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Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications 总被引:1,自引:0,他引:1
Michael J. Thomson Namrata Singh Maria S. Dwiyanti Diane R. Wang Mark H. Wright Francisco Agosto Perez Genevieve DeClerck Joong Hyoun Chin Geraldine A. Malitic-Layaoen Venice Margarette Juanillas Christine J. Dilla-Ermita Ramil Mauleon Tobias Kretzschmar Susan R. McCouch 《Rice》2017,10(1):40
Background
Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.Results
Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.Conclusions
The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.3.
Geosmin depuration from European eel (Anguilla anguilla) is not affected by the water renewal rate of depuration tanks 下载免费PDF全文
Edward Schram Tobias van Kooten Jan W van de Heul Johan W Schrama Johan A J Verreth Albertinka J Murk 《Aquaculture Research》2017,48(9):4646-4655
This study established that geosmin depuration from European eel is not affected by the water renewal rate of depuration tanks. A general fish bioaccumulation model extended with terms that account for effects of tank water renewal rate and system losses of chemicals, predicted strong effects of the water renewal rate of depuration tanks on geosmin depuration from European eel. Model predictions were validated in a depuration experiment with geosmin‐loaded European eel (n = 95) with a mean (SD) individual weight of 134.4 (5.0) g and a mean (SD) lipid content of 33.7 (2.8) % (w/w). Fish were depurated for 24, 48 or 72 h at three different tank water renewal rates (0.3, 3.3 and 33 day?1). Treatments were installed by three different mean (SD) water flow rates (13.8 (1.3), 143.5 (9.2) and 1511 (80) L kg fish?1 day?1) over 30‐L tanks. Eels eliminated geosmin from their bodies, but unlike the model predicted, this was independent of the water renewal rate of the depuration tanks. Although being eliminated from the fish, geosmin hardly appeared and certainly did not accumulate in the water of the depuration tanks as the model predicted. This observation may be explained by geosmin being eliminated from eel as metabolite rather than the parent compound. Geosmin elimination from eel seems not to occur according to the generally accepted passive diffusion mechanism for excretion of lipophilic chemicals, and geosmin biotransformation by the eel seems indicated. Clearly geosmin depuration from European eel cannot be enhanced by increasing water renewal rates of depuration tanks. 相似文献
4.
EFFECTS OF FLUID AND COMPUTED TOMOGRAPHIC TECHNICAL FACTORS ON CONSPICUITY OF CANINE AND FELINE NASAL TURBINATES 下载免费PDF全文
Raimonda Uosyte Darren J. Shaw Danielle A. Gunn‐Moore Eduardo Fraga‐Manteiga Tobias Schwarz 《Veterinary radiology & ultrasound》2015,56(5):494-502
Turbinate destruction is an important diagnostic criterion in canine and feline nasal computed tomography (CT). However decreased turbinate visibility may also be caused by technical CT settings and nasal fluid. The purpose of this experimental, crossover study was to determine whether fluid reduces conspicuity of canine and feline nasal turbinates in CT and if so, whether CT settings can maximize conspicuity. Three canine and three feline cadaver heads were used. Nasal slabs were CT‐scanned before and after submerging them in a water bath; using sequential, helical, and ultrahigh resolution modes; with images in low, medium, and high frequency image reconstruction kernels; and with application of additional posterior fossa optimization and high contrast enhancing filters. Visible turbinate length was measured by a single observer using manual tracing. Nasal density heterogeneity was measured using the standard deviation (SD) of mean nasal density from a region of interest in each nasal cavity. Linear mixed‐effect models using the R package ‘nlme’, multivariable models and standard post hoc Tukey pair‐wise comparisons were performed to investigate the effect of several variables (nasal content, scanning mode, image reconstruction kernel, application of post reconstruction filters) on measured visible total turbinate length and SD of mean nasal density. All canine and feline water‐filled nasal slabs showed significantly decreased visibility of nasal turbinates (P < 0.001). High frequency kernels provided the best turbinate visibility and highest SD of aerated nasal slabs, whereas medium frequency kernels were optimal for water‐filled nasal slabs. Scanning mode and filter application had no effect on turbinate visibility. 相似文献
5.
Assessing the influence of mechanical ventilation on blood gases and blood pressure in rattlesnakes 下载免费PDF全文
Mads F Bertelsen Rasmus Buchanan Heidi M Jensen Cleo AC Leite Augusto S Abe Søren S Nielsen Tobias Wang 《Veterinary anaesthesia and analgesia》2015,42(4):386-393
ObjectiveTo characterize the impact of mechanical positive pressure ventilation on heart rate (HR), arterial blood pressure, blood gases, lactate, glucose, sodium, potassium and calcium concentrations in rattlesnakes during anesthesia and the subsequent recovery period.Study designProspective, randomized trial.AnimalsTwenty one fasted adult South American rattlesnakes (Crotalus durissus terrificus).MethodsSnakes were anesthetized with propofol (15 mg kg−1) intravenously, endotracheally intubated and assigned to one of four ventilation regimens: Spontaneous ventilation, or mechanical ventilation at a tidal volume of 30 mL kg−1 at 1 breath every 90 seconds, 5 breaths minute−1, or 15 breaths minute−1. Arterial blood was collected from indwelling catheters at 30, 40, and 60 minutes and 2, 6, and 24 hours following induction of anesthesia and analyzed for pH, PaO2, PaCO2, and selected variables. Mean arterial blood pressure (MAP) and HR were recorded at 30, 40, 60 minutes and 24 hours.ResultsSpontaneous ventilation and 1 breath every 90 seconds resulted in a mild hypercapnia (PaCO2 22.4 ± 4.3 mmHg [3.0 ± 0.6 kPa] and 24.5 ± 1.6 mmHg [3.3 ± 0.2 kPa], respectively), 5 breaths minute−1 resulted in normocapnia (14.2 ± 2.7 mmHg [1.9 ± 0.4 kPa]), while 15 breaths minute−1 caused marked hypocapnia (8.2 ± 2.5 mmHg [1.1 ± 0.3 kPa]). Following recovery, blood gases of the four groups were similar from 2 hours. Anesthesia, independent of ventilation was associated with significantly elevated glucose, lactate and potassium concentrations compared to values at 24 hours (p < 0.0001). MAP increased significantly with increasing ventilation frequency (p < 0.001). HR did not vary among regimens.Conclusions and clinical relevanceMechanical ventilation had a profound impact on blood gases and blood pressure. The results support the use of mechanical ventilation with a frequency of 1–2 breaths minute−1 at a tidal volume of 30 mL kg−1 during anesthesia in fasted snakes. 相似文献
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7.
Maria Garcia-Martin Nora Fagerholm Claudia Bieling Dimitris Gounaridis Thanasis Kizos Anu Printsmann Matthias Müller Juraj Lieskovský Tobias Plieninger 《Landscape Ecology》2017,32(11):2133-2150
Context
Human–nature interactions are reflected in the values people assign to landscapes. These values shape our understanding and actions as landscape co-creators, and need to be taken into account to achieve an integrated management of the landscape that involves civil society.Objectives
The aim of this research was to increase the current knowledge on the most and least common landscape values perceived by local stakeholders, the patterns in the spatial distribution of values, and their connection to different socio-economic backgrounds and landscape characteristics across Europe.Methods
The research consisted of a cross-site comparison study on how landscape values are perceived in six areas of Europe using Public Participation GIS surveys. Answers were analysed combining contingency tables, spatial autocorrelation and bivariate correlation methods, kernel densities, land cover ratios, and viewshed analyses. Results were discussed in the light of findings derived from other European participatory mapping studies.Results
We identified shared patterns in the perception of landscape values across Europe. Recreation, aesthetics, and social fulfilment were the most common values. Landscape values showed common spatial patterns mainly related to accessibility and the presence of water, settlements, and cultural heritage. However, respondents in each study site had their own preferences connected to the intrinsic characteristics of the local landscape and culture.Conclusions
The results encourage land planners and researchers to approach landscape values in relation to socio-cultural and bio-physical land characteristics comprehensibly, acknowledging the complexity in the relationship between people’s perception and the landscape, to foster more effective and inclusive landscape management strategies.8.
Johannes Trini Hans Peter Maurer Sigrid Weissmann Tobias Würschum 《Plant Breeding》2020,139(5):906-915
Accurate hybrid prediction and knowledge about the relative contribution of general (GCA) and specific combining ability (SCA) are of utmost importance for efficient hybrid breeding. We therefore evaluated 91 triticale single-cross hybrids in field trials at seven environments for plant height, heading time, fresh biomass, dry matter content and dry biomass. Fresh and dry biomass showed the highest proportion (23%) of variance due to SCA. Prediction accuracies based on GCA were slightly higher than based on mid-parent values. Utilizing parental kinship information yielded the highest prediction accuracies when both parental lines have been tested in other hybrid combinations, but still moderate-to-low prediction accuracies for two untested parents. Thus, hybrid prediction for biomass traits in triticale is currently promising based on mid-parent values as emphasized by our simulation study, but can be expected to shift to GCA-based prediction with an increasing importance of GCA due to selection in hybrid breeding. Moreover, the performance of potential hybrids between newly developed lines can be predicted with moderate accuracy using genomic relationship information. 相似文献
9.
Stephanie Kramer-Schadt Tobias S. Kaiser Karin Frank Thorsten Wiegand 《Landscape Ecology》2011,26(4):501-513
With habitat loss and fragmentation having become two of the major threats to the viability of species, the question of how
to manage landscapes for species conservation has attracted much attention. In this context, the planning of stepping stones
has been proposed to increase connectivity in fragmented landscapes. We present a simulation study with a neutral landscape
approach to assess the effects of stepping stones on colonization success. To that end, we used a spatially explicit, calibrated
population model of the European lynx (Lynx lynx) coupled with structured landscapes, in which we could control the landscape parameters of dispersal habitat coverage and
contagion, as well as the number and size of stepping stones available for breeding. In general, we found that colonization
success increased with increasing habitat coverage but decreased with increasing habitat contagion, while the introduction
of stepping stones had significant effects in critical situations. Especially at low to medium dispersal habitat coverage
and high disperser mortality, stepping stones had a positive effect on colonization success when they were large enough to
produce new dispersers, but negative effects when they were small and located in a way that dispersers would be distracted
from more suitable breeding habitat patches. The latter clearly constituted a shading effect and argues for a thorough consideration
of the trade-offs related to stepping stone size and location when implementing stepping stones as a conservation measure,
especially when the number of individuals of conservation concern is low. 相似文献
10.
From wine to pepper: rotundone, an obscure sesquiterpene, is a potent spicy aroma compound 总被引:1,自引:0,他引:1
Wood C Siebert TE Parker M Capone DL Elsey GM Pollnitz AP Eggers M Meier M Vössing T Widder S Krammer G Sefton MA Herderich MJ 《Journal of agricultural and food chemistry》2008,56(10):3738-3744
An obscure sesquiterpene, rotundone, has been identified as a hitherto unrecognized important aroma impact compound with a strong spicy, peppercorn aroma. Excellent correlations were observed between the concentration of rotundone and the mean 'black pepper' aroma intensity rated by sensory panels for both grape and wine samples, indicating that rotundone is a major contributor to peppery characters in Shiraz grapes and wine (and to a lesser extent in wine of other varieties). Approximately 80% of a sensory panel were very sensitive to the aroma of rotundone (aroma detection threshold levels of 16 ng/L in red wine and 8 ng/L in water). Above these concentrations, these panelists described the spiked samples as more 'peppery' and 'spicy'. However, approximately 20% of panelists could not detect this compound at the highest concentration tested (4000 ng/L), even in water. Thus, the sensory experiences of two consumers enjoying the same glass of Shiraz wine might be very different. Rotundone was found in much higher amounts in other common herbs and spices, especially black and white peppercorns, where it was present at approximately 10000 times the level found in very 'peppery' wine. Rotundone is the first compound found in black or white peppercorns that has a distinctive peppery aroma. Rotundone has an odor activity value in pepper on the order of 50000-250000 and is, on this criterion, by far the most powerful aroma compound yet found in that most important spice. 相似文献