Partitioning of photosynthates originating from bent shoots in the arching and high-rack culture systems of cut rose production

The arching and high-rack culture systems were developed and patented by Japanese rose growers. Both culture systems have bent canopies (lower bent shoots). In the arching culture system, shoots sprouting from the crown are harvested as cut flowers. However, the high-rack culture system also has a bent canopy originating from the mother stem (upper bent shoots) and flower stems sprout and is harvested at the top of each mother stem. Partitioning of photosynthates originating from bent shoots in arching and high-rack culture systems of rose production was investigated to elucidate how carbohydrates are re-allocated from the bent shoots in different culture systems of roses. At the flowering stage in both culture systems, 50–70% of ¹³C-photosynthates originated from bent shoots were exported to other parts within 72 h after ¹³CO₂ feeding to the bent shoot. In the arching culture system, photosynthates from lower bent shoots were partitioned mainly to the roots and crown. Similarly, in the high-rack culture system, between 71 and 86% of the exported carbon from the bent shoots were allocated to below the point of bending (roots + crown + mother stems) and only 9–28% was allocated to flowering shoots above the point of bending. In both culture systems, photosynthate translocation from the lower bent shoot directly to flowers was low. Accordingly, bent shoots in rose plants acted as a source of photosynthates, independent of culture system. The height of the bent shoots determined for a great deal in the re-allocation of the photosynthates, and provides a partial explanation for difference in production of cut roses.     

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.     

Occurrence of rocket larkspur witches’ broom caused by “<Emphasis Type="Italic">Candidatus</Emphasis> Phytoplasma asteris” in Japan

In October 2001, a disease of rocket larkspur (Cosolida ambigua (L.) P. W. Ball et Heyw), characterized by witches’ broom, yellows and virescence of flowers, was found in Yakage Town in Okayama Prefecture. Electron microscopy revealed the presence of phytoplasma-like bodies in the phloem of diseased plants. The causal phytoplasma was identified as “Candidatus Phytoplasma asteris” based on 16S rDNA sequence analysis, and demonstrated to be acquired by the leafhopper Macrosteles striifrons. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession number AB258330.     

Genotypes and allele frequencies of buried SNPs in a bovine single‐nucleotide polymorphism array in Japanese Black cattle

Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position‐unassigned SNPs, or “buried SNPs” include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.     

The cumulative methane production from dairy cattle slurry can be explained by its volatile solid,temperature and length of storage

In order to refine the national estimate of methane emission from stored cattle slurry, it is important to comprehend the basic characteristics of methane production. Two dairy cattle slurries were obtained from livestock farms located in Hokkaido (a northern island) and Kyushu (a southern island). The slurries were diluted with water into three levels: undiluted, three times diluted, and 10 times diluted. Three hundred mL of the slurries were put into a bottle with a headspace volume of 2.0 L, which was filled with nitrogen gas and then sealed by butyl rubber. Four levels of temperature were used for incubation: 35, 25, 15 and 5 °C. The time course of the cumulative methane production per volatile solid (VS) was satisfactorily expressed by an asymptotic regression model. The effect of dilution on the methane production per VS was not distinctive, but that of temperature was of primary importance. In particular, higher temperature yields a higher potential production and a shorter time when the cumulative production reaches half of the potential production. The inclusive and simple models obtained in this study indicate that the cumulative methane production from stored cattle slurry can be explained by VS, temperature and length of storage.     

Genetic organization and preferential distribution of putative pilus gene clusters in Streptococcus suis

Recent analyses of Streptococcus suis isolates using multilocus sequence typing (MLST) suggested the importance of sequence type (ST) 1 and ST27 complexes for animal hygiene and public health. In this study, to investigate whether pilus-associated genes in S. suis can be used as novel genetic markers for important clonal groups, we examined the correlation between STs and putative pilus-associated gene profiles in S. suis. Genomic searches using sequenced genomes and sequence data determined in several isolates revealed the presence of at least four distinct putative pilus gene clusters in S. suis (srtBCD, srtE, srtF, and srtG clusters). On the basis of the presence or absence of genes in the four clusters, 108 S. suis isolates from various origins were classified into 12 genotypes (genotypes A–L). Genotypes A and B, which possessed srtBCD plus srtF clusters and srtF plus srtG clusters, respectively, were the most common in isolates from diseased pigs and humans, and 29.9% and 59.8% of the isolates belonged to genotypes A and B, respectively. In contrast, only 4.8% and 28.6% of isolates from healthy carriers were genotypes A and B, respectively. MLST analysis showed the associations of genotypes A and B with ST1 and ST27 complexes, respectively. In addition, srtBCD and srtG clusters were preferentially distributed to ST1 and ST27 complex members, respectively. These results suggest that profiling of selected pilus-associated genes could be used as an easy screening method to monitor isolates important for S. suis infection.     

Spectral sensitivity of juvenile chub mackerel (<Emphasis Type="Italic">Scomber japonicus</Emphasis>) in visible and ultraviolet light

Although chub mackerel (Scomber japonicus) is widely distributed all over the world, the relevance of its visual sensitivity to its ecology is not yet fully understood. We investigated spectral sensitivity in juvenile chub mackerel in the range of ultraviolet (UV) to visible light (369–652 nm) by electroretinogram (ERG) using light-emitting diodes (LEDs). Sensitivity peaked at a wavelength of approximately 482 nm in dark-adapted fish and 525 nm in light-adapted fish. A secondary sensitivity peak in the UV range at approximately 382 nm was found in both dark- and light-adapted fish. The UV sensitivity of chub mackerel may be attributable to UV transmissibility of the optical media and to the presence of a beta-band of visible light-sensitive visual pigments, and not to an alpha-band of UV visual pigments. This UV sensitivity may be useful for feeding or communication with other fishes.     

Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole‐genome resequencing in Japanese Black cattle

In our previous study, we performed genome‐wide association study (GWAS) to identify the genomic region associated with Fat area ratio to rib eye area (FAR) and detected a candidate in BTA7 at 10–30 Mbp. The present study aims to comprehensively detect all polymorphisms in the candidate region using whole‐genome resequencing data. Based on whole‐genome resequencing of eight animals, we detected 127,090 polymorphisms within the region. Of these, 31,945 were located within the genes. We further narrowed the polymorphisms to 6,044 with more than five allele differences between the high and low FAR groups that were located within 179 genes. We subsequently investigated the functions of these genes and selected 170 polymorphisms in eight genes as possible candidate polymorphisms. We focused on SLC27A6 K81M as a putative candidate polymorphism. We genotyped the SNP in a Japanese Black population (n = 904) to investigate the effect on FAR. Analysis of variance revealed that SLC27A6 K81M had a lower p‐value (p = .0009) than the most significant SNP in GWAS (p = .0049). Although only SLC27A6 K81M was verified in the present study, subsequent verification of the remaining candidate genes and polymorphisms could lead to the identification of genes and polymorphisms responsible for FAR.