Mapping QTLs using a novel source of salinity tolerance from Hasawi and their interaction with environments in rice

Background

Salinity is one of the most severe and widespread abiotic stresses that affect rice production. The identification of major-effect quantitative trait loci (QTLs) for traits related to salinity tolerance and understanding of QTL × environment interactions (QEIs) can help in more precise and faster development of salinity-tolerant rice varieties through marker-assisted breeding. Recombinant inbred lines (RILs) derived from IR29/Hasawi (a novel source of salinity) were screened for salinity tolerance in the IRRI phytotron in the Philippines (E1) and in two other diverse environments in Senegal (E2) and Tanzania (E3). QTLs were mapped for traits related to salinity tolerance at the seedling stage.

Results

The RILs were genotyped using 194 polymorphic SNPs (single nucleotide polymorphisms). After removing segregation distortion markers (SDM), a total of 145 and 135 SNPs were used to construct a genetic linkage map with a length of 1655 and 1662 cM, with an average marker density of 11.4 cM in E1 and 12.3 cM in E2 and E3, respectively. A total of 34 QTLs were identified on 10 chromosomes for five traits using ICIM-ADD and segregation distortion locus (SDL) mapping (IM-ADD) under salinity stress across environments. Eight major genomic regions on chromosome 1 between 170 and 175 cM (qSES1.3, qSES1.4, qSL1.2, qSL1.3, qRL1.1, qRL1.2, qFWsht1.2, qDWsht1.2), chromosome 4 at 32 cM (qSES4.1, qFWsht4.2, qDWsht4.2), chromosome 6 at 115 cM (qFWsht6.1, qDWsht6.1), chromosome 8 at 105 cM (qFWsht8.1, qDWsht8.1), and chromosome 12 at 78 cM (qFWsht12.1, qDWsht12.1) have co-localized QTLs for the multiple traits that might be governing seedling stage salinity tolerance through multiple traits in different phenotyping environments, thus suggesting these as hot spots for tolerance of salinity. Forty-nine and 30 significant pair-wise epistatic interactions were detected between QTL-linked and QTL-unlinked regions using single-environment and multi-environment analyses.

Conclusions

The identification of genomic regions for salinity tolerance in the RILs showed that Hasawi possesses alleles that are novel for salinity tolerance. The common regions for the multiple QTLs across environments as co-localized regions on chromosomes 1, 4, 6, 8, and 12 could be due to linkage or pleiotropic effect, which might be helpful for multiple QTL introgression for marker-assisted breeding programs to improve the salinity tolerance of adaptive and popular but otherwise salinity-sensitive rice varieties.

     

Local adaptation studies and conservation: Parasite–host interactions between the endangered freshwater mussel Unio crassus and its host fish

1. Parasite–host interactions can involve strong reciprocal selection pressure, and may lead to locally adapted specializations. The highly threatened unionoid mussels are temporary parasites on fish, but local adaptation has not yet been investigated for many species.
2. Patterns of local adaptation of one of Europe's most threatened unionoids, the thick‐shelled river mussel (Unio crassus) were investigated. Eurasian minnows (Phoxinus phoxinus) from two rivers (separate drainage areas) were cross‐infested in the laboratory with sympatric and allopatric mussel larvae, while bullheads (Cottus gobio), inhabiting only one of the rivers, were infested with sympatric or allopatric mussel larvae. Larval encystment, juvenile mussel excystment and survival were measured.
3. For one river, but not the other, juvenile excystment from P. phoxinus was highest when infested with sympatric mussels. The opposite pattern was found for C. gobio in this river, where juvenile excystment and post‐parasitic juvenile survival from allopatric C. gobio were highest. The results thus cannot confirm local adaptation of U. crassus to P. phoxinus in the study rivers, as excystment was not consistently higher in all sympatric mussel–host combinations, whereas there were potential maladaptive signs of U. crassus in relation to C. gobio. There was no loss of encysted larvae 3 days after infestation until juvenile excystment. Most juveniles were excysted between 17 and 29 days after infestation, and the numbers of excysted juveniles increased with fish size.
4. The results have implications for parasite–host ecology and conservation management with regard to unionoid propagation and re‐introduction. This includes the need to (1) test suitability and adaptation patterns between U. crassus and multiple host fish species, (2) evaluate the suitability of certain unionoids and host fish strains after more than 3 days, and (3) determine whether large fish produce more juvenile mussels than smaller fish.

     

Otolith chemistry indicates walleye movement and entrainment in a large serial reservoir system

Understanding fish movement in impounded river systems is important for fisheries management. Otolith chemistry was used to examine walleye Sander vitreus (Mitchill) intra‐ and inter‐reservoir movement in four Missouri River impoundments. Age‐0 individuals were reclassified with 75%–93% accuracy to known natal sites, allowing for reliable evaluation of movement patterns of age‐1 and older fish. Nearly half of walleye occupied the same location annually (i.e. site residency) between 2009 and 2010. In 2011, during the largest flood on record since 1898, downstream movement (49% of age‐1 and older fish) exceeded upstream movement (7%) and site residency (33%) across the study area. After the flood, most walleye moved downstream within reservoirs (45%) or were site residents (37%). Entrainment occurred most frequently during the flood year and was proportionally greatest in downstream reservoirs. Otolith chemistry is useful for understanding walleye movement and entrainment and is a tool for fisheries management with applications such as informing reservoir water releases, harvest regulations and habitat protection and rehabilitation within and outside the Missouri River reservoir system.     

Drivers of Setaria pumila (Poir.) Roem. et Schult growth and impact on forage quality in lowland Switzerland meadows

Invasive grasses (especially Setaria pumila (Poir.) Roem. et Schult) increasingly threaten meadows and pastures as a consequence of human impact and climate change. We conducted a study in 2012 and in 2013 to better understand the growing cycle and the influence of S. pumila on forage quality of lowland meadows. We observed a rapid increase of S. pumila presence and phytomass on the southern side of the Alps across the growing season. We measured (i) above‐ground phytomass, with a modified Corral‐Fenlon method; (ii) botanical composition using the linear point quadrat method; and (iii) grassland chemical composition by NIRs (near‐infrared spectroscopy) analyses. To test the hypothesis that S. pumila summer growth is related to specific climatic conditions, meteorological data (temperature, precipitation and evapotranspiration) were collected from meteorological stations near the study sites. Total phytomass was sorted into S. pumila and other species. We used a generalized linear mixed models (GLMM) and found the abundance of S. pumila to be inversely correlated with rainfall and the presence of other species, but positively correlated with temperature increase. The increase of S. pumila above‐ground phytomass production was linked to a reduction of forage quality.     

Ultrastructural analysis of sequential cyprinid herpesvirus 3 morphogenesis in vitro

Cyprinid herpesvirus 3 (CyHV‐3) is an alloherpesvirus, and it is the aetiological agent of koi herpesvirus disease. Although the complex morphogenic stages of the replication cycle of CyHV‐3 were shown to resemble that of other members of the Herpesvirales, detailed analysis of the sequence and timing of these events was not definitively determined. This study describes these features through a time course using cyprinid cell cultures (KF‐1 and CCB) infected with CyHV‐3 (KHV isolate, H361) and analysed by transmission electron microscopy. Rapid viral entry was noted, with high levels of intracellular virus within 1–4 h post‐infection (hpi). Intranuclear capsid assembly, paracrystalline array formation and primary envelopment of capsids occurred within 4 hpi. Between 1 and 3 days post‐infection (dpi), intracytoplasmic secondary envelopment occurred, as well as budding of infectious virions at the plasma membrane. At 5–7 dpi, the cytoplasm contained cytopathic vacuoles, enveloped virions within vesicles, and abundant non‐enveloped capsids; also there was frequent nuclear deformation. Several morphological features are suggestive of inefficient viral assembly, with production of non‐infectious particles, particularly in KF‐1 cells. The timing of this alloherpesvirus morphogenesis is similar to other members of the Herpesvirales, but there may be possible implications of using different cell lines for CyHV‐3 propagation.     

Interactions of baseflow habitat constraints: Macroinvertebrate drift,stream temperature,and physical habitat for anadromous salmon in the Calapooia River,Oregon

1. The Calapooia River in western Oregon supports a small winter steelhead trout (Oncorhynchus mykiss) population and historically supported spring Chinook salmon (Oncorhynchus tshawytscha). Early timber harvesting removed the riparian forest, and log transportation practices simplified the channel. Those disturbance legacies continue to affect fish habitat by limiting shade and channel complexity, complicating conservation efforts.
2. To evaluate juvenile salmonid rearing potential, macroinvertebrate drift, thermal regime and physical habitat were measured at eight sites in 24 km of the upper river during late summer baseflow.
3. Overall physical habitat was simple, with few functioning instream structures or pools. During the 22‐day drift study, flows declined and maximum site stream temperatures ranged from 23.1°C at the lower end to 16.4°C 24 km upstream.
4. Macroinvertebrate drift concentrations ranged from 0.7–13.7 ind. m^?3 with biomasses from 0.02–1.23 mg m^?3. Drift concentration biomass was higher upstream (P  = 0.006) than downstream and declined overall (P  < 0.001) during the study. Drift biomass was dominated by five taxon groups – Baetis tricaudatus, Calineuria californica, Hesperoperla pacifica, Simulium spp., and Chironomidae, which were 65% of total biomass. During twilight, total biomass and biomass of B. tricaudatus, Simulium spp., and Chironomidae (both larvae and adults) were higher.
5. Total drift declined dramatically over the study period owing to decreases in drift concentration and a 58% decline in discharge, greatly reducing overall drift and available food resources for juvenile‐rearing salmonids.
6. The upper catchment, both with cooler temperatures and higher food availability, provided the best conditions for juvenile anadromous salmonids to survive late summer conditions. Conservation consequences of climate change‐induced alterations in flow and temperature may further affect habitat quality for juvenile salmonids in this catchment in the coming decades.

     

Linking small pelagic fish and cetacean distribution to model suitable habitat for coastal dolphin species,Delphinus delphis and Tursiops truncatus,in the Greek Seas (Eastern Mediterranean)

1. A large‐scale assessment of the summertime suitable habitat for Delphinus delphis (short‐beaked common dolphin) and Tursiops truncatus (common bottlenose dolphin) in Greek Seas (Eastern Mediterranean) was conducted using data from dedicated and opportunistic cetacean surveys and published data records.
2. Using a presence/absence approach, generalized additive models were applied to define a suite of environmental, bathymetric and biotic factors that best describe common and bottlenose dolphin spatial distribution, during early (May, June, July) and late (August, September) summer.
3. A geographic information system (GIS) was used to integrate sightings data with environmental characteristics, distance from the coast and sardine probability of presence. These variables were considered as good proxies for defining species‐suitable habitat within the study area's coastal environment.
4. The final selected models were used to produce annual probability maps of the presence of the species in the entire Greek Seas, as a measure of habitat suitability. Based on the mean probability and standard deviation maps for the study period GIS techniques were subsequently used to determine the persistent (areas with high mean and low variation) and occasional (high mean and high variation) habitat of each species.
5. Results showed that there was a high probability of common dolphin presence in areas with a high probability of sardine presence. For bottlenose dolphin, higher probability of the presence of species occurred in areas closer to the shore, with a high probability of sardine presence and with high concentrations of chlorophyll‐a.
6. In both seasons, the North Aegean Sea and the Inner Ionian Sea Archipelago were indicated as the most suitable areas for common dolphin distribution. Persistent habitat areas of the bottlenose dolphin included enclosed seas, continental shelf waters, and waters surrounding islands. The indicated suitable areas are discussed along with deficiencies of the models and future implications for conservation.

Copyright © 2016 John Wiley & Sons, Ltd.     

Predation by invasive signal crayfish on early life stages of European barbel may be limited

1. To determine whether or not signal crayfish Pacifastacus leniusculus and native white‐clawed crayfish Austropotamobius pallipes prey on European barbel Barbus barbus eggs, interstitial free‐embryos and emergent larvae, experiments were undertaken in salmonid (substratum) incubators (six treatments, four controls) fitted with video recorders.
2. No corpses or remains of emergent barbel larvae or eggs, or parts thereof, were observed in any of the incubators containing buried eggs, and no emergent larvae showed any sign of attack. However, video evidence of a signal crayfish catching and consuming a barbel larva was obtained.
3. There were no statistically significant differences between white‐clawed and signal crayfish either in carapace length or weight at the beginning and end of the experiments. The conservation implications of these results are discussed.

     

Phosphorus utilization in juvenile Clarias gariepinus fed phytase-supplemented diets based on soya bean (oil-extracted) and full-fat (roasted): A comparison

The effect of microbial phytase on phosphorus utilization in juvenile Clarias gariepinus (initial fish body weight 11.55 ± 0.2 g) was tested on two different diets based on oil-extracted soya bean (Experiment 1) and roasted soya bean meal (Experiment 2) using a 5 × 5 experimental design for 84 days. The basal isonitrogenous and isocaloric diets for oil-extracted and roasted soya bean were formulated to replace fish meal at 25% (S1E), 50% (S2E), 75% (S3E), 100% (S4E); and 25% (S1), 50% (S2), 75% (S3), 100% (S4), respectively. Each treatment was replicated four times. Microbial phytase was supplemented in each replicate at 250 FTU/g (P1), 500 FTU/g (P2), 750 FTU/g (P3), and 1,000 FTU/g (P4). Basal controls, which included a fish meal-based diet (S0), were not supplemented with phytase (P0). The result in Experiment 1 showed that there was a significant increase in whole-body protein and reduction in fat with phytase compared to a diet without phytase (P < 0.05). Serum total protein declined significantly with phytase supplementation (P < 0.05). Serum phosphorus and glucose were higher with phytase supplementation compared to control (P < 0.05). Bone minerals declined significantly with increasing level of soya bean compared to fish meal diet (P < 0.05). In Experiment 2, serum phosphorus was improved with phytase compared to control with no phytase (P > 0.05). A significant reduction in whole-body protein and increase in fat was observed for fish fed phytase diets compared to diets with no phytase, regardless of soya bean level (P < 0.05); however, ash content was improved with phytase (250 FTU/g) compared to control (P < 0.05). Phytase supplementation improved bone phosphorus (250 FTU/g), calcium (250 FTU/g), magnesium (250–500 FTU/g), and zinc (250–1,000 FTU/g) compared to control (P < 0.05). In conclusion, the research has demonstrated that improved bone phosphorus (P) and growth could be achieved with the supplementation of dietary phytase.     

Responses of Australian sea lions,Neophoca cinerea,to anthropogenic activities in the Perth metropolitan area,Western Australia

1. Tourist‐based activities, partly due to their rapid increase, have raised concerns regarding the impacts of anthropogenic activity on marine fauna. Documented effects on pinnipeds in proximity to humans include changes in behaviour, site use and potentially higher aggression levels towards people. Effects vary considerably between populations and sites, thus requiring separate assessment of human impacts on activity and energy budgets.
2. Responses of the endangered Australian sea lion, Neophoca cinerea, to human visitation were recorded from November 2013 through April 2014. Exposure levels and response types to anthropogenic activities were assessed at two easily accessible locations with different management schemes, Seal (landing prohibited) and Carnac (landing permitted) islands, Western Australia. Exposure levels were measured as both stimulus type (i.e. ‘People’, ‘Paddlers’, ‘Small’, ‘Medium’, and ‘Large vessels’, ‘Tour vessels’, and ‘Jet skies’), and people (‘Direct’, ‘Attract’, ‘Interact’, ‘View’, ‘Incidental’, ‘Water’, ‘Low‐level’), and vessel activities (‘Interact’, ‘Approach/Follow’, ‘Anchor noise’, ‘Engine noise’, ‘Close to beach’, ‘Moderate/Fast travel’, ‘Slow travel’, ‘Transit’, ‘Drift/At anchor’, ‘Aircraft noise’).
3. Exposure levels varied significantly between the islands in numbers, stimuli type, duration and minimum approach distances. The instantaneous behaviours of ‘Lift head’, ‘Interact’ and ‘Sit’ were the most frequent responses. ‘Aggressive’ and ‘Retreat’ responses, the highest disturbance levels measured, occurred on Carnac approximately once per day, but rarely on Seal Island. ‘Aggressive’ behaviour towards ‘People’ was observed only on Carnac Island and elicited only by ‘People’. ‘People’, ‘Tour vessels’, and scenic ‘Aircrafts’ on both islands as well as ‘Jet skis’ on Carnac Island had the highest probability of triggering responses. Owing to their relatively high visitation at Seal Island, ‘Paddle powered vessels’, followed by ‘Tour vessels’ elicited the highest number of responses, compared with ‘People’, ‘Small’, and ‘Medium vessels’ at Carnac Island. The majority of responses occurred when any stimulus type was at short‐range (≤10 m), and ‘People’ ‘Viewing’ N. cinerea elicited most. Vessels triggered more responses at larger ranges than ‘People’.
4. To limit close‐range access to N. cinerea, one possibility is to close the beach at Carnac Island to human visitation and increase the minimum approach distance by vessels and ‘People’ by installing marker buoys at least 15 m from the shore.

© 2016 The Authors. Aquatic Conservation: Marine and Freshwater Ecosystems published by John Wiley & Sons, Ltd.