Accuracy of imputation of single nucleotide polymorphism marker genotypes from low‐density panels in Japanese Black cattle

Using target and reference fattened steer populations, the performance of genotype imputation using lower‐density marker panels in Japanese Black cattle was evaluated. Population imputation was performed using BEAGLE software. Genotype information for approximately 40 000 single nucleotide polymorphism (SNP) markers by Illumina BovineSNP50 BeadChip was available, and imputation accuracy was assessed based on the average concordance rates of the genotypes, varying equally spaced SNP densities, and the number of individuals in the reference population. Two additional statistics were also calculated as indicators of imputation performance. The concordance rates tended to be lower for SNPs with greater minor allele frequencies, or those located near the ends of the chromosomes. Longer autosomes yielded greater imputation accuracies than shorter ones. When SNPs were selected based on linkage disequilibrium information, relative imputation accuracy was slightly improved. When 3000 and 10 000 equally spaced SNPs were used, the imputation accuracies were greater than 90% and approximately 97%, respectively. These results indicate that combining genotyping using a lower‐density SNP chip with genotype imputation based on a population of individuals genotyped using a higher‐density SNP chip is a cost‐effective and valid approach for genomic prediction.     

Mycoplasma pneumonia of swine (MPS) resistance and immune characteristics of pig lines generated by crossing an MPS pulmonary lesion selected Landrace line and a highly immune capacity selected Large White line

To understand the influence of crossbreeding on Mycoplasma pneumonia of swine (MPS) resistance and immune characteristics, two crossbred lines were characterized. One crossbred line, LaWa, was generated by crossing the MPS pulmonary lesion selected Landrace line (La) and the highly immune‐selected Large White line (Wa). The second crossbred line, LaWb, was generated by crossing the La line and the nonselected Large White line (Wb). The crossbred LbWb line (nonselected Landrace line × nonselected Large White line) and the La line were used as controls. The LaWa and LaWb lines had an intermediate level of MPS lung lesions between La and LbWb lines, although the difference was not statistically significant. After stimulation with sheep red blood cells (SRBCs), the LaWb and LaWa lines showed immune characteristics similar to that of the La line; the number of monocytes in peripheral blood increased, while B cells, T cells, secretion of SRBC‐specific immunoglobulin G, and interleukin (IL)‐13 decreased. Additionally, the number of natural killer (NK) cells and the expression of IL‐4 and IL‐17 were significantly higher in the LaWb and LaWa lines, respectively. These data suggested that crossbreeding of La and Wa lines resulted in the inheritance of some of the selected immune responses.     

In vitro effects of reactive oxygen metabolites, with and without flunixin meglumine, on equine colonic mucosa

OBJECTIVE: To determine effects of reactive oxygen metabolites (ROMs), with and without flunixin meglumine, on equine right ventral colon (RVC) in vitro. ANIMALS: 18 healthy horses and ponies. PROCEDURES: In 3 groups of 6 animals each, short-circuit current and conductance were measured in RVC mucosa in Ussing chambers. The 3 groups received physiologic saline (0.9% NaCl) solution, IV, 10 minutes before euthanasia and tissue incubation in Krebs-Ringer-bicarbonate (KRB) solution; flunixin meglumine (1.1 mg/kg, IV) 10 minutes before euthanasia and tissue incubation in KRB solution; or physiologic saline solution, IV, 10 minutes before euthanasia and incubation in KRB solution with 2.7 x 10(5)M flunixin meglumine. Incubation conditions included control (no addition) and ROM systems, including addition of 1 mM xanthine and 80 mU of xanthine oxidase (to produce the superoxide radical), 1 mM H(2)O(2), and 1 mM H(2)O(2) and 0.5 mM ferrous sulfate (to produce the hydroxyl radical). RESULTS: All ROMs that were added or generated significantly increased the short-circuit current except in tissues coincubated with flunixin meglumine, and they induced mild epithelial vacuolation and apoptosis, but did not disrupt the epithelium nor change conductance, lactate dehydrogenase release, or [(3)H]mannitol flux. CONCLUSIONS AND CLINICAL RELEVANCE: Responses to ROMs could be attributed to increased chloride secretion and inhibited neutral NaCl absorption in equine RVC, possibly by stimulating prostaglandin production. The ROMs examined under conditions of this study could play a role in prostaglandin-mediated colonic secretion in horses with enterocolitis without causing direct mucosal injury.     

Phylogenetic characterization of rabies virus isolates from Carnivora in Brazil

The incidence of canine rabies has been widely reported in Brazil, and new rabies virus (RV) variants, genetically similar to canine RV, have recently been isolated from foxes. In order to derive the epidemiological characteristics of Brazilian Carnivora RV, Brazilian RVs isolated from dogs, cats, and foxes were genetically analyzed. Brazilian Carnivora RV isolates were divided into 2 main lineages. The predominant lineage was found in dogs and cats, which included the Argentinean and Bolivian Carnivora RV isolates, and was extensively distributed throughout Brazil and surrounding countries. The other lineage consisted of three sublineages containing Brazilian dog and fox RV isolates, with the dog sublineages located on an internal branch of 2 fox sublineages, suggesting that RV transmission events might have occurred between foxes and dogs in the past. These results suggest that contact between dogs and wildlife has the potential to generate new rabies variants and that it is important to control RV infection cycles in both dogs and wildlife to prevent spread of rabies infection.     

Role of active aluminum in the formation of water-stable macroaggregates

Soil structure is determined by the arrangement of particles in soil and the particles of sand, silt, and clay bind together into aggregates of various sizes by organic and inorganic materials. Structural stability which is the ability of the aggregates and pores to remain intact when subjected to stress, markedly affects crop production and soil erosion (Tisdall 1996). Since water, either directly as rainfall or as surface runoff is the main agent of aggregate breakdown, in the analyzes of stable soil aggregation, the term water-stable aggregation is generally used (Lynch and Bragg 1985). Water-stable aggregates have been divided into micro aggregates < 0.25 mm dia.) and macro aggregates (> 0.25 mm dia.) (Edwards and Bremner 1967; Tisdall and Oades 1982). Microaggregates show a relatively high stability against physical disruption (Edwards and Bremner 1967). On the other hand, macro aggregates are sensitive to soil management (Tisdall and Oades 1982).

There are many reports on the relationships between the aggregate stability and the soil physicochemical properties. For example, significant correlations were found between the aggregate stability and the amounts of organic C (Tisdall and Oades 1982), total N, and carbohydrates or the CEC (Chaney and Swift 1984). However, most of these studies were conducted in non-volcanic ash soils. Volcanic ash soils are widely distributed in Japan and are very important soils for crop production. The objective of this study was, therefore, to obtain more information on the relationship between the degree of macro aggregation and the soil physicochemical properties in non-volcanic and volcanic ash soils.     

Effects of genes increasing the number of spikelets per panicle,TAW1 and APO1, on yield and yield-related traits in rice

The genes TAWAWA1 (TAW1) and ABERRANT PANICLE ORGANIZATION1 (APO1) increase the number of spikelets per panicle (SN). In the present study, we examined the effects of these genes on morphological traits, yield, and yield-related traits including yield components using the near-isogenic lines (NILs) in the genetic background of a japonica rice variety, Koshihikari – NIL-taw1, NIL-apo1-D3, and NIL-apo1-D4 – in a field experiment. The SN and total number of spikelets per area of the three NILs were larger than those of Koshihikari. However, the yield of the three NILs did not exceed that of Koshihikari due to their low filling ability. Interestingly, our field experiments indicated that TAW1 did not affect the diameter of internodes and the PN, whereas APO1 decreased the PN and increased the diameter of internodes. These results suggest that TAW1 and APO1 differently affect yield-related traits.     

Beneficial effects on meat quality of yellowtail Seriola quinqueradiata induced by diets containing red pepper

The meat quality of farmed yellowtail Seriola quinqueradiata fed on extruded pellets (EP) containing 0.5% (v/v) red pepper (experimental group) was compared with yellowtail of the same age fed on EP (control group). In 1-year-old yellowtail, the crude lipid content of the dorsal muscle of the experimental group tended to be lower than that of the control group. In contrast, there was no difference in the lipid content of the dorsal muscle between the control group and the experimental group in 2-year-old yellowtail. The muscle texture of the experimental group was significantly firmer than that of the control group, with the effect of red pepper unrelated to fish age and lipid content. Color change of red muscle of the experimental group was significantly lower than that of the control group, and the content of thiobarbituric acid-reactive substances in the red muscle was significantly lower in the experimental group than in the control group. These results are the first to demonstrate that the inclusion of red pepper in the diet is able to reduce the loss of muscle texture firmness and to slow down color change in red muscle of yellowtail.