Application of SSR markers for assessment of genetic similarity and genotype identification in local winter wheat breeding program

Background. Simple sequence repeat (SSR) markers are widely used for genetic analysis in plant breeding, allowing for the investigation of genetic divergence and similarity of genotypes, identification of unique alleles and determination of levels of genetic diversity. Materials and Methods. Analysis of 42 wheat cultivars and lines from the bree­ding program of Poltava State Agrarian University was carried out using 11 SSR mar­kers located on different chromosomes. A set of 11 microsatellite single locus primer pairs was used in this study (Xgwm 11, Xgwm 44, Xgwm 46, Xgwm 135, Xgwm 174, Xgwm 186, Xgwm 194, Xgwm 219, Xgwm 312, Xgwm 372, Xgwm 389). Amplification of 11 loci was performed using the Kapa2G FastHotStart PCR Kit (Kapa Biosystems, Boston, USA). The mixture for PCR amplification contained 1.5 x Kapa2G buffer, 0.5 mM dNTP mix, 0.5 μM of each primer (Sigma-Aldrich), 1 unit of Kapa2G FastHotStart DNA Polymerase and 11.8 ng of template DNA in a volume of 25 μl. Fragment lengths were determined using GeneMapper 4.0 software (Applied Biosystems). Dendrogram was constructed using UPGMA (unweighted pair-group method with arithmetic average) in DarWin 6.0 software (Perrier and Jacquemoud-Collet 2006) for clustering analysis. Results and Discussion. The number of alleles detected per locus varied from 5 (Xgwm 11, Xgwm 135, Xgwm 219) to 12 (Xgwm 174). A total of 80 alleles were identified for the 11 loci studied. Among these, 25 unique alleles were found, each of which was present in only one genotype. The polimorphism information content (PIC) values ranged from 0.48 to 0.87. The markers Xgwm 174 (PIC = 0.87), Xgwm 389 (PIC = 0.84) and Xgwm 372 (PIC = 0.83) were the most polymorphic in our study. We obtained a distribution of cultivars and lines by genetic similarity into five clusters. Conclusion. The use of SSR markers made it possible to identify rare alleles within the varieties presented. The study of the genetic similarity of the presented geno­types showed their relationship according to their origin. It was shown that unique alleles tended to occur in certain local breeding genotypes. This study has shown that genotypes representing the local Ukrainian breeding program often have the same allelic variants and at the same time some genotypes have unique allelic variants. The results obtained from the study of 42 winter wheat genotypes based on 11 SSR markers showed that molecular markers can be very useful in assessing genetic similarity and identifying genotypes in the local breeding program

GPS tracking data of Eurasian oystercatchers (Haematopus ostralegus) from the Netherlands and Belgium

We describe six datasets that contain GPS and accelerometer data of 202 Eurasian oystercatchers (Haematopus ostralegus) spanning the period 2008–2021. Birds were equipped with GPS trackers in breeding and wintering areas in the Netherlands and Belgium. We used GPS trackers from the University of Amsterdam Bird Tracking System (UvA-BiTS) for several study purposes, including the study of space use during the breeding season, habitat use and foraging behaviour in the winter season, and impacts of human disturbance. To enable broader usage, all data have now been made open access. Combined, the datasets contain 6.0 million GPS positions, 164 million acceleration measurements and 7.0 million classified behaviour events (i.e., flying, walking, foraging, preening, and inactive). The datasets are deposited on the research repository Zenodo, but are also accessible on Movebank and as down-sampled occurrence datasets on the Global Biodiversity Information Facility (GBIF) and Ocean Biodiversity Information System (OBIS)

Use of Self-Organizing Map to Analyze Images of Fungi Colonies Grown from Triticum aestivum

We submitted to ozone treatment Triticum aestivum (common wheat) seeds severely contaminated by fungi. Fungi colonies developed when seeds were placed over malt agar medium in Petri dishes; Fusarium sp. and Alternaria sp. were identified. However, conventional colonies counting did not allow a clear assessment of the effect of ozone disinfection. We thus used self-organizing maps (SOMs) to perform an image analysis of colonies surface area that clearly showed a significant disinfection effect on Fusarium sp

Root Morphological Traits of Seedlings Are Predictors of Seed Yield and Quality in Winter Oilseed Rape Hybrid Cultivars

The root system is responsible for soil resources acquisition. Hence, optimizing crop root characteristics has considerable implications for agricultural production. This study evaluated a panel of twenty-eight European modern cultivars of oilseed rape (Brassica napus L.) cultivated in laboratory and field environments. Root morphology was screened using a high-throughput hydroponic growth system with two divergent nitrogen supplies. The panel showed an important diversity for biomass production and root morphological traits. Differences in root and shoot dry biomasses and lateral root length were mainly explained by the genotype, and differences in primary root length by nitrogen nutrition. The cultivars were tested in a pluriannual field trial. The field variation for yield and seed quality traits attributed to the genotype was more important than the year or the genotype × year interaction effects. The total root length measured at the seedling stage could predict the proportion of nitrogen taken up from the field and reallocated to seed organs, a component of the nitrogen use efficiency. The genetic interrelationship between cultivars, established with simple sequence repeat markers, indicated a very narrow genetic base. Positive correlations were found between the genetic distance measures, root morphological traits during nitrogen depletion and yield components. This study illustrates a root phenotyping screen in the laboratory with a proof of concept evaluation in the field. The results could assist future genetic improvements in oilseed rape for desirable root characteristics to reduce nutrient losses in the environment.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Genetic Diversity Trends in the Cultivated Potato: A Spatiotemporal Overview

International audienceSimple Summary Monitoring the change in genetic diversity over time and space in crop species is essential to facilitating further improvement. As the world's most important tuber crop for human consumption, and an ideal candidate to help address global food security, the cultivated potato deserves in-depth study in this regard. In this overview, some aspects of spatiotemporal diversity assessment in the cultivated potato are examined with the aim of promoting appropriate strategies for breeding programs in line with challenges relating to sustainable crop production. We investigated the changes in genetic diversity over time and space of the cultivated potato (Solanum tuberosum L.) for the period pre-1800 to 2021. A substantial panel of 1219 potato varieties, belonging to different spatiotemporal groups, was examined using a set of 35 microsatellite markers (SSR). Genotypic data covering a total of 407 alleles was analyzed using both self-organizing map (SOM) and discriminant analysis of principal components (DAPC) de novo and a priori clustering methods, respectively. Data analysis based on different models of genetic structuring provided evidence of (1) at least two early lineages that have been maintained since their initial introduction from the Andes into Europe in the 16th century, followed by later ones coming from reintroduction events from the US in the mid-1800s; (2) a level of diversity that has gradually evolved throughout the studied time periods and areas, with the most modern variety groups encompassing most of the diversity found in earlier decades; (3) the emergence of new genetic groups within the current population due to increases in the use of germplasm enhancement practices using exotic germplasms. In addition, analysis revealed significant genetic differentiation both among and within the spatiotemporal groups of germplasm studied. Our results therefore highlight that no major genetic narrowing events have occurred within the cultivated potato over the past three centuries. On the contrary, the genetic base shows promising signs of improvement, thanks to extensive breeding work that is gaining momentum. This overview could be drawn on not only to understand better how past decisions have impacted the current genetic cultivated potato resources, but also to develop appropriate new strategies for breeding programs consistent with the socio-economic and sustainability challenges faced by agrifood systems

Measurement of translesion synthesis by fluorescent capillary electrophoresis: 7,8-Dihydro-8-oxodeoxyguanosine bypass modulation by natural products

Translesion synthesis (TLS) relies on a series of specialized DNA polymerases able to insert a base either correctly or incorrectly opposite a lesion on a DNA template strand during replication or post-repair synthesis. To measure the correct or mutagenic outcome of 7,8-dihydro-8-oxodeoxyguanosine (8-oxodG) bypass by TLS DNA polymerases, a capillary electrophoresis (CE) method with fluorescent label has been developed. Two oligonucleotides were designed and hybridized: (i) a 72-mer oligonucleotide framing one 8-oxodG at position 40 and (ii) the 39-mer oligonucleotide complementary to the first strand from the 30 end to the lesion and labeled at the 50 end with a fluorochrome. After incubation with FHs 74 Int human intestinal epithelial cell nuclear proteins, in the presence of either deoxyadenosine triphosphate (dATP) or deoxycytidine triphosphate (dCTP), and denaturation, the resulting elongated oligomers were analyzed by fluorescent capillary electrophoresis. This primer extension assay was then validated in terms of linearity (linear range = 0.5-2.5 nM), detectability (limits of detection and quantification = 0.023 and 0.091 nM, respectively), and precision (total precisions = 8.1% and 3.7% for dATP and dCTP, respectively, n = 9). The addition of some natural phytochemicals to the reaction mix significantly influences the outcome of TLS either in an error-free way or in a mutagenic way. © 2013 Elsevier Inc. All rights reserved.SCOPUS: ar.jinfo:eu-repo/semantics/publishe