Morphological and Genetic Clonal Diversity within the ‘Greco Bianco’ Grapevine (Vitis vinifera L.) Variety

: Grapevine (Vitis vinifera L.) has been propagated vegetatively for hundreds of years. Therefore, plants tend to accumulate somatic mutations that can result in an intra-varietal diversity capable of generating distinct clones. Although it is common that winemakers request specific clones or selections for planting new vineyards, relatively limited information is available on the extent, degree, and morphological impact of the clonal diversity in traditional, highly valued grapevine varieties within production areas protected by geographical denomination of origin. Here, we present a morphological and genetic investigation of the intra-varietal diversity in 'Greco Bianco', the grapevine variety used to produce the DOCG and PDO "Greco di Tufo" wine. Seventeen clones from different farms (all within the allowed production area) were phenotypically characterized using ampelographic and ampelometric traits. The clones were also genotyped with Simple Sequence Repeats (SSR) and retrotransposon-based DNA markers (REMAP). The morphological analysis indicated a uniformity in the qualitatively scored traits, and a limited variability for the quantitative traits of the bunch and of the berry composition. The molecular markers also depicted variability among clones, which was more evident with the use of REMAPs. The comparison of the discriminatory information of the three analyses indicated that they provided different estimates of the level of diversity. The evaluation described herein of the clonal variability has implications for the management and protection of clonal selections in 'Greco Bianco' and prompts for further multidisciplinary investigations on its possible role in winemaking

Intra- and Inter-Population Genetic Diversity of “Russello” and “Timilia” Landraces from Sicily: A Proxy towards the Identification of Favorable Alleles in Durum Wheat

Climate change and global population growth call for urgent recovery of genetic variation from underexploited or unexplored durum wheat (Triticum turgidum ssp. durum) landraces. Indeed, these untapped genetic resources can be a valuable source of favorable alleles for environmental adaptation and tolerance or resistance to (a)biotic stress. In southern Italy, in addition to the widespread modern and highly productive durum wheat cultivars, various landraces have been rediscovered and reused for their adaptation to sustainable and low-input cropping systems and for their peculiar qualitative characteristics. Sicily is a semiarid area rich in landraces, some of which are independently reproduced by many farmers. Among these, “Timilia” and “Russello” have been independently grown in various areas and are now cultivated, mostly under organic systems, for their hypothetical greater benefits and height, which give them a high level of competitiveness against weeds despite their low yield potential. So far, there is little information on the genetic variations of “Timilia” and “Russello” despite their putative origin from a common funder. This work aims to dissect the genetic variation patterns of two large germplasm collections of “Timilia” and “Russello” using SNP genotyping. The analysis of intra- and inter-population genetic variation and the identification of divergent loci between genetic groups showed that (i) there are two “Russello” genetic groups associated with different Sicilian geographical areas, which differ in important traits related to gluten quality and adaptation, and (ii) the individuals of “Timilia”, although presenting wide genetic variation, have undergone a conservative selection, likely associated with their distinctive traits. This work paves the way for a deeper exploration of the wide genetic diversity in Sicilian landraces, which could be conveniently exploited in future breeding programs, and points out that intra-population genetic diversity should be taken into account when ‘conservation varieties’ are to be registered in national registers of crop

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation

Defining the lentiviral integrome in human hematopoietic cells

Retroviral integration is a non-random process, whereby pre-integration complexes of different viruses recognize components or features of the host cell chromatin in a specific fashion. By using deep sequencing technology, we mapped >60,000 MLV and HIV integration sites in the genome of human CD34+ hematopoietic stem/progenitor cells and >16,000 sites in peripheral blood T-lymphocytes, and defined genome-wide integration maps in both cell types. MLV integrations cluster around regulatory elements (promoters, enhancers, and evolutionarily conserved non-coding regions) of genes involved in hematopoietic functions, and to chromatin regions bearing epigenetic marks of active or poised transcription. On the contrary, HIV integrations are clustered in regions marked by histone modifications associated to the body of transcribed genes (H3K36me3 and H2BK5me1), and are under-represented in regulatory regions. Although >90% of the genes targeted by HIV integration are expressed by Affymetrix analysis, expressed genes are not equally targeted. By a rigorous statistical analysis, we define a set of <400 genes that are targeted by HIV at significantly higher frequency than matched random controls after normalization for gene length, and a smaller set of genes that are targeted at significantly lower frequency. Functional clustering analysis shows that highly targeted genes are involved in chromatin remodeling and transcription, and are enriched in housekeeping functions. This analysis identifies a set of “high-risk” genes in hematopoietic cells, the function of which is more likely to be influenced by lentiviral vector integration in clinical gene therapy. Many of these genes are over-represented in collections of lentiviral vector integrations from patients treated by gene therapy, indicating that lentiviral “common integration sites” are determined by the HIV target site selection rather than clonal dominance in vivo

Chromatin organization at the nuclear pore favours HIV replication.

International audienceThe molecular mechanisms that allow HIV to integrate into particular sites of the host genome are poorly understood. Here we tested if the nuclear pore complex (NPC) facilitates the targeting of HIV integration by acting on chromatin topology. We show that the integrity of the nuclear side of the NPC, which is mainly composed of Tpr, is not required for HIV nuclear import, but that Nup153 is essential. Depletion of Tpr markedly reduces HIV infectivity, but not the level of integration. HIV integration sites in Tpr-depleted cells are less associated with marks of active genes, consistent with the state of chromatin proximal to the NPC, as analysed by super-resolution microscopy. LEDGF/p75, which promotes viral integration into active genes, stabilizes Tpr at the nuclear periphery and vice versa. Our data support a model in which HIV nuclear import and integration are concerted steps, and where Tpr maintains a chromatin environment favourable for HIV replication

Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina

Abstract Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

Although sexual reproduction has resulted in an extraordinary degree of Q7 variability among cultivated grapevine (Vitis vinifera L.), spontaneous somatic mutations have further shaped the kaleidoscope of grapevine agrobiodiversity. For centuries, growers have been collecting and propagating these various selections, calling them “clones”. The objective of this work was to analyse the population structure and the genetic diversity of six grapevine varieties from Campania and Apulia considered as panels of clones. In detail, more than 130 clones were genotyped by two reduced representation sequencing methods. Inter- and intra-varietal genetic diversity was analysed using metrics such as population structure and fixation index (FST) between populations and at single loci. Varieties belonging to the same area showed high levels of genetic similarity. The obtained Single-Nucleotide Polymorphism (SNP) data were used to identify Q6 two hundred loci with divergent markers (FST ≥ 0.80) within annotated exons. Some of them were found to be associated with phenotypic plasticity, adaptation to environmental conditions and other key traits interesting and useful for grapevine breeding. The results presented here allowed to increase our knowledge about the genetic variability of valuable traditional grapevines, highlighting the need to recover these promising genetic resources, characterise them and conserve their intra-varietal diversity