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Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design

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G3-GENES GENOMES GENETICS 2021年第2期11卷 jkaa053页

作者： Chen, Yuhua Wu, Hainan Yang, Wenguo Zhao, Wei Tong, Chunfa Nanjing Forestry Univ Coinnovat Ctr Sustainable Forestry Southern China Key Lab Forest Genet & Biotechnol Minist Educ Nanjing 210037 Peoples R China Jingling Inst Technol Sch Anim Sci & Technol Nanjing 210038 Peoples R China

With the advances in high-throughput sequencing technologies, it is not difficult to extract tens of thousands of single-nucleotide polymorphisms (SNPs) across many individuals in a fast and cheap way, making it possible to perform genome-wide association studies (GWAS) of quantitative traits in outbred forest trees. It is very valuable to apply traditional breeding experiments in GWAS for identifying genome variants associated with ecologically and economically important traits in Populus. Here, we reported a GWAS of tree height measured at multiple time points from a randomized complete block design (RCBD), which was established with clones from an F 1 hybrid population of Populus deltoides and Populus simonii. A total of 22,670 SNPs across 172 clones in the RCBD were obtained with restriction site-associated DNA sequencing (RADseq) technology. The multivariate mixed linear model was applied by incorporating the pedigree relationship matrix of individuals to test the association of each SNP to the tree heights over 8 time points. Consequently, 41 SNPs were identified significantly associated with the tree height under the P-value threshold determined by Bonferroni correction at the significant level of 0.01. These SNPs were distributed on all but two chromosomes (Chr02 and Chr18) and explained the phenotypic variance ranged from 0.26% to 2.64%, amounting to 63.68% in total. Comparison with previous mapping studies for poplar height as well as the candidate genes of these detected SNPs were also investigated. We therefore showed that the application of multivariate linear mixed model to the longitudinal phenotypic data from the traditional breeding experimental design facilitated to identify far more genome-wide variants for tree height in poplar. The significant SNPs identified in this study would enhance understanding of molecular mechanism for growth traits and would accelerate marker-assisted breeding programs in Populus.

关键词： genome-wide association study randomized complete block design mixed linear model single-nucleotide polymorphism Populus GENETIC ARCHITECTURE POPULUS TRAITS GROWTH QTLS POPULATION DISCOVERY SELECTION ALIGNMENT SOFTWARE

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An application of the augmented randomized complete block design to poultry research

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POULTRY SCIENCE 1996年第5期75卷 601-607页

作者： Boyle, CR Montgomery, RD College of Veterinary Medicine Mississippi State University Mississippi State Mississippi 39762-9825

Avian health researchers are often faced with the need to evaluate large numbers of potential disease agents, but limited facilities and the desire to minimize animal usage and costs prohibit large, all-inclusive experiments. Plant breeders encounter a similar problem with variety screening experiments in which a large number of varieties must be evaluated, but the supply of seed may be limited. In that situation, the use of augmented experimental designs has proven effective for obtaining the replication needed for valid statistical analysis. Those designs rely on the use of multiple trials consisting of different sets of plant varieties;standard varieties are included as controls or checks in every trial to provide an estimate of experimental error. Although the comparisons among varieties are not all equally precise and the estimate of experimental error may be biased, use of augmented designs can reduce the time and number of experimental units needed to isolate the most promising new varieties for further in-depth study. Augmented designs can similarly be applied to screening experiments in poultry research. This paper describes the augmented randomized complete block design and its application in an avian health setting. Data collected in an exploratory study of infectious enteritis in chickens illustrate details of the statistical analysis. Suggestions for implementing this analysis using the SAS(R) statistical analysis package are also given.

关键词： augmented design experimental design partially balanced incomplete block design randomized complete block design statistical analysis

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ANALYSIS OF MEANS USING RANKS FOR THE randomized complete block design

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COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION 1994年第2期23卷 547-568页

作者： BAKIR, ST ALABAMA STATE UNIV COLL BUSINESS ADMMONTGOMERYAL 36101

A nonparametric test procedure is proposed for the analysis of randomized complete block designs. Such a procedure may be carried out graphically in the form of a Shewhart control chart. Exact and asymptotic critical values are given for the implementation of the proposed procedure. A Monte Carlo study is made to compare the powers of the proposed procedure to those of the analysis of variance, the analysis of means, and the Friedman procedures. Results of the study indicate that the proposed procedure has superior power performance when testing against slippage alternative hypotheses under heavy-tailed distributions such as the Cauchy distribution. However, when testing against symmetric alternatives under light-tailed distributions, the proposed procedure does not perform well.

关键词： ANALYSIS OF MEANS ANALYSIS OF VARIANCE FRIEDMAN TEST MONTE-CARLO RANKS randomized complete block design

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TESTING THE EFFECT OF blockING IN A randomized complete block design (RCBD)

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COMMUNICATIONS IN STATISTICS PART A-THEORY AND METHODS 1981年第23期10卷 2447-2459页

作者： PERES, CA National Institute of Environmental Health Sciences North Carolina 27709 p n Box12233 Research Triangle Park United States

In the RCBD, the block system causes, for most applications, strong correlation between responses from experimental units in the same block. Therefore, the usual modelwith the usual assumptions about zi j. (i.i.d. N(0,σ2)) is not realistic. In this paper we study the consequences of more realistic assumptions about zi j. and verify that the usual F test, for testing treatment effects, can be used even if there is a constant covariance between responses from experimental units in the same block. When the variances associated with each treatment are not the same we give an approximate solution for testing treatment effects.

关键词： randomized complete block design effect of blocking restriction error

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Γ-Optimal decision procedures for selecting the best population in randomized complete block design

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Communications in Statistics - Theory and Methods 1983年第3期12卷 341-354页

In randomized complete block design, we face the problem of selecting the best population. If some partial information about the unknown parameters is available, then we wish to delermine the optimal decisin rule to select the best *** this paper, in the class of natural selection rules, we employ the Γ-optimal criterion to determine optimal decision rules that will minimize the maximum expected risk over the class of some partial information. Furthermore, the traditional hypothesis testing is briefly discussed from the view point of ranking and selecting.

关键词： selection procedures randomized complete block design Γ-optimal decision rule best population

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Evaluation of different Maximum Allowable Deficit (MAD) levels for rice under raised bed planting and flat sowing in Pakistan

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COGENT FOOD & AGRICULTURE 2025年第1期11卷

作者： Iqbal, Shahzad Si, Qiaorui Ali, Asad Wang, Jian Abid, Muhammad Shahid, Muhammad Adnan Jiangsu Univ Natl Res Ctr Pumps Zhenjiang 212013 Peoples R China Govt Coll Univ Dept Stat Faisalabad Pakistan Univ Agr Faisalabad Dept Irrigat & Drainage Faisalabad Pakistan

Efficient water management in rice cultivation is crucial due to global freshwater scarcity and the need for sustainable agriculture. Freshwater scarcity is a growing global concern, and Pakistan, a water-scarce country, faces further reductions in available water. This study examined the effects of different Maximum Allowable Deficit (MAD) levels on rice growth and yield under raised bed and flat sowing methods. The experiment was conducted at the Water Management Research Centre, Faisalabad, Punjab, Pakistan, using a randomized complete block design with three replications and six treatments. Flat (conventional) and bed sowing methods were compared, with irrigation scheduled at MAD levels of I1 = 0%, I2 = 20%, and I3 = 40% during the 2021 and 2022 rice seasons. Treatments T4(I1) and T5(I2) used 3236 and 3248 m(3) ha(-1) of water, respectively, compared to T1(I1) and T2(I2) with 4022 and 4040 m(3) ha(-1). The highest water productivity was recorded under T4(I1) (2.94 kg m(-3)), with T5(I2) (2.90 kg m(-3)) statistically at par. Bed planting saved 28.06% more water than flat sowing. The current study advances sustainable agriculture by optimizing water use in rice cultivation, showing that raised bed-planting with controlled irrigation enhances water productivity and yield.

关键词： Water productivity Maximum Allowable Deficit randomized complete block design irrigation scheduling

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Comparison of unweighted and weighted rank based tests for an ordered alternative in randomized complete block designs

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COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION 2017年第6期46卷 4452-4464页

作者： Zhang, Hua Shan, Guogen Young, Daniel Zhejiang Gongshang Univ Sch Comp & Informat Engn Hangzhou Zhejiang Peoples R China Univ Nevada Sch Community Hlth Sci Dept Environm & Occupat Hlth Epidemiol & Biostat Program Las Vegas NV 89154 USA Univ Nevada Div Hlth Sci Las Vegas NV 89154 USA

In randomized complete block designs, a monotonic relationship among treatment groups may already be established from prior information, e.g., a study with different dose levels of a drug. The test statistic developed by Page and another from Jonckheere and Terpstra are two unweighted rank based tests used to detect ordered alternatives when the assumptions in the traditional two-way analysis of variance are not satisfied. We consider a new weighted rank based test by utilizing a weight for each subject based on the sample variance in computing the new test statistic. The new weighted rank based test is compared with the two commonly used unweighted tests with regard to power under various conditions. The weighted test is generally more powerful than the two unweighted tests when the number of treatment groups is small to moderate.

关键词： Jonckheere-Terpstra test Nonparametric test Page test randomized complete block design Repeated measurements

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A modified Friedman test for randomized complete block designs

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COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION 2017年第2期46卷 1508-1519页

作者： Xu, Jianbo Shan, Guogen Amei, Amei Zhao, Jiwei Young, Daniel Clark, Sheila Univ Nevada Dept Math Sci Nevada NV 89154 USA Univ Nevada Sch Community Hlth Sci Dept Environm & Occupat Hlth Epidemiol & Biostat Program Nevada NV 89154 USA Univ Buffalo Dept Biostat New York NY USA Univ Nevada Div Hlth Sci Las Vegas NV 89154 USA

The Friedman test is often used for a randomized complete block design when the normality assumption is not satisfied or the data are ordinal. The Friedman test can be viewed as an extension of the sign test for multiple measurements within each subject or block. We propose a modified Friedman test based on the Wilcoxon sign rank approach. Coincidentally, Tukey proposed a test statistic similar to our proposed test, but blocks are ranked by the minimum difference within each block. In the proposed test, we use the variance of block to rank the blocks, with the least variance being ranked the smallest. In both Tukey test and the modified Friedman test, linear ranks are used for blocks and treatments. The Tukey test belongs to the family of weighted-ranking test from Quade (1979).The modified Friedman test, the Friedman test and the Tukey test are compared under various conditions and the results indicate that the proposed test is generally more powerful than the Friedman test and the Tukey test when the number of groups is small.

关键词： Friedman test Nonparametric test Power study randomized complete block design Repeated measurements

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DETECTING AND HANDLING HETEROSCEDASTICITY IN YIELD TRIAL DATA

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COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION 1995年第1期24卷 243-274页

作者： PIEPHO, HP UNIV KASSEL FAC AGRD-37212 WITZENHAUSENGERMANY

Data from yield trials conducted in different environments are frequently analysed by ordinary analysis of variance. One of the preconditions for such analyses is that error variances be homogeneous across treatments and replicates. If a mixed model with fixed genotypes and random environments is assumed, genotype-environmental interaction is a random effect. For the ordinary ANOVA to be valid in this case, it is then also required that interaction variances be homogeneous for different genotypes. This paper suggests Box's correction of the ANOVA degrees of freedom for the case of heterogeneous interaction and error variances. Different estimators of the correction factors are compared via Monte Carlo simulation.

关键词： 2-WAY LAYOUT randomized complete block design HETEROSCEDASTICITY BOXS CORRECTION ANOVA TEST INTERACTION

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Assessment of dermal absorption of DEET-containing insect repellent and oxybenzone-containing sunscreen using human urinary metabolites

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ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH 2015年第9期22卷 7062-7070页

作者： Yiin, Lih-Ming Tian, Jia-Ni Hung, Chien-Che Tzu Chi Univ Dept Publ Hlth Hualien 97004 Taiwan Natl Hlth Res Inst Inst Biotechnol & Pharmaceut Res Zhunan 35053 Miaoli Taiwan Tzu Chi Univ Inst Med Sci Hualien 97004 Taiwan

Mutual enhancement of dermal absorption of N,N-diethyl-m-toluamide (DEET) and oxybenzone (OBZ) has been reported recently with DEET and OBZ being active ingredients of insect repellent and sunscreen, respectively. To assess the reported enhancing effect directly, we used human urinary metabolites as biomarkers;besides, we also sought to determine the best way for concurrent use of these two products without extra absorption of either. Four dermal application methods were used: DEET only (S1), OBZ only (S2), DEET on top of OBZ (S3), and OBZ on top of DEET (S4). Among the study methods, there was a significant difference (p = 0.013), which was attributed to the difference between S1 and S4, suggesting that applying OBZ over DEET on the skin lead to significantly higher absorption of DEET. Using both products in reverse order, (S3) did not result in extra DEET absorption significantly. As for OBZ permeation, no significant difference was observed among the methods. In summary, the enhancement of DEET absorption is confirmed for OBZ being applied over DEET on the skin;should concurrent use of both be necessary, applying sunscreen (OBZ) first and then insect repellent (DEET) with a 15-min interval is recommended.

关键词： Biomarker DEET Dermal absorption Oxybenzone randomized complete block design Urinary metabolite

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