Genetic diversity of wild mekong giant catfish Pangasianodon gigas collected from Thailand and Cambodia

The Mekong giant catfish Pangasianodon gigas is endemic to the Mekong River and is a critically endangered species. The genotypes of the microsatellite DNA (msDNA) and mitochondrial DNA (mtDNA) markers (right domain of the control region) were detected to evaluate the present status of genetic divergence of this species from the Mekong River in Thailand and Cambodia. The observed and expected heterozygosity values of Mekong giant catfish in Thailand and Cambodia were relatively low in comparison with those of other nonendangered freshwater fish species. These two populations from Thailand and Cambodia showed similar levels of genetic diversity, as evaluated by the 384 nucleotides of the mtDNA control region with 13 haplotypes. The pairwise F _ST value between the two populations based on the genotype frequencies of msDNA and mtDNA markers suggested a close genetic relationship between the populations in Thailand and Cambodia. The results of this study support the conclusion that the Mekong giant catfish is critically endangered. Care should be taken to sustain the genetic diversity of this species, as the level of genetic variability has already decreased in the wild population. This species is a target species for an ongoing stock enhancement program in the Mekong River in Thailand. It is proposed to apply these markers for proper broodstock management, such as for minimal kinship selective breeding in the hatchery.     

Estimation of sequestered carbon in Article-3.4 private planted forests in the first commitment period in Japan

The purpose of this study was to predict the likely amounts of carbon sequestration on a national scale for Japan in the Article-3.4 private planted forests of the Kyoto Protocol during the first commitment period. We regarded the planted forests that had undergone silvicultural practices such as weeding, pruning, and thinning since 1990 as Article-3.4 planted forests in accordance with the definition given by the Forestry Agency of Japan. Regression models were developed to predict the forest areas that had undergone silvicultural practices, employing silvicultural subsidies and forest workers' wages as predictor variables. Then the time series changes in the predictor variables were provided by extending their recent trends, with the result being that the forest areas that have undergone silvicultural practices were predicted on the basis of the three scenarios of the variables. Thus, the Article-3.4 forest area was calculated considering overlaps of silvicultural practices over fixed stands, and the area was converted into the amount of carbon sequestration by multiplying it by coefficients such as a volume table, biomass expansion factor, and others. The result implied that Article-3.4 private planted forests were expected to sequester 8.16–8.87 Mt-C year⁻¹ during the first commitment period. These amounts cover 63%–68% of the carbon sequestration goal by land-use change and forestry activities capped under the Marrakesh Accords. To realize this prediction, it is important to provide a sufficient silvicultural subsidy to last until the end of the first commitment period and to implement silvicultural practices on the forest stands that have not undergone such practices since 1990.     

Monitoring of the genetic variability of the hatchery and recaptured fish in the stock enhancement program of the rare species barfin flounder <Emphasis Type="Italic">Verasper moseri</Emphasis>

ABSTRACT:   In relation to the stock enhancement program for barfin flounder, hatchery juveniles produced in 2001 were genotyped using microsatellite DNA markers (msDNA) and then released to natural waters. Subsequently, recaptured individuals, designated as 'tentative recaptured', were examined using msDNA. In order to evaluate the effectiveness of the stock enhancement program, pairwise F _ST and genic differentiation tests were used to estimate the genetic divergence between the wild samples, the hatchery broodstock, and the tentative recaptured samples. Analysis showed significant differentiation among these three groups. Pedigree determination by msDNA was used to establish the origin of the tentative recaptured individuals, in order to elucidate whether they were hatchery produced, 'real recaptured', or wild specimens. Wild individuals were not found. The effective population size of the real recaptured stock was very low ( N _e = 16.6). Equal family survivability was observed between the released and real recaptured stocks, indicating that the genetic variability of the released stock was maintained in the natural environment. Future broodstock management, breeding designs, and family contribution equalization of the offspring to be released will be required in this rare species to avoid unintended genetic differentiation between the wild population and the hatchery broodstock.     

Genetic variation of mitochondrial and nuclear genomes in carrots revealed by random amplified polymorphic DNA (RAPD)

Mitochondrial and nuclear genomic diversities of 8 carrot (Daucus carota ssp. sativus) varieties, including 6 pure lines and 2 cytoplasmic male sterile (cms) lines, were taxonomically identified using PCR with 19 RAPD primers. Dendrograms based on polymorphisms of both mitochondrial and nuclear genomes were constructed. According to the dendrogram of the mitochondrial genome revealed by RAPD, 4 differentiated clusters formed, in good accordance with the classification based on analyses with restriction enzyme digestion. Two cms lines were grouped into the same cluster, as genetically separated from the others. Thus, the cytoplasm donors of these male sterile lines were thought to be wild carrots. Conversely, RAPD analysis of the nuclear genome for these eight cultivars revealed no evident clusters although some cultivars were of a similar origin or place of cultivation. A correlation between nuclear and mitochondrial dendrograms was absent. RAPD has proved to be a useful tool for identifying mitochondrial and nuclear genomes. This technique will greatly aid in promoting efficient improvement of carrots. This revised version was published online in July 2006 with corrections to the Cover Date.     

Biological control of Fusarium wilt by <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> IUMC7 isolated from mushroom compost

Bacillus amyloliquefaciens IUMC7 isolated from mushroom compost inhibited growth of Fusarium oxysporum f. sp. lycopersici (FOL) on culture plates, and a culture supernatant of IUMC7 inhibited in vitro germ tube elongation of FOL. When compared with control soils, mushroom compost inoculated with IUMC7 significantly reduced disease severity caused by FOL in tomato plants. PCR tests for expression of PR genes indicated that IUMC7 did not induce resistance in tomato plants. These results suggested that the suppression of disease was mainly caused by antimicrobial compounds produced by IUMC7.     

Dynamics of soil biota at different depths under two contrasting tillage practices

One aim of conservation tillage is to preserve soil biological properties. This study was conducted to examine the effects of two contrasting tillage treatments on soil biota at different depths. We investigated the population dynamics and vertical distributions of microbes and several soil faunal groups for 2 years in field Andosols in northeastern Japan. The experimental plots were under no tillage (NT) or conventional tillage (CT, rotary tilled to 20 cm) management. In the 0–10-cm soil layer, bacterial and fungal substrate-induced respiration (SIR) and the population density of enchytraeids were higher under NT than under CT, but the population densities of protozoa, mites, and collembolans did not differ significantly. In contrast, at 10–20 cm, both SIR values were higher under CT, where larger populations of mites and collembolans were recorded. At both depths, nematodes were more abundant under CT. Thus, the effects of tillage on these soil organisms differed according to soil depth, and negative impacts of tillage were smaller in the deeper layer. Larger amounts of earthworm casts at the soil surface in NT plots showed a greater biomass of earthworms than in CT. To evaluate the activities of soil biota, we buried litterbags with three different mesh sizes at the two depths and examined the rate of decomposition. The daily decay constant of litter in the surface soil layer (1.5–8.5 cm) was greater under NT. We suppose that the activities of soil biota in this layer were stimulated under NT, and that especially microbes and enchytraeids, which were abundant at 0–10 cm, contributed greatly to the decomposition.     

Effects of feeding calves genetically modified corn bt11: a clinico-biochemical study

Genetically modified corn Bt11 is insect-resistant and expresses Cry1Ab toxin, an insecticidal protein, in kernels. Although Bt11 corn is considered safe based on animal performance, there are no reports available on the clinico-biochemical effects of feeding it to cattle. In this study, we evaluated the effects of feeding Bt11 to calves, using blood and ruminal clinico-biochemical parameters. Our three-month-long feeding experiment demonstrated that calves (n=6), fed with a ration containing 43.3% of Bt11 corn kernels as dry matter, did not develop any discernible clinical, hematological, biochemical, or ruminal abnormalities as compared with control calves (n=6) fed non-Bt11 corn. The results suggest that the transgenic Bt11 has no negative clinico-biochemical effects on calves.     

Soil organic carbon pools in ploughed and no‐till Alfisols of central Ohio

No‐till (NT) farming can restore the soil organic carbon (SOC) pool of agricultural soils, but the SOC pool size and retention rate can vary with soil type and duration of NT. Therefore, the objectives of this study were to determine the effects of NT and soil drainage characteristics on SOC accumulation across a series of NT fields on Alfisols in Ohio, USA. Sites under NT for 9 (NT9), 13 (NT13), 36 (NT36), 48 (NT48) and 49 (NT49) years were selected for the study. Soil was somewhat poorly drained at the NT48 site but moderately well drained at the other sites. The NT48 and NT49 on‐station sites were under continuous corn (Zea mays), while the other sites were farmers' fields in a corn–soybean (Glycine max) rotation. At each location, the SOC pool (0–30 cm) in the NT field was compared to that of an adjacent plough‐till (PT) and woodlot (WL). At the NT36, NT48 and NT49 sites, the retention rate of corn‐derived C was determined using stable C isotope (¹³C) techniques. In the 0‐ to 10‐cm soil layer, SOC concentration was significantly larger under NT than PT, but a tillage effect was rarely detected below that depth. Across sites, the SOC pool in that layer averaged 36.4, 20 and 40.8 Mg C/ha at the NT, PT and WL sites, respectively. For the 0‐ to 30‐cm layer, the SOC pool for NT (83.4 Mg C/ha) was still 57% greater than under PT. However, there was no consistent trend in the SOC pool with NT duration probably due to the legacy of past management practices and SOC content differences that may have existed among the study sites prior to their conversion to NT. The retention rate of corn‐derived C was 524, 263 and 203 kg C/ha/yr at the NT36, NT48 and NT49 sites. In contrast, the retention rate of corn‐C under PT averaged 25 and 153 kg C/ha/yr at the NT49 (moderately well‐drained) and NT48 (somewhat poorly drained) sites, respectively. The conversion from PT to NT resulted in greater retention of corn‐derived C. Thus, adoption of NT would be beneficial to SOC sequestration in agricultural soils of the region.     

Pool‐based genome‐wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle

Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool‐based genome‐wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full‐length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo.     

Effect of calcined lime (CaO) on chlamydospores of the rice false smut pathogen,Villosiclava virens,and their root attachment and infection

Rice false smut caused by Villosiclava virens is a devastating disease. The smut balls contain chlamydospores, which fall onto paddy soils to become the primary inoculum. After transplanting, the chlamydospores subsequently germinate and infect rice roots. The application of a CaO-containing fertilizer to paddy soils can inhibit the development of rice false smut disease; however, the underlying mechanism is unknown. In this study, we evaluated the suppression of chlamydospore behaviour due to CaO. Specifically, we clarified the effects of the following on chlamydospore morphology and germination: (a) pH, (b) calcium (Ca) concentration, (c) Ca concentration (pH adjusted to 6.5), and (d) CaO-added soil solution. Germination was suppressed at pH 4 and 10, in contrast with the normal germination at pH 6, 7, and 8. Treatments with more than 10 mg/L Ca melted the outer layer of chlamydospores and suppressed germination regardless of whether the pH was adjusted to 6.5. A saturated CaO solution induced bursting of chlamydospores. Suppressed germination and a melted outer chlamydospore layer were also observed, even though the soil buffering effect initially prevented the CaO-mediated pH increase. Furthermore, the chlamydospores within 15 mm from the CaO small lump exhibited suppressed germination in soil. In addition, there was no effect of CaO treatment on chlamydospore attachment to rice roots and hyphal invasion of rice roots in in vitro inoculation tests. These results suggest that Ca concentration is an important factor for inhibiting the occurrence of rice false smut disease.