Advances in Statistical Methods for the Genetic Dissection of Complex Traits in Plants

Advances in Statistical Methods for the Genetic Dissection of Complex Traits in Plants PDF

Author: Yuan-Ming Zhang

Publisher: Frontiers Media SA

Published: 2024-01-26

Total Pages: 278

ISBN-13: 2832543693

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Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. However, there are still limits in current GWAS statistics. For example, (1) almost all the existing methods do not estimate additive and dominance effects in quantitative trait nucleotide (QTN) detection; (2) the methods for detecting QTN-by-environment interaction (QEI) are not straightforward and do not estimate additive and dominance effects as well as additive-by-environment and dominance-by-environment interaction effects, leading to unreliable results; and (3) no or too simple polygenic background controls have been employed in QTN-by-QTN interaction (QQI) detection. As a result, few studies of QEI and QQI for complex traits have been reported based on multiple-environment experiments. Recently, new statistical tools, including 3VmrMLM, have been developed to address these needs in GWAS. In 3VmrMLM, all the trait-associated effects, including QTN, QEI and QQI related effects, are compressed into a single effect-related vector, while all the polygenic backgrounds are compressed into a single polygenic effect matrix. These compressed parameters can be accurately and efficiently estimated through a unified mixed model analysis. To further validate these new GWAS methods, particularly 3VmrMLM, they should be rigorously tested in real data of various plants and a wide range of other species.

Bioinformatics for agriculture: High-throughput approaches

Bioinformatics for agriculture: High-throughput approaches PDF

Author: Atul Kumar Upadhyay

Publisher: Springer Nature

Published: 2021-03-19

Total Pages: 160

ISBN-13: 9813347910

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This book illustrates the importance and significance of bioinformatics in the field of agriculture. It first introduces the basic concepts of bioinformatics, such as homologous sequence and gene function analyses, determination of protein structures, and discusses machine learning applications for an in-depth understanding of the desired genes and proteins based on commonly used bioinformatics software and tools, e.g. BLAST, molecular modelling, molecular-docking and simulations, protein-protein and domain-domain interactions. The book also describes recent advances in the high-throughput analysis of whole genome and transcriptome using next-generation sequencing platforms, and functional proteome studies. It also examines the role of computational biology in understanding and improving the nutrient quality and yield of crops. Lastly, the book explores a comprehensive list of applications of bioinformatics to improve plant yield, biomass, and health, and the challenges involved.

Omics in Plant Breeding

Omics in Plant Breeding PDF

Author: Aluízio Borém

Publisher: John Wiley & Sons

Published: 2014-06-03

Total Pages: 253

ISBN-13: 1118820843

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Computational and high-throughput methods, such as genomics, proteomics, and transcriptomics, known collectively as “-omics,” have been used to study plant biology for well over a decade now. As these technologies mature, plant and crop scientists have started using these methods to improve crop varieties. Omics in Plant Breeding provides a timely introduction to key omicsbased methods and their application in plant breeding. Omics in Plant Breeding is a practical and accessible overview of specific omics-based methods ranging from metabolomics to phenomics. Covering a single methodology within each chapter, this book provides thorough coverage that ensures a strong understanding of each methodology both in its application to, and improvement of, plant breeding. Accessible to advanced students, researchers, and professionals, Omics in Plant Breeding will be an essential entry point into this innovative and exciting field. • A valuable overview of high-throughput, genomics-based technologies and their applications to plant breeding • Each chapter explores a single methodology, allowing for detailed and thorough coverage • Coverage ranges from well-established methodologies, such as genomics and proteomics, to emerging technologies, including phenomics and physionomics Aluízio Borém is a Professor of Plant Breeding at the University of Viçosa in Brazil. Roberto Fritsche-Neto is a Professor of Genetics and Plant Breeding at the University of São Paulo in Brazil.

Forest Genomics and Biotechnology

Forest Genomics and Biotechnology PDF

Author: Isabel Allona

Publisher: Frontiers Media SA

Published: 2019-11-27

Total Pages: 185

ISBN-13: 2889631788

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This Research Topic addresses research in genomics and biotechnology to improve the growth and quality of forest trees for wood, pulp, biorefineries and carbon capture. Forests are the world’s greatest repository of terrestrial biomass and biodiversity. Forests serve critical ecological services, supporting the preservation of fauna and flora, and water resources. Planted forests also offer a renewable source of timber, for pulp and paper production, and the biorefinery. Despite their fundamental role for society, thousands of hectares of forests are lost annually due to deforestation, pests, pathogens and urban development. As a consequence, there is an increasing need to develop trees that are more productive under lower inputs, while understanding how they adapt to the environment and respond to biotic and abiotic stress. Forest genomics and biotechnology, disciplines that study the genetic composition of trees and the methods required to modify them, began over a quarter of a century ago with the development of the first genetic maps and establishment of early methods of genetic transformation. Since then, genomics and biotechnology have impacted all research areas of forestry. Genome analyses of tree populations have uncovered genes involved in adaptation and response to biotic and abiotic stress. Genes that regulate growth and development have been identified, and in many cases their mechanisms of action have been described. Genetic transformation is now widely used to understand the roles of genes and to develop germplasm that is more suitable for commercial tree plantations. However, in contrast to many annual crops that have benefited from centuries of domestication and extensive genomic and biotechnology research, in forestry the field is still in its infancy. Thus, tremendous opportunities remain unexplored. This Research Topic aims to briefly summarize recent findings, to discuss long-term goals and to think ahead about future developments and how this can be applied to improve growth and quality of forest trees.

Neglected and Underutilized Crop Species for Sustainable Food and Nutritional Security: Prospects and Hidden Potential

Neglected and Underutilized Crop Species for Sustainable Food and Nutritional Security: Prospects and Hidden Potential PDF

Author: Omena Bernard Ojuederie

Publisher: Frontiers Media SA

Published: 2024-01-23

Total Pages: 151

ISBN-13: 2832543324

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Global demand for food is rising as a result of increases in the global population as well as dietary changes. Furthermore, climate change exerts additional pressure on the food supply, adversely affecting sustainable food production. Increased temperatures and drought stresses coupled with the migration of pests limit crop yields and affect their nutritional quality. Many staple crops are unable to adapt to these changing climatic conditions. To achieve the Sustainable Development Goals of the United Nation to end hunger and promote good health and well-being, concerted efforts need to be made to enhance food production while mitigating the effects of climate change through the promotion of climate-smart agricultural practices and the utilization of neglected and underutilized crop species. These species can be highly nutritious and well-adapted to different agroecologies and climatic conditions, meaning that they offer the possibility of improving food and nutritional security.

Omics in Horticultural Crops

Omics in Horticultural Crops PDF

Author: Gyana Ranjan Rout

Publisher: Academic Press

Published: 2022-07-16

Total Pages: 664

ISBN-13: 0323899137

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Omics in Horticulture Crops presents a comprehensive view of germplasm diversity, genetic evolution, genomics, proteomics and transcriptomics of fruit crops (temperate, tropical and subtropical fruits, fruit nuts, berries), vegetables, tuberous crops, ornamental and floricultural crops and medicinal aromatic plants. Information covering phenomics, genetic diversity, phylogenetic studies, genome sequencing, and genome barcoding through the utilization of molecular markers plays an imperative role in the characterization and effective utilization of diverse germplasm are included in the book. This is a valuable reference for researchers and academics seeking to improve cultivar productivity through enhanced genetic diversity while also retaining optimal traits and protecting the growing environment. Highlights perspectives, progress and promises of -omics application Provides a systematic overview of origin, progenitor and domestication process as well as genetic insights Includes full range of horticultural crops

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