scholarly journals SAMPLING VARIANCE FOR MOLECULAR MARKER DATA WITH RESPECT TO GENETIC DISTANCE

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 573f-573
Author(s):  
Jan Tiväng ◽  
Jim Nienhuis ◽  
O.S Smith
Keyword(s):  
Molecular Marker ◽  
Genetic Distance ◽  
Sample Size ◽  
Sampling Method ◽  
Simulation Models ◽  
Sampling Variance ◽  
Data Set ◽  
Random Simulation ◽  
Marker Data ◽  
Molecular Marker Analysis

The sampling method was applied to a data-set generated by RFLP molecular marker analysis, representing 37 Zea maize cultivars. A total of 251 enzyme probe-combinations were used yielding a total of 1,205 scores per genotype. Genetic distance was calculated among all 37 entries from subsets of arbitrary and increasing sample size. Each score entry in the subset was selected at random from all possible scores with replacement following each selection. The variance for genetic distance was calculated among all subsets of equal size for all possible cultivar pairs. The pooled pair variance was plotted and compared to random simulation models. Additional comparisons were made contrasting closely vs. distantly related cultivars.

Estimation of sampling variance of molecular marker data using the bootstrap procedure

1994 ◽  
Vol 89-89 (2-3) ◽  
pp. 259-264 ◽  
Author(s):  
J. G. Tivang ◽  
J. Nienhuis ◽  
O. S. Smith
Keyword(s):  
Molecular Marker ◽  
Sampling Variance ◽  
Bootstrap Procedure ◽  
Marker Data

PSVI-8 Meta-regression Analysis to Determine the Relationship Between Growing Pig Body Weight and Variation

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 218-219
Author(s):  
Andres Fernando T Russi ◽  
Mike D Tokach ◽  
Jason C Woodworth ◽  
Joel M DeRouchey ◽  
Robert D Goodband ◽  
...  
Keyword(s):  
Body Weight ◽  
Regression Analysis ◽  
Sample Size ◽  
Polynomial Regression ◽  
Data Sets ◽  
Regression Equations ◽  
Prediction Equations ◽  
Data Set ◽  
Rate Of Increase ◽  
The Relationship

Abstract The swine industry has been constantly evolving to select animals with improved performance traits and to minimize variation in body weight (BW) in order to meet packer specifications. Therefore, understanding variation presents an opportunity for producers to find strategies that could help reduce, manage, or deal with variation of pigs in a barn. A systematic review and meta-analysis was conducted by collecting data from multiple studies and available data sets in order to develop prediction equations for coefficient of variation (CV) and standard deviation (SD) as a function of BW. Information regarding BW variation from 16 papers was recorded to provide approximately 204 data points. Together, these data included 117,268 individually weighed pigs with a sample size that ranged from 104 to 4,108 pigs. A random-effects model with study used as a random effect was developed. Observations were weighted using sample size as an estimate for precision on the analysis, where larger data sets accounted for increased accuracy in the model. Regression equations were developed using the nlme package of R to determine the relationship between BW and its variation. Polynomial regression analysis was conducted separately for each variation measurement. When CV was reported in the data set, SD was calculated and vice versa. The resulting prediction equations were: CV (%) = 20.04 – 0.135 × (BW) + 0.00043 × (BW)2, R2=0.79; SD = 0.41 + 0.150 × (BW) - 0.00041 × (BW)2, R2 = 0.95. These equations suggest that there is evidence for a decreasing quadratic relationship between mean CV of a population and BW of pigs whereby the rate of decrease is smaller as mean pig BW increases from birth to market. Conversely, the rate of increase of SD of a population of pigs is smaller as mean pig BW increases from birth to market.

scholarly journals Optimal breeding-value prediction using a Sparse Selection Index

Genetics ◽  
2021 ◽  
Author(s):  
Marco Lopez-Cruz ◽  
Gustavo de los Campos
Keyword(s):  
Sample Size ◽  
Dna Sequences ◽  
Genomic Prediction ◽  
Prediction Accuracy ◽  
Regularization Parameter ◽  
Selection Index ◽  
Prediction Method ◽  
Training Data ◽  
Breeding Value ◽  
Data Set

Abstract Genomic prediction uses DNA sequences and phenotypes to predict genetic values. In homogeneous populations, theory indicates that the accuracy of genomic prediction increases with sample size. However, differences in allele frequencies and in linkage disequilibrium patterns can lead to heterogeneity in SNP effects. In this context, calibrating genomic predictions using a large, potentially heterogeneous, training data set may not lead to optimal prediction accuracy. Some studies tried to address this sample size/homogeneity trade-off using training set optimization algorithms; however, this approach assumes that a single training data set is optimum for all individuals in the prediction set. Here, we propose an approach that identifies, for each individual in the prediction set, a subset from the training data (i.e., a set of support points) from which predictions are derived. The methodology that we propose is a Sparse Selection Index (SSI) that integrates Selection Index methodology with sparsity-inducing techniques commonly used for high-dimensional regression. The sparsity of the resulting index is controlled by a regularization parameter (λ); the G-BLUP (the prediction method most commonly used in plant and animal breeding) appears as a special case which happens when λ = 0. In this study, we present the methodology and demonstrate (using two wheat data sets with phenotypes collected in ten different environments) that the SSI can achieve significant (anywhere between 5-10%) gains in prediction accuracy relative to the G-BLUP.

Molecular marker analysis of F1 progenies and their parents for carotenoids inheritance in African cassava (Manihot esculenta Crantz)

2014 ◽  
Vol 13 (40) ◽  
pp. 3999-4007 ◽  
Author(s):  
D. N. Njoku, ◽  
V. E Gracen, ◽  
S. K. Offei, ◽  
I. K. Asante, ◽  
E. Y. Danquah, ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Manihot Esculenta ◽  
Manihot Esculenta Crantz ◽  
Marker Analysis ◽  
Molecular Marker Analysis

scholarly journals Examination of Different Item Response Theory Models on Tests Composed of Testlets

2017 ◽  
Vol 6 (4) ◽  
pp. 113
Author(s):  
Esin Yilmaz Kogar ◽  
Hülya Kelecioglu
Keyword(s):  
Item Response Theory ◽  
Sample Size ◽  
Item Response ◽  
Data Sets ◽  
Meaningful Difference ◽  
Response Theory ◽  
Size Change ◽  
Data Set ◽  
Testlet Response Theory ◽  
Item Response Theory Models

The purpose of this research is to first estimate the item and ability parameters and the standard error values related to those parameters obtained from Unidimensional Item Response Theory (UIRT), bifactor (BIF) and Testlet Response Theory models (TRT) in the tests including testlets, when the number of testlets, number of independent items, and sample size change, and then to compare the obtained results. Mathematic test in PISA 2012 was employed as the data collection tool, and 36 items were used to constitute six different data sets containing different numbers of testlets and independent items. Subsequently, from these constituted data sets, three different sample sizes of 250, 500 and 1000 persons were selected randomly. When the findings of the research were examined, it was determined that, generally the lowest mean error values were those obtained from UIRT, and TRT yielded a mean of error estimation lower than that of BIF. It was found that, under all conditions, models which take into consideration the local dependency have provided a better model-data compatibility than UIRT, generally there is no meaningful difference between BIF and TRT, and both models can be used for those data sets. It can be said that when there is a meaningful difference between those two models, generally BIF yields a better result. In addition, it has been determined that, in each sample size and data set, item and ability parameters and correlations of errors of the parameters are generally high.

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