Download or read book Effects of Evolution on Repetitive and Genic Sequences of the Maize Genome written by Wade Eugene Odland and published by . This book was released on 2006 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Evolution of Repetitive Content in the Genus Zea written by Paul Bilinski and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Even across related organisms, genome size is known to differ greatly, though the causes and consequences of this variation are unclear. Genome size variation is most pronounced within plants, where differences in repetitive sequence content have been identified as the cause of large scale structural variation. Though many plants show differences across species and genera, genome size variation in maize (Zea mays ssp. mays) is known vary greatly within the species and subspecies. Here, we aim to better understand whether maize taxa utilize genome size variation in adaptation or whether stochastic forces better explain variation in total nucleic content. To better inform our investigation of genome-wide patterns of repeat variation, the first component of the dissertation focused on the evolutionary dynamics of one class of repeat, the maize centromere repeat CentC. Centromere repeats are found in most eukaryotes, play a critical role in kinetochore formation, and contribute considerably to overall genome size. We investigated how a complex history of polyploidy, subsequent fractionation, and recent domestication impacted the diversity of the maize centromeric repeat. Looking at copies of CentC genome-wide, we found the highest genetic similarity among repeats was highest within long tandem arrays, suggesting that tandem duplications are the primary mechanism for the generation of new CentC copies. Though further clustering analyses identified similar sequences amongst physically distant repeats, we used simulations to suggest that this pattern may be due to homoplasious mutation. We also examined how the allopolyploid origin of maize has impacted centromere repeats. We showed that although the two ancestral subgenomes of maize contributed nearly equal numbers of centromeres, the majority of all CentC repeats derive from one of the parental genomes. By comparing maize with its wild progenitor, teosinte, we found that the abundance of CentC likely decreased after domestication. Having studied the evolutionary dynamics of one class of repeat, we then shifted our focus to understanding whether and how natural selection and adaptation impact repetitive content genome wide. The second chapter of the dissertation investigated how genome size and its repetitive components respond to altitudinal adaptation. We identified genome-wide changes in repetitive content of maize landraces and highland teosinte across altitudinal gradients in Mexico and South America. We mapped low coverage whole genome sequence against a curated set of reference repeats to discover the percentage of the genome comprised of each repeat and convert the proportion to a basepair value using flow cytometry estimates of genome size. We verified the accuracy of our bioinformatic approach using flourescent in-situ hybridization (FISH) data from the same populations. With confidence in our abundance measures, we used the data to test for evidence of selection on overall genome size and individual repeat abundances using models of phenotypic and genetic covariance among populations. We found that population structure and genetic drift alone cannot explain observed clinal patterns of genome size in Zea mays landraces, suggesting natural selection is responsible for the decrease in genome size at high altitude. However, we found no evidence of selection on individual repeat classes when controlling for overall genome size, suggesting that repetitive sequence is under selection pressure inasmuch as it contributes basepairs to the genome. Given the observed selection on genome size in maize landraces, we were curious as to whether natural populations of teosinte experienced similar selective pressures as domesticated maize. We therefore sampled 10 populations of the highland teosinte, Z. mays ssp. mexicana, along an altitudinal gradient in the Sierra Madre mountain range in central Mexico, excluding populations that showed evidence of admixture. Analysis of genome size in these highland teosinte showed evidence for selection along an altitudinal gradient. With multiple examples of a parallel response of genome size to altitude, we wanted to connect our observed selection pressure to a phenotype. Previously, other researchers had shown a correlation between selection for earlier flowering and a reduction in genome size, while other works found that genome size correlates with mitotic index. We hypothesized that the reduction in genome size would help plants move through the cell cycle more quickly, as a smaller genome needed less time for replication. We conducted a growth chamber experiment using one of our highland teosinte populations showing genome size variation, and tracked cell size, leaf elongation, and genome size of each plant. We developed a Bayesian model for the relationship between genome size and leaf elongation. Although the effect size was small, our model showed modest statistical support for a negative correlation between cell production and genome size, suggesting that smaller genome sizes may spur faster development through more rapid cell production. Surprisingly, we found no correlation between genome size and cell size as previous hypotheses had suggested. In contrast to longstanding hypotheses that genome size is an artifact of stochastic processes, we documented the case for selection shaping genome size variation in maize and its related taxa.
Download or read book The Maize Genome written by Jeffrey Bennetzen and published by Springer. This book was released on 2018-11-24 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics.
Download or read book Plant Genomes written by Jean-Nicolas Volff and published by Karger Medical and Scientific Publishers. This book was released on 2008-01-01 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.
Download or read book Handbook of Maize written by Jeff L. Bennetzen and published by Springer Science & Business Media. This book was released on 2009-01-16 with total page 785 pages. Available in PDF, EPUB and Kindle. Book excerpt: Maize is one of the world’s highest value crops, with a multibillion dollar annual contribution to agriculture. The great adaptability and high yields available for maize as a food, feed and forage crop have led to its current production on over 140 million hectares worldwide, with acreage continuing to grow at the expense of other crops. In terms of tons of cereal grain produced worldwide, maize has been number one for many years. Moreover, maize is expanding its contribution to non-food uses, including as a major source of ethanol as a fuel additive or fuel alternative in the US. In addition, maize has been at the center of the transgenic plant controversy, serving as the first food crop with released transgenic varieties. By 2008, maize will have its genome sequence released, providing the sequence of the first average-size plant genome (the four plant genomes that are now sequenced come from unusually tiny genomes) and of the most complex genome sequenced from any organism. Among plant science researchers, maize has the second largest and most productive research community, trailing only the Arabidopsis community in scale and significance. At the applied research and commercial improvement levels, maize has no peers in agriculture, and consists of thousands of contributors worthwhile. A comprehensive book on the biology of maize has not been published. The "Handbook of Maize: the Genetics and Genomics" center on the past, present and future of maize as a model for plant science research and crop improvement. The books include brief, focused chapters from the foremost maize experts and feature a succinct collection of informative images representing the maize germplasm collection.
Download or read book Maize Domestication and Molecular Evolution written by Edward St. Clair Buckler and published by . This book was released on 1997 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: To examine the history of maize domestication, I evaluated the phylogenetics of genus Zea. Ribosomal internal transcribed spacer (ITS) sequences were used to evaluate the phylogenetics of Zea and Tripsacum. The phylogenetic position of Z. mays ssp. huehuetenangensis was clearly established as basal to the other Z. mays. The ITS data indicated a near contemporary divergence of domesticated maize and its two closest wild relatives. Since maize domestication was part of paleo-Amerinds transition from foragers to farmers, I examined the subsistence patterns of early Central Mexicans to understand their activities at the dawn of maize domestication. Human plant exploitation from 11000 to 4000 BP was correlated with the predicted changes in plant community composition caused by the major regional climate changes. These correlations with climate suggest that the early residents of semiarid Central Mexico were predominantly foraging on the most abundant local plants. Cultivation appears to be insignificant and none of the major New World crops appear important for subsistence in these semiarid regions of Central Mexico. The second phase of my doctoral research examined the processes of maize genome evolution. Zea and Tripsacum nuclear ribosomal ITS sequences were used to evaluate patterns of concerted evolution, rates of substitutions, patterns of methylation-induced deamination, and structural constraints of the ITS. Selection was important in shaping the distribution of polymorphisms and substitutions observed in the ITS. By examining a wide range of plant taxa I found many examples of diverse paralogous rDNA. Some of these divergent paralogues were probably rDNA pseudogenes, since they had low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. These divergent paralogues can have a major impact on phylogeny reconstruction. Chromosomal knobs are repeated tandem DNA sequences that form large blocks of heterochromatin in the maize genome. I have shown that chromosomal meiotic drive has driven knob evolution and may be a powerful force in genome evolution. We demonstrate the evolutionary relationship between the meiotic drive factor Ab10 and the knobs.
Download or read book Plant Genome Diversity Volume 1 written by Jonathan Wendel and published by Springer Science & Business Media. This book was released on 2012-03-23 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this timely new 2-volume treatise, experts from around the world have banded together to produce a first-of-its-kind synopsis of the exciting and fast moving field of plant evolutionary genomics. In Volume I of Plant Genome Diversity, an update is provided on what we have learned from plant genome sequencing projects. This is followed by more focused chapters on the various genomic “residents” of plant genomes, including transposable elements, centromeres, small RNAs, and the evolutionary dynamics of genes and non-coding sequences. Attention is drawn to advances in our understanding of plant mitochondrial and plastid genomes, as well as the significance of duplication in genic evolution and the non-independent evolution among sequences in plant genomes. Finally, Volume I provides an introduction to the vibrant new frontier of plant epigenomics, describing the current state of our knowledge and the evolutionary implications of the epigenomic landscape.
Download or read book Genome Duplication written by Melvin DePamphilis and published by Garland Science. This book was released on 2010-10-06 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome Duplication provides a comprehensive and readable overview of the underlying principles that govern genome duplication in all forms of life, from the simplest cell to the most complex multicellular organism. Using examples from the three domains of life - bacteria, archaea, and eukarya - Genome Duplication shows how all living organisms store their genome as DNA and how they all use the same evolutionary-conserved mechanism to duplicate it: semi-conservative DNA replication by the replication fork. The text shows how the replication fork determines where organisms begin genome duplication, how they produce a complete copy of their genome each time a cell divides, and how they link genome duplication to cell division. Genome Duplication explains how mistakes in genome duplication are associated with genetic disorders and cancer, and how understanding genome duplication, its regulation, and how the mechanisms differ between different forms of life, is critical to the understanding and treatment of human disease.
Download or read book Plant Molecular Biology Labfax written by R. R. D. Croy and published by Wiley-Blackwell. This book was released on 1993 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: For an active scientist, tracking down the data needed for planning and carrying out experiments can be time-consuming and frustrating. Now the Labfax series of reference databooks provides all the essential information required, quickly and accurately. Plant Molecular Biology Labfax is a unique single source of reference to key data and information required by the plant molecular biologist on an almost daily basis. A select team of editors and contributors have compiled this manual to provide a guide to researchers in the most important basic and applied aspects of plant molecular biology. All the data a plant molecular biologist is ever likely to need. Spiral bound and laminated for durability and ease of use in the lab. Contains comprehensive tables listing plant genes published and submitted to sequence databases up to 1992.
Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.
Download or read book Evolution Composition and Regulation of Supernumerary B Chromosomes written by Andreas Houben and published by MDPI. This book was released on 2019-04-25 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: Supernumerary B chromosomes (Bs) are dispensable genetic elements found in thousands of species of plants and animals, and some fungi. Since their discovery more than a century ago, they have been a source of puzzlement, as they only occur in some members of a population and are absent from others. When they do occur, they are often harmful, and in the absence of “selfishness”, based on mechanisms of mitotic and meiotic drive, there appears to be no obvious reason for their existence. Cytogeneticists have long wrestled with questions about the biological existence of these enigmatic elements, including their lack of any adaptive properties, apparent absence of functional genes, their origin, sequence organization, and co-evolution as nuclear parasites. Emerging new technologies are now enabling researchers to step up a gear, to look enthusiastically beyond the previous limits of the horizon, and to uncover the secrets of these “silent” chromosomes. This book provides a comprehensive guide to theoretical advancements in the field of B chromosome research in both animal and plant systems.
Download or read book Replacing Darwin written by Nathaniel T Jeanson and published by New Leaf Publishing Group. This book was released on 2017-09-01 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: If Darwin were to examine the evidence today using modern science, would his conclusions be the same? Charles Darwin’s On the Origin of Species, published over 150 years ago, is considered one of history’s most influential books and continues to serve as the foundation of thought for evolutionary biology. Since Darwin’s time, however, new fields of science have immerged that simply give us better answers to the question of origins. With a Ph.D. in cell and developmental biology from Harvard University, Dr. Nathaniel Jeanson is uniquely qualified to investigate what genetics reveal about origins. The Origins Puzzle Comes Together If the science surrounding origins were a puzzle, Darwin would have had fewer than 15% of the pieces to work with when he developed his theory of evolution. We now have a much greater percentage of the pieces because of modern scientific research. As Dr. Jeanson puts the new pieces together, a whole new picture emerges, giving us a testable, predictive model to explain the origin of species. A New Scientific Revolution Begins Darwin’s theory of evolution may be one of science’s “sacred cows,” but genetics research is proving it wrong. Changing an entrenched narrative, even if it’s wrong, is no easy task. Replacing Darwin asks you to consider the possibility that, based on genetics research, our origins are more easily understood in the context of . . . In the beginning . . . God, with the timeline found in the biblical narrative of Genesis. There is a better answer to the origins debate than what we have been led to believe. Let the revolution begin! About the Author Dr. Nathaniel Jeanson is a scientist and a scholar, trained in one of the most prestigious universities in the world. He earned his B.S. in Molecular Biology and Bioinformatics from the University of Wisconsin-Parkside and his PhD in Cell and Developmental Biology from Harvard University. As an undergraduate, he researched the molecular control of photosynthesis, and his graduate work involved investigating the molecular and physiological control of adult blood stem cells. His findings have been presented at regional and national conferences and have been published in peer-reviewed journals, such as Blood, Nature, and Cell. Since 2009, he has been actively researching the origin of species, both at the Institute for Creation Research and at Answers in Genesis.
Download or read book Genetically Engineered Crops written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-01-28 with total page 607 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetically engineered (GE) crops were first introduced commercially in the 1990s. After two decades of production, some groups and individuals remain critical of the technology based on their concerns about possible adverse effects on human health, the environment, and ethical considerations. At the same time, others are concerned that the technology is not reaching its potential to improve human health and the environment because of stringent regulations and reduced public funding to develop products offering more benefits to society. While the debate about these and other questions related to the genetic engineering techniques of the first 20 years goes on, emerging genetic-engineering technologies are adding new complexities to the conversation. Genetically Engineered Crops builds on previous related Academies reports published between 1987 and 2010 by undertaking a retrospective examination of the purported positive and adverse effects of GE crops and to anticipate what emerging genetic-engineering technologies hold for the future. This report indicates where there are uncertainties about the economic, agronomic, health, safety, or other impacts of GE crops and food, and makes recommendations to fill gaps in safety assessments, increase regulatory clarity, and improve innovations in and access to GE technology.
Download or read book Gene Drives on the Horizon written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-08-28 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators.
Download or read book Evolution and Impact of Transposable Elements written by Pierre Capy and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: During the last 50 years, the perception oftransposable elements (TEs) has changed considerably from selfish DNA to sequences that may contribute significantly to genome function and evolution. The recent increased interest in TEs is based on the realization that they are a major genetic component (at least 10--20%) of all organisms and a major contributor to the mutation process. It is currently estimated that 70--80% of spontaneous mutations are the result of TE-mediated insertions, deletions, or chromosomal rearrangements. Thus, it seems at least plausible that TEs may playa significant role in the adaptation and evolution of natural populations and species. The ubiquity of TEs suggests that they are an old component of genomes which have been vertically transmitted through generations over evolutionary time. However, detailed analyses carried out over the last 20 years have revealed several unusual features of TE evolution: (i) TEs can be horizontally transferred between species; (ii) TE evolutionary rates can be dramatically increased by specific inactivation processes, such as the RIP (Repeat Induced Point mutation) mechanism in fungi; (iii) TEs can influence the regulation of other TEs by insertion or deletion; (iv) different classes of TEs in even distantly related species can be remarkably similar in both structure and function.
Download or read book The Oil Palm Genome written by Maizura Ithnin and published by Springer Nature. This book was released on 2020-06-12 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book compiles the fundamental advances resulting from of oil-palm genome and transcriptome sequencing, and describes the challenges faced and strategies applied in sequencing, assembling and annotating oil palm genome sequences. The availability of genome and transcriptome data has made the mining of a high number of new molecular markers useful for genetic diversity as well as marker-trait association studies and the book presents high-throughput genotyping platforms, which allow the detection of QTL regions associated with interesting oil palm traits such as oil unsaturation and yield components using classical genetic and association mapping approaches. Lastly, it also presents the discovery of major genes governing economically important traits of the oil palm. Covering the history of oil palm expansion, classical and molecular cytogenetics, improvements based on wild and advanced genetic materials, and the science of oil palm breeding, the book is a valuable resource for scientists involved in plant genetic research.
Download or read book Variation and Evolution in Plants and Microorganisms written by National Academy of Sciences and published by National Academies Press. This book was released on 2000-10-11 with total page 353 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The present book is intended as a progress report on [the] synthetic approach to evolution as it applies to the plant kingdom." With this simple statement, G. Ledyard Stebbins formulated the objectives of Variation and Evolution in Plants, published in 1950, setting forth for plants what became known as the "synthetic theory of evolution" or "the modern synthesis." The pervading conceit of the book was the molding of Darwin's evolution by natural selection within the framework of rapidly advancing genetic knowledge. At the time, Variation and Evolution in Plants significantly extended the scope of the science of plants. Plants, with their unique genetic, physiological, and evolutionary features, had all but been left completely out of the synthesis until that point. Fifty years later, the National Academy of Sciences convened a colloquium to update the advances made by Stebbins. This collection of 17 papers marks the 50th anniversary of the publication of Stebbins' classic. Organized into five sections, the book covers: early evolution and the origin of cells, virus and bacterial models, protoctist models, population variation, and trends and patterns in plant evolution.
