Agronomic fortification of rice grains with secondary and micronutrients under differing crop management and soil moisture regimes in the north Indian Plains

Although the System of Rice Intensification (SRI) has been reported to produce higher paddy (Oryza sativa L.) yields with better-quality grains, little research has addressed the latter claim. This study investigated the interactive effects of rice cultivation methods with different irrigation schedules and plant density on the uptake and concentration of sulfur (S), zinc (Zn), iron (Fe), manganese (Mn) and copper (Cu) in the grain and straw of two rice cultivars during two rainy seasons in the northern plains of India. As the two seasons differed in amounts of rainfall, there were impacts of soil moisture differences on nutrient uptake. Plots with SRI cultivation methods enhanced the grain uptake and concentrations of S, Zn, Fe, Mn and Cu by 36, 32, 28, 32 and 63%, respectively, compared to conventional transplanting (CT). Under SRI management, the highest concentrations of S, Zn and Cu in the grain and straw occurred with irrigation intervals scheduled at 3 days after disappearance of ponded water (DADPW; 3_D), whereas Fe and Mn concentrations in the grain and straw were higher with irrigation at 1 DADPW (1 _D ) compared with plots under 3 _D or 5 DADPW (5 _D ). The higher nutrient uptakes were also manifested in higher grain yield in 1 _D and 3 _D plots (by 9 and 6%, respectively) compared with 5 _D . Wider spacing (25 × 25 cm) compared with closer spacing (20 × 20 cm) significantly increased yield and the uptake and concentrations of all the said nutrients in the grains. When comparing the performance of two cultivars, the total uptakes of Zn, Fe, Mn and Cu in both grain and straw were significantly more in Hybrid 6444 than the improved variety Pant Dhan 4. Overall, SRI crop management compared to CT practices led to more biological fortification of rice grains with respect to S and the four micronutrients studied, giving a concomitant yield advantage of about 17% on average in this region.     

Rapid salinity changes affect the survival and physiology of a penaeid prawn: Implications of flood events on recruitment to the fishery

Estuaries act as nurseries for many penaeid prawns, but these habitats are highly susceptible to salinity decline through flooding. The rate of salinity decline and duration of exposure to non‐optimal salinity may affect survival and subsequent recruitment of prawns to the fishery. This study aimed to determine the effect of salinity fluctuations observed in local estuaries during flood events using a novel dilution approach. Mortality of juvenile Melicertus plebejus (Hess) was assessed after 24 hr exposure to 24 rates of salinity decline ranging from 0.01% to 20% per hr. After the salinity decline, prawns were held at the final salinities for five days before again assessing mortality as well as aerobic metabolic rate and prawn water content. Salinity decline from 36 to ~0.8 led to 50% mortality, but continued exposure to low salinity for five days increased mortality at this salinity to 99% and shifted the 50% mortality point to salinity ~5. Aerobic metabolic rate and water content data suggested the cause of mortality due to exposure to salinities < 5 was osmoregulatory failure. Rapid salinity declines over 24 hr and sustained low salinity due to flooding could compromise the survival of juvenile prawns, potentially reducing recruitment to the fishery.     

Investigations into the temporal development of epitheliocystis infections in brown trout: a histological study

Epitheliocystis in Swiss brown trout (Salmo trutta) is a chlamydial infection, mainly caused by Candidatus Piscichlamydia salmonis and Candidatus Clavichlamydia salmonicola. To gain a better understanding of the temporal development of infections in wild brown trout, we investigated epitheliocystis infections during the course of the summer and autumn months of a single year (2015), and compared this to sampling points over the span of the years 2012–2014. The survey focused on tributaries (Venoge and Boiron) of the Rhone flowing in to Lake Geneva. When evaluated histologically, epitheliocystis infections were found throughout the period of investigation with the exception of the month of June. Fifty to 86 animals per sampling were investigated. Highest prevalence and infection intensities were seen in September. A correlation between epitheliocystis infection and water temperatures was not evident. Interyear comparison revealed consistent levels of prevalence and infection intensities in late summer. The absence of infections in June, combined with the consistent interyear results, indicates seasonal fluctuation of epitheliocystis infections in brown trout with a reservoir persisting during winter months from which infections can re‐initiate each year. This could either be at levels below detection limits within the brown trout population itself or in an alternative host.     

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.

     

The efficiency of nitrogen in cattle manures when applied to a double‐annual forage cropping system

The use of cattle manure (CM) for fertilization presents challenges for optimizing nitrogen (N) use. Our work aimed to assess N efficiencies, in a 6‐year experiment with three biennial rotations of four crops: oat–sorghum (first year) and ryegrass–maize (second year) in a rainfed humid Mediterranean area of Spain. Fertilization treatments included the following: control (no N), 250 kg mineral N ha^?1 year^?1 (250MN), three CM rates (supplying 170, 250 and 500 kg N ha^?1 year^?1) and four treatments where the two lowest CM rates were complemented with either 80 or 160 kg mineral N ha^?1 year^?1. Treatments were distributed randomly in each of three blocks. Maximum dry‐matter yield (~44–49 t ha^?1 rotation^?1) was achieved in the third rotation, and only the control and the 170CM yielded significantly less. Within the limitations of the EU Nitrate Directive, the N steady state supply of 170CM always requires a complement of mineral N (80 kg N ha^?1) to maximize N agronomic efficiency. The maximum N‐fertilizer replacement value (250CM vs. 250MN) was 0·67, without significant differences between the two treatments in other N‐related efficiency indexes, which indicates that plants took advantage of residual‐N effects. Nitrogen losses by leaching in the 250CM treatment were around 5–7% of the N applied. This reinforces the sustainability of manure recycling in long cropping seasons.     

Herbage production,nutritive value and animal productivity within hardwood silvopasture,open and mixed pasture systems in Appalachia,United States

Demand for livestock food products is projected to increase dramatically through to 2050. Increased livestock production capacity on marginal lands will be critical to meeting this demand. A 5‐year research effort was undertaken to evaluate lamb and sward productivity within open and hardwood silvopasture (SP) systems in Appalachia, USA. Grazing began in mid to late April each year, with the grazing season averaging 141 d. Grazing system treatments during 2002 and 2003 grazing seasons were as follows: 100% open pasture (OP), 67% OP and 33% SP, and 67% OP and 33% SP with delayed SP grazing initiation (OSD). In 2004, a 100% SP (SP) system was added. Animals were rotationally stocked through either 6 (2002–2004) or 7 (2005–2006) paddocks. Open pasture produced greater (P < 0·001) grazing season herbage yield, while all systems generated similar animal performance. Based on summer solstice, herbage production in spring was greater (P < 0·001) than summer, except in 2003. Total non‐structural carbohydrate (TNC) content was greater (P < 0·05) in spring than in summer, except in 2004. Animal performance was superior in spring versus summer (P < 0·001). Animal plasma urea nitrogen (PUN) was lower (P < 0·05) for OP in 2003. When PUN was correlated with nutritive value indicators, the ratio of TNC to crude protein (CP) had the strongest correlation. The strong correlation indicates the need for synchronized ruminal energy and CP availability. Development of silvopasture from existing woodlots has potential to improve whole farm productivity on marginal lands.     

Efficiency of fisheries is increasing at the ecosystem level

Managing fisheries presents trade‐offs between objectives, for example yields, profits, minimizing ecosystem impact, that have to be weighed against one another. These trade‐offs are compounded by interacting species and fisheries at the ecosystem level. Weighing objectives becomes increasingly challenging when managers have to consider opposing objectives from different stakeholders. An alternative to weighing incomparable and conflicting objectives is to focus on win–wins until Pareto efficiency is achieved: a state from which it is impossible to improve with respect to any objective without regressing at least one other. We investigate the ecosystem‐level efficiency of fisheries in five large marine ecosystems (LMEs) with respect to yield and an aggregate measure of ecosystem impact using a novel calibration of size‐based ecosystem models. We estimate that fishing patterns in three LMEs (North Sea, Barents Sea and Benguela Current) are nearly efficient with respect to long‐term yield and ecosystem impact and that efficiency has improved over the last 30 years. In two LMEs (Baltic Sea and North East US Continental Shelf), fishing is inefficient and win–wins remain available. We additionally examine the efficiency of North Sea and Baltic Sea fisheries with respect to economic rent and ecosystem impact, finding both to be inefficient but steadily improving. Our results suggest the following: (i) a broad and encouraging trend towards ecosystem‐level efficiency of fisheries; (ii) that ecosystem‐scale win–wins, especially with respect to conservation and profits, may still be common; and (iii) single‐species assessment approaches may overestimate the availability of win–wins by failing to account for trade‐offs across interacting species.     

Effect of substitution of dietary fish meal by soybean meal on different sizes of gibel carp (Carassius auratus gibelio): digestive enzyme gene expressions and activities,and intestinal and hepatic histology

A 7‐week growth trial was conducted to evaluate the effects of dietary soybean meal (SBM) on digestive enzyme activity of intestinal mucosa, mRNA levels of digestive enzymes in hepatopancreas, and the mid‐intestinal and hepatopancreas histology of gibel carp CAS III (Carassius auratus gibelio). Four different growth phases of gibel carp (initial body weight: fry, 0.8 g; juvenile, 5.0 g; 1‐year‐old, 62.7 g; and broodstock, 135.6 g) were tested. Seven isonitrogenous and iso‐energetic diets were formulated to contain different SBM replacement levels (0%, 20%, 40%, 60%, 80% and 100% of dietary fish meal protein), and another diet (SBMAA) contained all SBM protein and supplied crystalline amino acids. The results showed that the activities of mid‐intestine trypsin, α‐amylase and gamma glutamyl transpeptidase reduced with increased dietary SBM, while the chymotrypsin activity increased first and then decreased. The ultrastructures of intestinal epithelial cells and hepatopancreas cells in fry and broodstock fish were distinctly affected by 200 g kg^‐1 dietary SBM. Supplementation of dietary amino acid to the highest replacement groups was not sufficient to improve digestive and absorptive capacities and growth performance. Gibel carp may be adapted to dietary SBM through increase in gene expression of hepatopancreas digestive enzymes and has potential to utilize proceeded SBM as feedstuffs.     

Natural bixin as a potential carotenoid for enhancing pigmentation and colour in goldfish (Carassius auratus)

Discovering natural carotenoids for colour enhancement and health benefits of fish is important to develop new feed formulations. We have purified natural bixin from achiote seeds and evaluated the effect of colour enhancing and pigmentation in goldfish. Varying levels of bixin‐based diets were prepared with 420 g kg^?1 of crude protein and 120 g kg^?1 of lipid content. Our results clearly showed that bixin (0.05, 0.10, 0.20 and 0.60 g kg^?1) based diets significantly (P < 0.05) enhanced the skin and fin colour at 30 and 60 days compared to diet without bixin. Interestingly, diet which contains 0.20 g kg^?1 bixin and commercial feed (with astaxanthin) had similar effect on carotenoid deposition in skin. Moreover, total carotenoid deposition in fin was higher than in skin of all bixin‐containing diets. However, 0.60 g kg^?1 bixin‐containing diet had lower specific growth rate (1.01 ± 0.01) and higher feed conversion ratio (2.05 ± 0.19) compared to the control group. The present results demonstrate that achiote bixin can be successfully used as an alternative natural carotenoid source against synthetic astaxanthin in fish feed. Our data indicate that 0.20 g kg^?1 is a suitable dietary level of bixin to ensure strong pigmentation, acceptable growth and feed utilization in goldfish.     

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.