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Some Methods For Analyzing Multi Trait Genotype By Environment Interactions
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Book Synopsis Some Methods for Analyzing Multi-trait Genotype-by-environment Interactions by : Muhammad Yaseen
Download or read book Some Methods for Analyzing Multi-trait Genotype-by-environment Interactions written by Muhammad Yaseen and published by . This book was released on 2012 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling complex interactions involving multiple response variables is a difficult problem. Response variables are often correlated with each other, have causal relationships and are influenced by factor main effects, interactions and covariates. When analyzing these types of data, the covariance(s) and causal structure among the traits and the random structure due to factor and/or the experimental design should be taken into consideration. Ignoring anyone or more of them, during the analysis process, can limit the scope of the analysis and reduce the inference space. Modeling both causal structure and random structure is difficult and either totally ignored or estimated via Bayesian methods. Use of a classical mixed model framework has been avoided since causal modeling is often considered too complex. We propose a simple modification to the classical causal model that allows using restricted maximum likelihood (REML) to estimate both causal and random structures. We call this model a linear system with random effects (LSRE) and we show it has good statistical properties in that the estimates are consistent and asymptotically normal. The LSRE model is a special form of the multivariate linear mixed model that can be fitted with methods for multivariate linear mixed models using the modified Cholesky decomposition. The proposed model can account for complex covariance structures due to random effects and/or the experimental design and can fit recursive causal structures among the traits simultaneously. This model also allows incorporation of any correlation structure among the observations. This model can be used to produce BLUPs that when used with other methods, e.g. Tucker's three mode decomposition, give increased explanatory power compared to traditional fixed effects methods. Tucker's three mode decomposition breaks down the three-way interaction into a smaller number of multiplicative terms with the presumption that most of the three-way interaction can be explained by the first few meaningful components of each mode. BLUPs shrink towards their means and therefore, the predictors are smoother than means obtained using fixed effects approaches and has additional advantage over the means approaches when data are unbalanced or missing.^ The LSRE model was implemented on simulated data and a real wheat genetics data set. The analysis on simulated data gave results very close to the true parameters. The results obtained from real data set made biological sense and provided a clearer understanding than traditional methods for the analysis of genotype-by-environment interaction in wheat.
Download or read book GGE Biplot Analysis written by Weikai Yan and published by CRC Press. This book was released on 2002-08-28 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research data is expensive and precious, yet it is seldom fully utilized due to our ability of comprehension. Graphical display is desirable, if not absolutely necessary, for fully understanding large data sets with complex interconnectedness and interactions. The newly developed GGE biplot methodology is a superior approach to the graphical analys
Book Synopsis Genotype by Environment Interaction by : Manjit S. Kang
Download or read book Genotype by Environment Interaction written by Manjit S. Kang and published by CRC-Press. This book was released on 1996-02-06 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genotype-by-Environment Interaction (GEI) is a prevalent issue among crop farmers, plant breeders, geneticists, and production agronomists. This book brings together contributions from expert plant breeders and quantitative geneticists to better understand the relationship between crop performance and environment. This information can reduce the cost of extensive genotype evaluation by eliminating unnecessary testing sites and by fine-tuning breeding programs. Molecular aspects of GEI are discussed for the first time and key bibliographical references on GEI are included in an appendix.
Book Synopsis Statistical Analysis of Regional Yield Trials: AMMI Analysis of Factorial Designs by : Hugh G. Gauch (Jr.)
Download or read book Statistical Analysis of Regional Yield Trials: AMMI Analysis of Factorial Designs written by Hugh G. Gauch (Jr.) and published by . This book was released on 1992-11-06 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Basic statistical concepts. AMMI and related models. Estimation. Selection. Modeling. Efficient experiments.
Book Synopsis Adaptation and Fitness in Animal Populations by : Julius van der Werf
Download or read book Adaptation and Fitness in Animal Populations written by Julius van der Werf and published by Springer Science & Business Media. This book was released on 2008-10-17 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fitness and adaptation are fundamental characteristics of plant and animal species, enabling them to survive in their environment and to adapt to the inevitable changes in this environment. This is true for both the genetic resources of natural ecosystems as well as those used in agricultural production. Extensive genetic variation exists between varieties/breeds in a species and amongst individuals within breeds. This variation has developed over very long periods of time. A major ongoing challenge is how to best utilize this variation to meet short-term demands whilst also conserving it for longer-term possible use. Many animal breeding programs have led to increased performance for production traits but this has often been accompanied by reduced fitness. In addition, the global use of genetic resources prompts the question whether introduced genotypes are adapted to local production systems. Understanding the genetic nature of fitness and adaptation will enable us to better manage genetic resources allowing us to make efficient and sustainable decisions for the improvement or breeding of these resources. This book had an ambitious goal in bringing together a sample of the world’s leading scientists in animal breeding and evolutionary genetics to exchange knowledge to advance our understanding of these vital issues.
Book Synopsis Gene-Environment Interaction Analysis by : Sumiko Anno
Download or read book Gene-Environment Interaction Analysis written by Sumiko Anno and published by CRC Press. This book was released on 2016-03-30 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene-environment (GE) interaction analysis is a statistical method for clarifying GE interactions applicable to a phenotype or a disease that is the result of interactions between genes and the environment. This book is the first to deal with the theme of GE interaction analysis. It compiles and details cutting-edge research in bioinformatics
Book Synopsis Applied Quantitative Genetics by : Manjit S. Kang
Download or read book Applied Quantitative Genetics written by Manjit S. Kang and published by . This book was released on 1994 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: APPLIED QUANTITATIVE GENETICS resulted from several years of teaching a graduate course on Quantitative Genetics in Plant Improvement. This book fills a critical need in that it presents topics for students from a practical standpoint & makes available some essential computer software. The book should also be useful to teachers & researchers in the areas of quantitative genetics & plant breeding. This publication covers the following topics: 1. Gene Action, genetic variances & effects, & mean; 2. Inbreeding & mating designs; 3. Diallel analyses; 4 . Generation mean analysis; 5. North Carolina designs I, II, III; 6. Path coefficient analysis; 7. Heritability & selection; 8. Heterosis; 9. Genotype-by- environment interaction & stability analyses; & 10. Locating quantitative trait loci. The book places special emphasis on Diallel analyses, Stability analyses, & locating quantitative trait loci; these three important topics either have not been covered at all or have been inadequately covered in currently available texts. The book is available for $28.50 (shipping & handling included) to individuals or libraries. For students or for orders of four or more copies, the cost is $24.50 per book. Payment in full may be sent to Dr. M. S. Kang, 2477 Creekside Dr., Baton Rouge, LA 70810- 6966.
Book Synopsis Genotype X Environment Interactions by : Paolo Annicchiarico
Download or read book Genotype X Environment Interactions written by Paolo Annicchiarico and published by Food & Agriculture Org.. This book was released on 2002 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt: The projected increase in world population levels and the subsequent rise in food demand represents a huge challenge for agricultural production systems worldwide. This publication examines the opportunities and challenges raised by the use of plant genetic resources and highlights the contribution that data from multi-environment yield trials can provide for the definition of adaptation strategies and yield stability targets in plant breeding programmes. It contains a case study about a durum wheat crop programme in Algeria, and also includes a CD-ROM with data from IRRISTAT, a programme developed by the International Rice Research Institute (IRRI).
Book Synopsis Genetic Data Analysis for Plant and Animal Breeding by : Fikret Isik
Download or read book Genetic Data Analysis for Plant and Animal Breeding written by Fikret Isik and published by Springer. This book was released on 2017-09-09 with total page 409 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book fills the gap between textbooks of quantitative genetic theory, and software manuals that provide details on analytical methods but little context or perspective on which methods may be most appropriate for a particular application. Accordingly this book is composed of two sections. The first section (Chapters 1 to 8) covers topics of classical phenotypic data analysis for prediction of breeding values in animal and plant breeding programs. In the second section (Chapters 9 to 13) we provide the concept and overall review of available tools for using DNA markers for predictions of genetic merits in breeding populations. With advances in DNA sequencing technologies, genomic data, especially single nucleotide polymorphism (SNP) markers, have become available for animal and plant breeding programs in recent years. Analysis of DNA markers for prediction of genetic merit is a relatively new and active research area. The algorithms and software to implement these algorithms are changing rapidly. This section represents state-of-the-art knowledge on the tools and technologies available for genetic analysis of plants and animals. However, readers should be aware that the methods or statistical packages covered here may not be available or they might be out of date in a few years. Ultimately the book is intended for professional breeders interested in utilizing these tools and approaches in their breeding programs. Lastly, we anticipate the usage of this volume for advanced level graduate courses in agricultural and breeding courses.
Book Synopsis The Oxford Handbook of Quantitative Methods in Psychology: Vol. 2 by : Todd D. Little
Download or read book The Oxford Handbook of Quantitative Methods in Psychology: Vol. 2 written by Todd D. Little and published by . This book was released on 2013-03-21 with total page 785 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Oxford Handbook of Quantitative Methods in Psychology provides an accessible and comprehensive review of the current state-of-the-science and a one-stop source for learning and reviewing current best-practices in a quantitative methods across the social, behavioral, and educational sciences.
Book Synopsis Wheat Landraces by : Nusret Zencirci
Download or read book Wheat Landraces written by Nusret Zencirci and published by Springer Nature. This book was released on 2021-09-15 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Landraces possess a very large genetic base in population structure and are dynamic populations of cultivated plants with historical origin, distinct identity, and without any formal crop improvement. They are often genetically diverse, locally adapted, and associated with traditional farming systems. Resistance genes to biotic and abiotic stress factors, which are especially diversified in landraces, are of great interest to plant breeders, faced with global climate challenge. In addition, gene pools made of different landraces grown in different ecological conditions can be used for wheat breeding to enhance quality; yield and other desirable agricultural parameters. An estimated 75% of the genetic diversity of crop plants was lost in the last century due to the replacement of high yielding modern varieties. There is, thus, an urgent need to preserve existing species, not only for posterity but also as a means to secure food supply for a rising world population. In this book, we provide an overview of wheat landraces with special attention to genetic diversities, conservation, and utilization.
Book Synopsis Genetics and Analysis of Quantitative Traits by : Michael Lynch
Download or read book Genetics and Analysis of Quantitative Traits written by Michael Lynch and published by Sinauer Associates Incorporated. This book was released on 1998-01 with total page 980 pages. Available in PDF, EPUB and Kindle. Book excerpt: Professors Lynch and Walsh bring together the diverse array of theoretical and empirical applications of quantitative genetics in a work that is comprehensive and accessible to anyone with a rudimentary understanding of statistics and genetics.
Book Synopsis Genome-Wide Association Studies and Genomic Prediction by : Cedric Gondro
Download or read book Genome-Wide Association Studies and Genomic Prediction written by Cedric Gondro and published by Humana Press. This book was released on 2013-06-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the detailed genomic information that is now becoming available, we have a plethora of data that allows researchers to address questions in a variety of areas. Genome-wide association studies (GWAS) have become a vital approach to identify candidate regions associated with complex diseases in human medicine, production traits in agriculture, and variation in wild populations. Genomic prediction goes a step further, attempting to predict phenotypic variation in these traits from genomic information. Genome-Wide Association Studies and Genomic Prediction pulls together expert contributions to address this important area of study. The volume begins with a section covering the phenotypes of interest as well as design issues for GWAS, then moves on to discuss efficient computational methods to store and handle large datasets, quality control measures, phasing, haplotype inference, and imputation. Later chapters deal with statistical approaches to data analysis where the experimental objective is either to confirm the biology by identifying genomic regions associated to a trait or to use the data to make genomic predictions about a future phenotypic outcome (e.g. predict onset of disease). As part of the Methods in Molecular Biology series, chapters provide helpful, real-world implementation advice.
Book Synopsis Forest Genetics by : Timothy L. White
Download or read book Forest Genetics written by Timothy L. White and published by Cabi. This book was released on 2007 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, which contains 20 chapters, integrates the varied subdisciplines of genetics and their applications in gene conservation, tree improvement and biotechnology. Topics covered include: genetic variation in natural forests, the application of genetics in tree improvement and breeding programmes, and genomic sequences and molecular technologies. This book will be a valuable resource for students, scientists and professionals in the plant sciences, especially forest geneticists, tree breeders, forest managers and other natural resource specialists.
Book Synopsis Handbook of Statistical Genomics by : David J. Balding
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Book Synopsis Quantitative Genetics in Maize Breeding by : Arnel R. Hallauer
Download or read book Quantitative Genetics in Maize Breeding written by Arnel R. Hallauer and published by Springer Science & Business Media. This book was released on 2010-09-28 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Maize is used in an endless list of products that are directly or indirectly related to human nutrition and food security. Maize is grown in producer farms, farmers depend on genetically improved cultivars, and maize breeders develop improved maize cultivars for farmers. Nikolai I. Vavilov defined plant breeding as plant evolution directed by man. Among crops, maize is one of the most successful examples for breeder-directed evolution. Maize is a cross-pollinated species with unique and separate male and female organs allowing techniques from both self and cross-pollinated crops to be utilized. As a consequence, a diverse set of breeding methods can be utilized for the development of various maize cultivar types for all economic conditions (e.g., improved populations, inbred lines, and their hybrids for different types of markets). Maize breeding is the science of maize cultivar development. Public investment in maize breeding from 1865 to 1996 was $3 billion (Crosbie et al., 2004) and the return on investment was $260 billion as a consequence of applied maize breeding, even without full understanding of the genetic basis of heterosis. The principles of quantitative genetics have been successfully applied by maize breeders worldwide to adapt and improve germplasm sources of cultivars for very simple traits (e.g. maize flowering) and very complex ones (e.g., grain yield). For instance, genomic efforts have isolated early-maturing genes and QTL for potential MAS but very simple and low cost phenotypic efforts have caused significant and fast genetic progress across genotypes moving elite tropical and late temperate maize northward with minimal investment. Quantitative genetics has allowed the integration of pre-breeding with cultivar development by characterizing populations genetically, adapting them to places never thought of (e.g., tropical to short-seasons), improving them by all sorts of intra- and inter-population recurrent selection methods, extracting lines with more probability of success, and exploiting inbreeding and heterosis. Quantitative genetics in maize breeding has improved the odds of developing outstanding maize cultivars from genetically broad based improved populations such as B73. The inbred-hybrid concept in maize was a public sector invention 100 years ago and it is still considered one of the greatest achievements in plant breeding. Maize hybrids grown by farmers today are still produced following this methodology and there is still no limit to genetic improvement when most genes are targeted in the breeding process. Heterotic effects are unique for each hybrid and exotic genetic materials (e.g., tropical, early maturing) carry useful alleles for complex traits not present in the B73 genome just sequenced while increasing the genetic diversity of U.S. hybrids. Breeding programs based on classical quantitative genetics and selection methods will be the basis for proving theoretical approaches on breeding plans based on molecular markers. Mating designs still offer large sample sizes when compared to QTL approaches and there is still a need to successful integration of these methods. There is a need to increase the genetic diversity of maize hybrids available in the market (e.g., there is a need to increase the number of early maturing testers in the northern U.S.). Public programs can still develop new and genetically diverse products not available in industry. However, public U.S. maize breeding programs have either been discontinued or are eroding because of decreasing state and federal funding toward basic science. Future significant genetic gains in maize are dependent on the incorporation of useful and unique genetic diversity not available in industry (e.g., NDSU EarlyGEM lines). The integration of pre-breeding methods with cultivar development should enhance future breeding efforts to maintain active public breeding programs not only adapting and improving genetically broad-based germplasm but also developing unique products and training the next generation of maize breeders producing research dissertations directly linked to breeding programs. This is especially important in areas where commercial hybrids are not locally bred. More than ever public and private institutions are encouraged to cooperate in order to share breeding rights, research goals, winter nurseries, managed stress environments, and latest technology for the benefit of producing the best possible hybrids for farmers with the least cost. We have the opportunity to link both classical and modern technology for the benefit of breeding in close cooperation with industry without the need for investing in academic labs and time (e.g., industry labs take a week vs months/years in academic labs for the same work). This volume, as part of the Handbook of Plant Breeding series, aims to increase awareness of the relative value and impact of maize breeding for food, feed, and fuel security. Without breeding programs continuously developing improved germplasm, no technology can develop improved cultivars. Quantitative Genetics in Maize Breeding presents principles and data that can be applied to maximize genetic improvement of germplasm and develop superior genotypes in different crops. The topics included should be of interest of graduate students and breeders conducting research not only on breeding and selection methods but also developing pure lines and hybrid cultivars in crop species. This volume is a unique and permanent contribution to breeders, geneticists, students, policy makers, and land-grant institutions still promoting quality research in applied plant breeding as opposed to promoting grant monies and indirect costs at any short-term cost. The book is dedicated to those who envision the development of the next generation of cultivars with less need of water and inputs, with better nutrition; and with higher percentages of exotic germplasm as well as those that pursue independent research goals before searching for funding. Scientists are encouraged to use all possible breeding methodologies available (e.g., transgenics, classical breeding, MAS, and all possible combinations could be used with specific sound long and short-term goals on mind) once germplasm is chosen making wise decisions with proven and scientifically sound technologies for assisting current breeding efforts depending on the particular trait under selection. Arnel R. Hallauer is C. F. Curtiss Distinguished Professor in Agriculture (Emeritus) at Iowa State University (ISU). Dr. Hallauer has led maize-breeding research for mid-season maturity at ISU since 1958. His work has had a worldwide impact on plant-breeding programs, industry, and students and was named a member of the National Academy of Sciences. Hallauer is a native of Kansas, USA. José B. Miranda Filho is full-professor in the Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz - University of São Paulo located at Piracicaba, Brazil. His research interests have emphasized development of quantitative genetic theory and its application to maize breeding. Miranda Filho is native of Pirassununga, São Paulo, Brazil. M.J. Carena is professor of plant sciences at North Dakota State University (NDSU). Dr. Carena has led maize-breeding research for short-season maturity at NDSU since 1999. This program is currently one the of the few public U.S. programs left integrating pre-breeding with cultivar development and training in applied maize breeding. He teaches Quantitative Genetics and Crop Breeding Techniques at NDSU. Carena is a native of Buenos Aires, Argentina. http://www.ag.ndsu.nodak.edu/plantsci/faculty/Carena.htm
Book Synopsis Proceedings of FSTP3 Congress - A Sustainable Durum Wheat Chain for Food Security and Healthy Lives by : Brian L. Beres
Download or read book Proceedings of FSTP3 Congress - A Sustainable Durum Wheat Chain for Food Security and Healthy Lives written by Brian L. Beres and published by Frontiers Media SA. This book was released on 2021-06-04 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt:
