Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle

Marker‐assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.     

Oxidation of quercetin by salivary components. Quercetin-dependent reduction of salivary nitrite under acidic conditions producing nitric oxide

Under acidic conditions, nitrite is protonated to nitrous acid (pK(a) = 3.2-3.4) that can be transformed into nitric oxide by self-decomposition and reduction. When sodium nitrite was mixed with quercetin at pH 1-2, quercetin was oxidized producing nitric oxide. In addition to quercetin, kaempferol and quercetin 4'-glucoside were also oxidized by nitrous acid, but oxidation of apigenin, luteolin, and rutin was slow compared to oxidation of the above flavonols. These results suggested that flavonols, which have a free hydroxyl group at carbon position 3, can readily reduce nitrous acid to nitric oxide. When the pH of saliva was decreased to 1-2, formation of nitric oxide was observed. The nitric oxide formation was enhanced by quercetin, and during this process quercetin was oxidized. These results indicate that there is a possibility of reactions between phenolics and nitrous acid derived from salivary nitrite in the stomach.     

Breeding and brewing quality of the Canadian malting barley variety ‘CDC Goldstar’ lacking lipoxygenase-1

Various types of malt quality profiles have been investigated to benefit the North American brewing industry. Herein, we report the development and brewing quality of the hulled, two-row malting barley (Hordeum vulgare L.) variety ‘CDC Goldstar’ lacking lipoxygenase-1 (LOX-1-less). This new variety offers a novel malt type for the improvement of beer flavor stability. The agronomic performance of ‘CDC Goldstar’ was tested in the Western Cooperative Two Row Barley Registration Trials during 2013–2014. In addition to high lodging tolerance, the new variety showed 6% higher yield than the current leading variety ‘CDC Copeland’. The malt quality of ‘CDC Goldstar’ showed higher diastatic power and lower wort β-glucan content than ‘CDC Copeland’ and controllable proteolytic modification (soluble nitrogen and Kolbach Index). Pilot- (100 L) and commercial-scale (5,000 L) brewing trials were conducted using ‘CDC PlatinumStar’, another LOX-1-less variety with a low enzymatic profile, as the control variety. Absence of the LOX-1 trait from ‘CDC Goldstar’ maintained trans-2-nonenal levels in aged beers as low as those in other LOX-1-less varieties without affecting major beer parameters, such as ester and aldehyde content or foam stability. The newly developed ‘CDC Goldstar’ malting barley provides added value for the beer industry and consumers.     

Heritability estimates for racing performance in Japanese Thoroughbred racehorses using linear and non-linear model analyses

This study evaluated the differences between linear and non‐linear modelled heritability estimates of racing performance based on lifetime earnings (LE) and lifetime ranking (LR) in Japanese Thoroughbred racehorses. The heritability estimate (h² = 0.25) obtained from a non‐linear model based on formal Japan Racing Association ranking was much higher than that obtained from a linear model based on the original trait phenotype (h² = 0.11). The linear models showed slightly higher heritability estimates under the trait categorizations than under the original phenotypes, while the non‐linear categorical trait models showed much higher heritability estimates than the linear models, especially for binary trait categorizations (h² = 0.34) with non‐winning and winning horses. The binary trait categorizations were consistent with the case and control classifications in the previous genome‐wide association study (GWAS), which identified possible sequence variants on ECA18 that affect racing performance in Japanese Thoroughbred racehorses. Those findings suggested that the different heritability estimates obtained from several trait categorizations would reflect the possible presence of susceptibility gene segregations in the analyzed population, indicating that heritability estimates from non‐linear models are useful for the selection of case and control populations in GWAS.     

Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags

We have collected more than 190 000 porcine expressed sequence tags (ESTs) from full‐length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three‐way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor‐joining tree showed that the pig groups were classified into two large clusters, namely, Euro‐American and East Asian pig populations. F‐statistics and the analysis of molecular variance of Euro‐American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F_IS values were less than the F_ST values_, the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples.     

Impaired postnatal development in C/EBPbeta-deficient mice

Tail DNA genotyping of fetal and neonatal mice from C/EBPbeta heterozygous parents was performed to determine whether the decreased number of surviving C/EBPbeta mutants was caused by prenatal or postnatal death. Eighty-four 3-week-old mice born of heterozygous parents had significantly lower numbers of C/EBPbeta-deficient offspring than the expected Mendelian ratio (29.8%+/+, 65.5%+/-, 4.76%-/-, P<0.05). The genotypes of 72 fetal mice from intercrossed heterozygotes showed approximately the expected 1:2:1 Mendelian ratio (18.1% +/+, 52.8% +/-, 29.2% -/-, P>0.05). No difference in the proportions by sex could be detected in these perinates. This data indicates that C/EBPbeta-deficient mice have unknown lethal problems between the embryonic stage and weaning.     

Humus composition and humification degree of humic acids of alpine meadow soils in the northeastern part of the Qinghai–Tibet Plateau

The characteristics of humus composition are important for understanding the mechanism of carbon storage in the Qinghai–Tibet Plateau. The aim of this study was to characterize the quality of soil organic matter (SOM) in this region. Soil samples from four soil profiles in fenced study sites in the alpine grassland were collected at altitudes of 4200, 4000, 3800, and 3400 m, along the southwest facing slope in the Qilian Mountains. The humus composition and humification degree of the humic acid (HA) were determined by two methods: (1) extraction with 0.5% sodium hydroxide (NaOH) followed by 0.1 M sodium pyrophosphate (Na₄P₂O₇) (OH-PP method); and (2) treating once with 0.1 M hydrochloric acid (HCl) followed by extracting with 0.5% NaOH (Cl-OH method). Physico-chemical analysis revealed higher exchangeable cation content and higher base saturation ratios could be related to slightly acidic to neutral soils, which could be regarded as calcium (Ca)-rich soils. The amounts of combined-form HAs obtained by HCl pretreatment (HA_Cl – HA_OH; ?HA_Cl) were remarkably higher than those extracted with Na₄P₂O₇ (HA_PP), indicating that the combined form of HAs is mainly Ca. In addition, the proportion of HA_PP in the total HAs extracted with both NaOH and Na₄P₂O₇ (HA_OH + HA_PP) obtained in the OH-PP method increased with soil depth and decreasing elevation, indicating that HAs associated with aluminum (Al) and iron (Fe) were distinguished in the subsoils of lower elevation. Therefore, the formation of the organo-mineral complex may contribute to stabilizing SOM in the Qinghai–Tibet Plateau. Moreover, Type A-HA with the highest degree of humification was obtained from the deeper horizons with the Cl-OH method and almost all horizons by extraction with Na₄P₂O₇ in the OH-PP method. Further studies using various spectroscopic analyses are necessary to elucidate the chemical properties of SOM in this region.     

Identification of novel haze-active beer proteins by proteome analysis

Colloidal haze reduces beer quality considerably. Four haze samples were analyzed by two-dimensional gel electrophoresis (2DE) in order to identify haze-active proteins. Several protein spots were observed in all of the four haze samples. Using mass spectrometry analysis followed by a database search identified these spots as barley dimeric alpha-amylase inhibitor (BDAI-1), CMb component of tetrameric alpha-amylase inhibitor (CMb) and trypsin inhibitor CMe precursor (CMe). These proteins were considered to be haze-active. Since haze-active proteins are adsorbed by silica gel in the beer filtration process, we eluted proteins adsorbed onto silica gel (PAS) and identified their species. These major PAS were identified as protein Z4, protein Z7 and trypsin/amylase inhibitor pUP13 (TAI), rather than BDAI-1, CMb and CMe. Furthermore, we analyzed proline compositions in the beer proteins, PAS and the haze proteins. Consequently, we found that the proline compositions of PAS were higher (ca. 20 mol%) than those in the beer proteins (ca. 10 mol%), although those of the haze-active proteins such as BDAI-1, CMb and CMe were 6.6–8.7 mol%. Our results suggest that BDAI-1, CMb and CMe are not predominant haze-active proteins, but growth factors of beer colloidal haze.     

Brewing Performance of Malted Lipoxygenase‐1 Null Barley and Effect on the Flavor Stability of Beer

We examined the malting and brewing performances of a lipoxygenase‐1 (LOX‐1) null line of barley (Hordeum vulgare L.). The LOX‐normal malt and the LOX‐null malt were prepared from F₄ populations derived from a single cross. We could not observe any major differences in the general malt characteristics between the two malts. A brewing trial was performed using these malts. The analysis of the wort and beer revealed that the absence of LOX‐1 had little effect on the general characteristics of the wort and beer. In contrast, beer made from the LOX‐null malt showed reduced levels of beer‐deteriorating substances, trans‐2‐nonenal (T2N), and trihydroxyoctadecenoic acid (THOD). In the sensory evaluation, well‐trained panel members recognized the significant superiority of the aged LOX‐null beer in terms of staleness. These results show that the LOX‐1 null barley line can be effectively used to improve the flavor stability of beer without changing the other important beer qualities.