Genetic diversity of the Andean blackberry (Rubus glaucus Benth.) in Ecuador assessed by AFLP markers

Andean blackberry (Rubus glaucus Benth.) is an emerging fruit crop with significant commercial potential. Despite its growing popularity, basic research about its genetic resources and breeding remains insufficient. The aim of this study was to assess the genetic diversity of Andean blackberry cultivars and related berries species from the main production areas in Ecuador. We analysed a total of 106 samples and performed DNA screening with different molecular markers: random-amplified polymorphic DNAs (RAPDs), inter-simple sequence repeats (ISSRs) and a set of representative samples with amplified fragment length polymorphisms (AFLPs). The tested RAPD primers did not reveal any differentiation among accessions identified as R. glaucus, however one ISSR primer was useful to find polymorphisms allowing the selection of 29 accessions for the analysis with AFLP markers. AFLP-M13 technology was used for screen genetic variations among these accessions and eight wild Rubus accessions. We scored 203 bands using five primer combinations; out of these 152 were informative in R. glaucus. AFLP markers clearly distinguish R. glaucus from the screened wild Rubus species, also an unexpected genetic structure was revealed among R. glaucus cultivars. This genetic differentiation and detection of admixed genotypes suggest a possible introgression of wild Rubus species in R. glaucus. Our findings are relevant for blackberry genetic breeding and use of these genetic resources.

Native and invasive populations of the ectomycorrhizal death cap Amanita phalloides are highly sexual but dispersal limited

The ectomycorrhizal death cap Amanita phalloides is native to Europe but invasive in North America. To understand whether the fungus spreads underground using hyphae, or above ground using sexual spores, we mapped and genotyped sporocarps from European and American populations. Larger genetic individuals (genets) would suggest spread mediated by vegetative growth, while many small genets would suggest dispersal mediated by spores. To test whether genets are ephemeral or persistent, we also sampled from the same invasive populations over time.We mapped 13 European and American populations between 2004-2007 and characterized each using amplified fragment length polymorphisms (AFLP). In 2014 and 2015, we resampled populations in California and added three new European populations. These populations and a subset of the specimens originally collected in 2004 were characterized using whole genome sequencing.In every population and across all time points, sporocarps resolve into small, apparently short-lived genets. Sporocarps nearer each other are more closely related, suggesting spores land and germinate near parent sporocarps.A. phalloides uses spores to move across landscapes. Spores travel very short distances and individuals appear ephemeral. The death cap’s life history suggests yearly sporocarp removal as a strategy for control of this deadly fungus.

The morphometrics of autopolyploidy: insignificant differentiation among sexual–apomictic cytotypes

Polyploidization of the plant genome affects the phenotype of individuals including their morphology, i.e. size and form. In autopolyploids, we expect mainly nucleotypic effects, from a number of monoploid genomes (i.e. chromosome sets) or genome size, seen from an increase in size or dimension of the polyploids compared with the diploids (or lower ploids). To identify nucleotypic effects, confounding effects of hybridity (observed in allopolyploids), postpolyploidization processes or environmental effects need to be considered. We morphometrically analysed five ploidy cytotypes of the sexual–apomictic species Potentilla puberula cultivated ex situ under the same experimental conditions. Sexuals are mainly tetraploid, while higher ploidy (penta- to octoploidy) is typically associated with the expression of apomixis. The cytotypes likely arose via autopolyploidization although historic involvement of another species in the origin of apomicts cannot be fully ruled out, suggested by a slight molecular differentiation among reproductive modes. We (i) revisited molecular differentiation using amplified fragment length polymorphisms and performed a morphometric analysis to test (ii) if cytotypes are morphologically differentiated from each other and (iii) if the size of individuals is related to their ploidy. Weak molecular differentiation of sexual versus apomictic individuals was confirmed. Cytotypes and reproductive modes were also morphologically poorly differentiated from each other, i.e. apomicts largely resampled the variation of the sexuals and did not exhibit a unique morphology. Overall size of individuals increased moderately but significantly with ploidy (ca. 14 % in the comparison of octo- with tetraploids). The results support an autopolyploid origin of the P. puberula apomicts and suggest a nucleotypic effect on overall plant size. We discuss taxonomic consequences of the results in the context of data on reproductive relationships among cytotypes and their ecological preferences and evolutionary origin, and conclude that cytotypes are best treated as intraspecific variants within a single species.

Genetic variability assessment in ‘Muscat’ grapevines including ‘Muscat of Alexandria’ clones from selection programs

Genetic variability is needed to face environmental changes and pathogen constrains. In addition, the search for intravarietal variability contributes to the avoidance of genetic erosion, preserving clones that are adapted to particular conditions. Variability is also important to diversify grapevine-derived products. In this work, we have analyzed the genetic variability of ‘Muscat germplasm’ including samples from neglected vineyards from Alicante and Valencia provinces, accessions of the germplasm collections of ‘Colección de Vides de El Encín’ (Alcalá de Henares, Madrid) and ‘La Casa de las Vides’ (Agullent, Valencia), accessions supplied by nurseries of Valencia province, and ‘Muscat of Alexandria’ clones selected using differential ampelographic characteristics in selection programs (La Marina, Alicante). Fifteen microsatellites (SSRs) were used to study intervarietal variability. The SSR fingerprinting allowed the identification of some accessions, variants, and synonymies. Amplified Fragment Length Polymorphisms (AFLPs) markers and Microsatellite-AFLPs were used to determine the variability attended in ‘Muscat of Alexandria’ accessions. A CAPs (Cleaved Amplified Polymorphic Sequences) marker, recently developed for the discrimination of ‘Muscat’ flavor genotypes using the SNP1822 G>T, was assessed and showed that all the analyzed accessions were ‘Muscat’ flavored. The variation found among the analyzed germplasm is very interesting because variants within ‘Muscat of Alexandria’, ‘Muscat Italia’, and ‘Muscat d’Istambul’ have been identified. In addition, intravarietal genetic variation was found among the analyzed accessions in ‘Muscat of Alexandria’ from selection programs.

Occasional hybridization between a native and invasiveSeneciospecies in Australia is unlikely to contribute to invasive success

BackgroundHybridization between native and invasive species can facilitate introgression of native genes that increase invasive potential by providing exotic species with pre-adapted genes suitable for new environments. In this study we assessed the outcome of hybridization between nativeSenecio pinnatifoliusvar.pinnatifoliusA.Rich. (dune ecotype) and invasiveSenecio madagascariensisPoir. to investigate the potential for introgression of adaptive genes to have facilitatedS. madagascariensisspread in Australia.MethodsWe used amplified fragment length polymorphisms (141 loci) and nuclear microsatellites (2 loci) to genotype a total of 118 adults and 223 seeds fromS. pinnatifoliusvar.pinnatifoliusandS. madagascariensisat one allopatric and two shared sites. We used model based clustering and assignment methods to establish whether hybrid seed set and mature hybrids occur in the field.ResultsWe detected no adult hybrids in any population. Low incidence of hybrid seed set was found at Lennox Head where the contact zone overlapped for 20 m (6% and 22% of total seeds sampled forS. pinnatifoliusvar.pinnatifoliusandS. madagascariensisrespectively). One hybrid seed was detected at Ballina where a gap of approximately 150 m was present between species (2% of total seeds sampled forS. madagascariensis).ConclusionsWe found no evidence of adult hybrid plants at two shared sites. Hybrid seed set from both species was identified at low levels. Based on these findings we conclude that introgression of adaptive genes fromS. pinnatifoliusvar.pinnatifoliusis unlikely to have facilitatedS. madagascariensisinvasions in Australia. Revisitation of one site after two years could find no remainingS. pinnatifoliusvar. pinnatifolius, suggesting that contact zones between these species are dynamic and thatS. pinnatifoliusvar. pinnatifoliusmay be at risk of displacement byS. madagascariensisin coastal areas.

Invasive Russian Knapweed (Acroptilon repens) Creates Large Patches Almost Entirely by Rhizomic Growth

Russian knapweed is an outcrossing perennial invasive weed in North America that can spread by both seed and horizontal rhizomic growth leading to new shoots. The predominant mode of spread at the local scale and dispersal at the long-distance scale informs control but has not been quantitatively researched. We used amplified fragment-length polymorphisms (AFLPs) of DNA collected from 174 shoots in two discrete patches of Russian knapweed at each of three locations in Montana. Out of the 174 shoots collected, we found nine AFLP genotypes. Three out of the six patches were monotypic; the other three patches each had one rare genotype. No genotypes were shared between patches. The maximum diameter of a genet (a genetic individual) was 56.5 m. These results indicate that patch expansion at the local scale is almost entirely by rhizomes that spread and develop new shoots. At the long-distance scale, dispersal is by seed. Controlling seed development through biological control and herbicide use may be effective at stopping long-distance dispersal but may not affect expansion of existing patches.

Amplified fragment length polymorphisms (AFLP's)

AFLP is a combination restriction fragment/PCR molecular marker technique which detects polymorphisms due to changes at or in the vicinity of restriction enzyme sites. The technique detects multiple polymorphic loci throughout the genome and may be used for fingerprinting and mapping purposes. The main advantages of the method are the consistency and reliability of the technique due to stringent PCR conditions and the ability to rapidly detect many polymorphic loci.

Spatial genetic structure in four Pinus species in the Sierra Madre Occidental, Durango, Mexico

In this study, we examined the spatial genetic structure (SGS) in extensively managed, but naturally regenerated forest stands of Pinus cembroides Zucc., Pinus discolor Bailey et Hawksworth, Pinus durangensis Martínez, and Pinus teocote Schiede ex Schltdl. & Cham. at local (within the stands) and large (among the stands) scales using amplified fragment length polymorphisms (AFLP), with respect to conservation and sustainable management of genetic resources of these species. Because these four pine species grow in different landscape structures, we expected to find differences in their SGS, although all of them are widely spread, wind pollinated, and often occur at high population densities. At the local scale, there was no evidence of significant SGS in the four species under study (except in 1 out of 18 seed stands), suggesting that the genetic variants of these species are almost always randomly distributed in space, probably due to high wind pollination and seed dispersal. At a larger scale, the significant SGS found may be the result of isolation by distance among populations. We recommend (i) establishing a tight network of seed stands, with a maximum distance of 3–11 km between seed stands, to prevent greater loss of local genetic structure, and (ii) using these seeds to establish reforestations within a maximal radius of 3–5 km from seed provenances.