Gene constitution of South-East Asian native chickens, commercial chickens and jungle fowl using polymorphisms of four calpain genes

The gene constitution of polymorphisms of the four calpain genes (µ‐calpain, m‐calpain, p94, and µ/m‐calpain) were analyzed in South‐East Asian native chickens, White Leghorn and Broiler commercial chickens, and Red and Green jungle fowl. Polymorphisms were detected at all loci in chickens and Red jungle fowl, but only for CAPN1 (µ‐calpain gene) in Green jungle fowl. CAPN2 and CAPN1.5 are linked on chicken chromosome 3, and the genotype for these loci were treated as haplotype. Some combinations of calpain loci were tested using principal component analysis, and the best combination (CAPN1, CAPN3, and CAPN1.5) was determined. The proportion of polymorphic loci (P_poly) and heterozygosity (H?) were 1.00 and 0.316–0.465 in domestic chickens and red jungle fowl, and 0.33 and 0.137 in Green jungle fowl, respectively. G_ST values suggested that the degree of subdivision among native chickens was relatively low except for Thailand, which was highest. Pair‐wise F_ST testing, dendrogram and principal component analysis from the results of calpain loci showed that the four South‐East Asian native and commercial chicken populations were close genetically.     

Nationwide survey of hepatitis E virus infection among wildlife in Japan

In Japan, hepatitis E virus (HEV) causes hepatitis in humans through the consumption of raw or undercooked meat, including game meat. In the present study, nationwide surveillance of HEV infection among a total of 5,557 wild animals, including 15 species, was conducted in Japan. The prevalence of anti-HEV antibodies in wild boar was 12.4%, with higher positive rates in big boars (over 50 kg, 18.4%) than in small individuals (less than 30 kg, 5.3%). Furthermore, HEV RNA was more frequently detected in piglets than in older boars. Interestingly, the detection of HEV among wildlife by ELISA and RT-PCR suggested that HEV infection in Sika deer was a very rare event, and that there was no HEV infection among wild animals except for wild boar, Sika deer and Japanese monkeys. In conclusion, wild boar, especially piglets, are at high risk of HEV infection, while other wild animals showed less risk or no risk of HEV transmission.     

Identification of QTLs for fruit quality traits in Japanese apples: QTLs for early ripening are tightly related to preharvest fruit drop

Many important apple (Malus × domestica Borkh.) fruit quality traits are regulated by multiple genes, and more information about quantitative trait loci (QTLs) for these traits is required for marker-assisted selection. In this study, we constructed genetic linkage maps of the Japanese apple cultivars ‘Orin’ and ‘Akane’ using F₁ seedlings derived from a cross between these cultivars. The ‘Orin’ map consisted of 251 loci covering 17 linkage groups (LGs; total length 1095.3 cM), and the ‘Akane’ map consisted of 291 loci covering 18 LGs (total length 1098.2 cM). We performed QTL analysis for 16 important traits, and found that four QTLs related to harvest time explained about 70% of genetic variation, and these will be useful for marker-assisted selection. The QTL for early harvest time in LG15 was located very close to the QTL for preharvest fruit drop. The QTL for skin color depth was located around the position of MYB1 in LG9, which suggested that alleles harbored by ‘Akane’ are regulating red color depth with different degrees of effect. We also analyzed soluble solids and sugar component contents, and found that a QTL for soluble solids content in LG16 could be explained by the amount of sorbitol and fructose.     

Life in the fast lane: Revisiting the fast growth—High survival paradigm during the early life stages of fishes

Early life survival is critical to successful replenishment of fish populations, and hypotheses developed under the Growth-Survival Paradigm (GSP) have guided investigations of controlling processes. The GSP postulates that recruitment depends on growth and mortality rates during early life stages, as well as their duration, after which the mortality declines substantially. The GSP predicts a shift in the frequency distribution of growth histories with age towards faster growth rates relative to the initial population because slow-growing individuals are subject to high mortality (via starvation and predation). However, mortality data compiled from 387 cases published in 153 studies (1971–2022) showed that the GSP was only supported in 56% of cases. Selection against slow growth occurred in two-thirds of field studies, leaving a non-negligible fraction of cases showing either an absence of or inverse growth-selective survival, suggesting the growth-survival relationship is more complex than currently considered within the GSP framework. Stochastic simulations allowed us to assess the influence of key intrinsic and extrinsic factors on the characteristics of surviving larvae and identify knowledge gaps on the drivers of variability in growth-selective survival. We suggest caution when interpreting patterns of growth selection because changes in variance and autocorrelation of individual growth rates among cohorts can invalidate fundamental GSP assumptions. We argue that breakthroughs in recruitment research require a comprehensive, population-specific characterization of the role of predation and intrinsic factors in driving variability in the distribution and autocorrelation of larval growth rates, and of the life stage corresponding to the endpoint of pre-recruited life.     

Impacts of invasive Iris pseudacorus L. (yellow flag) establishing in an abandoned urban pond on native semi-wetland vegetation

Iris pseudacorus L., intentionally introduced in Japan as an ornamental plant and to improve aquatic environments, has been declared a noxious species in the Invasive Alien Species Act of Japan due to the suspected high ecological risks to the local species and ecosystems. Although prompt responses to I. pseudacorus have been sought to conserve local biodiversity, knowledge about its invasiveness is lacking. Here, we report the relationship between the establishment of I. pseudacorus and floristic changes in semi-wetland vegetation of an abandoned urban pond (Aoike), Nara City, Nara Prepecture, Japan. In total, 64 vascular plants were recorded in the pond, of which 50 were native species, seven were naturalized non-native, and seven were invasive species. On the other hand, most of these vascular plants (42 species) were grassland species and only several aquatic plants (10 species) were found in this study pond. The number of vascular plant species decreased significantly at quadrats with a coverage of I. pseudacorus above 50%. In addition, tendencies of lower number of native species and concomitant higher number of invasive species were found with increasing coverage of I. pseudacorus. From these results, we suggest that it is important to preferentially manage sites where the coverage of I. pseudacorus is above 50%, in order to preserve the local biodiversity. Additionally, as recommended in the literature, it is essential that the cut reproductive organs are kept submerged under deep water for an effective control of I. pseudacorus.     

H2 15O translocation in rice was enhanced by 10 μm 5-aminolevulinic acid as monitored by positron emitting tracer imaging system (PETIS)

5-Aminolevulinic acid (ALA) acts to increase chlorophyll biosynthesis, photosynthesis, cold stress tolerance, and salt tolerance at low concentrations. We studied the effects of ALA on H₂ ¹⁵O translocation from the roots to the shoots of rice plants (Oryza sativa L. cv. Nipponbare) in real time by a positron-emitting tracer imaging system (PETIS). When the plant was treated with 10 μm ALA, the velocity of the H₂ ¹⁵O translocation from 2 to 12 min after absorption increased to 126, 137, 140% that of the control at 1.5, 2.5, and 3.5 h after ALA treatment, respectively. However, ALA did not affect the H₂ ¹⁵O translocation within 0.5 h of treatment. When the plant was treated with 0.1 mM ABA at 4 h after 10 μm ALA treatment, the velocity of the H₂ ¹⁵O translocation decreased at 0.5 h after ABA treatment. Those observations suggested ALA might be absorbed and transported to the guard cells within 1.5 h and functioned to expand the stomatal aperture.     

Formation of asparagine from 14C-labelled aspartate in different parts of rice plant at the panicle formation stage

Dynamics of asparagine formation and appearance have previously been studied, but it was particularly considered necessary to study the mode of asparagine formation in different parts of rice plant at the stage of panicle formation using ¹⁴C-labelled aspartate. During this investigation the place and velocity of asparagine were studied.     

Nitrate Loss for Denitrification during High Frequency Research in Floodplain Groundwater of the Tama River

This study aims to identify the possible roles of a floodplain inbiogeochemical nitrogen cycles, based on analysis of groundwaterdynamics of inorganic nitrogen species. Groundwater samples collected from boreholes made of poly vinyl chloride located onthe floodplain in the middle reach of the Tama River, Nagata district were analyzed for dissolved organic carbon, dissolved oxygen, inorganic nitrogen compounds, major anions and the stableisotope ratio of nitrate-nitrogen.Dissolved oxygen in groundwater samples collected from marked borehole (G-5) was low (50 ± 16 μM) and nitrate decreasedfrom 63 μM to < 10 μM during our research period. Concentrations of nitrate, nitrite and nitrous oxide decreased one after the other. These decreases in concentration, combinedwith ¹⁵N-enrichment of groundwater nitrate suggest denitrification as a significant nitrate sink, yielding an isotopic fractionation of nitrate-nitrogen with an enrichment factor (ε= –17.9‰) that is comparable tothose in various soil and groundwater systems. This study provesthat floodplains can perform as nitrogen sinks for groundwaterin river catchments.