically significant inhibition or a significant enhancement of virus reproduction. Possible mechanisms of the antistress effect of POA, in connection with their effect on virus reproduction, are discussed.     

Effects of clonality on the genetic variability of rare,insular species: the case of Ruta microcarpa from the Canary Islands

Many plant species combine sexual and clonal reproduction. Clonal propagation has ecological costs mainly related to inbreeding depression and pollen discounting; at the same time, species able to reproduce clonally have ecological and evolutionary advantages being able to persist when conditions are not favorable for sexual reproduction. The presence of clonality has profound consequences on the genetic structure of populations, especially when it represents the predominant reproductive strategy in a population. Theoretical studies suggest that high rate of clonal propagation should increase the effective number of alleles and heterozygosity in a population, while an opposite effect is expected on genetic differentiation among populations and on genotypic diversity. In this study, we ask how clonal propagation affects the genetic diversity of rare insular species, which are often characterized by low levels of genetic diversity, hence at risk of extinction. We used eight polymorphic microsatellite markers to study the genetic structure of the critically endangered insular endemic Ruta microcarpa. We found that clonality appears to positively affect the genetic diversity of R. microcarpa by increasing allelic diversity, polymorphism, and heterozygosity. Moreover, clonal propagation seems to be a more successful reproductive strategy in small, isolated population subjected to environmental stress. Our results suggest that clonal propagation may benefit rare species. However, the advantage of clonal growth may be only short‐lived for prolonged clonal growth could ultimately lead to monoclonal populations. Some degree of sexual reproduction may be needed in a predominantly clonal species to ensure long‐term viability.     

Effects of contemporary agricultural land cover on Colorado potato beetle genetic differentiation in the Columbia Basin and Central Sands

Landscape structure, which can be manipulated in agricultural landscapes through crop rotation and modification of field edge habitats, can have important effects on connectivity among local populations of insects. Though crop rotation is known to influence the abundance of Colorado potato beetle (CPB; Leptinotarsa decemlineata Say) in potato (Solanum tuberosum L.) fields each year, whether crop rotation and intervening edge habitat also affect genetic variation among populations is unknown. We investigated the role of landscape configuration and composition in shaping patterns of genetic variation in CPB populations in the Columbia Basin of Oregon and Washington, and the Central Sands of Wisconsin, USA. We compared landscape structure and its potential suitability for dispersal, tested for effects of specific land cover types on genetic differentiation among CPB populations, and examined the relationship between crop rotation distances and genetic diversity. We found higher genetic differentiation between populations separated by low potato land cover, and lower genetic diversity in populations occupying areas with greater crop rotation distances. Importantly, these relationships were only observed in the Columbia Basin, and no other land cover types influenced CPB genetic variation. The lack of signal in Wisconsin may arise as a consequence of greater effective population size and less pronounced genetic drift. Our results suggest that the degree to which host plant land cover connectivity affects CPB genetic variation depends on population size and that power to detect landscape effects on genetic differentiation might be reduced in agricultural insect pest systems.     

Protocol for DNA extraction from potato tubers

A method to extract high-quality DNA from potato tubers was developed and tested on 3 wild potato species (Solanum raphanifolium, S. megistracrolobum, S. bukasovii) and on the tetraploid B3 bred population, (population number 393228, derived fromS. tuberosum subsp.tuberosum). The average yield of extracted DNA varied from 10–30 μg of DNA per gram of processed tissue. The DNA was pure and suitable for ligation-mediated polymerase chain reaction (LM-PCR) amplification, producing clear, distinctive, and reproducible banding patterns in polyacrylamide gels.     

Fertilization fitness and offspring ploidy in 3x × 2x matings in potato

Abstract

The main objective of the current research was to study the reproductive behaviour of artificial triploid potato hybrids between wild Solanum commersonii and the cultivated potato Solanum tuberosum. When used in 3x × 2x crosses, triploids gave aneuploid progenies with somatic chromosome number ranging from 29 to 36. Fertilization fitness data suggested that the survival rate of gametes produced by the triploid parents may be related to their chromosome number. In addition, consistent with molecular data, our results indicated that fitness of gametes and chromosome number of progenies are influenced by the genome dosage of interspecific triploids. Since a main route to polyploidy formation is via 2n gametes and triploids, our study may contribute to a better understanding of polyploid plant reproduction, evolution and breeding.     

Field assessment of dihaploid Solatium tuberosum and S. brevidens somatic hybrids

Summary Following both chemical and electrical fusion of protoplasts of a dihaploid line of potato (Solanum tuberosum), (PDH40), with those of the wild species, Solanum brevidens, 11 and 40 somatic hybrid plants, respectively were obtained. Fifteen of these somatic hybrid genotypes and the two parents were studied further in a small field trial to assess field performance and phenotypic variability. In the UK, somatic hybrid plants are classified as genetically engineered organisms, and the UK Advisory Committee on Genetic Manipulation have imposed various restrictions on field experiments. Examination of the somatic hybrids in the field showed extensive phenotypic variability, and no two genotypes were identical. Some of the variation reflected changes in chromosome numbers, but other factors were also involved. Half the somatic hybrid genotypes produced tubers in the field, although the tubers were smaller and differed morphologically from those of PDH40. The results of the study suggest that the extent of somaclonal variation manifested in somatic hybrids is greater than that found in protoplast-derived plants of potato. The implications of this observation and the current regulations concerning field experiments of somatic hybrid plants in the UK are discussed.     

Genetic diversity and reproductive ecology of the sage-leaved rockrose,Cistus salviifolius L., in the Swiss Alps

Range marginal populations are often perceived to have lower conservation value compared to those in the core area. The allocation of resources to maintain peripheral populations is therefore often questioned. The sage-leaved rockrose (Cistus salviifolius L.) is a self-incompatible and obligate seeder widely distributed in the Mediterranean area but rare and patchily distributed in Switzerland at its range margin on the southern slopes of the Alps. Here, we combined analysis of genetic diversity with pollinator surveys and field studies of reproductive ecology to compare peripheral Cistus populations in the Alps with range central populations in the Mediterranean. Our results showed no differences in genetic diversity between peripheral and central populations and between fragmented and connected ones at its range margin in the Alps. Although the fragmented populations were visited by more abundant and species richer pollinators (bees and wasps), they showed lower number of seeds and higher self-compatibility compared to the connected ones, which excludes the pollination limitation hypothesis. Overall, our study highlights that peripheral populations of C. salviifolius in the Alps are likely to contribute to maintain genetic diversity, while showing variation in reproductive ecology, and are therefore important for the conservation of this species.

     

Measuring variation in potato roots in both field and glasshouse: the search for useful yield predictors and a simple screen for root traits

Aims

Potatoes have an inadequate rooting system for efficient acquisition of water and minerals and use disproportionate amounts of irrigation and fertilizer. This research determines whether significant variation in rooting characteristics of potato exists, which characters correlate with final yield and whether a simple screen for rooting traits could be developed.

Methods

Twenty-eight genotypes of Solanum tuberosum groups Tuberosum and Phureja were grown in the field; eight replicate blocks to final harvest, while entire root systems were excavated from four blocks. Root classes were categorised and measured. The same measurements were made on these genotypes in the glasshouse, 2 weeks post emergence.

Results

In the field, total root length varied from 40 m to 112 m per plant. Final yield was correlated negatively with basal root specific root length and weakly but positively with total root weight. Solanum tuberosum group Phureja genotypes had more numerous roots and proportionally more basal than stolon roots compared with Solanum tuberosum, group Tuberosum genotypes. There were significant correlations between glasshouse and field measurements.

Conclusions

Our data demonstrate that variability in rooting traits amongst commercially available potato genotypes exists and a robust glasshouse screen has been developed. By measuring potato roots as described in this study, it is now possible to assess rooting traits of large populations of potato genotypes.     

Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum × rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation‐sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments.     

Genetic diversity in water frog hybrids (Pelophylax esculentus) varies with population structure and geographic location

Pelophylax esculentus is a hybridogenetic frog originating from matings between P. ridibundus (RR) and P. lessonae (LL). Typically, diploid hybrids (LR) live in sympatry with one of their parental species, upon which they depend for successful reproduction. In parts of their range, however, pure hybrid populations can be found. These hybrid populations have achieved reproductive independence from their parental species by using triploid hybrids (LLR, LRR) rather than LL and RR as their sexual hosts. These different breeding systems also entail differences in reproduction (clonal versus sexual) and hence offer the opportunity to study how genetic diversity is affected by reproductive mode, population structure and geographic location. We investigated 33 populations in the Scania region (South Sweden) and 18 additional populations from Northern and Central Europe. Within both genomes (L, R), genetic variability increases with the potential for recombination and declines from the main species distribution area southeast of the Baltic Sea to the fringe populations northwest of the Baltic Sea. Within the main study area in Scania, genetic diversity is low and decreases from a core area to the periphery. Genetic differentiation between Scania populations is small but significant and best explained by ‘isolation by distance’. Despite the low genetic variability within the discrete genomes, all‐hybrid P. esculentus populations in southern Sweden are apparently not suffering from direct negative fitness effects. This is probably because of its somatic hybrid status, which increases diversity through the combination of genomes from two species.     

Strategy differences of two potato species in response to nitrogen starvation. Do plants have a genetic switch for nitrogen signalling?

Survival responses to nitrogen starvation are well known in micro‐organisms but little studied in plants. To construct a framework for study of the plant responses, we investigated the strategy differences of tubers from two closely related potato species. Solanum tuberosum conserves tuber nitrogen by inhibiting shoot growth, but S. phureja mobilizes tuber nitrogen to grow shoots, flowers and seeds. Genetic analysis of progeny from S. phureja–haploid S. tuberosum crosses uncovered segregation of a single dominant gene for the S. tuberosum inhibition strategy. Within S. tuberosum, haploid progeny closely resembled their tetraploid parents, suggesting strong genetic control of the inhibition. Growth of the inhibited shoots was proportional to sub‐optimal levels of added nitrate, and was triggered by exogenous gibberellic acid (GA₃). These observations support the notion that potato plants can closely tie shoot growth to ambient nitrogen levels – probably by a root–shoot nitrogen signal transduction pathway, and that this can be overridden by emergency mobilization of nitrogen reserves, perhaps by GA signalling from the tuber. Furthermore, genes for such developmental switches can be identified by classical genetic analysis of closely related species, such as S. tuberosum and S. phureja, that exhibit opposite survival strategies.     

Managing Potato Biodiversity to Cope with Frost Risk in the High Andes: A Modeling Perspective

Austral summer frosts in the Andean highlands are ubiquitous throughout the crop cycle, causing yield losses. In spite of the existing warming trend, climate change models forecast high variability, including freezing temperatures. As the potato center of origin, the region has a rich biodiversity which includes a set of frost resistant genotypes. Four contrasting potato genotypes –representing genetic variability- were considered in the present study: two species of frost resistant native potatoes (the bitter Solanum juzepczukii, var. Luki, and the non-bitter Solanum ajanhuiri, var. Ajanhuiri) and two commercial frost susceptible genotypes (Solanum tuberosum ssp. tuberosum var. Alpha and Solanum tuberosum ssp. andigenum var. Gendarme). The objective of the study was to conduct a comparative growth analysis of four genotypes and modeling their agronomic response under frost events. It included assessing their performance under Andean contrasting agroecological conditions. Independent subsets of data from four field experiments were used to parameterize, calibrate and validate a potato growth model. The validated model was used to ascertain the importance of biodiversity, represented by the four genotypes tested, as constituents of germplasm mixtures in single plots used by local farmers, a coping strategy in the face of climate variability. Also scenarios with a frost routine incorporated in the model were constructed. Luki and Ajanhuiri were the most frost resistant varieties whereas Alpha was the most susceptible. Luki and Ajanhuiri, as monoculture, outperformed the yield obtained with the mixtures under severe frosts. These results highlight the role played by local frost tolerant varieties, and featured the management importance –e.g. clean seed, strategic watering- to attain the yields reported in our experiments. The mixtures of local and introduced potatoes can thus not only provide the products demanded by the markets but also reduce the impact of frosts and thus the vulnerability of the system to abiotic stressors.