Estimation of variance components for carcass traits in Japanese Black cattle using 50K SNP genotype data

Genomic selection using high‐density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy‐three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score. Additive polygenic variance and the variance attributable to a set of SNPs that had statistically significant effects on the trait were estimated via Gibbs sampling with two models: (i) a model with the chosen SNPs and the additive polygenic effects; and (ii) a model with the polygenic effects alone. The proportion of the estimated variance attributable to the SNPs became higher as the number of SNP effects that fit increased. High correlations between breeding values estimated with the model containing the polygenic effect alone and those estimated by chosen SNPs were obtained. No fraction of the total genetic variance was explained by SNPs associated with the trait at P ≥ 0.1. Our results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.     

Molecular relationships between Australian annual wild rice,Oryza meridionalis,and two related perennial forms

Background

The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice.

Results

Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets.

Conclusion

Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon. One lineage is closely related to O. meridionalis and another to Asian O. rufipogon. The first was presumed to have evolved by divergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon, possibly arrived in Australia later.     

Towards the partial resumption of agriculture with buckwheat cultivation in fields physically decontaminated of radioactive cesium after the nuclear power plant accident in 2011: a case study in Yamakiya District,Fukushima

ABSTRACT

Yamakiya District in the town of Kawamata, Fukushima Prefecture, was evacuated after the nuclear accident at the Tokyo Electric Power Company’s Fukushima Dai-ichi nuclear power plant in 2011. Since then, nuclear decontamination procedures have been applied to the surrounding environment, including agricultural fields. The decontamination procedure for agricultural fields consists of the removal of radiation-contaminated surface soil, followed by soil dressing and plowing. However, radioactive cesium (RCs) remains in the soil even after decontamination. In this study, we investigated the effect of applying nitrogen, potassium fertilizers, and cattle manure compost on buckwheat growth and the concentration of RCs in the grain of buckwheat cultivated in a decontaminated field from 2014 to 2016. Applications of potassium fertilizer and cattle manure compost increased the soil exchangeable potassium content and decreased the RCs concentration in the grain of buckwheat cultivated in the decontaminated field. Before the cultivation of the first buckwheat crop, the RCs concentration in soil varied widely and there were ‘hot spots’ with high RCs concentrations because of insufficient mixing of the original and the dressed soils. Therefore, soil had to be adequately mixed to avoid producing grain with a high RCs concentration. Buckwheat grew better when supplied with more nitrogen fertilizer than the conventional amount at the first cultivation, indicating that the dressed soil had low fertility. We also monitored buckwheat cultivation by local farmers in decontaminated fields from 2015 to 2017. By using potassium fertilizer, the farmers produced buckwheat grain with low RCs concentrations from 2015 to 2017.     

Nondestructive evaluation of drying stress level on wood surface using near-infrared spectroscopy

A nondestructive technique for swiftly measuring the stress level of the surface of wood is proposed, which is important for process control in timber drying. Partial least squares (PLS) regression models for predicting surface-released strain (ε) were developed using NIR spectra obtained from Sugi (Cryptomeria japonica D. Don) samples during drying. The predictive ability of the models was evaluated by PLS analysis and by comparing NIR-predicted ε with laboratory-measured values. The PLS regression model using the NIR spectra pre-processed by MSC and second derivatives with a wavelength range of 2,000–2,220 nm showed good agreement with the measurement (R ² = 0.72). PLS analysis identified the wavelengths around 2,035 nm as making significant contributions to the prediction of ε. Orthogonal signal correction (OSC) was an effective pre-processing technique to reduce the number of factors required for the model using the wavelength range 1,300–2,500 nm. However, the predictive ability of the OSC-corrected model was not improved. Elapsed times to reach the maximum tensile stress (T _max) and the stress reversal point (T _rev) at the wood surface during drying were detected correctly for 75 % of the samples. The results show that NIR spectroscopy has potential to predict the drying stress level of the timber surface and to detect critical periods in drying, such as T _max and T _rev.     

Clinical Study Report on Milk Production in the Offspring of a Somatic Cell Cloned Holstein Cow

This study examined two female offspring of a somatic cell cloned Holstein cow that had reproduction problems and milk production performance issues. The two offspring heifers, which showed healthy appearances and normal reproductive characteristics, calved on two separate occasions. The mean milk yields of the heifers in the first lactation period were 9,037 kg and 7,228 kg. The relative mean milk yields of these cows were 111.2% and 88.9%, respectively, when compared with that of the control group. No particular clinical abnormalities were revealed in milk yields and milk composition rate [e.g., fat, protein and solids-not-fat (SNF)], and reproductive characteristics of the offspring of the somatic cell cloned Holstein cow suggested that the cloned offspring had normal milk production.     

Production of bioactive bovine fibroblast growth factor 4 in E. coli based on the common nucleotide sequence of its structural gene in three breeds

Fibroblast growth factor 4 (FGF4) is considered a crucial gene in the proper development of bovine embryos. We recently determined the FGF4 gene sequence in eight cattle derived from three breeds and revealed a common nucleotide sequence of the structural gene encoding FGF4, which leads to the deletion and mutation of amino acid sequences in the mature FGF4 (Pro³²‐Leu²⁰⁶) compared with the sequence previously reported. In the present study, HisbFGF4, a 6× histidine‐tagged bovine FGF4 (Pro³²‐Leu²⁰⁶), was produced in Escherichia coli based on the validated nucleotide sequence and purified by heparin column chromatography. In primary bovine fibroblasts, HisbFGF4 showed significant mitogenic activity, whereas, intriguingly, the activity of a commercially available recombinant human FGF4 (Gly²⁵‐Leu²⁰⁶) produced in E. coli was weaker than that of HisbFGF4. In conclusion, the present study provides a simple method for the production of a bioactive bovine FGF4 derivative in E. coli utilizing its structural gene elucidated by us.     

Effects of single caging and cage size on behavior and stress level of domestic neutered cats housed in an animal shelter

Cats need a minimum amount of space even in animal shelters. In this study the effects of single caging and cage size on the behavior and stress level of domestic cats were investigated. Six neutered cats (2–15 years old) that had been housed in a group for at least 7 months were moved to three kinds of single cages (small, medium and large) by rotation on a Latin square design. They experienced each cage size for 6 days. Cats could use vertical dimensions when housed in a group room and the large cage. Behavioral observation was conducted for 3 h in the evening, and stress levels were assessed by urine cortisol‐to‐creatinine ratios. The amounts (estimated proportions) of time spent in locomotion and social/solitary play were lower even in large cages than in group housing (both P < 0.05). Conversely, the amount of time spent resting tended to increase when housed singly (P = 0.104). The urine cortisol‐to‐creatinine ratios of singly housed cats tended to be higher than that of group‐housed cats (P = 0.086). The results indicate that cats become less active when they are housed singly in cages regardless of the cage size. Cats seem to feel no undue stress even in small cages if the stay is short.     

Comparison of the effects explained by variations in the bovine PLAG1 and NCAPG genes on daily body weight gain,linear skeletal measurements and carcass traits in Japanese Black steers from a progeny testing program

The c.1326T>G single nucleotide polymorphism (SNP) in the NCAPG gene, which leads to an amino acid change of Ile442 to Met442, was previously identified as a candidate causative variation for a bovine carcass weight quantitative trait loci (QTL) on chromosome 6, which was associated with linear skeletal measurement gains and daily body weight gain at puberty. Recently, we identified the stature quantitative trait nucleotides (QTNs) in the PLAG1‐CHCHD7 intergenic region as the causative variations for another carcass weight QTL on chromosome 14. This study aimed to compare the effects of the two QTL on growth and carcass traits using 768 Japanese Black steers from a progeny testing program and to determine whether a genetic interaction was present between them. The FJX_250879 SNP representing the stature QTL was associated with linear skeletal measurements and average daily body weight gain at early and late periods during adolescence. A genetic interaction between FJX_250879 and NCAPG c.1326T>G was detected only for body and rump lengths. Both were associated with increased carcass weight and Longissimus muscle area, and NCAPG c.1326T>G was also associated with reduced subcutaneous fat thickness and increased carcass yield estimate. These results will provide useful information to improve carcass weight in Japanese Black cattle.