Effects of starvation,subsequent feeding and photoperiod on flesh quality in farmed cod (Gadus morhua)

The study was designed to investigate the effect of four cycles of 5 weeks starvation followed by 10‐week refeeding compared with daily feeding under either natural photoperiod or continuous light (LL) regime on body composition and flesh quality in Atlantic cod in sea cages, northern Norway. The fish were sampled for body composition and flesh quality parameters at the start of the trial, twice at the end of a 10‐week feeding period and twice at the end of a 5‐week starvation period. There was effect of both feeding and light regime on growth, the two starving groups losing weight during starvation and regaining weight during refeeding, and the group under LL being heavier. But, the mean overall growth did not vary between groups. Starvation/refeeding regime resulted in higher slaughter yield, but no overall effect was seen on hepatosomatic index, water content, water holding capacity (WHC), muscle pH, hardness or flesh colour compared with control groups. Continuous light increased gutted weight and slaughter yield, lowered WHC and depressed maturation compared with fish under natural light regime. Increased growth rate resulted in softer fillets and lower muscle pH.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

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.

     

High fluid shear strain causes injury in silver shark: Preliminary implications for Mekong hydropower turbine design

The Lower Mekong Basin is facing unprecedented threats to fish diversity from hydropower development. There is increasing pressure on developers and construction authorities to design solutions to improve fish survival through turbines, thus protecting the resources in regions being developed for hydropower. A hydraulic characteristic of hydropower turbines with known fisheries impacts is fluid shear stress. Elevated shear stress occurs where rapidly flowing water passes near spillways, screens and within turbine draft tubes. Shear stress can have adverse impacts on fish, but no work has assessed whether this holds true for Mekong River species. A flume was used to determine critical tolerances of silver shark, Balantiocheilos melanopterus (Bleeker), to shear stress rates at a high‐velocity jet which simulated a hydropower turbine. Fish were assessed for injury or mortality following exposure. Results were compared against a no‐shear control. Injury and mortality were greater at higher shear stress exposures. Injuries occurred at all shear exposure levels with mortality at shear levels higher than 600/s. This approach should help design future hydropower turbines if data on other species demonstrate similar results. If the likelihood of adverse impact is high, then shear stress will need to be considered in the design of future hydropower facilities.     

Impact of grassland contract policy on soil organic carbon losses from alpine grassland on the Qinghai–Tibetan Plateau

Carbon storage in the soils on the Qinghai–Tibetan Plateau plays a very important role in the global carbon budget. In the 1990s, a policy of contracting collective grasslands to smaller units was implemented, resulting in a change from the traditional collective grassland management to two new management patterns: a multi‐household management pattern (MMP: grassland shared by several households without enclosures) and a single‐household management pattern (SMP: grassland enclosed and used by only one household). In 2016, 50 MMP and 54 SMP winter pastures on the Qinghai–Tibetan Plateau were sampled to assess the differences in soil organic carbon (SOC) between the two management patterns. Results showed that average SOC was significantly greater under MMP than under SMP, with an estimated 0.41 Mg C/ha/yr lost due to SMP following the new grassland contract. Based on the government's grassland policy, four grassland utilization scenarios were developed for both summer and winter pastures. We found that if the grassland were managed under SMP, likely C losses ranged between 0.31 × 10⁷ and 6.15 × 10⁷ Mg C/yr across the Qinghai–Tibetan Plateau relative to MMP, which more closely resembles pre‐1990s grassland management. Previous estimates of C losses have only considered land use change (with cover change) and ignored the impacts driven by land management pattern changes (without cover change). The new data suggest that C losses from the Qinghai–Tibetan Plateau are greater than previously estimated, and therefore that the grassland contract policy should be reviewed and SMP households should be encouraged to reunite into the MMP. These findings have potential implications for land management strategies not only on the Qinghai–Tibetan Plateau but also other grazing regions globally where such practices may exist.     

Effects of conservation tillage drills on soil quality indicators in a wheat–oilseed rape rotation: organic carbon,earthworms and water-stable aggregates

The effects of five conservation tillage drills with crop residue levels covering between 17% and 79% of the soil, and tillage depths ranging from 25 to 200 mm, were examined over 3 years. The tillage systems ranged from a relatively disruptive Farm System to a Low Disruption system, with three intermediate treatments labelled Sumo DTS, Claydon and Mzuri. The study involved field sites on a clay or clay loam soil, where winter wheat and oilseed rape were grown in rotation. In the clay field, the Mzuri and Low Disruption treatments, which produced the highest residue coverage, showed the greatest increase in surface total soil organic carbon (1.1 and 0.48 Mg C ha⁻¹, respectively) between years 1 and 3. The least disruptive tillage system also resulted in the highest density of earthworms (181–228 m⁻²), and the most disruptive system produced the lowest densities (75–98 m⁻²). In the third year, the least disruptive system also showed a higher proportion of water-stable aggregates (29.8%) than the other treatments (22.7%–25.3%). Linear regressions showed positive relationships of both soil organic carbon and earthworm density with surface residue cover, and of the proportion of water-stable aggregates with soil organic carbon.     

P0 protein of cotton leafroll dwarf virus-atypical isolate is a weak RNA silencing suppressor and the avirulence determinant that breaks the cotton Cbd gene-based resistance

Cotton blue disease (CBD) is the most important disease present in cotton crops in South America and cotton leafroll dwarf virus (CLRDV) is the causal agent. The disease has been controlled by sowing cotton varieties resistant to CLRDV. However, in the 2009/10 growing season, an outbreak due to an atypical CLRDV isolate (CLRDV-at) occurred in northwest Argentina. Although CLRDV and CLRDV-at genomes are very closely related, the symptoms they produce in cotton plants are quite different. P0 is the most divergent protein between the isolates and in CLRDV is a silencing suppressor protein. This work characterized the silencing suppressor activity of the P0 protein encoded by CLRDV-at (P0^CL-at) and evaluated its role in Cbd-resistance break in cotton plants. It was demonstrated that P0^CL-at, despite having a mutation in the consensus of the F-box-like motif, was able to suppress local RNA silencing, but displayed lower activity than P0^CL. P0^CL and P0^CL-at showed no differences in the interaction with Gossypium hirsutum SKP1 orthologue (GSK1) and Nicotiana benthamiana SKP1 and both P0 proteins triggered destabilization of ARGONAUTE1. However, when the ability to enhance PVX symptoms was evaluated, P0^CL-at was shown to be a weaker pathogenicity factor than P0^CL in N. benthamiana. Interestingly, trans-expressed P0^CL-at enabled CLRDV to systemically infect CBD-resistant plants, and a chimeric CLRDV-P0^CL-at infectious clone succeeded in establishing infection in CBD-resistant cotton varieties with symptoms resembling those produced by CLRDV-at. These results strongly suggest that P0^CL-at is the avirulence (Avr) determinant involved in breaking cotton Cbd gene-based resistance.     

Strategy to identify resistance to white mould associated with high yield for irrigated common bean in Brazil

Development of common bean cultivars with partial white mould resistance through breeding techniques has been a challenge in Brazil. As yet, lines/cultivars from breeding programmes have not been investigated for resistance; therefore, this study screened 107 lines/cultivars for their reactions to white mould in 14 preliminary trials conducted under irrigation. Thirteen resistant lines/cultivars (three of Andean origin) and six Mesoamerican cultivars (three intermediately resistant and three susceptible) were selected for further investigation. These lines/cultivars and the resistant control A195 were evaluated in six advanced trials and two straw tests to assess the effectiveness of the screening procedure. In 11 preliminary trials, screenings were performed under moderate/high or higher disease pressure. These pressures occurred in two advanced trials in which, when yields were averaged across moderate/high and high pressures, 10 Mesoamerican lines/cultivars selected for resistance yielded 14%, 23%, and 38% more than intermediately resistant cultivars, A195, and susceptible cultivars, with median disease ratings (1–9 scale) of 4.5, 5.7, 5.7, and 6.7, respectively. In the straw test, three Andean lines/cultivars (A195 included) and two susceptible cultivars in the field were among those with the highest levels of physiological resistance. Thus, field rating under high disease pressure and greenhouse rating did not correlate significantly, suggesting that field trials are critical to evaluating resistance and to identifying high-yielding beans. Therefore, lines/cultivars from breeding programmes assessed in field trials may provide a low cost and fast way to identify high-yielding bean cultivars with partial resistance to white mould in the subtropical southern hemisphere.