Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium

The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP‐LD). In the three GBLUP‐LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP‐LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation data. When quantitative trait loci (QTL) were located at weak LD regions, the predictive abilities of the three GBLUP‐LD methods were superior to those of GBLUP and Bayesian lasso except when the number of QTL was small. In particular, the superiority of GBLUP‐LD increased with decreasing trait heritability. The rates of QTL at weak LD regions would increase when selection by GBLUP continues; this consequently decreases the predictive ability of GBLUP. Thus, the GBLUP‐LD could be applicable for populations selected by GBLUP for a long time. However, if QTL were located at strong LD regions, the accuracies of three GBLUP‐LD methods were lower than GBLUP and Bayesian lasso.     

Genetic analysis of fat‐to‐protein ratio,milk yield and somatic cell score of Holstein cows in Japan in the first three lactations by using a random regression model

We estimated the genetic parameters of fat‐to‐protein ratio (FPR) and the genetic correlations between FPR and milk yield or somatic cell score in the first three lactations in dairy cows. Data included 3 079 517 test‐day records of 201 138 Holstein cows in Japan from 2006 to 2011. Genetic parameters were estimated with a multiple‐trait random regression model in which the records within and between parities were treated as separate traits. The phenotypic values of FPR increased soon after parturition and peaked at 10 to 20 days in milk, then decreased slowly in mid‐ and late lactation. Heritability estimates for FPR yielded moderate values. Genetic correlations of FPR among parities were low in early lactation. Genetic correlations between FPR and milk yield were positive and low in early lactation, but only in the first lactation. Genetic correlations between FPR and somatic cell score were positive in early lactation and decreased to become negative in mid‐ to late lactation. By using these results for genetic evaluation it should be possible to improve energy balance in dairy cows.     

Carbon source and trophic position of pelagic fish in coastal waters of south-eastern Izu Peninsula,Japan, identified by stable isotope analysis

ABSTRACT:   It is important to clarify trophic dynamics in marine ecosystems for management of the fishing ground. Organic carbon sources and trophic position of pelagic fishes in the coastal waters of the south-eastern Izu Peninsula, Japan, were examined on the basis of carbon and nitrogen stable isotope distributions. The δ¹³C of the fishes was mostly distributed from −19 to −16‰ for nektonic fishes (13 species of adults and immatures) and planktonic fishes (10 species of larvae and juveniles), close to the δ¹³C values of particulate organic matter and planktonic decapods. These δ¹³C signatures for the inhabitants of the water column were in contrast with the high δ¹³C values (mainly −16 to −13‰) for demersal fishes of Scorpaeniformes and benthic polychaetes collected in the surf zone. These results indicate that nektonic and planktonic fishes depend on phytoplankton for carbon supply. The δ¹⁵N signatures suggest that the trophic position ranged 3.1–4.5 for the nektonic fishes and 2.9–3.7 for the planktonic fishes, premised on trophic level 3 for larval Japanese anchovy Engraulis japonicus . Thus, planktivorous fishes should be mainly assigned to trophic levels 3 and 4 in this area.     

Bioavailability of amino acids chelated and glass embedded zinc to rainbow trout, Oncorhynchus mykiss, fingerlings

A 2 × 4 factorial experiment was conducted to determine the bioavailability of zinc (Zn) from amino acids chelated (Zn–Am) and glass embedded Zn (Zn–Gl) as sources for rainbow trout, Oncorhynchus mykiss , fed practical type diets. Two levels of Zn (20 and 40 mg kg⁻¹) were supplemented to the diets using either zinc sulphate (Zn–Sf), zinc methionine (Zn–Mt), Zn–Am or Zn–Gl. Rainbow trout with an average weight of 2 g were fed the experimental diets for 15 weeks. Growth and feed gain ratio (FGR) were not significantly influenced by the dietary Zn content and forms. Alkaline phosphatase (ALP) activity for both levels of Zn–Am was significantly higher than that of Zn–Sf and Zn–Gl at 20 mg supplementation. In another experiment, fish of about 95 g were fed the same experimental diets to determine the absorption of Zn and it was found to be significantly higher from Zn–Am compared with the rest. Retention from Zn–Am at 20 mg was significantly higher than the rest, excluding Zn–Sf. The results suggest that the availability of Zn from Zn–Am might be superior among the sources compared.     

Role of sodium bicarbonate on the initiation of sperm motility in the Japanese eel

ABSTRACT:   In order to find out the role of sodium bicarbonate (NaHCO₃) on the initiation of sperm motility in the Japanese eel Anguilla japonica , interactions were investigated between NaHCO₃ and various reagents (K⁺ channel blocker 4-aminopyridine [4-AP], ammonium chloride [NH₄Cl], sodium acetate and calcium chloride [CaCl₂]) that could regulate internal factors (intracellular K⁺, intracellular pH [[pH]_i] and intracellular Ca²⁺) in sperm motility. Contradictory effects of NaHCO₃ were observed (i.e. an inhibitory effect when 4-AP was absent and a promoting effect when 4-AP was present). Sodium bicarbonate inhibited the initiation of sperm motility in the Japanese eel. However, NaHCO₃ restored the motility of immotile sperm that 4-AP inhibited. The inhibitory effect of NaHCO₃ disappeared with the addition of NH₄Cl, which raised [pH]_i, but the promoting effect was not affected by [pH]_i. Although NaHCO₃ recovered motility in the presence of 4-AP, this recovery was also observed with the addition of CaCl₂ instead of NaHCO₃. In the initiation of sperm motility in the Japanese eel, two roles for NaHCO₃ are suggested: an inhibitory role relating to the regulation of [pH]_i and a promoting role relating to the uptake of another initiation factor, which could be Ca²⁺.     

Patterns of stable carbon and nitrogen isotopes in the baleen of common minke whale Balaenoptera acutorostrata from the western North Pacific

ABSTRACT:   Stable carbon and nitrogen isotope ratios were determined in the baleen plates of 17 common minke whales Balaenoptera acutorostrata from the north-western Pacific Ocean off Japan, as well as prey species (krill Euphausia pacifica , Japanese anchovy Engraulis japonicus and Pacific saury Cololabis saira ) collected in the stomach contents, to investigate the trophic relationship between the minke whales and their prey. A few δ¹⁵N-depleted peaks occurred along the length of baleen plates for 10 males irrespective of stomach content (anchovies and sauries). Similar δ¹⁵N-depleted peaks were also found for one female and two immature individuals. It was likely that these δ¹⁵N-depleted peaks formed in early summer. The stable nitrogen isotope ratio (δ¹⁵N) values in Pacific saury (9.3 ± 1.4‰) did not differ significantly from that in Japanese anchovy (8.8 ± 0.9‰). In contrast, δ¹⁵N in krill (7.2 ± 0.5‰ in July and 8.0 ± 0.2‰ in September) were significantly lower than in the Pacific saury. Thus, these peaks may reflect the dietary change from krill to fishes in the feeding migration of the whales. Growth rate of the baleen plate was estimated to be 129 mm/y, and it appeared that a dietary record of about 1.4 years remained in the baleen plate. For two immature whales, the maximum value of δ¹⁵N occurred at the tip of baleen. This δ¹⁵N enrichment may possibly be useful for discriminating weanlings and older whales.     

Supplementation of Citric Acid and Amino Acid Chelated Trace Elements in Low‐Fish Meal Diet for Rainbow Trout Affect Growth and Phosphorus Utilization

This study was conducted to evaluate the effect of citric acid (CA) and amino acid chelated trace elements (AA) on the growth, phosphorus (P) utilization efficiency and loading in rainbow trout fed a diet formulated with a low‐fish meal (FM) concentration. A low‐FM basal diet with or without monocalcium phosphate supplementation served as positive and negative control correspondingly. Dietary treatments consisted of the basal diet supplemented either with 1% CA, AA (equivalent to 40 Zn, 20 Mn, and 4 Cu mg/Kg of diet instead of inorganic trace element mix) or a combination of both. Duplicate groups of 35 fish (13.2 g) were fed until apparent satiation during 12 wk. Group of fish fed diets supplemented with 1% CA or AA had a final growth and feed utilization similar to that observed in fish fed the positive control diet (P > 0.05). P absorption was increased with the addition of CA or AA. P retention efficiency rates for these diets were higher in comparison with the rest of the treatments consequently showing the lowest P loading values (P < 0.05). The results indicate that addition of 1% CA or AA, to a low‐FM diet without inorganic P supplementation enhanced fish growth, P retention, and decreased P load to the environment.