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1.
Bayesian analysis via Gibbs sampling, restricted maximum likelihood (REML), and Method R were used to estimate variance components for several models of simulated data. Four simulated data sets that included direct genetic effects and different combinations of maternal, permanent environmental, and dominance effects were used. Parents were selected randomly, on phenotype across or within contemporary groups, or on BLUP of genetic value. Estimates by Bayesian analysis and REML were always empirically unbiased in large data sets. Estimates by Method R were biased only with phenotypic selection across contemporary groups; estimates of the additive variance were biased upward, and all the other estimates were biased downward. No empirical bias was observed for Method R under selection within contemporary groups or in data without contemporary group effects. The bias of Method R estimates in small data sets was evaluated using a simple direct additive model. Method R gave biased estimates in small data sets in all types of selection except BLUP. In populations where the selection is based on BLUP of genetic value or where phenotypic selection is practiced mostly within contemporary groups, estimates by Method R are likely to be unbiased. In this case, Method R is an alternative to single-trait REML and Bayesian analysis for analyses of large data sets when the other methods are too expensive to apply. 相似文献
2.
Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study 
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下载免费PDF全文 B.O. Fragomeni D.A.L. Lourenco S. Tsuruta Y. Masuda I. Aguilar I. Misztal 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2015,132(5):340-345
The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ?1 and the approximated G ?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method. 相似文献
3.
The cell-associated adsorption of thorium or uranium from the solution containing each metal only at pH 3.50 using various microorganisms was examined. Among the species tested, high thorium adsorption abilities were exhibited by strains of the gram-positive bacteria Arthrobacter nicotianae IAM12342, Bacillus megaterium IAM1166, B. Subtilis IAM1026, Micrococcus luteus IAM1056, Rhodococcus erythropolis IAM1399, and Streptomyces levoris HUT6156. And high uranium adsorption abilities were found in some gram-positive bacterial strains S. albus HUT6047, S. levoris HUT6156, and A. nicotianae IAM12342. Among these highly efficient thorium and uranium adsorbing microorganisms, S. levoris, which could adsorb the largest amount of uranium from the aqueous solution at pH 3.50, could adsorb about 383 mol thorium and 390 mol uranium per gram dry weight of microbial cells from the solution containing thorium or uranium at pH 3.50. The amount and time course of thorium adsorbed were almost unaffected by co-existing uranium; however, the adsorption of thorium was faster when carried out after the adsorption of uranium. Thorium adsorption also became faster when uranium was added after thorium adsorption. The effect of pH on thorium adsorption was also discussed. 相似文献
4.
Up to 109,447 records of 49,656 Large White sows were used to evaluate the genetic relationship between number of pigs born dead (BD) and number born alive (BA) in first and later parities. Performance data (n = 30,832) for ultrasound backfat (BF) at the end of the test and days to reach 113.5 kg (AD) were used to estimate their relationships with BD and BA at first parity in a four-trait threshold-linear analysis (TL). Effects were year-farm, contemporary group (CG: farm-farrowing year-farrowing month) and animal additive genetic. At first parity, estimates of heritability were 0.09, 0.09, 0.37, and 0.31 for BA, BD, AD, and BF, respectively. The estimate of genetic correlation between BD and litter size was -0.04 (BD-BA). Corresponding values with test traits were both -0.14 (BD-AD, BD-BF). Estimates of genetic correlation between BA and performance traits were 0.08 (BA-AD) and 0.05 (BA-BF). The two test traits were moderately negatively correlated (-0.22). For later parities, a six-trait (BD, BA in three parities) TL model was implemented. The estimates of additive genetic variances and heritability increased with parity for BD and BA. Estimates of heritabilities were: 0.09, 0.10, and 0.11 for BD, and 0.09, 0.12, and 0.12 for BA in parities one to three, respectively. Estimates of genetic correlations between different parities were high (0.91 to 0.96) for BD, and slightly lower (0.74 to 0.95) for BA. Genetic correlations between BD and BA were low and positive (0.02 to 0.17) for BA in Parities 1 and 2, but negative (-0.04 to -0.10) for BA in Parity 3. Selection for increased litter size should have little effect on farrowing piglet mortality. Intense selection for faster growth and increased leanness should increase farrowing piglet mortality of first-parity sows. A repeatability model with a simple correction for the heterogeneity of variances over parities could be implemented to select against farrowing mortality. The genetic components of perinatal piglet mortality are independent of the ones for litter size in the first parity, and they show an undesirable, but not strong, genetic association in second parity. 相似文献
5.
Hiromi Saijo Kazuya Tsuruta Norihisa Kusumoto Tatsuya Ashitani Koetsu Takahashi 《Journal of Wood Science》2013,59(3):238-242
In our ongoing efforts to develop new uses for wood-based waste streams, the growth inhibition activities of extracts obtained from Sugi (Cryptomeria japonica) bark were examined against Heterosigma akashiwo, otherwise known as red tide plankton. The Sugi bark was separated into its outer and inner barks and then extracted sequentially with hexane, ethyl acetate, and methanol. Strong inhibitory activities against H. akashiwo were observed in the tests involving the hexane extract from the inner and outer barks, as well as the ethyl acetate extract from the inner bark. Gas chromatography mass spectroscopy (GC–MS) analysis revealed that cubebol, phyllocladanol, 6,7-dehydroferruginol, ferruginol, and sugiol were the main components in the active extracts. These components themselves were then tested for their growth inhibition activities against H. akashiwo. Cubebol and ferruginol showed potent inhibitory activities, whereas phyllocladanol, 6,7-dehydroferruginol, and sugiol were only weakly active. Taken together, these results suggested that the Sugi bark extracts could be used as inhibition reagents against red tide plankton. 相似文献
6.
Jorge Hidalgo Daniela Lourenco Shogo Tsuruta Yutaka Masuda Vivian Breen Rachel Hawken Matias Bermann Ignacy Misztal 《Journal of animal science》2021,99(9)
Accuracy of genomic predictions is an important component of the selection response. The objectives of this research were: 1) to investigate trends for prediction accuracies over time in a broiler population of accumulated phenotypes, genotypes, and pedigrees and 2) to test if data from distant generations are useful to maintain prediction accuracies in selection candidates. The data contained 820K phenotypes for a growth trait (GT), 200K for two feed efficiency traits (FE1 and FE2), and 42K for a carcass yield trait (CY). The pedigree included 1,252,619 birds hatched over 7 years, of which 154,318 from the last 4 years were genotyped. Training populations were constructed adding 1 year of data sequentially, persistency of accuracy over time was evaluated using predictions from birds hatched in the three generations following or in the years after the training populations. In the first generation, before genotypes became available for the training populations (first 3 years of data), accuracies remained almost stable with successive additions of phenotypes and pedigree to the accumulated dataset. The inclusion of 1 year of genotypes in addition to 4 years of phenotypes and pedigree in the training population led to increases in accuracy of 54% for GT, 76% for FE1, 110% for CY, and 38% for FE2; on average, 74% of the increase was due to genomics. Prediction accuracies declined faster without than with genomic information in the training populations. When genotypes were unavailable, the average decline in prediction accuracy across traits was 41% from the first to the second generation of validation, and 51% from the second to the third generation of validation. When genotypes were available, the average decline across traits was 14% from the first to the second generation of validation, and 3% from the second to the third generation of validation. Prediction accuracies in the last three generations were the same when the training population included 5 or 2 years of data, and a decrease of ~7% was observed when the training population included only 1 year of data. Training sets including genomic information provided an increase in accuracy and persistence of genomic predictions compared with training sets without genomic data. The two most recent years of pedigree, phenotypic, and genomic data were sufficient to maintain prediction accuracies in selection candidates. Similar conclusions were obtained using validation populations per year. 相似文献
7.
Zumbach B Misztal I Tsuruta S Sanchez JP Azain M Herring W Holl J Long T Culbertson M 《Journal of animal science》2008,86(9):2082-2088
The objective of this study was to quantify the effect of heat stress during the life of a pig on its final weight, as a first step toward a genetic evaluation for heat tolerance. Data included carcass weights of 23,556 crossbred pigs [Duroc x (Landrace x Large White)] raised on 2 farms in North Carolina and slaughtered from May 2005 through December 2006. Weather data were available from a nearby weather station. Lifetime of a pig was assumed to be partitioned into 2 periods. During an initial period, the effect of heat stress was assumed to be negligible or compensated for later. During the second period ending in slaughtering, the ADG was assumed to be affected linearly by heat load. Weekly heat load was calculated as degrees of average temperature-humidity index in excess of a threshold (18 degrees C). The total heat load (H) was the sum of weekly heat loads during the second period. During the months of January to May H was 0; H reached a peak in September. The final BW during the peak of heat stress decreased about 6 kg compared with BW during months of non-heat stress. Weekly and monthly averages of carcass weight generally moved similarly to H. However, there were large fluctuations unrelated to H; the fluctuations were different on the 2 farms. The model included the effects of farm-year of slaughter, sex, age at slaughter, and H, where age at slaughter and H were linear regressions. In analyses, the threshold was varied from 16 to 20 degrees C, and the second period was varied from 8 to 16 wk. The greatest R(2) (10.4%) was at the threshold of temperature-humidity index = 18 degrees C for a period of 10 wk. Varying the threshold and the length of time reduced R(2) less than 1%. Least squares means of year-month and year-week of carcass weight were calculated using a model with the fixed effects farm-year-month or farm-year-week of slaughter, sex, and age at slaughter (linear covariate), and the random effect of birth litter. Changes in BW of finisher pigs due to heat stress can be quantified by H during the last 10 wk of the life of the pig. 相似文献
8.
Kenji Tsuruta Tomonori Kume Hikaru Komatsu Naoko Higashi Toshihiro Umebayashi Tomo’omi Kumagai Kyoichi Otsuki 《Journal of Forest Research》2010,15(6):398-403
Sap flow techniques are practical tools for estimating tree transpiration. Though many previous studies using sap flow techniques
did not consider azimuthal variations of sap flux density (F
d) on xylem trunk to estimate tree transpiration, a few studies reported that ignoring the azimuthal variations in F
d could cause large errors in tree transpiration estimates for some tree species. Therefore, examining azimuthal variations
in F
d for major plantation tree species is critical for estimating tree transpiration. Using the thermal dissipation method, we
examined azimuthal variations in F
d in six trees of Japanese cypress Chamaecyparis obtusa (Sieb. et Zucc.) Endl., which is one of the most common plantation tree species in Japan. We recorded considerable variations
among F
d at four different azimuthal directions. The F
d value for one aspect was more than 100% larger than those for the other aspects. We calculated differences between tree transpiration
estimates based on F
d for one to three azimuthal directions and those based on F
d for four aspects. The differences relative to tree transpiration estimates based on F
d for four aspects were typically 30, 20, and 10% in accordance with the F
d for one, two, and three measurement aspects, respectively. This finding indicates that ignoring azimuthal variations could
cause large errors in tree transpiration estimates for Japanese cypress. 相似文献
9.
Abstract Emission rates of dimethyl sulficle (DMS), carbonyl sulfide (COS), and carbon disulfide (CS2) to the atmosphere from paddy fields at Ryugasaki, Ibaraki Prefecture, Japan were measured by using the closed chamber method. DMS was emitted mainly through the rice plant and its emission rate was much higher than those of COS and CS2. During a cropping period COS was slightly absorbed by the rice plant. Significant diurnal and seasonal variations of DMS iuxes were observed. The highest DMS iux was observed immediately after the heading day of rice plant. The annual DMS emission rate was in the order of mineral plot > straw plot > no-N plot, ranging from 4.5 to 6.9 mg S m-2 yr-1. The annual COS emission rate was in the order of straw plot > no-N plot > mineral plot, ranging from -0.2 to 1.8 mg S m-2 yr-1. The annual CS2 emission rate was slightly higher in the straw plot, ranging from 0.9 to 2.0 mg S m-2 yr-1. 相似文献
10.
土壤水分状况和质地对稻田N2O 排放的影响 总被引：34，自引：0，他引：34
１９９４年中国科学院封丘生态试验站通过小区试验研究了土壤质地和水分状况对稻田Ｎ２Ｏ排放的影响。结果表明稻田Ｎ２Ｏ排放主要受土壤水分状况的影响,淹水状态下,Ｎ２Ｏ排放很少,水分落于期间Ｎ２Ｏ排放量占水稻生长期Ｎ２Ｏ排放总量的８７．５０％～９８．６５％。土壤质地显影响稻田平均Ｎ２Ｏ排放通量,砂质土壤排放的Ｎ２Ｏ显或极显高于壤质和粘质土壤,水稻生长期砂质、壤质及粘质土壤的平均Ｎ２Ｏ排放通量分别为１３７．６３、８７．５４和６３．６μｇＮ２Ｏ－Ｎ／ｍ＾２．ｈ。 相似文献