An optimised protocol for molecular identification of Eimeria from chickens

Molecular approaches supporting identification of Eimeria parasites infecting chickens have been available for more than 20 years, although they have largely failed to replace traditional measures such as microscopy and pathology. Limitations of microscopy-led diagnostics, including a requirement for specialist parasitological expertise and low sample throughput, are yet to be outweighed by the difficulties associated with accessing genomic DNA from environmental Eimeria samples. A key step towards the use of Eimeria species-specific PCR as a sensitive and reproducible discriminatory tool for use in the field is the production of a standardised protocol that includes sample collection and DNA template preparation, as well as primer selection from the numerous PCR assays now published. Such a protocol will facilitate development of valuable epidemiological datasets which may be easily compared between studies and laboratories. The outcome of an optimisation process undertaken in laboratories in India and the UK is described here, identifying four steps. First, samples were collected into a 2% (w/v) potassium dichromate solution. Second, oocysts were enriched by flotation in saturated saline. Third, genomic DNA was extracted using a QIAamp DNA Stool mini kit protocol including a mechanical homogenisation step. Finally, nested PCR was carried out using previously published primers targeting the internal transcribed spacer region 1 (ITS-1). Alternative methods tested included sample processing in the presence of faecal material, DNA extraction using a traditional phenol/chloroform protocol, the use of SCAR multiplex PCR (one tube and two tube versions) and speciation using the morphometric tool COCCIMORPH for the first time with field samples.     

Effects of increasing the stocking density of large carps by 20% on 'cash' carp–small fish polyculture of Bangladesh

This experiment was carried out in the framework of a project to develop a viable fish polyculture technology under Bangladeshi conditions that allows simultaneous fish production of small indigenous species for the farmers' family consumption and of large carp species as a cash crop. The objectives of this experiment were to assess the effects on fish performance and on the environment of adding 20% large fish to the basic ‘cash crop’ carp–small fish polyculture consisting of 10 000 fish ha^?1 of the large carp rohu Labeo rohita (Hamilton), catla Catla catla (Hamilton) and common carp Cyprinus carpio (L.) at a species ratio 1:1:1, and 15 000 fish ha^?1 of each small indigenous fish punti Puntius sophore (Hamilton) and mola Amblypharyngodon mola (Hamilton) (control). The treatment ponds were stocked with additional 2000 large fish ha^?1, either all rohu, or all catla, or all common carp, or half rohu and half common carp, or half catla and half common carp. The results obtained and the analysis of interactions through the food web that affect food resource availability of the different fish species and account for the trends and differences observed among treatments confirm the positive effect of common carp on rohu reported in previous experiments and show that a 20% increase in large carps stocking neither affect the survival of the large carps nor reduce harvesting biomass of the small fish for the farmer's family consumption. Increased stocking densities of each large carp species did not significantly reduce its own harvesting weight and mean growth rate, while significantly increased rohu and catla (but not common carp) harvesting biomass and yield. The complex relations between species led to inter‐ and intraspecific competition, which in some treatments increased growth or yield of one species and in other treatments of other species, so that the gains on one species and the losses on the other led to no significant total harvested biomass differences between treatments. Yet, the results herein reported may help farmers to select their species stocking ratios. Thus, if the main target of the farmer is rohu, then a stocking density increase of 10% common carp and 10% rohu would improve rohu growth rate (due to common carp) and result in 50% higher rohu harvesting biomass and yield. If the main target of the farmer is catla, then a 20% increase in catla stocking density would lead to 20% higher catla harvesting biomass.     

Capture for culture: artificial shelters for grouper collection in SE Asia

This paper addresses a little‐discussed relationship between wild capture and mariculture, when the latter involves grow‐out of small wild‐caught fish or invertebrates in captivity. Seafood generated in this way is typically considered to be a form of aquaculture because it is assumed that, for animals removed from the wild when natural mortality is still very high, the protection conferred by culture operations will improve survivorship and enhance production. This assumption does not necessarily, however, apply when animals are removed well past the time of early high mortality. As one example of the implications of an early life‐history phase (ELP) fishery supplying culture operations, a preliminary study was conducted on an ELP fishery supplying live reef fish, especially groupers, in Southeast Asia. Grouper culture depends on both hatchery‐produced and wild‐caught fish which are then grown out to market size. Following interest to develop grow‐out operations in Indonesia, a pilot study was conducted to determine the sizes and capture rates of species of interest to the live fish trade, and to determine the likely environmental footprint of an artificial shelter (gango) type of capture method. From the results of the 15‐month study, we drew inferences regarding the sustainability of this fishing method and requirements of space, fish and materials for a viable grow‐out operation. The results showed that gangos were unselective for either species or size. Only 1.4% of the total fish catch (by number) were target species, mainly the grouper Epinephelus coioides, and most were large (mean total length was 13.6 cm) enough to have bypassed the early high mortality phase. Moreover, there were large non‐target catches that included many food fish species too small to be useful in catches. Given the large number and area of gangos needed for a viable operation, and that many groupers captured could probably have survived to reproduce, the ecological footprint of this approach could be substantial. These results, and literature on other ELP fisheries, suggest that these may often need management, have important links to other capture fishery sectors, and require careful evaluation of potential costs and benefits before introduction or development.     

Potential for productivity improvements by implementing improved management practices in pond polyculture of Indian major carps in Bangladesh

The present study aims to assess the impact of improved management practices on productivity, profit, and consumption expenditure of carp farmers. This study was carried out in three of Bangladesh’s top carp-producing districts (administrative units). A total of 300 carp farmers were surveyed through face-to-face interviews. Data were analyzed with propensity score matching (PSM), inverse probability weighting (IPW), and inverse probability weighted regression adjustment (IPWRA). Improved management practices, such as improved fingerling variety, stocking density, feeding, pond water change, lime application, and proper drainage facilities, were considered to achieve the study’s objectives. Improved management practices were classified into simple, intermediate, and complex practices based on their complexity. Adopters of improved management practices achieved significantly higher productivity (248–299 kg ha^?1) based on various matching techniques compared to non-adopters. The impact of adoption on profitability and consumption expenditure was 22% and 34% on the basis of IPW. Due to higher productivity and profit, adopters were able to spend more on consumption. Findings also revealed that adopting simple management practice is insufficient to boost productivity and profit. More research is needed to develop and optimize the improved management practices as a package. Improvement in extension services is suggested to improve the adoption.

     

Multi-criteria evaluation approach to GIS-based land-suitability classification for tilapia farming in Bangladesh

Site selection is a key factor in any aquaculture operation, because it affects both success and sustainability. It can, moreover, solve conflicts between different activities, making rational use of the land. This study was conducted to identify suitable sites for development of Nile tilapia (Oreochromis niloticus) farming in Sitakunda Upazila (sub-district), Bangladesh, using GIS-based multi-criteria evaluation of water and soil quality, topography, infrastructure and socio-economic factors. ASTER image and eighteen thematic layers were analyzed using ENVI and ArcView software to identify the suitable areas for tilapia farm development. A constraint layer was used to exclude areas from suitability maps that cannot be allowed to implement tilapia farming. A series of GIS models were developed to identify and prioritize the most suitable areas for tilapia farming. The output of the model clearly indicates the location and extent of tilapia farming areas on different suitability scales, i.e. most suitable (7,744 ha), moderately suitable (2,479 ha), and not suitable (838 ha). Model outputs were assessed against field verification data, and were consistent. Because existing aquaculture covers only 1,540 ha of land in the study area, the potential for expanding tilapia farms should take into consideration socio-political and environmental issues. The results are encouraging in terms of tilapia culture development and suggest that grassland–agriculture areas could be used for sustainable development of tilapia farming to diversify the economic activities of rural communities.     

Methodology for measuring fAPAR in crops using a combination of active optical and linear irradiance sensors: a case study in Triticale (X Triticosecale Wittmack)

The amount of photosynthetically active radiation (PAR, 0.4–0.7 μm) absorbed by plants for photosynthesis relative to incident radiation is defined as the fraction of absorbed photosynthetically active radiation (fAPAR). This is an important variable in both plant biomass production and plant growth modeling. This study investigates the application of a newly developed, linear irradiance sensor (LightScout Quantum Bar Sensor, LightScout, Spectrum Technologies, Inc. USA), to quantify fAPAR for a demonstrator crop, Triticale (X Triticosecale Wittmack). A protocol was devised for sensor placement to determine reflected PAR components of fAPAR and to determine the optimal time of day and sensor orientation for data collection. Coincident, top of canopy, normalized difference vegetation index (NDVI) measurements were also acquired with a CropCircle? ACS-210 sensor and measurements correlated with derived fAPAR values. The optimum height of the linear irradiance sensor above soil or plant canopy was found to be 0.4 m while measuring reflected PAR. Measurement of fAPAR was found to be stable when conducted within 1 h of local solar noon in order to avoid significant bidirectional effects resulting from diurnal changes of leaf orientation relative to the vertically-placed sensor. In the row crop studied, averaging fAPAR readings derived from the linear irradiance sensor orientated across and along the plant row provided an R² = 0.81 correlation with above-canopy NDVI. Across row sensor orientation also gave a similar correlation of R² = 0.76 allowing the user to reduce sampling time.     

Current and future strategies in breeding lentil for resistance to biotic and abiotic stresses

Lentil production is limited by lack of moisture and unfavorable temperatures throughout its distribution. Waterlogging and salinity are only locally important. Progress has been made in breeding for tolerance to drought through selection for an appropriate phenology and increased water use efficiency and in breeding for winter hardiness through selection for cold tolerance.The diseases rust, vascular wilt, and Ascochyta blight, caused by Uromyces viciae-fabae, Fusarium oxysporum f. sp. lentis, and Ascochyta fabae f. sp. lentis, respectively, are the key fungal pathogens of lentil. Cultivars with resistance to rust and Ascochyta blight have been released in several countries and resistant sources to vascular wilt are being exploited. Sources of resistance to several other fungal and viral diseases of regional importance are known. In contrast, although the pea leaf weevil (Sitona spp.) and the parasitic weed broomrape (Orobanche spp.), and to a lesser extent the cyst nematode (Heterodera ciceri), are significant yield reducers of lentil, no sources of resistance to these biotic stresses have been found. Directions for future research in lentil on both biotic and abiotic stresses are discussed.     

Fatty acid composition of resynthesized Brassica napus and trigenomic Brassica void of genes for erucic acid in their A genomes

The fatty acid composition of seed oil of four interspecific hybrids, resulting from crosses between zero erucic acid Brassica rapa (AA), and high erucic acid Brassica alboglabra/Brassica oleracea (CC) and Brassica carinata (BBCC), void of erucic acid genes in their A‐genomes was examined. The erucic acid content in resynthesized Brassica napus (AACC) lines derived from these crosses was only about half that of the high erucic acid CC genome parents, indicating equal contributions of the two genomes to oil (fatty acid) synthesis and accumulation. The differences in C18 fatty acid synthesis between the parents were also evident in the resulting resynthesized B. napus plants. Hexaploid Brassica plants of the genomic constitution AABBCC, in which the AA genome was incapable of erucic acid synthesis, had lower erucic acid contents than the B. carinata (BBCC) parent. This is plausible considering the fact that the zero erucic acid AA genome contributes to oil synthesis in AABBCC plants, thus reducing erucic acid content.     

Molecular markers for yield components in Brassica juncea – do these assist in breeding for high seed yield?

A population of 112 F₁-derived doubled haploid lines was produced from a reciprocal cross of Brassica juncea. The parents differed for seed quality, seed color and many agronomic traits. A detailed RFLP linkage map of this population, comprising 316 loci, had been constructed, and was used to map quantitative trait loci (QTL) for seed yield and yield components, viz. siliqua length, number of seeds per siliqua, number of siliques per main raceme and 1000-seed weight. Stable and significant QTLs were identified for all these yield components except seed yield. For yield components, a selection index based on combined phenotypic and molecular data (QTL effects) could double up the efficiency of selection compared to the expected genetic advance by phenotypic selection. Selection indices for high seed yield, based on the phenotypic data of yield and yield components, could only improve the efficiency of selection by 4% of the genetic advance that can be expected from direct phenotypic selection for yield alone. Inclusion of molecular data together with the phenotypic data of yield components in the selection indices did not improve the efficiency of selection for higher seed yield. This is probably due to often negative relationships among the yield components. Most of the QTLs for yield components were compensating each other, probably due to linkage, pleiotropy or developmentally induced relationships among them. The breeding strategy for B. juncea and challenges to marker assisted selection are discussed.     

Genetic control of spikelet number per ear with particular reference to rate of spikelet initiation in hexaploid wheat,Triticum aestivum L.em.Thell.Thell.

Summary Inheritance of spikelet number per ear and rate of spikelet initiation in wheat (Triticum aestivum L. em. Thell.) was studied in the land race spring wheats, 8–23 and 8–27 from Afghanistan, under controlled temperature and photoperiod. Spikelet number per ear was found to be under simple genetic control with dominance for high spikelet number. It is suggested that the gene determining spikelet number does so by determining the rate of spikelet initiation.