Riccardo Aversano

Loss of DNA methylation affects the recombination landscape in Arabidopsis

During sexual reproduction, one-half of the genetic material is deposited in gametes, and a complete set of chromosomes is restored upon fertilization. Reduction of the genetic information before gametogenesis occurs in meiosis, when cross-overs (COs) between homologous chromosomes secure an exchange of their genetic information. COs are not evenly distributed along chromosomes and are suppressed in chromosomal regions encompassing compact, hypermethylated centromeric and pericentromeric DNA. Therefore, it was postulated that DNA hypermethylation is inhibitory to COs. Here, when analyzing meiotic recombination in mutant plants with hypomethylated DNA, we observed unexpected and counterintuitive effects of DNA methylation losses on CO distribution. Recombination was further promoted in the hypomethylated chromosome arms while it was inhibited in heterochromatic regions encompassing pericentromeric DNA. Importantly, the total number of COs was not affected, implying that loss of DNA methylation led to a global redistribution of COs along chromosomes. To determine by which mechanisms altered levels of DNA methylation influence recombination—whether directly in cis or indirectly in trans by changing expression of genes encoding recombination components—we analyzed CO distribution in wild-type lines with randomly scattered and well-mapped hypomethylated chromosomal segments. The results of these experiments, supported by expression profiling data, suggest that DNA methylation affects meiotic recombination in cis. Because DNA methylation exhibits significant variation even within a single species, our results imply that it may influence the evolution of plant genomes through the control of meiotic recombination.

The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

The draft genome and transcriptome sequences of the wild potato species S. commersonii demonstrate the usefulness of genome sequences from wild relatives for elucidating evolutionary mechanisms contributing to Solanum species diversity and understanding changes in response to cold. Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.

Stochastic changes affect Solanum wild species following autopolyploidization

Polyploidy is very common within angiosperms, and several studies are in progress to ascertain the effects of early polyploidization at the molecular, physiological, and phenotypic level. Extensive studies are available only in synthetic allopolyploids. By contrast, less is known about the consequences of autopolyploidization. The current study aimed to assess the occurrence and extent of genetic, epigenetic, and anatomical changes occurring after oryzaline-induced polyploidization of Solanum commersonii Dunal and Solanum bulbocastanum Dunal, two diploid (2n=2×=24) potato species widely used in breeding programmes. Microsatellite analysis showed no polymorphisms between synthetic tetraploids and diploid progenitors. By contrast, analysis of DNA methylation levels indicated that subtle alterations at CG and CHG sites were present in tetraploids of both species. However, no change occurred concurrently in all tetraploids analysed with respect to their diploid parent, revealing a stochastic trend in the changes observed. The morpho-anatomical consequences of polyploidization were studied in leaf main veins and stomata. With only a few exceptions, analyses showed no clear superiority of tetraploids in terms of leaf thickness and area, vessel number, lumen size and vessel wall thickness, stomata pore length and width, guard cell width, and stomatal density compared with their diploid progenitors. These results are consistent with the hypothesis that there are no traits systematically associated with autopolyploidy.

Secondary Metabolite Profile in Induced Tetraploids of Wild Solanum commersoniiDun.

The main aim of this work was to study the leaf secondary metabolite profiles of artificially induced tetraploids (2n=4x=48) of Solanum commersonii, a diploid (2n=2x=24) wild potato species. The tetraploid genotypes of S. commersonii were produced by oryzalin treatment. Both HPLC‐UV and LC/MS analyses revealed that there were no qualitative differences in the metabolite profiles between the diploid S. commersonii and its tetraploids. By contrast, the results showed that the phenylpropanoid content was generally significantly higher in the tetraploids than in the diploid S. commersonii. Concerning the glycoalkaloids (GAs), the results provided evidence that the content of minor GAs (solanidenediol triose, solanidadienol lycotetraose, and solanidenol lycotetraose) was higher in tetraploids than in the diploid progenitor, while the content of major GAs (dehydrodemissine and dehydrocommersonine) was significantly higher in diploid S. commersonii than in its tetraploid genotypes. The results are discussed from the practical perspective of potato biodiversity enhancement.

Molecular Tools for Exploring Polyploid Genomes in Plants

Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

Resistance to Ralstonia solanacearum of Sexual Hybrids Between Solanum commersonii and S. tuberosum

This research was carried out to study the levels of bacterial wilt resistance and genetic diversity of (near)pentaploid sexual hybrids between S. commersonii (2n = 2x = 24, 1EBN) and cultivated S. tuberosum. Following artificial inoculations with Ralstonia solanacearum, wilting degree was estimated on a scale from 0 to 4, and seven genotypes of 26 (27%) displaying a S. commersonii like behavior were identified. Latent bacterial colonizations were detected in roots of symptomless S. commersonii and hybrids, whereas no bacterial populations were detected within stems. This suggests that the movement and/or growth of the bacterium in the aerial part were strongly inhibited. A molecular study with AFLP markers clustered hybrids into nine groups and provided evidence that resistant hybrids were slightly more similar to cultivated S. tuberosum than to the wild parent. This is important in view of the re-establishment of the cultivated genetic background through backcrosses. Hybrids displayed good fertility and are being used for further breeding efforts.ResumenEsta investigación fue realizada para estudiar los niveles de resistencia a la marchitez bacteriana y la diversidad genética de híbridos sexuales (casi) pentaploides entre S. commersoni y S. tuberosum cultivado. Después de las inoculaciones artificiales con Ralstonia solanacearum, la marchitez fue estimada en una escala de 0 a 4 y se identificaron siete genotipos de 26 (27%) que se comportaron como S. commersoni. Se detectaron colonizaciones bacterianas latentes en raíces que no presentaban síntomas de S. commersoni e híbridos mientras que no se detectó población bacteriana dentro de los tallos. Esto sugiere que el movimiento y/o crecimiento de la bacteria en la parte aérea fue fuertemente inhibido. Un estudio molecular con marcadores AFLP agrupó los híbridos en nueve grupos y dio la evidencia de que los híbridos fueron ligeramente más similares al S. tuberosum cultivado que sus progenitores silvestres. Esto es importante en vista del restablecimiento de los antecedentes genéticos de la especie cultivada por medio de retro cruzamientos. Los híbridos mostraron buena fertilidad y están siendo usados para mejoramiento.

Biochemical features of native red wines and genetic diversity of the corresponding grape varieties from Campania region.

Campania region has always been considered one of the most appreciated Italian districts for wine production. Wine distinctiveness arises from their native grapevines. To better define the chemical profile of Campania autochthonous red grape varieties, we analysed the phenolic composition of Aglianico di Taurasi, Aglianico del Vulture, Aglianico del Taburno, Piedirosso wines, and a minor native variety, Lingua di Femmina in comparison with Merlot and Cabernet Sauvignon, as reference cultivars. A genetic profiling was also carried out using microsatellite molecular markers with high polymorphic and unambiguous profiles. Principal component analysis applied to 72 wines based on the 18 biochemical parameters, explained 77.6% of the total variance and highlighted important biological entities providing insightful patterns. Moreover, comparison of SSR-based data with phenylpropanoid molecules exhibited a statistically significant correlation. Our approach might be reasonably adopted for future characterisations and traceability of grapevines and corresponding wines.

Genetic diversity among potato species as revealed by phenotypic resistances and SSR markers

The evolutionary diversity of wild potato species makes them excellent materials for improving the narrow genetic basis of the cultivated potato Solanum tuberosum. Understanding their genetic diversity is important not only to choose the best parents for breeding, but also to design proper crossing schemes and selection strategies. The objectives of this study were to determine the resistance response to Ralstonia solanacearum, Potato virus Y and low temperatures of 21 clones of 12 potato species, and to determine their genetic diversity through simple sequence repeat (SSR) markers. Sources of resistance have been found for all the investigated traits, with high resistance variability not only between but also within species. Combined resistances were also identified, with positive implications for efficient breeding. SSR analysis allowed the detection of 12 loci and 46 alleles across all genotypes, with an average value of 3.8 alleles per locus. Both unique and rare alleles useful for marker-assisted selection were found. SSR-based cluster analysis revealed that resistant genotypes were distributed among all clusters, suggesting that genetically different resistant genotypes were identified. The information obtained in this study is discussed from a breeding perspective.

Genome-wide identification and analysis of candidate genes for disease resistance in tomato

Tomato (Solanum lycopersicum L.) has served as an important model system for studying the genetics and molecular basis of resistance mechanisms in plants. An unprecedented challenge is now to capitalize on the genetic and genomic achievements obtained in this species. In this study, we show that information on the tomato genome can be used predictively to link resistance function with specific sequences. An integrated genomic approach for identifying new resistance (R) gene candidates was developed. An R gene functional map was created by co-localization of candidate pathogen recognition genes and anchoring molecular markers associated with resistance phenotypes. In-depth characterization of the identified pathogen recognition genes was performed. Finally, in order to highlight expressed pathogen recognition genes and to provide a first step in validation, the tomato transcriptome was explored and basic molecular analyses were conducted. Such methodology can help to better direct positional cloning, reducing the amount of effort required to identify a functional gene. The resulting candidate loci selected are available for exploiting their specific function.

Interspecific somatic hybrids between Solanum bulbocastanum and S. tuberosum and their haploidization for potato breeding

Protoplast fusion between incongruent Solanum bulbocastanum and S. tuberosum haploids was accomplished to produce hybrids combining elite traits from both parents. We identified 11 somatic hybrids out of 42 regenerants analyzed through ISSR markers. Some hybrids had loss or gain of fragments compared to the parents, likely due to rearrangements and deletions of chromosome segments after fusion, and/or to somaclonal variation during hybrid regeneration. Increased heterotic vigor for some traits as well as high diversity was observed as the effect of both ploidy and fusion combination. Microsporogenesis analysis indicated the occurrence of multivalent configurations and several meiotic abnormalities, such as chromosomes bridges and various spindle orientations. Since all hybrids were sterile, in vitro anther culture was employed for haploidization as a possible strategy to overcome barriers to hybridizations. Haploids were obtained from all the tetraploid S. bulbocastanum (+) S. tuberosum somatic hybrids tested, although with differences in both the number of embryos per 100 anthers cultured and the number of differentiated green plantlets. This is the first report on the successful production of haploid plants from S. bulbocastanum (+) S. tuberosum hybrids.