Blood biochemical values in Japanese Black calves in Kagoshima Prefecture,Japan

To obtain blood biochemical basic data of Japanese Black calves in Kagoshima Prefecture, Japan, blood samples were obtained from 582 clinically healthy calves on 27 farms. Calves were divided into three stages: the suckling stage (between 14 and 90 days of age, n=191), the early growing stage (between 91 and 180 days of age, n=200) and the late growing stage (between 181 and 270 days of age, n=191). The mean concentration of total cholesterol, triglyceride, nonesterified fatty acids, calcium and zinc, and the mean activities of γ-glutamyltransferase and alkaine phospatase in the suckling stage were significantly higher than those in the early and late growing stages (P<0.01). The mean concentration of total protein, albumin and globulin increased gradually with growing. The mean concentration of beta-hydroxybutyrate in the suckling stage was below 150 µmol/l, however, it elevated above 400 µmol/l in the early and late growing stages. The mean concentration of copper concentration was above 70 µg/dl in all stages. The mean concentration of zinc was between 90 and 110 µg/dl in all stages. These results suggest that the blood biochemical values of Japanese Black calves vary with growing stages, and the blood parameters obtained in this study are considered useful as indices for health management of Japanese Black calves.     

Amino acid substitution at position 95 in rabies virus matrix protein affects viral pathogenicity

We previously reported that rabies virus strain CE(NiM), but not the parental Ni-CE strain, killed mice after intracerebral inoculation. CE(NiM) and Ni-CE are genetically identical except for two amino acids at positions 29 and 95 in the M protein. In this study, to identify which residue determines the pathogenicity, we examined pathogenicities of two Ni-CE mutants, CE(NiM29) and CE(NiM95), which were established by replacement of an amino acid residue at position 29 or 95 in the Ni-CE M protein with the corresponding residue of CE(NiM), respectively. We found that CE(NiM95), but not CE(NiM29), killed mice, indicating that the amino acid at position 95 in the M protein is the pathogenic determinant.     

Effect of lodging on the level of mycotoxins in wheat,barley, and rice infected with the <Emphasis Type="Italic">Fusarium graminearum</Emphasis> species complex

Lodging is one possible risk factor that leads to increased cereal mycotoxin contamination, but few reports have been published on the subject. We examined the effects of lodging on the level of deoxynivalenol (DON) and nivalenol (NIV) contamination in wheat, barley, and rice infected with the Fusarium graminearum species complex. Case-control and intervention studies were applied to test the hypothesis that lodging increases the level of mycotoxin contamination. A total of 66 grain samples were collected from each field in 12 Japanese prefectures from 2002 to 2006. Each sample set consisted of grains from lodged and nonlodged plants. The concentration of DON + NIV in lodged plants was significantly higher than in nonlodged plants. All samples of wheat and barley were contaminated with DON and NIV; however, most of the lodged rice samples were contaminated only with NIV. In intervention trials to investigate the effects of lodging duration, a small area of wheat inoculated with the pathogen was completely lodged by trampling. Even with 5 days of lodging, the levels of DON + NIV in wheat grain at harvest increased by 27–51% compared to nonlodged control plots. For rice, half of each plot area was completely lodged by trampling 20 days before harvest. The level of NIV in lodged rice grain was significantly higher than that in nonlodged rice at optimum and delayed harvests, because lodging significantly increased the level of Fusarium mycotoxins in the three crops. Thus, practices (e.g., rational use of fertilizers) to avoid lodging should reduce the risk of mycotoxin contamination. This is the first epidemiological study on the effect of lodging on mycotoxin production by the F. graminearum species complex in wheat, barley, and rice.     

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and F_ST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.     

Foliar disease resistant and productive mutants from the introgression lines of peanut (Arachis hypogaea)

With an objective of developing the induced mutants for superior productivity and resistance to foliar diseases in peanut, two introgression lines (IL-3 and IL-4) derived from ABK genomes of peanut were subjected to gamma and sodium azide mutagenesis. Evaluation of M₁, M₂ and M₃ generations could identify foliar disease resistant and productive mutants. Large-scale evaluation of M₄ mutants during the rainy season of 2017 confirmed the superiority of 12 mutants over the respective parents and the best check (GPBD 4). The selected mutants were resistant to leaf spots (early and late) and rust diseases, and significantly more productive than the parents and GPBD 4. ddRAD-Sequencing of these mutants identified the single nucleotide polymorphisms (SNPs) when compared to their parents. The genes harbouring these structural mutations were also identified. However, no copy number variations (CNVs) were observed between the mutants and the parents. The selected mutants carried resistant-type alleles at the marker loci linked to foliar disease resistance. These promising mutants (M₈) are currently under initial trials of variety development for commercial release.     

Analysis of mitochondrial DNA protein-coding region in the Yeso Sika deer (Cervus nippon yesoensis)

In the present study, mitochondrial DNA sequences of the Yeso Sika deer (Cervus nippon yesoensis) were studied. Specifically, protein‐coding genes as mitochondrial NADH dehydrogenase subunits (ND1, ND2, ND3, ND4L, ND4, ND5 and ND6), cytochrome c oxidase subunits (CO I and CO III), ATP synthase subunits (ATPase8 and ATPase6) and cytochrome b. Also, phylogenetic analyses on eight mammalian species were performed, including the Muntjac deer (Muntiacus reevesi). The rate of amino‐acid substitution was lowest (3.74%) between Yeso Sika deer and Muntjac deer, and the values between Yeso Sika deer and other species (sheep, cattle, horse, pig, mouse, human and chimpanzee) were 6.63%, 7.30%, 12.55%, 13.03%, 23.59%, 24.82% and 25.04%, respectively. Among them, the highest value of divergence was recognized in ATPase8, and the second structure of ATPase8 showed a difference between the Yeso Sika deer and Muntjac deer as a result of the substitution of 34His→Tyr and 49Thr→Ile. In addition, we identified a substitution of an amino‐acid sequence (19Thr→Ala) between the Yeso Sika deer and Yakushima Sika deer (C. n. yakushimae). From these results, ATPase8 was also a variable region in Cervidae.     

Conformational change in hamster scrapie prion protein (PrP27-30) associated with proteinase K resistance and prion infectivity

The scrapie prion protein (PrP27-30) is a crucial component of the prion and is responsible for its transmissibility. Structural information on this protein is limited because it is insoluble and shows aggregated properties. In this study, PrP27-30 was effectively dispersed using sonication under the weak alkaline condition. Subsequently, the small PrP27-30 aggregates were subjected to different pH, heat, and denaturing conditions. The loss of proteinase K (PK) resistance of PrP27-30 and prion infectivity were monitored along with spectroscopic changes. Prion inactivation could not be achieved by the loss of PK resistance alone; a significant loss of the PrP27-30 amyloid structure, which was represented by a decrease in thioflavin T fluorescence, was required for the loss of transmissibility.     

Kazusa Marker DataBase: a database for genomics,genetics, and molecular breeding in plants

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.     

Relationships between nutrients and sucrose concentrations in sugarcane juice and use of juice analysis for nutrient diagnosis in Japan

Sugarcane is an important economic crop in southwest Japan, but its production is decreasing. To increase sugar production, both sugarcane yield and quality should be improved. Fertilizer management is one of the factors that influence sugarcane quality. We accordingly focused on nutrients present in sugarcane juice and attempted to identify the key factors affecting sugarcane quality. We collected sugarcane samples from 2013 to 2015 from all of the sugar mills in Japan and examined the relationships between juice nutrients and sucrose concentration. Juice analysis over 3 year showed that potassium (K⁺) and chloride (Cl^?) were the most abundant cation and anion in the juice and that both negatively correlated with the sucrose concentration. K⁺ and Cl^? concentrations significantly varied depending on production areas and those with higher K⁺ and Cl^? concentrations had a low sucrose concentration. This finding suggests that sugarcane in those areas may have been supplied with these two ions in excess. Electrical conductivity (EC) in the juice always positively correlated with K⁺ and Cl^? concentrations. EC may thus be a reliable indicator of K⁺ and Cl^? concentrations and could be used for nutrient diagnosis because of its ease of measurement. For improving sugarcane quality, we recommend that potassium chloride, which supplies both K⁺ and Cl^? and is a commonly used potassium fertilizer for sugarcane production in Japan, should be used in lower quantities in a year following one in which the EC of sugarcane juice at harvest is found to be high.