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Genotyping By Multiplexed Sequencing In Barley And Stripe Rust Resistance In Wheat
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Book Synopsis Genotyping by Multiplexed Sequencing in Barley and Stripe Rust Resistance in Wheat by : Jonathan Duran Eagle
Download or read book Genotyping by Multiplexed Sequencing in Barley and Stripe Rust Resistance in Wheat written by Jonathan Duran Eagle and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers that provide informative genotypic data and greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: 1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. 2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we used the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTLs for genes of interest. Good markers have a read depth of at least 5 amplicons and are reliably present across the population. Puccinia striiformis Westend. f. sp. tritici Erikss, causing wheat stripe rust, is an economically important pathogen of wheat (Triticum aestivum L.). The hexaploid club spring wheat cultivar JD contains both all-stage and adult plant resistance genes and is very resistant to stripe rust in the field. The objective of this study was to identify quantitative trait loci (QTL) for stripe rust resistance using a BC1F7 recombinant inbred line (RIL) population from parental line JD and backcross parent Avocet Susceptible (AvS). The population was phenotyped in field plots in Washington State at Pullman and Mount Vernon in 2014, 2015, and 2016. A major QTL conferring all-stage resistance from the JD background was identified on chromosome 1B using GBS markers. This QTL was further characterized with SSR markers and found to have the greatest effect at SSR marker WMC798, approximately 12 cM distal of WMC406. Additional QTL for adult-plant resistance were identified in the JD background on chromosomes 3A, 3B, 4A, 6B, and 7A having smaller effects.
Book Synopsis Genotyping by Multiplexed Sequencing by : Travis Merle Ruff
Download or read book Genotyping by Multiplexed Sequencing written by Travis Merle Ruff and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Genotyping of polyploid species, such as common wheat, has proven difficult with current technologies that combine high-throughput and multiplexing abilities that are suitable for genomic selection (GS). The most common methods for high-throughput genotyping of wheat samples have been with the Illumina Infinium 90K SNP chip and more recently genotyping-by-sequencing (GBS). While many researchers continue to use these genotyping technologies for genetic studies in wheat, each have issues. The key problems with GBS is that the data analysis requires in-depth bioinformatic knowledge and imputation is essential to fill in missing data. The main drawback with the Illumina Infinium 90K wheat SNP chip in polyploids is the co-hybridization of homoeoalleles resulting in improper heterozygous calls. To correct this issue with the SNP chip data, a researcher must manually annotate tens of thousands of results to fix these errors. In doing this, all real heterozygous samples are converted to homozygous samples, which lead to the loss of these heterozygous samples from the data set. Another issue with SNP chip technology is that it is expensive to customize. Genotyping by Multiplexed Sequencing (GMS) was developed to address the specific issues mentioned above. GMS is PCR based, multiplexes 1,709 SNP wheat markers, 248 syntenic barley markers and 60 known informative markers (KIMs) used for marker-assisted selection (MAS) in wheat. GMS amplicon libraries have the flexibility to be sequenced on either the Ion Torrent or Illumina next generation sequencing platforms. Direct sequencing of amplicon libraries confirms heterozygous samples, does not require broad bioinformatic knowledge or imputation, and allows researchers to customize GMS to fit their research needs.
Book Synopsis Use of Barley and Wheat Reference Sequences: Downstream Applications in Breeding, Gene Isolation, GWAS and Evolution, Volume II by : Dragan Perovic
Download or read book Use of Barley and Wheat Reference Sequences: Downstream Applications in Breeding, Gene Isolation, GWAS and Evolution, Volume II written by Dragan Perovic and published by Frontiers Media SA. This book was released on 2022-11-30 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Physiological, Molecular, and Genetic Perspectives of Wheat Improvement by : Shabir H Wani
Download or read book Physiological, Molecular, and Genetic Perspectives of Wheat Improvement written by Shabir H Wani and published by Springer Nature. This book was released on 2020-12-17 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: World population is growing at an alarming rate and may exceed 9.7 billion by 2050, whereas agricultural productivity has been negatively affected due to yield limiting factors such as biotic and abiotic stresses as a result of global climate change. Wheat is a staple crop for ~20% of the world population and its yield needs be augmented correspondingly in order to satisfy the demands of our increasing world population. “Green revolution”, the introduction of semi-dwarf, high yielding wheat varieties along with improved agronomic management practices, gave rise to a substantial increase in wheat production and self-sufficiency in developing countries that include Mexico, India and other south Asian countries. Since the late 1980’s, however, wheat yield is at a standoff with little fluctuation. The current trend is thus insufficient to meet the demands of an increasing world population. Therefore, while conventional breeding has had a great impact on wheat yield, with climate change becoming a reality, newer molecular breeding and management tools are needed to meet the goal of improving wheat yield for the future. With the advance in our understanding of the wheat genome and more importantly, the role of environmental interactions on productivity, the idea of genomic selection has been proposed to select for multi-genic quantitative traits early in the breeding cycle. Accordingly genomic selection may remodel wheat breeding with gain that is predicted to be 3 to 5 times that of crossbreeding. Phenomics (high-throughput phenotyping) is another fairly recent advancement using contemporary sensors for wheat germplasm screening and as a selection tool. Lastly, CRISPR/Cas9 ribonucleoprotein mediated genome editing technology has been successfully utilized for efficient and specific genome editing of hexaploid bread wheat. In summary, there has been exciting progresses in the development of non-GM wheat plants resistant to biotic and abiotic stress and/or wheat with improved nutritional quality. We believe it is important to highlight these novel research accomplishments for a broader audience, with the hope that our readers will ultimately adopt these powerful technologies for crops improvement in order to meet the demands of an expanding world population.
Book Synopsis Molecular Techniques in Crop Improvement by : Shri Mohan Jain
Download or read book Molecular Techniques in Crop Improvement written by Shri Mohan Jain and published by Springer Science & Business Media. This book was released on 2009-11-05 with total page 759 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides comprehensive information on the latest tools and techniques of molecular genetics and their applications in crop improvement. It thoroughly discusses advanced techniques used in molecular markers, QTL mapping, marker-assisted breeding, and molecular cytogenetics.
Download or read book The Alfalfa Genome written by Long-Xi Yu and published by Springer Nature. This book was released on 2021-07-17 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first comprehensive compilation of deliberations on whole genome sequencing of the diploid and tetraploid alfalfa genomes including sequence assembly, gene annotation, and comparative genomics with the model legume genome, functional genomics, and genomics of important agronomic characters. Other chapters describe the genetic diversity and germplasm collections of alfalfa, as well as development of genetic markers and genome-wide association and genomic selection for economical important traits, genome editing, genomics, and breeding targets to address current and future needs. Altogether, the book contains about 300 pages over 16 chapters authored by globally reputed experts on the relevant field in this crop. This book is useful to the students, teachers, and scientists in the academia and relevant private companies interested in genetics, breeding, pathology, physiology, molecular genetics and breeding, biotechnology, and structural and functional genomics. The work is also useful to seed and forage industries.
Download or read book Stripe Rust written by Xianming Chen and published by Springer. This book was released on 2017-07-11 with total page 723 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprehensively introduces stripe rust disease, its development and its integral control. Covering the biology, genetics, genome, and functional genomics of the pathogen, it also discusses host and non-host resistance, their interactions and the epidemiology of the disease. It is intended for scientists, postgraduates and undergraduate studying stripe rust, plant pathology, crop breeding, crop protection and agricultural science, but is also a valuable reference book for consultants and administrators in agricultural businesses and education.
Book Synopsis Plant Breeding: Past, Present and Future by : John E. Bradshaw
Download or read book Plant Breeding: Past, Present and Future written by John E. Bradshaw and published by Springer. This book was released on 2016-03-08 with total page 710 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book aims to help plant breeders by reviewing past achievements, currently successful practices, and emerging methods and techniques. Theoretical considerations are also presented to strike the right balance between being as simple as possible but as complex as necessary. The United Nations predicts that the global human population will continue rising to 9.0 billion by 2050. World food production will need to increase between 70-100 per cent in just 40 years. First generation bio-fuels are also using crops and cropland to produce energy rather than food. In addition, land area used for agriculture may remain static or even decrease as a result of degradation and climate change, despite more land being theoretically available, unless crops can be bred which tolerate associated abiotic stresses. Lastly, it is unlikely that steps can be taken to mitigate all of the climate change predicted to occur by 2050, and beyond, and hence adaptation of farming systems and crop production will be required to reduce predicted negative effects on yields that will occur without crop adaptation. Substantial progress will therefore be required in bridging the yield gap between what is currently achieved per unit of land and what should be possible in future, with the best farming methods and best storage and transportation of food, given the availability of suitably adapted cultivars, including adaptation to climate change. My book is divided into four parts: Part I is an historical introduction; Part II deals with the origin of genetic variation by mutation and recombination of DNA; Part III explains how the mating system of a crop species determines the genetic structure of its landraces; Part IV considers the three complementary options for future progress: use of sexual reproduction in further conventional breeding, base broadening and introgression; mutation breeding; and genetically modified crops.
Book Synopsis Smart Plant Breeding for Field Crops in Post-genomics Era by : Devender Sharma
Download or read book Smart Plant Breeding for Field Crops in Post-genomics Era written by Devender Sharma and published by Springer Nature. This book was released on 2023-04-28 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book emphasizes on cutting-edge next-generation smart plant breeding approaches for maximizing the use of genomic resources generated by high-throughput genomics in the post-genomic era. Through this book the readers would learn about the recent development in the genomic approaches such as genotype by sequencing (GBS) for genomic analysis (SNPs, Single Nucleotide Polymorphism), whole-genome re-sequencing (WGRS) and RNAseq for transcriptomic analysis (DEGs, Differentially Expressed Genes). To maximize the genetic gains in the cereal/food crops, the book covers topics on transgenic breeding, genome editing, high-throughput phenotyping, reliable/precision phenotyping and genomic information-based analysis. In the era of climate change and the ever-increasing population, food security and nutritional security are the primary concern of plant breeders, growers, and policymakers to address the UN’s sustainable development goals. Chapters of this book cohere around these goals and covers techniques such as (QTL mapping, association studies, candidate gene identification), omics, RNAi [through micro RNA (miRNA), small interfering RNA (siRNA) and artificial micro RNA (amiRNA)]. It also covers other genomic techniques like antisense technology, genome editing (CRISPR/cas9, base editing) and epigenomics that assist the crop improvement programmes to fulfil the UNs sustainable development goals. It explores the influence of rapidly available sequencing data assisting in the next generation breeding programmes. This volume is a productive resource for the students, researchers, scientists, teachers, public and private sector stakeholders involved in the genetic enhancement of cereal crops.
Book Synopsis Genetics and Genomics of Brachypodium by : John P. Vogel
Download or read book Genetics and Genomics of Brachypodium written by John P. Vogel and published by Springer. This book was released on 2016-02-17 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Grasses dominate many natural ecosystems and produce the bulk calories consumed by humans either directly in the form of grains or indirectly through forage/grain fed animals. In addition, grasses grown as biomass crops are poised to become a significant source of renewable energy. Despite their economic and environmental importance, research into the unique aspects of grass biology has been hampered by the lack of a truly tractable experimental model system. Over that past decade, the small, annual grass Brachypodium distachyon has emerged as a viable model system for the grasses. This book describes the development of extensive experimental resources (e.g. whole genome sequence, efficient transformation methods, insertional mutant collections, large germplasm collections, recombinant inbred lines, resequenced genomes) that have led many laboratories around the world to adopt B. distachyon as a model system. The use of B. distachyon to address a wide range of biological topics (e.g. disease resistance, cell wall composition, abiotic stress tolerance, root growth and development, floral development, natural diversity) is also discussed.
Book Synopsis Molecular Breeding of Forage Crops by : German Spangenberg
Download or read book Molecular Breeding of Forage Crops written by German Spangenberg and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 345 pages. Available in PDF, EPUB and Kindle. Book excerpt: Forage plant breeding has entered the genome era. This timely book reviews the latest advances in the development and application of molecular technologies which supplement conventional breeding efforts for our major forage crops. It describes the plethora of new technologies and tools now available for high-throughput gene discovery, genome-wide gene expression analysis, production of transgenic plants, genome analysis and marker-assisted selection as applied to forage plants. Detailed accounts are presented of current and future opportunities for innovative applications of these molecular tools and technologies in the identification, functional characterisation, and use of valuable genes in forage production systems and beyond. This book represents a valuable resource for plant breeders, geneticists, and molecular biologists, and will be of particular relevance to advanced undergraduates, postgraduates, and researchers with an interest in forage legumes and grasses.
Book Synopsis Genomics and Breeding for Climate-Resilient Crops by : Chittaranjan Kole
Download or read book Genomics and Breeding for Climate-Resilient Crops written by Chittaranjan Kole and published by Springer Science & Business Media. This book was released on 2013-06-18 with total page 556 pages. Available in PDF, EPUB and Kindle. Book excerpt: Climate change is expected to have a drastic impact on agronomic conditions including temperature, precipitation, soil nutrients, and the incidence of disease pests, to name a few. To face this looming threat, significant progress in developing new breeding strategies has been made over the last few decades. The first volume of Genomics and Breeding for Climate-Resilient Crops presents the basic concepts and strategies for developing climate-resilient crop varieties. Topics covered include: conservation, evaluation and utilization of biodiversity; identification of traits, genes and crops of the future; genomic and molecular tools; genetic engineering; participatory and evolutionary breeding; bioinformatics tools to support breeding; funding and networking support; and intellectual property, regulatory issues, social and political dimensions.
Book Synopsis Wheat Rust Diseases by : Sambasivam Periyannan
Download or read book Wheat Rust Diseases written by Sambasivam Periyannan and published by Humana. This book was released on 2018-06-12 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a collection of tools currently used for the characterization of rust, the host plant wheat, and their interactions. This book is divided into five parts: Parts I and II discuss advanced techniques for characterizing rust pathogens in rust surveillance, genotyping, and molecular pathogenicity; Part III describes protocols for genetic analysis of rust resistance; Part IV covers methods on rust resistance gene cloning; and Part V talks about the isolation and screening of bacterial endophytes as biocontrol agents for rust disease management. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Wheat Rust Disease: Methods and Protocols is a valuable resource for both established and novel wheat rust researchers and also the plant science and microbial research community.
Book Synopsis DNA Fingerprinting in Plants by : Kurt Weising
Download or read book DNA Fingerprinting in Plants written by Kurt Weising and published by CRC Press. This book was released on 2005-02-28 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: Given the explosive development of new molecular marker techniques over the last decade, newcomers and experts alike in the field of DNA fingerprinting will find an easy-to-follow guide to the multitude of techniques available in DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition. Along with step-by-step annotated p
Book Synopsis Gene Manipulation in Plant Improvement by : J. Perry Gustafson
Download or read book Gene Manipulation in Plant Improvement written by J. Perry Gustafson and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 667 pages. Available in PDF, EPUB and Kindle. Book excerpt: The results obtained to date involving the use of in ~ methods to facilitate wide hybridization in plants are voluminous and impressive. The techniques of embryo culture, ovule culture, and in~ pollination and fertilization represent an extension of the normal sexual hybridization process. Successes recorded in obtaining hybrids stem largely from circumventing prezygotic or postzygotic hybridization barriers. Numerous recent successful hybridizations were possible because of the development of improved tissue and cell culture systems for crop plants and attention given to genotypes used in hybridization attempts. Interspecific and intergeneric hybridization utilizing the process of protoplast fusion will bypass the limits set by all sexual me'thods. In addition to combining complete genomes from two different species through protoplast fusion, this system affords unique opportunities for creating novel cytoplasmic combinations, transfer of individual chromosomes, transfer of cytoplasmic organelles, manipulation of male sterility, and for single gene transfer. Some caution must be noted with regard to the extent of hybridization possible between distantly related species. Although practically no limit exists to the physical fusion of protoplasts from widely divergent species, the restrictions imposed by somatic incompatibility have not been adequately addressed. Regeneration of plants from the protoplast or single heterokaryon level is still a major hurdle for many important crop species before somatic cell fusion can be exploited to produce interspecific and intergeneric hybrids. Identification and selection of hybrids is also a limitation to the efficient application of cell fusion methods.
Book Synopsis Wheat Production in Stressed Environments by : H.T. Buck
Download or read book Wheat Production in Stressed Environments written by H.T. Buck and published by Springer Science & Business Media. This book was released on 2007-05-16 with total page 764 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a unique overview to wheat and related species, this book comprises the proceedings of the 7th International Wheat Conference, held in Mar del Plata, Argentina, at the end of 2005. Leading scientists from all over the world, specialized in different areas that contribute to the better understanding of wheat production and use, review the present achievements and discuss the future challenges for the wheat crop.
Book Synopsis Genome Engineering for Crop Improvement by : Bidyut Kumar Sarmah
Download or read book Genome Engineering for Crop Improvement written by Bidyut Kumar Sarmah and published by Springer Nature. This book was released on 2021-04-18 with total page 277 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book serves the teachers, researchers and the students as a handy and concise reference as well as guidebook while designing and planning for use of the advanced technologies for crop improvement. The content of the book is designed to cover the latest genome engineering techniques for crop improvement. The conventional breeding has got its limitations such as non-availability of desired genes within the genepool. In many cases, breeding has been highly used and it has nearly reached its highest limit so far as the productivity and production of crops are concerned. However, with increasing need of food and decreasing resources, including water, land, labour, etc., to feed the growing population, the alternative available ways of increasing crop productivity need to be explored and exploited. Genome engineering has a wide scope that includes technologies such as genetic engineering and transgenesis, RNA technologies, CRISPR, cisgenics and subgenics for better productivity and more efficient biotic and abiotic stress management. Therefore, the book is planned to enlighten the readers with the advanced technologies with examples and case studies, whenever possible. Efforts will be made to emphasize on general efforts on various major food crops; however, it would also be made clear that such efforts could be taken as proofs of concepts and that this could be extrapolated keeping the demand in mind.
