Long‐term changes in recruitment of age‐0 Pacific bluefin tuna (Thunnus orientalis) and environmental conditions around Japan

Recruitment of age‐0 Pacific bluefin tuna (Thunnus orientalis) from 1952 to 2014 was examined by a sequential regime shift detection method. The regime shifts in recruitment were detected in 1957, 1972, 1980, 1994 and 2009. The durations of regime shift ranged from 8–15 years and averaged 13.0 years. In both the total (1952–2014) and data rich (1980–2014) periods, negative relationships were found between recruitment and the Pacific Decadal Oscillation in autumn, and positive relationships were found between recruitment and sea surface temperature (SST) anomalies in the northern part of the East China Sea, in the southwestern part of the Sea of Japan, and in the waters off Shikoku and Tokai in summer and autumn. The 1994 and 2009 regime shifts in recruitment occurred in the same years as shifts in SST anomalies in the northern part of the East China Sea in summer. These results suggest that the ocean conditions in the northern part of the East China Sea are closely related to recruitment of Pacific bluefin tuna, and that the warmer conditions result in higher recruitment of the species.     

Evaluation of Zona Pellucida Function for Sperm Penetration During In Vitro Fertilization in Pigs

In porcine oocytes, the function of the zona pellucida (ZP) with regard to sperm penetration or prevention of polyspermy is not well understood. In the present study, we investigated the effects of the ZP on sperm penetration during in vitro fertilization (IVF). We collected in vitro-matured oocytes with a first polar body (ZP+ oocytes). Some of them were freed from the ZP (ZP− oocytes) by two treatments (pronase and mechanical pipetting), and the effects of these treatments on sperm penetration parameters (sperm penetration rate and numbers of penetrated sperm per oocyte) were evaluated. There was no evident difference in the parameters between the two groups. Secondly, we compared the sperm penetration parameters of ZP+ and ZP− oocytes using frozen-thawed epididymal spermatozoa from four boars. Sperm penetration into ZP+ oocytes was found to be accelerated relative to ZP− oocytes. Thirdly, we evaluated the sperm penetration of ZP+ and ZP− oocytes at 1−10 h after IVF (3 h gamete co-incubation). The proportions of oocytes penetrated by sperm increased significantly with time in both groups; however, the number of penetrated sperm per oocyte did not increase in ZP− oocytes. Finally, we performed IVF using ZP− oocytes divided into control (3 h) and prolonged gamete co-incubation (5 h) groups. Greater numbers of sperm penetrated in the 5 h group than in the control group. These results suggest that the ZP and oolemma are not competent factors for prevention of polyspermy in our present porcine IVF system. However, it appears that ZP removal is one of the possibilities for reducing polyspermic penetration in vitro in pigs.     

Identification of genomic regions regulating ammonium-dependent inhibition of primary root length in Arabidopsis thaliana

Plant roots grow into the soil for efficient acquisition of various nutrients, such as inorganic nitrogen, ammonium, and nitrate. A previous study has revealed the genetic diversity of foliar functions of Arabidopsis thaliana ecotypes in an environment containing ammonium; however, the function of roots remains unclear. This work focuses on the root system architecture (RSA) of Arabidopsis ecotypes to investigate the genetic factors regulating ammonium-dependent RSA changes. Arabidopsis ecotypes were grown on vertical agar medium containing ammonium as a major nitrogen source, and root growth and RSA were determined. Arabidopsis ecotypes showed differential sensitivity to ammonium. The shoot dry weight of some ecotypes decreased, whereas that of other ecotypes increased in ammonium medium. The RSA changes also varied among the different ecotypes in response to ammonium. The total root length, measured as the sum of primary root and lateral root length, of some ecotypes was reduced, whereas that of other ecotypes showed no significant difference in ammonium medium. Compared with lateral roots, the primary roots showed a sharp response to ammonium supply. Notably, the RSA showed a partial correlation with shoot dry weight in ammonium medium. Because Col-4 and Ler-0 showed opposite RSA responses to ammonium supply, these two ecotypes were selected for further genetic analysis. Quantitative trait locus (QTL) analysis of recombinant inbred lines of Col and Ler showed the involvement of several genetic factors in ammonium-dependent RSA changes. Moreover, QTL analysis revealed that the primary structure of nitrogen-related enzymes do not account for changes in RSA in response to ammonium supply.     

Characteristics of the soils developed under broad-leaved evergreen forests in okinawa prefecture and the kinki district with special reference to their pedogenetic processes

Abstract

Properties of sesquioxides, clay mineralogical composition, and charge characteristics of the soils developed under broad-leaved evergreen forests in Okinawa Prefecture (subtropical climate) and the Kinki District (warm temperate climate) were studied with special reference to their pedogenetic processes in order to reexamine the corresponding parameters of Brown Forest soils and related soils in Japan.

The soils in Okinawa Prefecture were characterized by a higher degree of weathering as compared to the soils in the Kinki District. Major differences involved the values of the Fed/Fet ratio for the soil samples throughout the profile, and those of the ratios of (Fed-Feo)/Fet, CEC/clay, and (Feo + Alo)/ clay and the content of CaO plus Na₂O for the B horizon. The soils in the Kinki District did not show andic soil properties, nor Al translocation in the profile and, both of which were characteristic of Brown Forest soils developed under cool temperate climatic conditions at high altitudes in the same District.

The difference in the degree of weathering were reflected on the charge characteristics at the very surface of the soils, i.e., the surface of the particles of the soils in Okinawa Prefecture exhibited a lower reactivity as compared with those of the soils in the Kinki District.     

QTL for spikelet number from a high-yielding rice variety, Hoshiaoba, detected in an introgression line with the genetic background of an indica rice variety, IR64

Total spikelet number per panicle (TSN) is thought to be one of the most important agronomic traits associated with grain production in rice (Oryza sativa L.). We previously reported the development of 334 introgression lines (ILs) with variations in agronomic traits in the genetic background of indica rice variety IR64. Among these, an IL derived from high-yielding rice variety Hoshiaoba showed significantly higher TSN than IR64. We therefore have conducted a quantitative trait locus (QTL) analysis for TSN in an F₂ population of IL × IR64 to ascertain the genetic basis for the high TSN of the IL. The analysis revealed the presence of a QTL for TSN on chromosome 7, where several QTLs for grain number have been previously reported. We developed a near-isogenic line (NIL) for this QTL by using DNA marker-assisted selection and characterized its effect. The NIL showed significantly higher TSN than IR64. These results suggest that the QTL and the NIL will be useful materials in breeding programs aimed at increasing TSN.     

Development of late-bolting F<Subscript>1</Subscript> hybrids of Chinese cabbage (<Emphasis Type="Italic">Brassica rapa</Emphasis> L.) allowing early spring cultivation without heating

We developed new F₁ hybrids of Chinese cabbage (Brassica rapa L. ssp. pekinensis) that allow cultivation earlier in spring without heating by introducing extremely late-bolting alleles at two homologs of the flowering repressor Flowering Locus C (BrFLC2 and BrFLC3) from non-heading ‘Leafy Green Parental Line No. 2’. These new F₁ hybrids were produced by the following four steps. First, the extremely late bolting selected lines were developed. These selected lines headed in spring after overwintering cultivation, whereas the conventional F₁ cultivars flowered. Secondly, an investigation of the three plantings showed that our F₁ hybrids formed heads when seeds were sown from mid-February to early March, whereas the conventional F₁ cultivar did not form heads because of premature bolting. Thirdly, we identified some F₁ hybrids with extremely late bolting during early spring cultivation in an investigation of many F₁ hybrids. Finally, based on an investigation across four cold regions for 2 years, we compared the commercialization rate, defined as the proportion of plants greater than 2000 g in weight and with a flowering stalk less than 10 cm long. Then we identified a F₁ of MS02 × 12-04 which had a high commercialization rate on average (92%), whereas the rates of three conventional F₁ cultivars were only 0–2%. In the near future, these F₁ hybrids will be valuable late-bolting cultivars despite climate change, permitting stable cultivation and harvest over wide regions.     

EDEM as an acceptor of terminally misfolded glycoproteins released from calnexin

Terminally misfolded proteins in the endoplasmic reticulum (ER) are retrotranslocated to the cytoplasm and degraded by proteasomes through a mechanism known as ER-associated degradation (ERAD). EDEM, a postulated Man8B-binding protein, accelerates the degradation of misfolded proteins in the ER. Here, EDEM was shown to interact with calnexin, but not with calreticulin, through its transmembrane region. Both binding of substrates to calnexin and their release from calnexin were required for ERAD to occur. Overexpression of EDEM accelerated ERAD by promoting the release of terminally misfolded proteins from calnexin. Thus, EDEM appeared to function in the ERAD pathway by accepting substrates from calnexin.     

Numerical simulation on effect of irrigation conditions on water temperature distribution in a paddy field

Water management methods regulate water temperature in paddy fields, which affects rice growth and the environment. To understand the effect of irrigation conditions on water temperature in a paddy field, water temperature distribution under 42 different irrigation models including the use of ICT water management, which enables remote and automatic irrigation, was simulated using a physical model of heat balance. The following results were obtained: (1) Irrigation water temperature had a more significant effect on paddy water temperature close to the inlet. As the distance from the inlet increased, the water temperature converged to an equilibrium, which was determined by meteorological conditions and changes in water depth. (2) Increasing the irrigation rate with higher irrigation water amount increased the extent and magnitude of the effects of the irrigation water temperature. (3) When total irrigation water amount was the same, increasing the irrigation rate decreased the time-averaged temperature gradient effect over time across the paddy field. (4) Irrigation during the lowest and highest paddy water temperatures effectively decreased and increased the equilibrium water temperature, respectively. The results indicate that irrigation management can be used to alter and control water temperature in paddy fields, and showed the potential of ICT water management in enhancing the effect of water management in paddy fields. Our results demonstrated that a numerical simulation using a physical model for water temperature distribution is useful for revealing effective water management techniques under various irrigation methods and meteorological conditions.

     

Genetic characterization of wild barley populations (Hordeum vulgare ssp. spontaneum) from Kazakhstan based on genome wide SNP analysis

The wild ancestral form of barley, Hordeum vulgare ssp. spontaneum, is a valuable source for gene enrichment of cultivated barley. The purpose of this work was to study the area of distribution as well as the extent and structure of genetic variation of wild barley populations grown in Kazakhstan. It was found that distribution of wild barley populations in Kazakhstan is restricted to the most southern province. A genome wide single nucleotide polymorphism (SNP) analysis was performed in order to study the level of the genetic diversity in 96 accessions representing 14 wild barley populations from Kazakhstan and 25 accessions from the Middle East which is the center of diversity of this subspecies. The oligonucleotide pooled assay was used to genotype 384 SNPs distributed throughout the genome. In total 233 polymorphic SNPs were selected for further statistical analysis. The level of genetic diversity of wild barley populations from Kazakhstan was predictably narrower (He = 0.19 ± 0.01) in comparison with wild barley samples from the Middle East (He = 0.29 ± 0.01). The results suggested that H. vulgare ssp. spontaneum populations in Kazakhstan probably represent a recent spread of a limited number of plants from the primary distribution area and might be well adapted to winter low temperature.     

Spatiotemporal catch distribution of age-0 Pacific bluefin tuna Thunnus orientalis caught by the Japanese troll fishery in relation to surface sea temperature and seasonal migration

This study used a delta-lognormal model to analyze monthly catches of age-0 Pacific bluefin tuna by the troll fishery. The model included fixed effects of month, area, and month–area interaction, and random effects of port, year and port–year interaction. The catch patterns by month and area predicted by the statistical model (standardized catch) revealed that main fishing grounds along the Tsushima Warm Current generally shifted from north to south as the season turned from autumn to winter. In contrast, the standardized catch along the Kuroshio Current did not show such clear spatiotemporal patterns. The standardized catch along the Tsushima Warm Current is significantly associated with average monthly sea surface temperatures in the fishing grounds and consistent with migration routes revealed by tagging experiments in previous studies. These associations indicate the spatiotemporal catch pattern in the Tsushima Warm Current region partly reflects seasonal migration. Knowledge of the possible associations among fish migration, environmental factors and spatiotemporal distribution of the catch will contribute to future management of this species.