Haplotype phasing after joint estimation of recombination and linkage disequilibrium in breeding populations

A novel method for haplotype phasing in families after joint estimation of recombination fraction and linkage disequilibrium is developed. Results from Monte Carlo computer simulations show that the newly developed E.M. algorithm is accurate if true recombination fraction is 0 even for single families of relatively small sizes. Estimates of recombination fraction and linkage disequilibrium were 0.00 （SD 0.00） and 0.19 （SD 0.03） for simulated recombination fraction and linkage disequilibrium of 0.00 and 0.20, respectively. A genome fragmentation phasing strategy was developed and used for phasing haplotypes in a sire and 36 progeny using the 50 k Illumina BeadChip by： a） estimation of the recombination fraction and LD in consecutive SNPs using family information, b） linkage analyses between fragments, c） phasing of haplotypes in parents and progeny and in following generations. Homozygous SNPs in progeny allowed determination of paternal fragment inheritance, and deduction of SNP sequence information of haplotypes from dams. The strategy also allowed detection of genotyping errors. A total of 613 recombination events were detected after linkage analysis was carried out between fragments. Hot and cold spots were identified at the individual （sire level）. SNPs for which the sire and calf were heterozygotes became informative （over 90%） after the phasing of haplotypes. Average of regions of identity between half-sibs when comparing its maternal inherited haplotypes （with at least 20 SNP） in common was 0.11 with a maximum of 0.29 and a minimum of 0.05. A Monte-Carlo simulation of BTA1 with the same linkage disequilibrium structure and genetic linkage as the cattle family yielded a 99.98 and 99.94% of correct phases for informative SNPs in sire and calves, respectively.     

Economies of scale for juvenile production of common snook (Centropomus undecimalis Bloch)

Abstract

Construction and operating costs for three common snook (Centropomus undecimalis) hatcheries in Florida, USA, are illustrated. Hypothetical capacities and targets of the three hatcheries (Scenarios I, II and III respectively) were 615, 000 juveniles (8 ‐ 10 g in weight) for stock enhancement, and 1, 275, 000 and 3, 000, 000 juveniles (1‐g in weight) for commercial grow‐out. Estimated production costs were lower than for many marine finfish species. The 20‐year mean costs per 1, 000 juveniles were estimated to be $324, $215, and $159, for hatcheries I, II, and III respectively, and the initial capital investments were $731, 660, $1, 162, 460, and $1, 896, 030¹, respectively. Major cost items of annual production were labor (22 ‐ 33%), supplies (14 ‐ 20%), fixed costs (15 ‐ 17%), and interest (13 ‐ 15%). The most profitable hatchery was the 3 million 1‐g juvenile hatchery due to the hatchery size effect, with a net present value (NPV) of $1, 760, 000, an internal rate of return (ERR) of 81%, a payback period of 3.6 years, and a profitability index of $2.86 for every dollar invested. Possible cost reductions to increase financial profitability were discussed.     

Performance of a photo‐heterotrophic,hypersaline system for intensive cultivation of white leg shrimp (Litopenaeus vannamei) with minimal water replacement in lined ponds using a stochastic approach

The aim of the study was to evaluate the performance of Litopenaeus vannamei in an intensive photo‐heterotrophic hypersaline system with minimal seawater replacement, and establish relationships between parameters of a stochastic production model and relevant water quality variables. Six experimental 1000 m² lined ponds were stocked at a density of 120 shrimp m^?2 for a 105‐day trial. Salinity increased from 37 to 45 ± 2 g/L, and the water level was maintained with the weekly addition of filtered seawater, equivalent to 1.6% per day. The stochastic model predicted that, at harvest, there is 95% confidence that the system produces between 12.1 and 14.7 t/ha with a mean final individual weight of 13.1 g and a mean survival of 84.2%. Sensitivity analyses showed that dissolved oxygen and individual final weight of shrimp were the main variables influencing yield variance. Nitrogenous compounds were maintained between optimal cultivation levels (NH₃–NH₄⁺ = 0.73 ± 0.43 mg/L, N–NO₂^? = 0.09 ± 0.05 mg/L, N–NO₃^? = 3.22 ± 0.11 mg/L). Heterotrophic bacteria (6.6 ± 3.4 × 10⁵ CFU/ml) and chlorophyll‐α concentration (108.5 ± 80.2 μg/L) showed a similar development pattern, indicating a strong relationship between bacteria and microalgae during cultivation. Vibrio spp. concentrations were low (1.24 ± 1.42 × 10³ CFU/ml). It was shown that the photo‐heterotrophic system could be used in hypersaline conditions, typical of semi‐arid regions, to consistently produce between 12.1 and 14.7 t/ha in 15 weeks.     

Lettuce response to organic and phosphate fertilizers and root mycorrhization

The response of lettuce to production system, organic and phosphate fertilizers and root mycorrhization, was evaluated in two pot trials with factorial treatment combination of: (i) soil type (from organic and from conventional production systems) and organic fertilizer (0, 2 and 4 t ha^?1) in the first trial; and (ii) mycorrhizal inoculation (mycorrhized and non-mycorrhized plants) and Gafsa phosphate (0, 100 and 200 kg P₂O₅ ha^?1) in the second. Lettuce growth decreased with increasing rates of the organic fertilizer because of its very high electrical conductivity (50.1 dS m^?1) and lack of maturation. However, the fertilizer harmful effects were minimized in the soil from organic production. The application of Gafsa phosphate significantly increased lettuce yield and nutrient uptake. However, for the highest rate of phosphate, mycorrhized lettuce yield decreased compared to non-mycorrhized lettuce, suggesting that high soil available P may have harmful effects on the activity of mycorrhizal fungi.     

Less is more: Little seed processing required for direct seeding in seasonal tropics

Seed processing and dormancy break treatments are recommended for rendering seeds restoration-ready. Conversely, fruit structures and seed coats may protect seeds from environmental harm in the field. We evaluated the effects of seed processing (by either keeping fruit structures or extracting seeds) and/or scarification (of physically dormant seeds) on the seedling emergence and establishment of 10 legume tree species from tropical forests and savannas of Central Brazil. We sowed seeds in a greenhouse for reference and in a field experiment conducted in tilled ready-to-seed sites. We monitored seedling emergence and survival for a year. We calculated the costs of harvesting, processing, and pretreating seeds, and considered the final cost of a 1-year-old seedling. Seed extraction resulted in lower emergence for most species in the greenhouse and in the field. It also accelerated emergence of three and four species in the greenhouse and the field, respectively. Scarification resulted in lower seedling emergence in the field for half of the species, while it increased emergence of three species in the greenhouse. Most species presented accelerated emergence both in the greenhouse and the field. The seedling cost was 1.6 to 74.6 times higher when seeds were processed, and 1.3 to 6.0 times when seeds were scarified, except for one species. Keeping fruit structures and seed coats reduced the costs of seeds and increased the success of direct seeding.

     

A preliminary equine abuse policy with potential application to veterinary practice

An equine abuse policy was developed as an adjunct to an equine management survey. If at least 3 of 5 categories caused concern, a report to the authorities was indicated. The policy was not used but, in the absence of other guidelines, it might assist veterinarians considering potential abuse cases.