Biodiversity of grapevines ( Vitis vinifera L.) grown in the Aosta Valley

Forensic genetics

Background Heterodera avenae, the cereal cyst nematode or European cyst nematode, is a plant pathogen and an obligate parasite of cereal crops including barley, oats, wheat, and rye. Cereal crops infected with this nematode are more susceptible to infection by fungal diseases such as Rhizoctonia root rot. Objective The main objective of the present study was to map Heterodera avenae resistance and to compare seven different species. This study also aimed to increase the efficiency and precision of standard procedures for testing the resistance of barley toward root-lesion nematodes. Materials and methods The genetic variability analysis of seven barley genotypes, of Egypt was achieved using 7 Inter simple sequence repeat (ISSR) primers. Phylogenetic relationships of seven accessions of (Hordeum vulgare L.) collected from different region of Egypt were assessed. The soil was sterilized in an autoclave of each pot was planted in the comparison experiment, as well as in the treatment experiment with nematode Heterdra avanae infected soil brought from an infected field, and this soil was added to the treated pots. Also (ISSR) molecular marker technique was used for DNA fingerprinting and assessing genetic diversity and phylogenetic relationships in barley germplasm. Results and conclusion A significant correlation was observed between the Jaccard’s dissimilarity matrices based on ISSR markers, as revealed by Mantel test using the Pearson correlation coefficient (r = 0.69; P < 0.05). The results showed that ISSR primers produced 37 bands their size ranged between 100-2000 bp with (87.5%). polymorphism percentage. Polymorphic information content PIC was 0.74 for ISSR. Unweighted Pair Group Method with Arithmetic (UPGMA), Dendrogram was divided into two clusters by morphological traits and ISSR analysis. Genetic similarity matrix was examined with Jaccard’s coefficient, maximum similarity was found between Giza126 and Giza127 (99%) with morphological analysis both and lowest similarity between Giza123 and Giza126 (6%) with ISSR analysis. Determination of genetic diversity between barley is of major importance for characterization of barley germplasm, breeding programs and conservation purposes. Morphological traits and ISSR analysis are effective tools for detecting genetic variations. The results showed that H. vulgare have high ratio of variation. This study may be considered as reference study for further studies on H. vulgare and may contribute to species concept and breeding programs.

Date palm (Phoenix dactylifera L., 2n = 36) is a fruit tree mainly cultivated in arid regions in the Middle East, where it has been domesticated for at least 5,000 years and is believed to have originated in Mesopotamia. Date palm (Phoenix dactylifera L) is the major factor of oasis environmental and economic stability (Zehdi et al., 2004). The major date producers in the world are located in the Middle East and North Africa (Rania et al., 2008). In Egypt, date palm is an important crop where the total number of fruitful female palm is about 10 million palm trees according to the statistics of the Central Administrations of Horticultural, Ministry of Agriculture (Rania et al., 2008). This crop is of a great socioeconomic importance in oases. The oasis of Siwa located in Egypt’s western desert is about 600 km away from Alexandria and 300 km South-West from Matrouh (Mediterranean coast) and about 65 km east from the Libyan borders. Siwa oasis is a natural isolated depression in the western desert of Egypt. However, little is known about the genetic characterization of Date palm cultivars. The date palm cultivation takes about 40% of all cultivated area. The pollen of the date palm has been found to exert a direct influence on the size, shape and color of the seed and also, on the size of the fruit, on the speed of development of the fruit and on the time of ripening of the fruit. This direct influence of the male parent on the development of the date fruit is precise and definite and varies with the particular male used to fertilize the female flowers. Each male is exerting approximately the same effect on fruit of all varieties and exerting the same effect in different years. Therefore, it is important to select and identify superior male in term of fertilization (Walter, 1928). Recently, study of genetic diversity for plant crops is the process by which variation among individuals or groups of individuals is analyzed by a specific genetically method or a combination of such methods. The most important measurements are data obtained by DNA based marker data that detect and monitor identification of different genomes. Many new markers can be identified in the same region using inter Simple Sequence Repeat (ISSR) markers linked to genes of interest. Furthermore, ISSR is informative about many loci and are suitable to discriminate closely related genotype variants and lastly, ISSR markers constitute discrete markers suitable in the DNA fingerprinting (Gupta and Varshney, 2000). The objectives of this study were designed to the determine morphological traits among nine date palm cultivars and six male trees grow in Siwa oasis and develop molecular fingerprints based RAPD and ISSR analysis. Moreover, through the obtained data, determine genetic relationships among these cultivars by applying morphological and molecular analysis.

Systematic evaluation of the early access applied biosystems precision ID Globalfiler mixture ID and Globalfiler NGS STR panels for the ion S5 system

Variety improvement program of citrus in Indonesia has still been prioritized, therefore, characterization and identification of varieties within and/or among citrus species are absolutely required in order to obtain desired varieties based on market demand needs. The aim of this research was to determine morphological characteristics, flowering periods, and the genetic relationship of four citrus species. This study was carried out at Indonesia Citrus and Subtropical Fruit Research Institute (ICISFRI). A total of 12 varieties derived from Citrus reticulata Blanco, Citrus sinensis L. Osbeck, Citrus aurantifolia (Christm.) Swingle), and Citrus lemon (L.) Burm. F was used for morphological description. The genetic relationship was evaluated by morphological and molecular analyses using Inter-simple Sequence Repeat (ISSR). The result showed that variations of morphological characters were identified either within or among four citrus species. Citrus reticulata Blanco had the highest physiochemical contents. In terms of flowering periods, varieties that belong to Citrus reticulata Blanco, and Ortaji (Citrus sinensis L. Osbeck) required 9 to 11 days for fully blooming after flower bud; whereas Montaji (Citrus limon (L.) Burm. F) and Nimas (Citrus aurantifolia (Christm.) Swingle) needed 16 days. In both morphological and molecular analyses, 12 varieties were classified into two main clusters, however, some differences were found between the two dendrograms. The genetic relationship of four citrus species based on similarity coefficient ranged from 1 to 25 (morphological analyses) and 0.62 to 0.90 (ISSR marker), respectively. The highest genetic relationship derived from both analyses was performed by Krisma versus Monita, and Krisma versus Orlinda Kuning, respectively. Morphological analyses are still needed to complement molecular analyses in citrus classification in order to produce desired new citrus varieties in order to create sustained citrus agribusiness in Indonesia.

The analysis and profiling of short tandem repeat (STR) loci is routinely used in forensic genetics. Current methods to investigate STR loci, including PCR-based standard fragment analyses and capillary electrophoresis, only provide amplicon lengths that are used to estimate the number of STR repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method in combination with a bioinformatic tool designed specifically to analyze sequence lengths and frequencies, we found that GS FLX STR sequence data are comparable to conventional capillary electrophoresis-based STR typing. Furthermore, we found DNA base substitutions and repeat sequence variations that would not have been identified using conventional STR typing.

Identifying germplasm is an important component for efficient and effective management of plant genetic resources. This investigation was undertaken for the identification and analysis of genetic variation within 9 species of Albizzia through 33 morphological parameters, and 15 Random Amplified Polymorphic DNA (RAPD) and 17 Inter Simple Sequence Repeat (ISSR) primers. The use of selected RAPD and ISSR primers generated a total of 163 and 201 amplified DNA fragments, respectively. High frequencies of polymorphism, 95.05% for RAPD and 96.02% for ISSR, were detected. Statistical approaches were employed to construct genetic relationships by RAPD, ISSR and morphological analysis. Cluster analysis by the unweighted pair-group method (UPGMA) of Nei's similarity generated dendograms with similar topology that gave a better reflection of the diversity and affinities between species. These molecular results were comparable to main morphological characteristics. The correlation matrices generated by RAPD and ISSR markers were highly correlated (r = 0.843 at p = 1.0), thereby indicating congruence between these two marker systems. Both morphometric data and molecular markers have the potential to analyse genetic variation among the nine species of Albizzia, thus providing a major input for management strategy of plant genetic resources.

Simultaneous carcinomas of the endometrium and ovary may represent a diagnostic dilemma and the clinical management of such cases may be problematic. In surgical pathology practice, we classify them either as double primary tumors (DP) or a single primary tumor with metastasis (PM), according to the conventional clinicopathologic criteria. The distinction has important therapeutic and prognostic implications, but it can be sometimes difficult, especially in advanced cases. In this study, in addition to the clinicopatho-logic classification, we assessed tumor cell clonality in 13 cases with synchronous endometrial and ovarian endometrioid adenocarcinomas using PCR-based microsatellite analysis of microdissected archival tissues for loss of heterozygosity (LOH) and microsatellite instability (MSI). All paired endometrial and ovarian tumors demonstrated either MSI or/and LOH except for 1 case, and therefore the microsatellite analysis was informative in 92.3% of the cases. Nine of 26 tumors (34.6%) exhibited MSI-H and 15 of 26 (57.7%) showed LOH. In contrast to 4 DP cases and 9 PM cases classified according to clinicopathologic criteria, microsatellite analysis suggested 10 DP cases and 2 PM cases. The molecular analysis was not informative in 1 case. Thus, analysis of microsatellite abnormality is a helpful adjunct in the assessment of synchronous tumors, especially to differentiate DP from PM cases in advanced tumor cases. Moreover, the combination of conventional clinicopathologic evaluation and molecular analysis is important and helpful in distinction between the two groups of synchronous tumors.

White clover is an important legume naturalized in China. But genetic variation of Chinese local white clover germplasm has not been reported. There is no information for parents’ selection and genetic resource conservation. The objective of this study was to investigate and characterize genetic variation of ten local white clover germplasms collected from different geographical regions of China. Morphological data analysis of white clover populations was coupled with molecular markers of random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) to investigate the genetic relationships among white clover germplasms of China, and four commercial cultivars were included for a comparison. The results revealed that the populations showed diverse morphological traits, RAPD and SSR patterns. Despite the certain similarities among the dendrograms of particular populations, the overall correlations among the distance matrices appeared to be rather low. In the present study, cluster analysis only slightly reflected the geographical origins of populations, and the dendrogram employing SSR data showed the closest agreement with collections’ geographical origins. The analysis of molecular variance (AMOVA) analysis based on both RAPD and SSR markers revealed higher levels of intra-population variation than inter-population variation. Neither RAPD nor SSR based grouping showed obvious agreement with variation of leaf sizes and other morphological traits. Our results suggest that the combination of morphological traits and SSR analysis could be a useful method for assessing genetic variation in white clover, and could be helpful for breeders to plan crosses for positive traits.

Sissoo or shisham (Dalbergia sissoo Roxb.) is one of the finest wood of South Asia. Fusarium solani is a causal organism of sissoo wilt, decline, or dieback. It is also a potential causal organism associated with other valuable tree species. Thirty-eight Fusarium isolates including 24 F. solani and 14 Fusarium sp., were obtained in 2005 from different geographical locations in India. All 38 (18 pathogenic and 20 non-pathogenic) isolates were characterized for genomic analysis, growth behaviour, pigmentation and sensitivity to carbendazim. Based on growth pattern, growth rate, pigmentation and sensitivity to carbendazim, all 38 isolates showed a wide range of variability, but no correlation with pathogenicity or geographical distribution. Three techniques were used for comparative genomic analysis: random amplified polymorphic DNA (RAPD); inter simple sequence repeats (ISSR); and simple sequence repeats (SSR). A total of 90 primers targeting different genome regions resulted a total of 1159 loci with an average of 12.88 loci per primer. These primers showed high genomic variability among the isolates. The maximum loci (14.64) per primer were obtained with RAPD. The total variation of the first five principal components for RAPD, ISSR, SSR and combined analysis were estimated as 47.42, 48.21, 46.30 and 46.78 %, respectively. Among the molecular markers, highest Pearson correlation value (r = 0.957) was recorded with combination of RAPD and SSR followed by RAPD and ISSR (r = 0.952), and SSR and ISSR (r = 0.942). The combination of these markers would be similarly effective as single marker system i.e. RAPD, ISSR and SSR. Based on polymorphic information content (PIC = 0.619) and highest coefficient (r = 0.995), RAPD was found to be the most efficient marker system compared to ISSR and SSR. This study will assist in understanding the population biology of wilt causing phytopathogen, F. solani, and in assisting with integrated disease management measures.

The development of Tifgreen bermudagrass, and the subsequent mutations of this cultivar, has revolutionized the game of golf in the southern United States as superintendents have access to high‐quality putting surface capable of withstanding hot summers. However, the lack of genetic diversity may make them vulnerable to various pests and the low tolerance to freeze temperatures may make them susceptible to winterkill. In recent years, Oklahoma State University and other universities have begun to create new interspecific F1 hybrids between common (Cynodon dactylon) and African bermudagrasses (C. transvaalensis) for putting greens. The objectives of this study were to investigate the genetic diversity and variation among 14 experimental genotypes and two standard cultivars (TifEagle and Tifdwarf). Simple sequence repeat (SSR) markers and morphological characteristics were used to evaluate the genetic relationships and variation among the 16 genotypes. Results showed significant variation for 11 vegetative traits and two reproductive traits. The phenotypic coefficient of variation was greatest for the third internode length and the least for the first leaf angle for both the field and greenhouse trials. The morphological cluster analysis also showed variation between the two trial environments. The SSR marker cluster analysis showed the 16 genotypes were grouped into four major groups, with a similarity coefficient ranging from 0.44 to 1. The highest similarity was found among the two commercial standards and an experimental ultradwarf from Florida. Several new genotypes (OKC3920, 5 × 23, 11 × 2, 19 × 19, and 34 × 20) were also grouped with the ultradwarf genotypes in the morphological cluster analysis, showing the possibility of achieving similar morphological traits with new genetics. Further field evaluations are needed to determine the performance of these genotypes under low mowing heights.

Gene flow connects populations and is necessary to sustain effective population sizes, and genetic diversity. In the Lower Central American (LCA) region, the complex topographic and climatic history have produced a wide variety of habitats resulting in high biodiversity. Phylogeographic studies of plants from this area are scarce, and to date none have been conducted on palms. We used SSR and chloroplast DNA (cpDNA) markers to study the genetic diversity and structure of populations of the understory palm Chamaedorea tepejilote in Costa Rica. We found that populations of C. tepejilote have moderate to high nuclear simple sequence repeat (SSR) genetic diversity, likely due to large population sizes and its outcrossing mating system. Habitat loss and fragmentation may have contributed to increased genetic structure within slopes. High-elevation mountain ranges appeared to be a significant barrier for gene flow among populations in the Caribbean and Pacific slopes; however, ranges are permeable through low-elevation passes. In contrast, most populations had a single distinct cpDNA haplotype, supporting the hypothesis of several isolated populations that experienced decline that likely resulted in eroded cytoplasmic genetic diversity within populations. The haplotype network and Bayesian analysis linked populations in the Caribbean and the southern Pacific coast, suggesting that gene flow between Pacific and Caribbean populations may have occurred through the southern extreme of the Talamanca Mountain range in Panama, a colonization pathway not previously suggested for LCA plants. This is one of the first phylogeographic studies conducted on tropical palms in the LCA region and the first in the genus Chamaedorea, which sheds light on possible gene flow and dispersal patterns of C. tepejilote in Costa Rica. Our results also highlight the importance of mountain ranges on shaping gene flow patterns of Neotropical plants.

Understanding the structure of intraspecific genetic and morphological diversity within and across habitats is a fundamental aspect of biodiversity research with conservation value. Atlin Lake is the largest lake in British Columbia, Canada, and contains relatively pristine populations of lake trout ( Salvelinus namaycush ) that are key components of the lake’s fish community and local fisheries. Lake trout from Atlin Lake were examined for genetic and phenotypic variation using eight microsatellite DNA loci, body form, and colouration. Genetic assays were also conducted on lake trout from the adjoining Tagish Lake and from 17 other localities to provide spatial context for the variation within Atlin Lake. The genetic data suggested that there were three genetic subpopulations within the Atlin–Tagish lake system. Morphological analysis identified two morphological groups of lake trout within Atlin Lake. Genetic and morphological groupings in Atlin Lake were not associated with each other. A mixed-stock analysis of samples collected from Atlin Lake commercial and recreational fisheries suggested that all genetic subpopulations contributed to the fishery and that there was some contribution from fish originating from within Tagish Lake.

To broaden and delve into the genomic information of Clausena excavata, an important medicinal plant in many Asian countries, RNA sequencing (RNA-seq) analysis was performed and a total of 16,638 non-redundant unigenes (≥300bp) with an average length of 755bp were generated by de novo assembly from 17,580,456 trimmed clear reads. The functional categorization of the identified unigenes by a gene ontology (GO) term resulted in 2305 genes in the cellular component, 5577 in the biological processes, and 8056 in the molecular functions, respectively. The top sub-category in biological processes was the metabolic process with 4374 genes. Among annotated genes, 3006 were mapped to 123 metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis tool. The search for simple sequence repeats (SSRs) resulted in 845 SSRs from 749 SSR-containing unigenes and the most abundant SSR motifs was AAG/CTT with 179 occurrences. Twelve SSR markers were tested for cross transferability among five Clausena species; eight of them exhibited polymorphism. Taken together, these data provide valuable resources for genomic or genetic studies of Clausena species and other relative studies. The transcriptome shotgun assembly data have been deposited at DDBJ/EMBL/GenBank under the accession GGEM00000000.

Despite the enormous advancements in breeding, fresh and accessible methods of plant development are preferred. Many research have been done to determine the impact of zinc oxide nanoparticles (ZnO NPs) and magnesium nanoparticles (MgONPs) on plant growth. ZnO NPs and MgONPs have been used extensively in agriculture. Few research have looked into the potential impact of ZnO NPs on grain Zn content or cereal yield formation to date. The goal of the study was to demonstrate how varied concentrations of nanoparticles affected root germination in three different rice types (Giza 177, Sakha super 300, and Sakha 108) and the fungus Fusariummoniliforme, which causes foot rot in rice. Here, we performed a pot experiment to assess the effects that ZnO nanoparticles and MgONPs had on the shoot length, root length, and germination of rice. The experiment involved three dosages of Zn and Mg nanoparticle solution at varying concentrations of 10, 20, and 100 ppm. The outcomes showed that, when compared to the control treatment, ZnO NPs and MgONPs increased the length of the shoot, the length of the roots, and the rate of germination. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers, the genetic makeup of plants treated with 10, 20, and 100 ppm AgNPs was also examined. In vitro rooted shoots were acclimated in a greenhouse before being tested for biochemical stability and phenotypic stability. In vitro, callogenesis and caulogenesis were both reduced by AgNPs at the greatest dose (100 ppm). In order to maximise genome coverage, three rice cultivars from distinct origins were chosen, and they were tested using three RAPD markers and seven selected ISSR markers. AgNPs-treated plants using ISSR markers produced 87 amplified bands in total, 45 polymorphic allelic variants, and 36 monomorphic allelic variations. The Pearson correlation coefficient was used in the Mantel test to determine whether there was a significant association between the Jaccard's dissimilarity matrices based on ISSR and RAPD markers (r = 0.69; P 0.05). Morphological characteristics, ISSR, and RAPD analysis were used to partition the UPGMA Dendrogram into two groupings. Jaccard's coefficient was used to analyse the genetic similarity matrix. Sakha Super 300 and Giza 177 had the most genetic similarity (95%) while Sakha 108 and Giza 177 had the lowest genetic similarity (90%) according to ISSR and RAPD study. The classification of rice germplasm, breeding initiatives, and conservation efforts all heavily rely on the determination of genetic diversity within the rice species. To find genetic variations, morphological characteristics, ISSR, and RAPD analysis are useful techniques. The findings demonstrated the large ratio of variation in rice. This work successfully established the possibility of using MgONPs and ZnO NPs as high-performing fertilisers to improve rice output and quality.This study could serve as a guide for future research on rice and could support efforts to understand the species and improve breeding stock.