Physical Sciences and Mathematics Commons^™

An Introduction To Model Selection For Quantitative Trait Locus Analysis In Polyploids, R. W. Doerge, Bruce A. Craig

Conference on Applied Statistics in Agriculture

Substantial gains have been made in locating regions of agricultural genomes associated with characteristics, diseases, and agroeconomic traits. These gains have relied heavily on the ability to estimate the association between DNA markers and regions of a genome (quantitative trait loci or QTL) related to a particular trait. The majority of these advances have focused on diploid species (two homologous chromosomes per set), even though many important agricultural crops are, in fact, polyploid (more than two homologous chromosomes per set). The purpose of our work is to initiate an algorithmic approach for model selection and QTL detection in polyploid species. …

A Fertilizer-Rate Experiment Involving Young Citrus Trees: Does More Fertilizer Mean Higher Producing Trees?, John A. Cornell

Conference on Applied Statistics in Agriculture

Citrus growers are interested in making money. So, the most common practice among growers is to push young trees into early production by the application of high amounts (rates) of fertilizer. This practice can lead to disaster in terms of tree formation (canopy shape) and production stress. In contrast, when the applied fertilizer approaches both the optimum rate and the optimum N -P -K -Ca ratio for citrus, then the trees are more uniform in size and with compact canopies and the incidence of decline is less. Cordieropolis station in Sao Paula, Brazil, is the site of a large 3-component …

Editor's Preface, Table Of Contents, And List Of Attendees, George A. Milliken

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the twelfth annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 30-May 2, 2000..

Changes In Alfalfa Breeding — Where Is Alfalfa Headed?, Becky Greenwald

Kentucky Alfalfa and Stored Forage Conference

Alfalfa didn't earn the title "Queen of the Forages" just because of its good looks on rolling hills or sweet smell at harvest. Alfalfa was first described nearly 2,500 years ago, in 490 B.C in the desert regions of what is now Iran. From the Middle East, alfalfa was taken into Europe and South America by invading armies, explorers, and missionaries.

Little Known Facts About Alfalfa, Don Ball

Kentucky Alfalfa and Stored Forage Conference

During the previous nineteen Kentucky Alfalfa Conferences, many topics pertaining to alfalfa have undoubtedly been addressed. In fact, some topics such as establishment techniques, varieties, and factors affecting yield are important enough that they have probably been discussed in one form or another during most of these conferences.

However, a twentieth-year state commodity conference is a milestone that deserves some special consideration, and which should justify inclusion of one or more unique topics on the program. This line of thinking led to idea that for this presentation it might be interesting to discuss some facts about alfalfa that are not …

Reducing Alfalfa Harvesting Losses, Michael Collins

Kentucky Alfalfa and Stored Forage Conference

In some areas of the country, producers store a substantial portion of their forage for winter feeding as silage or haylage. However, hay remains the most popular storage method for forage. Hay stores well for long periods and is better suited to cash sale and transportation than silage. Mechanical conditioning, which gained acceptance during the 1950's is probably still the greatest single change in hay harvesting and storage technology during this century. However, a number of other noteworthy changes and innovations have occurred in recent years which have helped to reduce the extent of losses during hay harvesting and storage.

Opportunities For Alfalfa As A Grazing Crop In Kentucky, Ken Johnson

Kentucky Alfalfa and Stored Forage Conference

Why do we continue to hear people talk about Alfalfa as a grazing crop? In my opinion there are two words that come to mind when I think of grazing Alfalfa, quality and yield. Alfalfa is without a doubt the highest quality forage we can graze. Alfalfa is also one of the highest yielding forages we can graze and maybe the highest yielding widely known and widely grown forage available to Kentucky farmers.

Hay Testing And New Marketing Program, Allen Johnson

Kentucky Alfalfa and Stored Forage Conference

The Kentucky Department of Agriculture (Hay & Grain Branch) Hay testing program is now entering its 13^th year of testing hay for Kentucky producers. The Department continues to use NIR forage analysis equipment. The program has made many improvements and much information has been gained. We continue to strive for quality control and producing accurate results. Recently, many new updates have occurred. New hardware and software have been added, along with the recent purchase of a second hay testing van. By placing a toll free call (1-800- 248-4628) to the Department of Agriculture in Frankfort, we will find a …

An Alfalfa Disease Calendar, Paul Vincelli

Kentucky Alfalfa and Stored Forage Conference

The following calendar provides producers and agricultural professionals with insights that may improve alfalfa production in several ways. First, knowing when to expect certain diseases improves one's ability to diagnose disease problems, which is a fundamental foundation for disease management. The many UK Extension Service publications on alfalfa as well as publications like the Alfalfa Analyst and the Compendium of Alfalfa Diseases, all are useful for diagnosis, but none provides a precise calendar of when to expect activity of alfalfa diseases in Kentucky. An alfalfa disease calendar can also provide occasional insights into timely management practices. For example, being …

Fertilizing Alfalfa For Profit, Monroe Rasnake, Steven G. Isaacs

Kentucky Alfalfa and Stored Forage Conference

Alfalfa has the potential for producing high yields of high quality forage with good management. A key component of good management is supplying plant nutrients in adequate quantities and proper balance. In Kentucky, this requires fertilizing soils with agricultural limestone, commercial fertilizers and/or animal manures. Good soil fertility is necessary for alfalfa stand establishment, high yields and long stand life.

Kentucky Alfalfa Conference After Twenty Years, Garry D. Lacefield

Kentucky Alfalfa and Stored Forage Conference

Today marks the 20th consecutive year we have come together for a full days conference featuring "Alfalfa- Queen of the Forages" as the theme and focal point. Only one other state in the U.S. has such an annual event.

Foreword [2000], Garry D. Lacefield

Kentucky Alfalfa and Stored Forage Conference

This is the front matter of the proceedings.

The Power Of Structured Designs And Mixed Models In A Real World Experiment, J. C. Galland, G. A. Milliken, D. R. Hyatt, M. Hornback, K. Cudjoe

Conference on Applied Statistics in Agriculture

Justifications usually given for adopting an automated system pertain to a reduction in labor and an improvement in quality control. A manufacturer of a prototype instrument that automated some of the steps for culturing bacteria wanted to compare the automated system to the manual system. The manufacturer wanted to compare the two systems in 1) Total time needed to isolate the target bacteria, 2) Ability to isolate the target bacteria, 3) Amount of interference from background (non-target) bacterial growth, and 1) Extent of cross (sample to sample) contamination.

This paper presents the experimental design used to make these comparisons and …

Investigating Power Of Analysis Of Covariance Methods, James R. Schwenke, J. Mark Donovan

Conference on Applied Statistics in Agriculture

Analysis of covariance is a well-utilized statistical methodology. The procedure involves a series of statistical tests to first construct a most significant analysis model to characterize the effect of the covariate on response. Pairwise comparisons among treatments are then based on the finalized model.

For traditional Normal error assumptions, each step of the process is based on exact statistical tests. However, the series of statistical tests defines a conditional probability scheme with possible multiplicity issues. The question then becomes if the analysis of covariance methodology considered in entirety is able to maintain a nominal level of significance with good power. …

Starting Values For Proc Mixed With Repeated Measures Data, J. C. Recknor, W. W. Stroup

Conference on Applied Statistics in Agriculture

A major advantage of PROC MIXED for repeated measures data is that one could choose from many different correlated error models. However, MIXED uses default starting values that may cause difficulty obtaining REML estimates of the covariance parameters for several of the models available. This can take the form of excessively long run times or even failure to converge. We have written a program to obtain initial covariance parameter estimates that result in greatly improved performance of the REML algorithm. We will use two covariance models frequently of interest in animal health experiments, the first-order ante-dependence model [ANTE(l)] and the …

Analysis Of Genotype-By-Environment Interaction With Ammi Models Using Sas Proc Mixed, Raul E. Macchiavelli, James S. Beaver

Conference on Applied Statistics in Agriculture

Genotype-by-environment (GE) interaction can be analyzed using different approaches. Among these, the additive main effects and multiplicative interaction model yields useful interpretations and can be applied successfully to plant breeding programs. In this paper we review fitting strategies for this model and show how to combine the capabilities of the Mixed and IML procedures in SAS to fit this model. This permits straightforward use of likelihood-based inference in standard and non standard situations like complex experimental designs. The proposed procedures were applied to data from red mottled bean variety trials conducted in the Dominican Republic and Puerto Rico in 9 …

The Analysis Of Count Data In A One-Way Layout, Yuhua Wang, Dallas E. Johnson, Linda J . Young

Conference on Applied Statistics in Agriculture

An efficient score statistic for testing the equality of the means of several groups of count data in the presence of a common dispersion parameter is introduced and a new approximation to its distribution is given. The performance of the efficient score statistic using this approximation, the original efficient score statistic approximated by X ² (t -1), the likelihood ratio statistic and four more ANOVA methods based on raw data or transformed data are compared in terms of size and power by using Monte Carlo simulations. The efficient score statistic with its new approximation is recommended. An application is given.

Hydrological Normalization Of Nutrient Deliveries From Agricultural Catchments, Per Stalnacke, Anders Grimvall

Conference on Applied Statistics in Agriculture

Nutrient deliveries from agricultural catchments are strongly influenced by natural fluctuations in water discharge. Hydrological normalization of such data may therefore facilitate estimation of human impact on the environment. In the present study, we compared conventional statistical normalization techniques with a recently proposed, semi-parametric regression technique, which can accommodate time-dependent relationships between nutrient deliveries and water discharge. Case studies of agricultural catchments in Sweden and Norway demonstrated that all of the tested normalization techniques were able to remove a substantial fraction of the interannual variation in nitrogen deliveries, whereas normalization of phosphorus loads was problematic. Semi-parametric regression models were found …

A Computationally Efficient Method For Determining Significance In Interval Mapping Of Quantitative Trait Loci, Dan Nettleton

Conference on Applied Statistics in Agriculture

This paper provides a brief introduction to the mapping of quantitative trait loci (QTL). An example on mapping QTL for root thickness in rice is presented to illustrate popular statistical methods used in QTL mapping. Interval mapping is used in conjunction with permutation testing techniques to detect significant associations between genetic positions and quantitative traits while controlling overall type I error rate. A review of a recent technique that can greatly reduce the computational expense of permutation testing in QTL mapping is discussed. Theory is provided for an extension of recent results that may lead to more powerful methods of …

An Improved Estimator For Assessing The Measure Of Agreement With A Gold Standard, Brent D. Burch, Ian R. Harris, Roy T. St. Laurent

Conference on Applied Statistics in Agriculture

St. Laurent (1998, Biometrics 54, 537-545) developed a measure of agreement for method comparison studies in which an approximate method of measurement is compared to a gold standard method of measurement. The measure of agreement proposed was shown to be related to a population intraclass correlation coefficient. This paper develops a family of estimators for the measure of agreement based on pivotal quantities. A blend of two particular members of the family is suggested as an estimator itself. In general, this estimator outperforms the maximum likelihood estimator in terms of bias and mean-squared error.

Nonlinear Models For Multi-Factor Plant Nutrition Experiments, R. D. Landes, W. W. Stroup, E. T. Paparozzi, M. E. Conley

Conference on Applied Statistics in Agriculture

Plant scientists are interested in measuring plant response to quantitative treatment factors, e.g. amount of nutrient applied. Response surface methods are often used for experiments with multiple quantitative factors. However, in many plant nutrition studies, second-order response surface models result in unacceptable lack of fit. This paper explores multi-factor nonlinear models as an alternative. We have developed multi-factor extensions of Mitscherlich and Gompertz models, and fit them to data from experiments conducted at the University of Nebraska-Lincoln Horticulture department. These data are typical of experiments for which conventional response surface models perform poorly. We propose design selection strategies to facilitate …

Using Isotonic Regression To Improve Estimation In Factorial Experiments With Ordered Factor Levels, Matt Strand, Jim Higgins

Conference on Applied Statistics in Agriculture

In many designed experiments in agriculture and the life sciences, a researcher can anticipate the direction that responses will take when treatments are varied. For example, in a 2-way factorial, a researcher may know that increasing the levels of nitrogen and phosphorus will increase yields of a crop. Classical analysis of variance does not take into account a known ordering among population means. However, it can be shown that by restricting the estimates of means to have the same ordering as the anticipated ordering of population means, a reduction in mean-squared errors of estimators will likely occur, often by more …

Characterizing The Statistical Distribution Of Organic Carbon And Extractable Phosphorus At A Regional Scale, John J. Brejda, David W. Meek, Douglas L. Karlen

Conference on Applied Statistics in Agriculture

Greater awareness of potential environmental problems has created the need to monitor total organic carbon (TOC) and extractable phosphorus (P) concentrations at a regional scale. The probability distribution of these soil properties can have a significant effect on the power of statistical tests and the quality of inferences applied to these properties. The objectives of this study were to: (1) evaluate the probability distribution of TOC and extractable P at the regional scale in three Major Land Resource Areas (MLRA), and (2) identify appropriate transformations that will result in a normal distribution. Both TOC and extractable P were non-normally distributed …

Analysis Of Nuclei Fluorescence Histograms Using Non-Linear Functions Or Wavelets, Susanne Aref, Maria Kocherginsky, Carrie A. Northcott, Lane A. Rayburn

Conference on Applied Statistics in Agriculture

Histograms based on 5,000 nuclei from cells (Chinese hamster ovary cells, bone marrow cells) are used to determine the coefficient of variation (CV) of observations surrounding the highest peak. The cells are subjected to various treatments, for example exposure to herbicides. By eyeballing the histogram, an interval under the highest peak is determined. The CV calculated from the histogram on the eyeballed interval is the response variable in an ANOVA. To avoid the subjectivity of eyeballing the histogram, non-linear functions such as the Gaussian density function can be used to model the histogram. The CV may then be determined from …

On Using Proc Mixed For Longitudinal Data, Walter W. Stroup

Conference on Applied Statistics in Agriculture

PROC MIXED has become a standard tool for analyzing repeated measures data. Its popularity results from a wide choice of correlated error models compared to other software, e.g. PROC GLM. However, PROC MIXED's versatility comes at a price. Users must take care. Problems may result from MIXED defaults. These include: questionable criteria for selecting correlated error models; starting values that may impede REML estimation of covariance components; and biased standard errors and test statistics. Problems may be induced by inadequate design. This paper is a survey of current knowledge about mixed model methods for repeated measures. Examples are presented using …

Modeling The Fate Of Toxic Chemicals In Soils, Anabayan Kessavalou, Anne M. Parkhurst

Conference on Applied Statistics in Agriculture

Studies on the fate of toxic chemicals in soils are often reported with a minimum of descriptive statistics. Use of modeling techniques to describe the kinetics of chemical degradation provides a better understanding of the fate of chemicals in soil systems. When modeling nonlinear systems, assumptions made about the error term greatly influence the parameter estimation. Inappropriate use of linearization and failure to account for autocorrelated errors may result in inaccurate models. Information is also needed about the effects of the magnitude of autocorrelation on parameter estimation. The exponential decay function was chosen to fit the data obtained from a …

Estimating The Likelihood Of Yellow Starthistle Occurrence Using An Empirically Derived Nonlinear Regression Model, Bahman Shafii, William J. Price, Lawrence W. Lass, Donn C. Thill

Conference on Applied Statistics in Agriculture

Yellow starthistle is a noxious weed common in the semiarid climate of Central Idaho and other western states. Early detection of yellow starthistle and predicting its infestation potential have important scientific and managerial implications. Weed detection and delineation are often carried out by visual observation or survey techniques. However, such methods may be ineffective in detecting sparse infestations. The distribution of yellow starthistle over a large region may be affected by various exogenous variables such as elevation, slope and aspect. These landscape variables can be used to develop prediction models to estimate the potential invasion of yellow starthistle into new …

Statistics In The New Millennium: Some Personal Views, Bryan F.J. Manly

Conference on Applied Statistics in Agriculture

In this paper I discuss three topics that I believe are relevant to the subject of statistics in the new millennium: (a) the impact of computers, and the state of computer-intensive methods as far as practical applications of statistics are concerned; (b) methods for the analysis of the extremely large data sets that are now becoming available; and (c) the use of statistics by scientists in general. For the first topic I suggest that the main advantage of computer-intensive methods is that they can under certain circumstances give simple and believable answers to questions when other methods fail. However, I …

Editor's Preface And Table Of Contents, George A. Milliken

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the eleventh annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 25-27, 1999.

Marketing Alfalfa Hay: What The Consumer Demands, Tom Keene

Kentucky Alfalfa and Stored Forage Conference

Anytime we address selling a product to the consumer; our first objective should always be to sell a quality product. However before we get into quality, I think we need to back up and understand that quality can vary from customer to customer depending upon the type of livestock he is feeding. For instance, if you are selling hay to a dairy operation, how is the hay being utilized? Is it being fed free choice? Is it going into a milking TMR (total mixed ration)? Is it going to feed young stock, breeding heifers, or sick animals? Each group of …