Diploid Populations Research Articles

Role of ploidy in colonization of alpine habitats in natural populations of Arabidopsis arenosa.

Polyploidy is an important driver of plant diversification and adaptation to novel environments. As a consequence of genome doubling, polyploids often exhibit greater colonizing ability or occupy a wider ecological niche than diploids. Although elevation has been traditionally considered as a key driver structuring ploidy variation, we do not know if environmental and phenotypic differentiation among ploidy cytotypes varies along an elevational gradient. Here, we tested for the consequences of genome duplication on genetic diversity, phenotypic variation and habitat preferences on closely related diploid and tetraploid populations that coexist along approx. 2300 m of varying elevation. We sampled and phenotyped 45 natural diploid and tetraploid populations of Arabidopsis arenosa in one mountain range in Central Europe (Western Carpathians) and recorded abiotic and biotic variables at each collection site. We inferred genetic variation, population structure and demographic history in a sub-set of 29 populations genotyped for approx. 36 000 single nucleotide polymorphisms. We found minor effects of polyploidy on colonization of alpine stands and low genetic differentiation between the two cytotypes, mirroring recent divergence of the polyploids from the local diploid lineage and repeated reticulation events among the cytotypes. This pattern was corroborated by the absence of ecological niche differentiation between the two cytotypes and overall phenotypic similarity at a given elevation. The case of A. arenosa contrasts with previous studies that frequently showed clear niche differentiation between cytotypes. Our work stresses the importance of considering genetic structure and past demographic processes when interpreting the patterns of ploidy distributions, especially in species that underwent recent polyploidization events.

Modeling the reproductive impact of aquaculture-produced sexually fertile triploids on conspecific diploid populations

AEI Aquaculture Environment Interactions Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections AEI 11:205-211 (2019) - DOI: https://doi.org/10.3354/aei00308 Modeling the reproductive impact of aquaculture-produced sexually fertile triploids on conspecific diploid populations Federico M. Winkler1,2,3,*, Miguel Concha4, Christopher Concha1 1Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile 2Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Larrondo 1281, Coquimbo 1780000, Chile 3Centro de Innovación Acuícola AquaPacífico, Universidad Católica del Norte, Larrondo 1281, Coquimbo 1780000, Chile 4Departamento de Física, Liceo Bicentenario Alejandro Álvarez Jofre, Victoria 150, Ovalle 1840000, Chile *Corresponding author: fwinkler@ucn.cl ABSTRACT: The use of artificially produced triploid (3n) organisms has been proposed as a strategy to produce total or partial sterility in a number of species in order to prevent the potential negative effects of escapees on the genetic structure and integrity of wild conspecific populations or to avoid having alien species become feral in a new environment. When infertility is incomplete, triploid organisms are able to produce gametes that compete with those produced by wild diploid populations or crops that share the same habitat during reproductive periods, which may adversely affect the reproductive success of the wild population. In the present study, a model was developed in order to estimate the effects of the production of gametes by triploid organisms on the reproductive efficiency of a sympatric diploid population of the same species. The chance of the production of balanced gametes by triploids rapidly reduced with the increase of haploid number of the species. It was concluded that, in most aquatic species, this effect depends on the relative contribution of gametes derived from triploid individuals ( pet), which is determined by the proportion of triploids in the population and their relative fecundity relative to normal diploids. The variation of the reproductive efficiency in a mixed population of diploids and triploids will be directly proportional to pet if only one sex is fertile in triploids but will have a logarithmic relationship if both sexes are fertile. KEY WORDS: Triploids · Risk assessment · Reproductive success · Sterility · Chromosome manipulation · Fecundity Full text in pdf format PreviousNextCite this article as: Winkler FM, Concha M, Concha C (2019) Modeling the reproductive impact of aquaculture-produced sexually fertile triploids on conspecific diploid populations. Aquacult Environ Interact 11:205-211. https://doi.org/10.3354/aei00308 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AEI Vol. 11. Online publication date: May 23, 2019 Print ISSN: 1869-215X; Online ISSN: 1869-7534 Copyright © 2019 Inter-Research.

Cytogeography and chromosomal variation of the endemic East Asian herb Lycoris radiata.

Information on the spatial distribution of cytotypes and karyotype variation in plants is critical for studies of the origin and evolution of polyploid complexes. Here, the spatial distribution of cytological races and intraspecific variation in the karyotype of Lycoris radiata, an endemic species to East Asia, is investigated. Conventional karyotype analysis methods were used to determine ploidy level and karyotypical characteristics in 2,420 individuals from 114 populations of L. radiata nearly covering the whole distribution areas in China. Of 114 populations studied, 52 (45.61%), 58 (50.88%), and 4 (3.51%) are diploid, triploid, and mixoploid populations, respectively, with 1,224, 1,195, and 1 individuals being diploid, triploid, and tetraploid, respectively. The triploid possesses a much wider distribution range than the diploid, with the former almost occupying the entire range of this complex species in East Asia and the latter distributing in the middle and east regions of China. Triploids tend to occur at high altitudes, and the relationship between the ploidy and altitude is significantly positive but low (r 2 = 0.103, p < 0.01). About 98.6% of examined bulbs have a common karyotype consisting of 22 or 33 acrocentric (A) chromosomes. Some aberrant chromosomes which should be generated from A‐type chromosome have been found including metacentrics (m), small metacentrics (m′), and B‐type chromosome. The results can provide a fundamental cytogeographic data for further studies on the evolutionary origins and adaptive divergences of polyploids, especially the triploid, within L. radiata using molecular and/or ecological methods in the future.

Evolution and phylogeography analysis of diploid and polyploid Misgurnus anguillicaudatus populations across China.

The origin and evolution of polyploid organisms have been extensively studied in plants, but this topic remains only partially understood in vertebrates, where polyploidy is relatively rare. In this study, we used Misgurnus anguillicaudatus, a fish that comprises five ploidy levels in nature, as a model animal to improve our understanding of biogeographic history and evolution of polyploid vertebrates. After collecting samples from different geographical populations in China, their ploidy levels were determined using flow cytometry. Two mitochondrial markers ( cytochrome b and control region) were then used for phylogeographic analyses to unravel the possible origins of diploids and tetraploids in China. The results showed that diploids have wider geographical distribution than tetraploids and triploids. There was no clear allopatric geographical range or boundary to divide diploid and polyploid populations. Rather, the analysis of mitochondrial DNA sequences indicated that tetraploids were autopolyploids, with lower genetic diversity than diploids. This suggests that tetraploids originated from sympatric diploids via multiple independent polyploidization events. Genetic structure patterns were similar between diploids and tetraploids, whereas complex genetic differentiation was found among different regions. The potential origin of M. anguillicaudatus was deduced to be in the Pearl River basin, which exhibited the highest nucleotide diversity and genetic differentiation. These findings provide insights into the evolution of polyploidy in vertebrates.

The Rise of Apomixis in Natural Plant Populations.

Apomixis, the asexual reproduction via seed, has many potential applications for plant breeding by maintaining desirable genotypes over generations. Since most major crops do not express natural apomixis, it is useful to understand the origin and maintenance of apomixis in natural plant systems. Here, we review the state of knowledge on origin, establishment and maintenance of natural apomixis. Many studies suggest that hybridization, either on diploid or polyploid cytotypes, is a major trigger for the formation of unreduced female gametophytes, which represents the first step toward apomixis, and must be combined to parthenogenesis, the development of an unfertilized egg cell. Nevertheless, fertilization of endosperm is still needed for most apomictic plants. Coupling of these three steps appears to be a major constraint for shifts to natural apomixis. Adventitious embryony is another developmental pathway toward apomixis. Establishment of a newly arisen apomictic lineage is often fostered by side-effects of polyploidy. Polyploidy creates an immediate reproductive barrier against the diploid parental and progenitor populations; it can cause a breakdown of genetic self-incompatibility (SI) systems which is needed to establish self-fertility of pseudogamous apomictic lineages; and finally, polyploidy could indirectly help to establish an apomictic cytotype in a novel ecological niche by increasing adaptive potentials of the plants. This step may be followed by a phase of diversification and range expansion, mostly described as geographical parthenogenesis. The utilization of apomixis in crops must consider the potential risks of pollen transfer and introgression into sexual crop fields, which might be overcome by using pollen-sterile or cleistogamous variants. Another risk is the escape into natural vegetation and potential invasiveness of apomictic plants which needs careful management and consideration of ecological conditions.

Polyploid breeding strategies for developing hop cultivars in New Zealand

The main objective of the New Zealand hop breeding programme is to develop triploid cultivars with unique brewing properties. Created from crosses between diploid and tetraploid parents, these genotypes have the advantage of being seedless as well as high yielding. Population improvement procedures are used independently for both diploid and tetraploid populations. Restricted maximum likelihood statistical procedures are used for the selection of both male and female genotypes for tetraploid and diploid parental material. In this regard, particular emphasis is placed on identifying sexually derived tetraploids to widen the gene pool. Crosses using tetraploids, as both female and male parents, hybridised with diploid genotypes, are described. Gender segregation ratios from recent triploid seedling populations vary considerably. The statistical analysis of triploid seedling female genotypes from these populations for several key traits is presented. A summary of main chemistry features of New Zealand bred polyploid cultivars is presented. Future breeding strategies for triploid hops are discussed.

The Effect of Consanguinity on Between-Individual Identity-by-Descent Sharing.

Consanguineous unions increase the rate at which identical genomic segments are paired within individuals to produce runs of homozygosity (ROH). The extent to which such unions affect identity-by-descent (IBD) genomic sharing between rather than within individuals in a population, however, is not immediately evident from within-individual ROH levels. Using the fact that the time to the most recent common ancestor for a pair of genomes at a specific locus is inversely related to the extent of IBD sharing between the genomes in the neighborhood of the locus, we study IBD sharing for a pair of genomes sampled either within the same individual or in different individuals. We develop a coalescent model for a set of mating pairs in a diploid population, treating the fraction of consanguineous unions as a parameter. Considering mating models that include unions between sibs, first cousins, and nth cousins, we determine the effect of the consanguinity rate on the mean for pairs of lineages sampled either within the same individual or in different individuals. The results indicate that consanguinity not only increases ROH sharing between the two genomes within an individual, it also increases IBD sharing between individuals in the population, the magnitude of the effect increasing with the kinship coefficient of the type of consanguineous union. Considering computations of ROH and between-individual IBD in Jewish populations whose consanguinity rates have been estimated from demographic data, we find that, in accord with the theoretical results, increases in consanguinity and ROH levels inflate levels of IBD sharing between individuals in a population. The results contribute more generally to the interpretation of runs of homozygosity, IBD sharing between individuals, and the relationship between ROH and IBD.

Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling.

Dissecting complex connections between cytogenetic traits (ploidy levels) and plant invasiveness has emerged as a popular research subject in the field of invasion biology. Although recent work suggests that polyploids are more likely to be invasive than their corresponding diploids, the molecular basis underlying the successful invasion of polyploids remains largely unexplored. To this end, we adopted an RNA‐seq and sRNA‐seq approach to describe how polyploids mediate invasiveness differences in two contrasting cytotypes of Solidago canadensis L., a widespread wild hexaploid invader with localized cultivated diploid populations. Our analysis of the leaf transcriptome revealed 116,801 unigenes, of which 12,897 unigenes displayed significant differences in expression levels. A substantial number of these differentially expressed unigenes (DEUs) were significantly associated with the biosynthesis of secondary metabolites, carbohydrate metabolism, lipid metabolism, and environmental adaptation pathways. Gene Ontology term enrichment‐based categorization of DEU‐functions was consistent with this observation, as terms related to single‐organism, cellular, and metabolic processes including catalytic, binding, transporter, and enzyme regulator activity were over‐represented. Concomitantly, 186 miRNAs belonging to 44 miRNA families were identified in the same leaf tissues, with 59 miRNAs being differentially expressed. Furthermore, we discovered 83 miRNA‐target interacting pairs that were oppositely regulated, and a meticulous study of these targets depicted that several unigenes encoding transcription factors, DNA methyltransferase, and leucine‐rich repeat receptor‐like kinases involved in the stress response were greatly influenced. Collectively, these transcriptional and epigenetic data provide new insights into miRNA‐mediated gene expression regulatory mechanisms that may operate in hexaploid cytotypes to favor successful invasion.

Complex genetic relationships within and among cytotypes in the Lepidosperma costale species complex (Cyperaceae) on rocky outcrops in Western Australia

There is a growing realisation that cytotype variation within species complexes plays an important role in plant evolution; however, there are relatively few investigations that describe the genetic diversity within and among related cytotypes. In the present study, we analysed patterns of genetic variation in 774 individuals from nine diploid, 14 tetraploid and five mixed ploidy populations of the Lepidosperma costale complex (Cyperaceae) from rocky outcrops in south-west Australia. Application of nuclear (nSSR) and chloroplast (cpSSR) microsatellites suggests that polyploids are of autopolyploid and allopolyploid origin and that polyploidisation is associated with a shift to facultative clonal reproduction, including apomictic reproduction. The newly-discovered putative allopolyploids were commonly associated with disturbed environments, an association commonly reported for allopolyploids. Diploid populations generally contained more genetic diversity than polyploid populations, and there was little genetic differentiation among diploid populations. In contrast, polyploids were characterised by higher heterozygosity and differentiation among populations, but possessed lower within-population diversity. The high differentiation among polyploid populations suggests that polyploids may have formed recurrently and are an important component of morphologically cryptic diversity within the species complex. Ploidy level is a critical factor affecting genetic diversity in this species complex, highlighting the potential contributions of polyploidy to genetic differentiation, and potentially speciation.

Fitness Cost and Competitive Ability to Different Ploidy Levels in Ryegrass Genotypes

ABSTRACT: The intergenotypic competition of tetraploid ryegrass with natural diploid population may be a tool to reduce the frequency of resistant individuals in an area. This study aimed to identify and compare the phenological development, fitness cost, and competitive ability between diploid and tetraploid ryegrass genotypes. Genotypes were grown in pots, and the morphological variables of genotype growth were assessed every 15 days up to 120 days after emergence to evaluate the fitness cost. Phenological development and seed yield components were measured in a single time together with the fitness cost. Competitive ability was determined in a replacement-series experiment with proportions of tetraploid and diploid ryegrass, in which the number of tillers, plant height, leaf area, and shoot dry weight were assessed at 50 days after emergence. The results of fitness cost showed that the number of tillers, leaf area, root dry weight, and the number of seeds were higher for tetraploid ryegrass, which presented a higher competitive ability than the diploid genotype regardless of the tested proportions. Tetraploid ryegrass may be useful for reducing the frequency of herbicide-resistant diploid ryegrass because of its higher competitive potential.

Animal conflicts in diploid populations with sexual reproduction

The classical, monomorphic, evolutionary games analyze competition among phenotypes while implicitly assuming monomorphic transmission of phenotypic attributes to successive generations. The recently formulated polymorphic evolutionary game theory (PEGT), which adds the underlying genetics and sexual reproduction to evolutionary games, has the potential to revolutionize game theoretical modeling of co-evolutionary processes.In this paper, I apply PEGT methods to the analysis of animal conflicts — the oldest, and one of the best-developed areas of evolutionary game modeling. Overall, the polymorphic results are consistent with the sequential assessment hypothesis. However, beyond the specific, the results indicate the need for a degree of caution applied to the existing evolutionary stability results — as the polymorphic analysis shows that monomorphic ESS can be destabilized by sexual recombination.Finally, due to the novelty of the analytical approach, I make a particular emphasis on methodology: in particular, demonstrating how to combine generation of pertinent phenotypes with genetic plausibility considerations in the design of PEGT models.

Divergent impact of actin isoforms on cell cycle regulation

ABSTRACTWe have shown that cytoplasmic actin isoforms play different roles in neoplastic cell transformation. β-Cytoplasmic actin acts as a tumor suppressor, affecting epithelial differentiation, cell growth, cell invasion and tumor growth of colon and lung carcinoma cells. In contrast, γ-cytoplasmic actin enhances malignant features of tumor cells whose actin network regulation is carried out via the γ-actin isoform. The goal of this study was to describe the role of cytoplasmic actins in cell cycle regulation of breast cancer cell lines MCF-7 and MDA-MB-231. The distinct roles of each cytoplasmic actin in the cell cycle driving were observed. β-Actin as well as γ-actin down-regulation inhibited proliferation of breast cancer cells, but only down-regulation of β-actin induced a significant decrease in diploid cell population and accumulation of tetraploid cells. Down-regulation of β-actin stimulated cyclin A2, B1 and D3 expression, whereas down-regulation of γ-actin reduced expression of these cyclins in both cell lines. Moreover, cyclin B1 and γ-actin were co-localized in mitotic control and β-actin-deficient cells. In mitotic MCF-7 cells down-regulation of β-actin caused an enrichment of prophase/metaphase population compared with control. γ-Actin down-regulation induced telophase enrichment.ERK1/2 and γ-actin co-localization and possible selective binding were revealed in MCF7 cells. β-Actin down-regulation induced ERK1/2 activation, while γ-actin down-regulation led to reduction of p-ERK1/2. A direct interaction of ERK1/2 with γ-actin and cyclin A2 in the same protein complex was also discovered. We suggest that γ-actin down-regulation leads to decrease of cyclin A2 level, inhibits ERK1/2 signaling and deceleration of breast cancer cells proliferation.

A member of the TERMINAL FLOWER 1/CENTRORADIALIS gene family controls sprout growth in potato tubers.

Potato tuber bud dormancy break followed by premature sprouting is a major commercial problem which results in quality losses and decreased tuber marketability. An approach to controlling premature tuber sprouting is to develop potato cultivars with a longer dormancy period and/or reduced rate of sprout growth. Our recent studies using a potato diploid population have identified several quantitative trait loci (QTLs) that are associated with tuber sprout growth. In the current study, we aim to characterize a candidate gene associated with one of the largest effect QTLs for rapid tuber sprout growth on potato chromosome 3. Underlying this QTL is a gene encoding a TERMINAL FLOWER 1/CENTRORADIALIS homologue (PGSC0003DMG400014322). Here, we use a transgenic approach to manipulate the expression level of the CEN family member in a potato tetraploid genotype (cv. Désirée). We demonstrate a clear effect of manipulation of StCEN expression, with decreased expression levels associated with an increased rate of sprout growth, and overexpressing lines showing a lower rate of sprout growth than controls. Associated with different levels of StCEN expression were different levels of abscisic acid and cytokinins, implying a role in controlling the levels of plant growth regulators in the apical meristem.

Maximum avoidance of inbreeding in haplodiploid populations

Maximum avoidance of inbreeding (MAI) is a mating system, in which mates are as distantly related as possible. Although theoretical aspects and applications of MAI in diploid populations have been studied by many researchers, extension of MAI to haplodiploid populations is an unresolved problem. In this paper, this problem is addressed, and the following conclusions are derived. For a haplodiploid population with a Fibonacci number of females, a set of mating systems (one cycle MAI-hd) to avoid inbreeding to the maximum after one cycle practice of the set can be defined. But unlike MAI in diploid populations, repetition of one cycle MAI-hd cannot be MAI in the global range of generations. Numerical comparison with random mating and circular half-sib mating shows that as in diploid populations, repetition of one cycle MAI-hd in haplodiploid populations attains a lower inbreeding coefficient in early generations at the expense of a higher asymptotic rate of inbreeding.

Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in Knautia serpentinicola (Caprifoliaceae).

Whole genome duplication is a key process in plant evolution and has direct phenotypic consequences. However, it remains unclear whether ploidy-related phenotypic changes can significantly alter the fitness of polyploids in nature and thus contribute to establishment of new polyploid mutants in diploid populations. We addressed this question using a unique natural system encompassing a diploid and its sympatric locally established autotetraploid derivative. By setting a common garden experiment with two manipulated environmental factors (presence/absence of serpentine substrate and competition), we tested whether these two locally important factors differently shape the phenotypic response of the two ploidy levels. Tetraploids attained significantly higher values of both above- and below-ground biomass, and root:shoot ratio compared to their diploid progenitors. Tetraploid superiority in vegetative fitness indicators was most prominent when they were cultivated together with a competitor in nutrient-rich nonserpentine substrate. We show that even genetically very closely related diploids and tetraploids can respond differently to key environmental factors. Provided there are sufficient nutrients, tetraploids can be more successful in tolerating interspecific competition than their diploid progenitors. Such superior performance might have provided an adaptive advantage for the newly established tetraploid promoting colonisation of new (micro-)habitats, which was indeed observed at the natural site.

Meiotic irregularities in diploid and tetraploid plants of Lolium multiflorum Lam.

The genus Lolium comprises several species of economical importance in temperate countries, mostly due to their high nutritional value and adaptability to cold environments, including southern regions of Brazil. Recently, several diploid cultivars and populations, as well as synthetic tetraploid cultivars have been explored. In order to viabilize or to direct crossings, it is important that the accessions present regular meiosis, thus, producing viable pollen grains. In this way, this study aimed at investigating the meiosis of nine accessions of Lolium multiflorum used in breeding programs, seeking to evaluate its viability in future crossings. The meiosis of diploid plants (2n = 2× = 14) is more regular than the artificially tetraploidized genotypes (2n = 4× = 28). In the tetraploids, univalent, bivalent, and multivalent configurations were observed. The irregularities were associated to mixoploidy, irregular segregation of chromosomes, spindle disorders, asynchrony, micronuclei, and cellular fusion and formation of syncyte. The abnormalities affected the meiotic index of tetraploid cultivars, characterizing them as unstable. Nevertheless, both diploid and tetraploid genotypes are considered able to participate in crossings because, although there are abnormalities, they do not occur at levels that could affect the production of viable pollen grains.

De novo construction of polyploid linkage maps using discrete graphical models.

Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. To remedy these issues, we propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a non-paranormal skeptic approach. We determine linkage groups, typically chromosomes, and the order of markers in each linkage group by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We apply the proposed method to three genotype datasets: barley, peanut and potato from diploid and polyploid populations. The method is implemented in the R package netgwas which is freely available at https://cran.r-project.org/web/packages/netgwas. Supplementary data are available at Bioinformatics online.

Efficient computation of the kinship coefficients.

For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations. Historically, computations of the inbreeding coefficient were used to prohibit inbred marriages and prohibit breeding of some pairs of pedigree animals. Such prohibitions foster genetic diversity and help prevent recessive Mendelian disease at a population level. This paper gives the fastest known algorithms for computing the kinship coefficient of a set of individuals with a known pedigree, especially for large pedigrees. These algorithms outperform existing methods. In addition, the algorithms given here consider the possibility that the founders of the known pedigree may themselves be inbred and compute the appropriate inbreeding-adjusted kinship coefficients, which has not been addressed in literature. The exact kinship algorithm has running-time O(n2) for an n-individual pedigree. The recursive-cut exact kinship algorithm has running time O(s2m) where s is the number of individuals in the largest segment of the pedigree and m is the number of cuts. The approximate algorithm has running-time O(nd) for an n-individual pedigree on which to estimate the kinship coefficients of n individuals of interest from n founder kinship coefficients and d is the number of samples. The above polynomial-time exact algorithm and the linear-time approximation algorithms are implemented as PedKin in C++ and are available under the GNU GPL v2.0 open source license. The PedKin source code is available at: http://www.intrepidnetcomputing.com/research/code/.

Novel gene Sen2 conferring broad-spectrum resistance to Synchytrium endobioticum mapped to potato chromosome XI

Key message Sen2gene for potato wart resistance, located on chromosome XI in a locus distinct fromSen1, provides resistance against eight wart pathotypes, including the virulent ones important in Europe.Synchytrium endobioticum causes potato wart disease imposing severe losses in potato production, and as a quarantine pathogen in many countries, it results in lost trade markets and land for potato cultivation. The resistance to S. endobioticum pathotype 1(D1) is widespread in potato cultivars but new virulent pathotypes appear and the problem re-emerges. To characterize and map a new gene for resistance to potato wart, we used diploid F1 potato population from a cross of potato clone resistant to S. endobioticum pathotype 1(D1) and virulent pathotypes: 2(G1), 6(O1), 8(F1), 18(T1), 2(Ch1), 3(M1) and 39(P1) with a potato clone resistant to pathotype 1(D1) only. The 176 progeny clones were tested for resistance to eight wart pathotypes with a modified Glynne–Lemmerzahl method. Bimodal distributions and co-segregation of resistance in the population show that a single resistance gene, Sen2, underlies the resistance to eight pathotypes. Resistance to pathotype 1(D1) was additionally conferred by the locus Sen1 inherited from both parents. Sen2 was mapped to chromosome XI using DArTseq markers. The genetic and physical distances between Sen1 and Sen2 loci were indirectly estimated at 63 cM and 32 Mbp, respectively. We developed PCR markers co-segregating with the Sen2 locus that can be applied in marker-assisted selection of potatoes resistant to eight important pathotypes of S. endobioticum. Wide spectrum of the Sen2 resistance may be an indication of durability which can be enhanced by the pyramiding of the Sen2 and Sen1 loci as in 61 clones selected within this study.

SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species.

QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations. Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references-A. duranensis V14167 genome sequence, and transcriptome sequences of A. duranensis KSSc38901 and OLin. More than 49,000 SNPs differentiated the parents, and 87.9% of the 190 SNP calls tested were validated. SNPs were then genotyped on 91 F2 lines using KASP chemistry on a Roche LightCycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1040cM. Comparison of the A-genome map to the A. duranensis genome sequence revealed a high degree of synteny. QTL analysis was also performed on the mapping population for important architectural traits. Fifteen definitive and 16 putative QTLs for petiole length, leaflet length and width, leaflet area, leaflet length/width ratio, main stem height, presence of flowers on the main stem, and seed mass were identified. Results demonstrate that SNPs identified from transcriptome sequencing could be converted to KASP or SNPType markers with a high success rate, and used to identify alleles with significant phenotypic effects, These could serve as information useful for introgression of alleles into cultivated peanut from wild species and have the potential to allow breeders to more easily fix these alleles using a marker-assisted backcrossing approach.