Genetic relationships between anther and stigma traits revealed by QTL analysis in two rice advanced-generation backcross populations

Anther and stigma size are critical floral traits that influence outcrossing in rice (Oryza sativa), a crop that is predominantly self-fertilizing. The efficiency of hybrid rice seed production depends on efficient outcrossing ability of parental lines, which is promoted by increased anther and stigma size. Phenotypic correlations between anther and stigma traits have been observed in many studies; however, evidence for this relationship is unclear and the genetic basis remains to be elucidated. To examine this relationship and to identify quantitative trait loci (QTLs) for increased anther and stigma size, we developed two advanced backcross QTL mapping populations derived from a cross between a Thai elite indica crop variety (SPR1) and an accession of common wild rice (O. rufipogon Griff.), which is predominantly outcrossing. One mapping population was selected for increased anther size while the other was selected for increased stigma size. We mapped QTLs for anther size and stigma size in both populations. Bulked segregant analysis was used to identify molecular markers associated with the selected traits. A total of 16 significant QTLs associated with anther and stigma traits were identified across the two populations, and these were located in five genomic regions on four chromosomes. Whereas three of these regions have been previously reported, two of them are newly identified and should be further explored for improving outcrossing ability in rice. The co-localization of QTL for anther and stigma traits strongly suggests some degree of shared developmental basis for these traits.     

Long-time 3D CFD modeling of sedimentation with dredging in a hydropower reservoir

Purpose

The purpose of the current study was to present a 3D computational fluid dynamics (CFD) model that can be used to predict long-term (11 years) bed changes in a reservoir due to sedimentation and dredging and that can be done with a reasonable computational time (18 h) on a desktop computer.

Materials and methods

The numerical model solved the Navier-Stokes equations on a 3D non-orthogonal unstructured grid to find the water velocities and turbulence. The convection-diffusion equation for suspended sediment transport was solved to find the sediment deposition pattern. Bed changes were computed and used to adjust the grid over time. Thereby, bed elevations over time were computed. The effect of dredging was also included in the model, and how this affected the bed elevation changes. The main feature of the numerical model enabling a reasonable computational time was implicit numerical methods giving the possibility to use long time steps.

Results and discussion

The results were compared with annually measured bed elevation changes in the reservoir over 11 years. This gave 11 figures of bed elevation changes, due to the combined effect of sedimentation and dredging. Comparing the annually computed and measured bed changes, there was a fair agreement for most of the years. The main deposition patterns were reproduced. The amount of sediments removed in three dredging campaigns were also computed numerically and compared with the measured values. Parameter tests were done for the grid size, fall velocity of the sediments, cohesion, and sediment transport formula. The deviation between computed and measured dredged sediment volumes was less than 16% for all these four parameters/formulas.

Conclusions

The 3D CFD numerical model was able to compute water flow, sediment transport, and bed elevation changes in a hydropower reservoir over a time period of 11 years. Field measurements showed reasonable agreement with the computed bed elevation changes. The results were most sensitive to the sediment particle fall velocity and cohesion of the bed material.

     

Genetic relationships of boxwood (<Emphasis Type="Italic">Buxus</Emphasis> L.) accessions based on genic simple sequence repeat markers

Boxwoods (Buxus L., Buxaceae) are popular woody landscape shrubs grown for their diverse forms and broad-leaved evergreen foliage. We used genic simple sequence repeat (genic-SSR) markers to assess genetic diversity and relatedness of 275 accessions from the National Boxwood Collection at the U.S. National Arboretum. Flow cytometry was conducted to determine the relative ploidy of each accession. Genic-SSR loci were highly variable among the accessions, detecting an average of 6.7 alleles per locus based on 17 primer pairs. Data were analyzed with a distance matrix based on Jaccard’s similarity index, followed by Unweighted Pair Group Method with Arithmetic Mean clustering. Two major clusters were identified, with four subclusters consisting of individual accessions from B. balearica Lam., B. bodinieri Lévl., B. harlandii Hance, B. microphylla Siebold et Zuccarini, B. sempervirens L., B. sinica (Rehd. et Wils.) M. Cheng, and their putative interspecific hybrids. The accessions generally clustered by cultivar, provenance, or species. Clustering within each group typically reflected breeding pedigrees, when known, and the clusters were supported by bootstrap results. This information will be used for breeding programs and collection management, and for identifying possible sources of disease tolerance for boxwood blight and other diseases and pests.     

Lipid digestibility and ultrastructural changes in the enterocytes of Arctic char (Salvelinus alpinus L.) fed linseed oil and soybean lecithin

Arctic char (Salvelinus alpinus L.) were fed two isocaloric diets supplemented with 15% linseed oil or soybean lecithin, and subsequently analysed for ultrastructural changes in various intestinal segments (pyloric caeca region, midgut and hindgut) as well as apparent digestibility coefficients (ADC) of the diets. The ADC of dry matter, lipid and individual fatty acids were always highest in fish fed the soybean lecithin diet. In hindgut for example, ADC of lipid and dry matter were 94 and 96%, respectively, in fish fed the soybean lecithin diet compared to 85 and 94% in fish fed linseed oil.There were major ultrastructural differences in the enterocytes between fish fed the two experimental diets. In char fed the linseed oil diet there were substantial accumulations of lipid droplets in the enterocytes from the pyloric caeca and midgut but not in hindgut. These accumulations were not observed in fish fed the soybean lecithin diet. In some cases, deposition of fat in the enterocytes was so great that it resulted in epithelial damage with lipid droplets and cell debris appearing in the intestinal lumen. These changes are likely to be pathological and may lead to intestinal malfunction and represent a major infection route to pathogenic bacteria. On the basis of these results it is suggested that endogenous phospholipid synthesis is insufficient to maintain lipoprotein synthesis in Arctic char when fed diets containing high levels of polyunsaturated fatty acid of total lipid, and that phospholipids should be supplied with such diets.     

Dominance hierarchies in Arctic charr, Salvelinus alpinus L.: differential cortisol profiles of dominant and subordinate individuals after handling stress

We examined the effect of social rank on plasma cortisol dynamics after handling stress in juvenile Arctic charr, Salvelinus alpinus L., reared in groups of 200 individuals in 1.5 m³ circular tanks (rearing density 0.022 kg L^–1). Fish obtained by dip-netting were categorized as either socially subordinate, dominant or as holding an intermediate position on the basis of size, skin coloration and occurrence of bite marks. In undisturbed fish, the highest cortisol levels were found in fish ranked as intermediate and the lowest in dominant fish. In contrast to what has been found under conditions of artificial rearing in small groups (two to ten individuals), cortisol was not significantly elevated in subordinates compared with dominant individuals. In small groups of fish, aggressive interactions and restricted access to food may be significant factors leading to increased stress in socially subordinate individuals. Following stress by dip-netting and transfer, the quickest and largest cortisol response was seen in dominant individuals. These results suggest that hypothalamus–pituitary–inter-renal/adrenal axis responsiveness as well as baseline cortisol production is influenced by social rank in fish, as has been shown in other vertebrates.     

鱼类消化道菌群与碳水化合物代谢

碳水化合物氧化分解是鱼类能量的重要来源。由于碳水化合物来源广泛、价格相对低廉,饲料中添加适量碳水化合物,不仅可以降低饲料成本,而且可以节约蛋白原料,减少氨氮排放。然而以往研究表明,鱼类摄入超量碳水化合物时会出现抗病力受损、生长迟缓、脂肪肝、死亡率升高等问题。鱼类消化道微生物参与宿主的糖、脂类和蛋白质等代谢过程,对动物营养代谢有重要的调控作用。提高鱼类对饲料的利用率,对鱼类增产、渔民增收具有重要的现实意义。本研究综述了鱼类对碳水化合物的代谢,以鱼类消化道微生物为出发点,阐述了鱼类消化道微生物调控碳水化合物代谢的方式与可能机制,旨在为鱼类高效利用碳水化合物以及节约饲料中蛋白质提供新视角。     

Anesthesia induces stress in Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis>), Atlantic cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>) and Atlantic halibut (<Emphasis Type="Italic">Hippoglossus hippoglossus</Emphasis>)

Stress in response to anesthesia with benzocaine, MS-222, metomidate and isoeugenol was studied in Atlantic salmon (Salmo salar), Atlantic halibut (Hippoglossus hippoglossus), and Atlantic cod (Gadus morhua) with no concomitant stress from handling or confinement in association with anesthesia or sampling. All of the anesthetics tested induced a stress response in all species, displayed by a release of cortisol to the water. MS-222 anesthesia elicited the highest cortisol release rates, reaching maximum levels 0.5 h post-exposure and returning to basal levels after 3–4 h. Benzocaine anesthesia caused a bimodal response where the initial peak in cortisol release rate was followed by a second increase lasting towards the end of the trial (6 h). This bimodality was more profound in Atlantic salmon than in Atlantic halibut and Atlantic cod. Metomidate anesthesia induced the lowest release of cortisol of the agents tested in both Atlantic halibut and Atlantic cod, but resulted in a bimodal response in Atlantic salmon where the initial increase in cortisol release was followed by a larger increase peaking at 2–2.5 h post exposure before returning to basal levels after 5 h. The stress induced in Atlantic salmon by isoeugenol anesthesia resembled that of MS-222, but did not reach the same elevated level. Overall, the cortisol release was most profound in Atlantic salmon followed by Atlantic halibut and Atlantic cod.     

Salmonid alphavirus (SAV) and pancreas disease (PD) in Atlantic salmon,Salmo salar L., in freshwater and seawater sites in Norway from 2006 to 2008

A cohort study was initiated in the spring of 2006 to investigate epidemiological aspects and pathogenesis of salmonid alphavirus (SAV) subtype 3 infections and pancreas disease (PD). The aims were to assess involvement of the freshwater production phase, the extent and frequency of subclinical infections and to follow PD‐affected populations throughout the entire seawater production cycle, as well as investigate possible risk factors for PD outbreaks. Fish groups from 46 different Atlantic salmon freshwater sites in six counties were sampled once prior to seawater transfer and followed onto their seawater sites. A total of 51 Atlantic salmon seawater sites were included, and fish groups were sampled three times during the seawater production phase. SAV subtype 3 was not identified by real‐time RT‐PCR from samples collected in the freshwater phase, nor were any SAV‐neutralizing antibodies or histopathological changes consistent with PD. In the seawater phase, SAV was detected in samples from 23 of 36 (63.9%) studied sites located within the endemic region. No SAV subtype 3 was detected in samples from seawater sites located outside the endemic region. The cumulative incidence of PD during the production cycle amongst sites with SAV detected was 87% (20 of 23 sites). Average fish weight at time of PD diagnosis ranged from 461 to 5978 g, because of a wide variation in the timing of disease occurrence throughout the production cycle. Mortality levels following a PD diagnosis varied greatly between populations. The mean percentage mortality was 6.9% (±7.06) (range 0.7–26.9), while the mean duration of increased mortality following PD diagnosis was 2.8 months (±1.11) (range 1–6).     

Pancreas disease (PD) in sea‐reared Atlantic salmon,Salmo salar L., in Norway; a prospective,longitudinal study of disease development and agreement between diagnostic test results

A prospective longitudinal study was performed on three cages at each of three Norwegian Atlantic salmon seawater sites that experienced outbreaks of pancreas disease (PD). Once salmonid alphavirus (SAV) ribonucleic acid (RNA) was detected by real‐time RT‐PCR (Rt RT‐PCR) at a site, it became detected in all studied cages and was persistently found until the end of the study period up to 19 months after first detection. SAV‐specific antibodies were detected at all sites until the end of the study period and were also found at a high prevalence in broodfish at the time of stripping. No evidence of increased viral activity was detected in these broodfish. One site tested negative over several months prior to the first detection of SAV by Rt RT‐PCR and SAV‐specific antibody, which occurred 1 month prior to clinical manifestations of PD. Moribund fish or thin fish/runts that were sampled after the first PD diagnosis had almost twice the risk of testing positive by one or more diagnostic tests compared to that of randomly selected apparently healthy individuals. This paper describes the first detailed investigation of the disease development of PD at site and cage level in Norway, as well as an assessment of the performance and agreement of the commonly used diagnostic tests.