Adjusting for heterogeneity of variance for carcass traits affects single and multiple trait selections in genetic evaluation of Japanese Black cattle

Heterogeneity of variance among subclasses of an effect is a potential source of bias in genetic evaluation. Degrees of the heterogeneity of variance among farm‐market‐year‐sex (FMYS) subclasses for carcass weight, beef marbling standard number, rib‐eye area, rib thickness and subcutaneous fat thickness were investigated in Japanese Black cattle. Consequences of adjusting for the heterogeneity on the predicted breeding values (PBVs) or on the genetic indexes derived from the PBVs of the five carcass traits were assessed. A total of 57 461 records were collected between 1997 and 2002 from steers and heifers fattened at farms across Japan. These records were grouped into 1591 FMYS subclasses. Bartlett's test showed that the degree of the heterogeneity of variance among the FMYS subclasses was sizeable in all traits (P < 0.0001). By applying a two‐step adjustment procedure it was possible to reduce the standard deviation, the coefficient of variation and the Gini coefficient of the phenotypic variances by 67.5% to 75.0% in the different traits. The applied adjustment caused a substantial re‐ranking of elite dams in the PBV for each trait as well as in the genetic index. This study provided evidence that the applied adjustment reduces the bias in the PBVs due to heterogeneous variances and increases the accuracy of bull‐dam selection.     

Effects of a probiotic bacterial <Emphasis Type="Italic">Lactobacillus rhamnosus</Emphasis> dietary supplement on the crowding stress response of juvenile Nile tilapia <Emphasis Type="Italic">Oreochromis niloticus</Emphasis>

To test the effects of probiotic bacteria against crowding stress, juvenile Nile tilapia Oreochromis niloticus were fed commercial feed supplemented with 1 × 10¹⁰ cfu/g pellets of Lactobacillus rhamnosus for 3 weeks. The fish were confined and subjected to crowding for 7 and 14 days after which their physiological condition was investigated. The administration of probiotic prophylaxis improved growth performance even in the stressed fish. After 7 days of stress exposure, fish receiving probiotic-supplemented feed showed proactive behavior and coping responses to the stressor, as evidenced by elevated plasma glucose levels and osmolality, stabilized plasma electrolytes, and a higher RNA:DNA ratio. Fish stressed for 7 days and fed normal commercial diet showed impairment of plasma electrolytes; after 14 days, the plasma osmolality, electrolytes, glucose, and RNA:DNA ratio decreased, indicating physiological maladaptation to the stressor. The growth rate was also found to be reduced, suggesting that energy demand exceeded the energy available from metabolism and dietary uptake. This latter effect was not observed in fish fed the probiotic-supplemented diet. The results suggest that probiotic bacteria prophylaxis may increase energy availability for metabolic support of the crowding stress response and improve the stress coping capacity of fish.     

Production of a desirable Brassica oleracea CMS line using an alloplasmic B. rapa CMS line carrying Diplotaxis erucoides cytoplasm as a bridge plant

In Brassica oleracea, production of F₁ hybrid seeds mainly makes use of the improved Ogura cytoplasmic male sterile (CMS) line. However, reliance on one particular line is a risk, and it would be advantageous to develop other CMS lines. In this study, we transferred Diplotaxis erucoides cytoplasm to B. oleracea cultivars using an alloplasmic B. rapaCMS line as a bridge plant to avoid incompatibility between donor and recipient plants. The new B. oleraceaCMS lines, which were derived by four generations of backcrossing, had small rudimentary anthers with no pollen grain and showed complete male sterility. There was no functional defect in other floral organs, and the ability to receive normal pollen did not appear to be impaired. Moreover, the B. oleraceaCMS lines carrying D. erucoides cytoplasm had larger leaf areas and a normal plastochron. As a consequence, the B. oleraceaCMS lines carrying D. erucoides cytoplasm have the potential to be valuable alternatives for use in commercial B. oleracea hybrid seed production.     

Two β-amylase genes,OsBAM2 and OsBAM3, are involved in starch remobilization in rice leaf sheaths

To identify mechanisms of starch degradation in rice leaf sheaths at the post-heading stage, we investigated the function of OsBAM2 and OsBAM3, which encode plastid-targeted active β-amylase isoforms, in starch remobilization in leaf sheaths. The starch content in the second leaf sheaths below the flag leaf (the third leaf sheaths) peaked at the flag leaf emergence stage and gradually decreased until 15 days after heading. The mRNA levels of OsBAM2 and OsBAM3 in the third leaf sheaths increased from the flag leaf emergence stage to the heading stage when the starch content began to decrease. However, these mRNA levels did not always remain high during post-heading. Overexpression of OsBAM2 or OsBAM3 markedly repressed starch accumulation in the third leaf sheaths, showing that OsBAM2 and OsBAM3 function in starch degradation in rice leaf sheaths. In contrast, no significant differences in starch content in the third leaf sheaths were detected between knockdown plants of OsBAM2 or OsBAM3 and non-transgenic wild-type plants. Our results suggest that reduced expression of the individual genes, OsBAM2 or OsBAM3, does not result in excess accumulation of starch in the leaf sheaths, probably because of the complementary function of another gene or the action of other genes encoding starch-degrading .     

Experimental evidence of a pathogenic change caused by homologous recombination between endogenous and introduced dysfunctional Avr-Pita genes in Pyricularia oryzae

To provide experimental evidence that somatic homologous recombination (HR) is involved in the instability and diversification of the avirulence gene Avr-Pita in Pyricularia oryzae, we generated a dysfunctional Avr-Pita homolog and integrated it into strain Hoku-1 containing Avr-Pita. In the transformants, the occurrence of somatic HR events between Avr-Pita and the dysfunctional homolog was confirmed by PCR–RFLP. Germlings from conidia from the HR-positive transformants had lost the avirulence function, which enabled it to infect rice cultivar Yashiromochi containing the corresponding resistant gene Pi-ta. These results suggested that genetic mutation caused by somatic HR is one of the mechanisms responsible for virulence diversity.     

N2O and NO emissions from an Andisol field as influenced by pelleted poultry manure

Animal manures from intensive livestock operations can be pelleted to improve handlings and recyclings of embodied nutrients. The aim of this study was to evaluate the influence of pelleted poultry manure on N₂O and NO fluxes from an Andisol field. In autumn 2006 and summer 2007, poultry manure (PM), pelleted poultry manure (PP), and chemical fertilizer (CF) were applied at a rate of 120 kg N ha⁻¹ in each cultivation period to Komatsuna (Brassica rapa var. peruviridis). Nitrous oxide and NO fluxes were measured using an automated monitoring system. A soil incubation experiment was also conducted to determine the influence of intact and ground pelleted manure on N₂O, NO, and CO₂ production with a water-filled pore space (WFPS) of 30 or 50%. In the field measurements, N₂O emission rates from the organic fertilizer treatments were larger than that from the CF treatment, possibly because organic C stimulated denitrification. The highest N₂O flux was observed from the PP treatment after a rainfall following fertilization, and the cumulative emission rate (2.72 ± 0.22 kg N ha⁻¹ y⁻¹) was 3.9 and 7.1 times that from the PM and CF treatments, respectively. In contrast, NO emission rates were highest from the CF treatment. The NO/N₂O flux ratio indicated that nitrification was the dominant process for NO and N₂O production from the CF treatment. Cumulative N₂O emission rates from all treatments were generally higher during the wetter cultivation period (autumn 2006) than during the drier cultivation period (summer 2007). In contrast, NO emission rates were higher in the drier than in the wetter cultivation period. The incubation experiment results showed a synergistic effect of soil moisture and the pelleted manure form on N₂O emission rates. The intact pelleted manure with the 50% WFPS treatment produced the highest N₂O and CO₂ fluxes and resulted in the lowest soil NO₃⁻ content after the incubation. These results indicate that anaerobic conditions inside the pellets, caused by rainfall and heterotrophic microbial activities, led to denitrification, resulting in high N₂O fluxes. Controlling the timing of N application by avoiding wet conditions might be one mitigation option to reduce N₂O emission rates from the PP treatment in this study field.     

Potential of near infrared spectroscopy to determine the lipid content of untreated garbage compost

The purpose of the present study was to evaluate the capability of near infrared spectroscopy (NIRS) as a simple method to monitor the lipid content of garbage compost, which is a potential inhibitor of plant growth. We conducted a cultivation experiment with vegetable mock pak choy ( Brassica rapa L. Parachinensis Group) using two application rates of four garbage composts that differed in lipid content. The input of lipid from the compost to the field showed a significant negative correlation with germination rate and plant height in the initial growth stage. Reflectance spectra of untreated and freeze-dried and milled compost samples were taken using a scanning monochromator. Second-derivative spectra and multiple regression analysis were used to develop calibration equations for lipid and moisture contents. The calibration was carried out with the short wavelength region ([SWR] 800–1100 nm) and the long wavelength region ([LWR] 1100–2500 nm) separately. The calibration equations with the LWR were more accurate than those with the SWR for lipid and moisture determinations. The accuracies of the calibration equations for untreated samples were comparable to those for freeze-dried and milled samples. In conclusion, we suggest that the application rate of garbage compost can be determined by measuring the lipid content of untreated samples by NIRS.     

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan

Background  

Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards.     

Vertical behavior of bigeye tuna (Thunnus obesus) in the northwestern Pacific Ocean based on archival tag data

The behavior of bigeye tuna (Thunnus obesus) in the northwestern Pacific Ocean was investigated using archival tag data for 28 fish [49–72 cm fork length (FL) at release, 3–503 days] released in Japanese waters around the Nansei Islands (24–29°N, 122–132°E) and east of central Honshu (Offshore central Honshu, 32–36°N, 142–148°E). Vertical behavior was classified into three types based on past studies: ‘characteristic’ (non‐associative), ‘associative’ (associated with floating objects) and ‘other’ (behavior not fitting into these two categories). The proportion of fish showing associative behavior decreased and that of characteristic behavior increased as fish grew, and this shift was pronounced at 60–70 cm FL. The fish usually stayed above the 20°C isotherm during the daytime and nighttime when showing associative behavior and below the 20°C isotherm during daytime for characteristic behavior. A higher proportion of characteristic behavior was seen between December and April around the Nansei Islands, and between September and December for offshore central Honshu. Seasonal changes in vertical position were also observed in conjunction with changes in water temperature. In this study, ‘other’ behavior was further classified into five types, of which ‘afternoon dive’ behavior, characterized by deep dives between around noon and evening, was the most frequent. The present study indicated that in the northwestern Pacific Ocean, the vertical behavior of bigeye tuna changes with size, as well as between seasons and regions.