1,721,060 research outputs found
QuantStudioTM 12K Flex OpenArray® System as a Tool for High-Throughput Genotyping and Gene Expression Analysis
No full textReal time technology provides great advancements over PCR-based methods for a broad range of applications. With the increased availability of sequencing information, there is a need for the development and application of high-throughput real time PCR genotyping and gene expression methods that significantly broaden the current screening capabilities. Thermo Fisher Scientific (USA) has released a platform (QuantStudioTM 12K Flex system coupled with OpenArray® technology) with key elements required for high-throughput SNP genotyping and gene expression analysis. This allows for a rapid screening of large numbers of TaqMan® assays (up to 256) in many samples (up to 480) per run. This advanced real-time method involves the use of an array composed of 3,000 through-holes running on the QuantStudioTM 12K with OpenArray® block. The aim of this chapter is to outline the OpenArray® approach while providing a comprehensive in-depth review of the scientific literature on this topic. In agreement with a large number of independent studies, we conclude that the use of OpenArray® technology is a rapid and accurate method for high-throughput and large-scale systems biology studies with high specificity and sensitivity
Combining abilities of sugar beet genotypes for root- and sugar-related traits under multi-environment trials
No full textThe improvement of sugar-related factors is associated with root traits in sugar beet. The objectives of the present study were to assess variations of sugar- and root yield (RY)-related traits and to estimate general (GCA) and specific (SCA) combining abilities of several lines, testers and hybrids under various environmental conditions. A line × tester mating design was used to develop 28 hybrids from seven lines × four testers. Presently, root- and sugar-related traits were recorded in parental lines, hybrids and five local ('Pars', 'Torbat' and 'Ekbatan') and international ('Kermit' and 'Tous') check varieties in the eight combinations of location and growing season. Mean RY and sugar yield (SY) were 44.81 t/ha and 7.57 t/ha, respectively. Genotypes tested had 16.91% sugar content (SC) and 13.64% white sugar content (WSC) across trials. No one genotype was found to have high levels for all traits, but several had above mean sugar-related or RY traits. L7T2 as the best hybrid for RY and SY yielded 37.0% and 34.4% more than the checks’ mean, whereas ratios for the best hybrid (L7T4) for SC and WSC were 8.2% and 4.3%, respectively. Additive variance was significant for all traits, whereas dominance component was only significant for RY. Several parental lines had stable GCA effects with respect to direction and magnitude for WSC, RY and SC in environments. L7 and T2 for RY and SY and L3 and T4 for SC and WSC were identified as the best combiners with high GCA effects, and their use might increase favourable alleles in further breeding programmes for traits tested. Estimated heritability for the combined environments was lower for sugar-related traits (54.01%–59.39%) compared with those for RY traits (73.68%–74.21%). Overall, given heritability and additive variances estimated the identification of environmentally stable GCA and SCA effects and might help to increase efficiency of selection of superior cultivars with respect to sugar traits
Bacteria profile of water and gills of Mytilus galloprovincialis from a North Italian lagoon
No full textThis study aimed to assess the microbiota in water and gills of Mytilus galloprovincialis collected at Scardovari lagoon (Po Delta, Italy). The seasonal and spatial dynamics microbial communities were investigated with a DNA metabarcoding approach, which simultaneously amplifies seven hypervariable regions of the bacterial 16S rRNA gene. Mussels and water were sampled in two areas of the lagoon (North-West and South-East) three times between April and June 2021. The most abundant bacterial taxa (Methylobacterium, Burkholderia, and Sphingomonas) in gill tissue found by DNA metabarcoding were confirmed using Sanger analysis and qPCR. Our results highlight a characteristic bacterial profile in mussels compared to water and the Principal Component Analysis (PCA) revealed the presence of separate community structures within gills and water samples. In gills tissues, the families of Sphingomonadaceae, Beijerinckiaceae, and Burkholderiaceae were abundant, while in seawater samples Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae families were the most represented. The gills of mussels sampled in the northern and southern areas presented a high similarity of microbial communities. The seasonal dynamic revealed structural variation of bacterial profile and alfa-diversity composition both in gills and water (P<0.05) and the unique presence of some pathogenic bacteria orders was highlighted in May and June when temperature raised. These findings enhance our understanding of the gill-associated microbiota with a space and time microbiota analysis approach. The relationship of gill bacteria communities with the surrounding environment was pointed out, enabling the development of a transferable method to other economically important seafood
Germination data analysis by time-to-event approaches
Full text linkGermination data are analyzed by several methods, which can be mainly classified as germination indexes and traditional regression techniques to fit non-linear parametric functions to the temporal sequence of cumulative germination. However, due to the nature of germination data, often different from other biological data, the abovementioned methods may present some limits, especially when ungerminated seeds are present at the end of an experiment. A class of methods that could allow addressing these issues is represented by the so-called “time-to-event analysis”, better known in other scientific fields as “survival analysis” or “reliability analysis”. There is relatively little literature about the application of these methods to germination data, and some reviews dealt only with parts of the possible approaches such as either non-parametric and semiparametric or parametric ones. The present study aims to give a contribution to the knowledge about the reliability of these methods by assessing all the main approaches to the same germination data provided by sugar beet (Beta vulgaris L.) seeds cohorts. The results obtained confirmed that although the different approaches present advantages and disadvantages, they could generally represent a valuable tool to analyze germination data providing parameters whose usefulness depends on the purpose of the research
Legumes of the Sardinia Island: Knowledge on Symbiotic and Endophytic Bacteria and Interactive Software Tool for Plant Species Determination
Full text linkA meta-analysis was carried out on published literature covering the topic of interactive plant microbiology for botanical species of legumes occurring within the boundary of the Italian island Sardinia, lying between the Tyrrhenian and the western Mediterranean seas. Reports were screened for the description of three types of bacterial occurrences; namely, (a) the nitrogen-fixing symbionts dwelling in root nodules; (b) other bacteria co-hosted in nodules but having the ancillary nature of endophytes; (c) other endophytes isolated from different non-nodular portions of the legume plants. For 105 plant species or subspecies, over a total of 290 valid taxonomical descriptions of bacteria belonging to either one or more of these three categories were found, yielding 85 taxa of symbionts, 142 taxa of endophytes in nodules, and 33 in other plant parts. The most frequent cases were within the Medicago, Trifolium, Lotus, Phaseolus, and Vicia genera, the majority of symbionts belonged to the Rhizobium, Mesorhizobium, Bradyrhizobium, and Sinorhizobium taxa. Both nodular and extra-nodular endophytes were highly represented by Gammaproteobacteria (Pseudomonas, Enterobacter, Pantoea) and Firmicutes (Bacillus, Paenibacillus), along with a surprisingly high diversity of the Actinobacteria genus Micromonospora. The most plant-promiscuous bacteria were Sinorhizobium meliloti as symbiont and Bacillus megaterium as endophyte. In addition to the microbial analyses we introduce a practical user-friendly software tool for plant taxonomy determination working in a Microsoft Excel spreadsheet that we have purposely elaborated for the classification of legume species of Sardinia. Its principle is based on subtractive keys that progressively filter off the plants that do not comply with the observed features, eventually leaving only the name of the specimen under examination
Genotyping by RAD sequencing analysis assessed the genetic distinctiveness of experimental lines and narrowed down the genomic region responsible for leaf shape in endive (Cichorium endivia L.)
Full text linkThe characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive
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