Optimal Designs In Genomic Selection
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Optimal Designs In Genomic Selection
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Author : Josafhat Salinas Ruiz
language : en
Publisher:
Release Date : 2015
Optimal Designs In Genomic Selection written by Josafhat Salinas Ruiz and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with categories.
Recently, many plant and animal breeders have been using genome-wide genetic markers and statistical methods to aid with selection of genetic material. These methods, termed genomic selection (GS), make selections based on estimates of breeding values obtained from a prediction model computed from phenotypic and genomic data of a training population. The precision of the predictions strongly depends on the genetic diversity of the training population (TP). The objectives of this research were (1) To present a new method for creating a TP that maximizes genetic diversity using either the most important genomic markers or the first few principal components (PCs) of the genomic data as inputs into A, D, and V optimal design algorithms; and (2) To evaluate the average predictive ability of the A, D, and V optimal TPs and compare their predictabilities with TPs based on random sampling, the commonly used approach. Using data from the University of Nebraska red winter wheat breeding program, results showed that when created the TP using either the most significant markers or the first PCs, the gain of the average predictive ability was higher in all optimal designs compared with random sampling with an average increase by 13.425% over random sampling. In addition, it was estimated that genetic gains of selection can be increased by 2.8348 and 3.3538 times when using the p1 significant markers and the first p1 PCs compared with the genetic gain of 1.8306 random sampling TP, respectively.
Genomic Selection In Plants
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Author : Ani A. Elias
language : en
Publisher: CRC Press
Release Date : 2022-08-18
Genomic Selection In Plants written by Ani A. Elias and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-08-18 with Science categories.
Genomic selection (GS) is a promising tool in the field of breeding especially in the era where genomic data is becoming cheaper. The potential of this tool has not been realized due to its limited adaptation in various crops. Marker Assisted Selection (MAS) has been the method of choice for plant breeders while using the genomic information in the breeding pipeline. MAS, however, fails to capture vital minor gene effects while focusing only on the major genes, which is not ideal for breeding advancement especially for quantitative traits such as yield. The main aim of statistical methodologies coming under the umbrella of GS on using the whole genome information is to predict potential candidates for breeding advancement while optimizing the use of resources such as land, manpower, and most importantly time. Lack of proper understanding of the methods and their applications is one of the reasons why breeders shy away from this tool. The book is meant for biologists, especially breeders, and provides a comprehensive idea of the statistical methodologies used in GS, guidance on the choice of models, and design of datasets. The book also encourages the readers to adopt GS by demonstrating the current scenarios of these models in some of the important crops among oilseeds, vegetables, legumes, tuber crops, and cereals. For ease of implementation of GS, the book also provides hands-on scripts on GS data design and modeling in a popular open-source statistical program. Additionally, prospective in GS model development and thereby enhancement in crop improvement programs is discussed.
Genomic Selection Lessons Learned And Perspectives
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Author : Johannes W. R. Martini
language : en
Publisher: Frontiers Media SA
Release Date : 2022-09-15
Genomic Selection Lessons Learned And Perspectives written by Johannes W. R. Martini and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-09-15 with Science categories.
Genomic selection (GS) has been the most prominent topic in breeding science in the last two decades. The continued interest is promoted by its huge potential impact on the efficiency of breeding. Predicting a breeding value based on molecular markers and phenotypic values of relatives may be used to manipulate three parameters of the breeder's equation. First, the accuracy of the selection may be improved by predicting the genetic value more reliably when considering the records of relatives and the realized genomic relationship. Secondly, genotyping and predicting may be more cost effective than comprehensive phenotyping. Resources can instead be allocated to increasing population sizes and selection intensity. The third, probably most important factor, is time. As shown in dairy cattle breeding, reducing cycle time by crossing selection candidates earlier may have the strongest impact on selection gain. Many different prediction models have been used, and different ways of using predicted values in a breeding program have been explored. We would like to address the questions: i. How did GS change breeding schemes of different crops in the last 20 years? ii. What was the impact on realized selection gain? iii. What would be the best structure of a crop-specific breeding scheme to exploit the full potential of GS? iv. What is the potential of hybrid prediction, epistasis effect models, deep learning methods and other extensions of the standard prediction of additive effects? v. What are the long-term effects of GS? vi. Can predictive breeding approaches also be used to harness genetic resources from germplasm banks in a more efficient way to adapt current germplasm to new environmental challenges? This Research Topic welcomes submissions of Original Research papers, Opinions, Perspectives, Reviews, and Mini-Reviews related to these themes: 1. Genomic selection: statistical methodology 2. The (optimal) use of GS in breeding schemes 3. Practical experiences with GS (selection gain, long-term effects, negative side effects) 4. Predictive approaches to harness genetic resources Concerning point 1): If an original research paper compares different methods empirically without theoretical considerations on when one or the other method should be better, the methods should be compared with at least five different data sets. The data sets should differ either in crop, genotyping method or its source, for instance from a breeding program or gene bank accessions. Concerning point 2): Manuscripts addressing the use of GS in breeding schemes should illustrate breeding schemes that are run in practice. General ideas about schemes that may be run in the future may be considered as 'Perspective' articles. Conflict of Interest statements: - Topic Editor Valentin Wimmer is affiliated to KWS SAAT SE & Co. KGaA, Germany. - Topic Editor Brian Gardunia is affiliated to Bayer Crop Sciences and has a collaboration with AbacusBio, and is an author on patents with Bayer Crop Sciences. The other Topic Editors did not disclose any conflicts of interest. Image credit: CIMMYT, reproduced under the CC BY-NC-SA 2.0 license
New Developments For Embracing Genomic Selection In Breeding Applications
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Author : Diego Jarquin
language : en
Publisher: Frontiers Media SA
Release Date : 2022-02-18
New Developments For Embracing Genomic Selection In Breeding Applications written by Diego Jarquin and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-02-18 with Science categories.
Genomic Selection For Crop Improvement
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Author : Rajeev K. Varshney
language : en
Publisher: Springer
Release Date : 2017-12-05
Genomic Selection For Crop Improvement written by Rajeev K. Varshney and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-12-05 with Technology & Engineering categories.
Genomic Selection for Crop Improvement serves as handbook for users by providing basic as well as advanced understandings of genomic selection. This useful review explains germplasm use, phenotyping evaluation, marker genotyping methods, and statistical models involved in genomic selection. It also includes examples of ongoing activities of genomic selection for crop improvement and efforts initiated to deploy the genomic selection in some important crops. In order to understand the potential of GS breeding, it is high time to bring complete information in the form of a book that can serve as a ready reference for geneticist and plant breeders.
Quantitative Approaches To Plant Breeding Concepts Strategies And Practical Applications
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Author : Suchismita Mondal
language : en
Publisher: Frontiers Media SA
Release Date : 2022-08-31
Quantitative Approaches To Plant Breeding Concepts Strategies And Practical Applications written by Suchismita Mondal and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-08-31 with Science categories.
Genomic Prediction Of Complex Traits
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Author : Nourollah Ahmadi
language : en
Publisher: Springer Nature
Release Date : 2022-04-22
Genomic Prediction Of Complex Traits written by Nourollah Ahmadi and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-04-22 with Science categories.
This volume explores the conceptual framework and the practical issues related to genomic prediction of complex traits in human medicine and in animal and plant breeding. The book is organized into five parts. Part One reminds molecular genetics approaches intending to predict phenotypic variations. Part Two presents the principles of genomic prediction of complex traits, and reviews factors that affect its reliability. Part Three describes genomic prediction methods, including machine-learning approaches, accounting for different degree of biological complexity, and reviews the associated computer-packages. Part Four reports on emerging trends such as phenomic prediction and incorporation into genomic prediction models of “omics” data and crop growth models. Part Five is dedicated to lessons learned from cases studies in the fields of human health and animal and plant breeding, and to methods for analysis of the economic effectiveness of genomic prediction. Written in the highly successful Methods in Molecular Biology series format, the book provides theoretical bases and practical guidelines for an informed decision making of practitioners and identifies pertinent routes for further methodological researches. Cutting-edge and thorough, Complex Trait Predictions: Methods and Protocols is a valuable resource for scientists and researchers who are interested in learning more about this important and developing field. Chapters 3, 9, 13, 14, and 21 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Population Genomics Crop Plants
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Author : Om P. Rajora
language : en
Publisher: Springer Nature
Release Date : 2024-06-08
Population Genomics Crop Plants written by Om P. Rajora and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-06-08 with Science categories.
Population genomics has revolutionized several disciplines of biology, genetic resource conservation and management, and breeding of crop plants by providing key and novel insights into population, evolutionary, ecological and conservation genetics, ecology, evolution and adaptation, and facilitating molecular breeding with an unprecedented power and accuracy. Crop plants have been domesticated from their wild progenitors over several centuries and have undergone severe genetic bottlenecks and selection sweeps. Population genomics research has unraveled novel insights into crop plants origin, evolution, demographic history, center of diversity, domestication history, genetic/genomic diversity and genetic structure of wild and domesticated populations and species, epigenomic diversity, genetic/genomic basis of domestication syndrome, genomic footprints of domestication, selection and breeding, de-domestication, speciation and admixture, taxonomy, phylogeny, ecology, biotic and abiotic stress tolerance, and ecological and climate adaptation. Population genomics has also facilitated the development of pangenomes, conservation and management of genetic diversity including in the pre-breeding and breeding programs, and genomics-assisted breeding via identifying genotype-phenotype associations and genomic selection in crop plants. This pioneering book presents the advances made and potential of population genomics in addressing the above crop plants aspects of basic and applied significance and brings together leading experts in crop plants population genomics to discuss these topics in major crop plants. Genomic, epigenomic, transcriptomic and plant resources available for population genomics research and challenges, opportunities and future perspectives of crop plants population genomics are also discussed. Chapters "Population Genomics of Yams: Evolution and Domestication of Dioscorea Species" and "Population Genomics Along With Quantitative Genetics Provides a More Efficient Valorization of Crop Plant Genetic Diversity in Breeding and Pre-breeding Programs" are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Plant Breeding Reviews Volume 45
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Author : Irwin Goldman
language : en
Publisher: John Wiley & Sons
Release Date : 2021-10-21
Plant Breeding Reviews Volume 45 written by Irwin Goldman and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-21 with Science categories.
Plant Breeding Reviews presents state-of-the-art reviews on plant genetics and the breeding of all types of crops by both traditional means and molecular methods. Many of the crops widely grown today stem from a very narrow genetic base; understanding and preserving crop genetic resources is vital to the security of food systems worldwide. The emphasis of the series is on methodology, a fundamental understanding of crop genetics, and applications to major crops.
Sustainable Poultry Production In Europe
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Author : Emily Burton
language : en
Publisher: CABI
Release Date : 2016-04-27
Sustainable Poultry Production In Europe written by Emily Burton and has been published by CABI this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-04-27 with Technology & Engineering categories.
Examining sustainable poultry production systems across Europe, this book contains a selected cross section of papers from the 2014 UK Poultry Science Symposium. It reviews essential topics such as resources and supply chains, the global poultry market, risk management, zoonoses and green issues. Providing a compilation of the most current research in the poultry science and production industry, this book is an important resource for both researchers and professionals.