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Books on the topic 'Genomic trait'

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Author: Grafiati

Published: 25 May 2024

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1

Fontanesi, Luca, ed. The genetics and genomics of the rabbit. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781780643342.0000.

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Abstract The purpose of the book is to present in one location a comprehensive overview of the progress of genetics in the rabbit, with a modern vision that integrates genomics to obtain a complete picture of the state of the art and of the applications in this species, defined according to the multiple uses and multi-faceted places that this species has in applied and fundamental biology. The 18 chapters cover several fields of genetics and genomics: Chapters 1 and 2 present the rabbit within the evolutionary framework, including the systematics, its domestication and an overview of the genetic resources (breeds and lines) that have been developed after domestication. Chapters 3-5 cover the rabbit genome, cytogenetics and genetic maps and immunogenetics in this species. Chapters 6-8 present the genetics and molecular genetics of coat colours, fibre traits and other morphological traits and defects. Chapters 9-13 cover the genetics of complex traits (disease resistance, growth and meat production traits, reproduction traits), reproduction technologies and genetic improvement in the meat rabbits. Chapters 14-18 present the omics vision, the biotech and biomodelling perspectives and applications of the rabbit. This book is addressed to a broad audience, including students, teachers, researchers, veterinarians and rabbit breeders.

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2

Lantbruksuniversitet, Sveriges, ed. Genome analysis of quantitative trait loci in the pig. Uppsala: Sveriges Lantbruksuniversitet, 1997.

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3

Gloyn, Anna L., and Mark I. McCarthy. Genetics in diabetes: Type 2 diabetes and related traits. Basel: Karger, 2014.

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4

1955-, Saxton Arnold Myron, and SAS Institute, eds. Genetic analysis of complex traits using SAS. Cary, N.C: SAS Institute, 2004.

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5

Nōrin Suisan Gijutsu Kaigi. Jimukyoku., ed. Yūyō idenshi katsuyō no tame no shokubutsu (ine) dōbutsu genomu kenkyū, ine genomu no jūyō keishitsu kanren idenshi no kinō kaimei =: Functional analysis of genes relevant to agriculturally important traits in rice genome. Tōkyō: Nōrin Suisan Gijutsu Kaigi Jimukyoku, 2009.

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6

Maroni, Gustavo. Molecular and Genetic Analysis of Human Traits. New York: John Wiley & Sons, Ltd., 2007.

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7

Nōrin Suisan Gijutsu Kaigi. Jimukyoku., ed. Genomu ikushu ni yoru kōritsuteki hinshu ikusei gijutsu no kaihatsu, QTL idenshi kaiseki no suishin =: Genetic and molecular dissection of quantitative traits in rice. Tōkyō: Nōrin Suisan Gijutsu Kaigi Jimukyoku, 2009.

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8

Nōrin Suisan Gijutsu Kaigi. Jimukyoku., ed. Genomu ikushu ni yoru kōritsuteki hinshu ikusei gijutsu no kaihatsu, QTL idenshi kaiseki no suishin =: Genetic and molecular dissection of quantitative traits in rice. Tōkyō: Nōrin Suisan Gijutsu Kaigi Jimukyoku, 2009.

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9

Saunak, Sen, and SpringerLink (Online service), eds. A Guide to QTL Mapping with R/qtl. New York, NY: Springer-Verlag New York, 2009.

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10

Genomic Selection in Animals. Wiley-Blackwell, 2016.

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11

Weller, Joel. Genomic Selection in Animals. Wiley & Sons, Limited, John, 2016.

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12

Weller, Joel. Genomic Selection in Animals. Wiley & Sons, Incorporated, John, 2016.

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13

Weller, Joel. Genomic Selection in Animals. Wiley & Sons, Incorporated, John, 2016.

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14

Walsh, Bruce, and Michael Lynch. Evolution and Selection of Quantitative Traits. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.001.0001.

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Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.

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15

Gianola, Daniel, and Gustavo De Los Campos. Prediction of Complex Traits Using Genomic Data. Taylor & Francis Group, 2023.

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16

Xu, Shizhong. Principles of Statistical Genomics. Springer London, Limited, 2012.

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17

Xu, Shizhong. Principles of Statistical Genomics. Springer, 2014.

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18

Principles Of Statistical Genomics. Springer-Verlag New York Inc., 2008.

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19

Renner, Tanya, Tianying Lan, Kimberly M. Farr, Enrique Ibarra-Laclette, Luis Herrera-Estrella, Stephan C. Schuster, Mitsuyasu Hasebe, Kenji Fukushima, and Victor A. Albert. Carnivorous plant genomes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198779841.003.0011.

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Carnivorous plant genome research has focused on members of the Lamiales and Oxalidales; the most complete sequences are for Utricularia gibba and Cephalotus follicularis. The size-limited U. gibba genome highlights the importance of small-scale tandem duplications, which likely play roles in this species’ carnivorous adaptation. Sequencing of the C. follicularis genome detected adaptive changes that may explain the evolution of traits associated with attraction, trapping, digestion, and absorption. Functional consequences of genes putatively missing in the U. gibba genome, yet present in other angiosperms, may have influenced the evolution of polyploidy, physiology, and a rootless Bauplan. Additional draft nuclear genomes and transcriptomes are available for carnivorous Caryophyllales, Ericales, Lamiales, and Poales, but are limited in quantity and quality. Chloroplast genomes of carnivorous Lentibulariaceae have revealed interesting patterns of gene loss, alterations in the proportion of repeat DNA, and plastome-wide increases in substitution rates.

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20

Xu, Peng, Lior David, Paulino Martinez, and Gen Hua Yue, eds. Genetic Dissection of Important Traits in Aquaculture: Genome-scale Tools Development, Trait Localization and Regulatory Mechanism Exploration. Frontiers Media SA, 2020. http://dx.doi.org/10.3389/978-2-88963-914-4.

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21

Lanciego, José Luis, Floris G. Wouterlood, and Laszlo Zaborszky. Neuroanatomical Tract-Tracing: Molecules, Neurons, and Systems. Springer, 2006.

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22

Lanciego, José Luis, Floris G. Wouterlood, and Laszlo Zaborszky. Neuroanatomical Tract-Tracing: Molecules, Neurons, and Systems. Springer, 2010.

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23

Kole, Chittaranjan. Genomics and Breeding for Climate-Resilient Crops: Vol. 2 Target Traits. Springer London, Limited, 2013.

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24

Kole, Chittaranjan. Genomics and Breeding for Climate-Resilient Crops: Vol. 2 Target Traits. Springer, 2015.

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25

Kole, Chittaranjan. Genomics and Breeding for Climate-Resilient Crops: Vol. 2 Target Traits. Springer, 2013.

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26

Hartl, Daniel L. A Primer of Population Genetics and Genomics. Oxford University Press, 2020. http://dx.doi.org/10.1093/oso/9780198862291.001.0001.

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A Primer of Population Genetics and Genomics, 4th edition, has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics. Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention. This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.

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27

Genetic Analysis of Complex Traits Using SAS. SAS Institute, 2004.

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28

Walsh, Bruce, and Michael Lynch. Changes in Quantitative Traits Over Time. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198830870.003.0001.

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Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. This chapter provides a historical overview of the study of such traits and their connections with traditional and molecular population genetics, applied breeding, and evolutionary theory.

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29

Pontarotti, Pierre. Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods. Springer, 2018.

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30

Pontarotti, Pierre. Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods. Springer, 2016.

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31

Pontarotti, Pierre. Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods. Springer London, Limited, 2016.

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32

Oziel, Adeline M. Mapping of quantitative trait loci for malting quality in a winter X spring barley (Hordeum vulgare, L.) cross. 1993.

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33

Haghighi, Afshin Borhani, and Bernadette Kalman. Other Proven and Putative Autoimmune Disorders of the CNS. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0094.

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Behcet’s Disease (BD) is a multiorgan disorder characterized by oral and genital ulceration, uveitis, and dermatological symptoms. BD is most prevalent in the Mediterranean countries and East Asia, but also occurs in Europe and North America. The etiology remains unknown. Evidence suggests that BD is an autoimmune disorder with complex traits. Neuro-Behcet’s Syndome (NBS) develops in about 5% to 30% of patients with BD and presents with parenchymal or nonparenchymal pathology. The course of NBS is highly variable. Treatment strategies include modulations of the immune response and tissue degeneration, along with symptomatic medications. Main directions of current research include genomic studies, biomarker discovery, and inventive drug- development strategies.

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34

Yūyō idenshi katsuyō no tame no shokubutsu (ine) dōbutsu genomu kenkyū, ine genomu no jūyō keishitsu kanren idenshi no kinō kaimei =: Functional analysis of genes relevant to agriculturally important traits in rice genome. Tōkyō: Nōrin Suisan Gijutsu Kaigi Jimukyoku, 2009.

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35

Pontarotti, Pierre. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. Springer, 2017.

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36

Pontarotti, Pierre. Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts. Springer, 2018.

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37

(Editor), Laszlo Zaborszky, Floris G. Wouterlood (Editor), and J. L. Lanciego (Editor), eds. Neuroanatomical Tract-Tracing: Molecules, Neurons, and Systems. Springer, 2006.

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38

Levinson, Douglas F., and Walter E. Nichols. Genetics of Depression. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0024.

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Major depressive disorder (MDD) is a common and heterogeneous complex trait. Twin heritability is 35%–40%, perhaps higher in severe/recurrent cases. Adverse life events (particularly during childhood) increase risk. Current evidence suggests some overlap in genetic factors among MDD, bipolar disorder, and schizophrenia. Large genome-wide association studies (GWAS) are now proving successful. Polygenic effects of common SNPs are substantial. Findings implicate genes with effects on synaptic development and function, including two obesity-associated genes (NEGR1 and OLFM4), but not previous “candidate genes.” It can now be expected that larger GWAS samples will produce additional associations that shed new light on MDD genetics.

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39

Molecular and Genetic Analysis of Human Traits. Blackwell Publishing Limited, 2001.

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40

Maroni, Gustavo. Molecular and Genetic Analysis of Human Traits. Wiley & Sons, Limited, John, 2008.

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41

Hochschild, Jennifer, and Maya Sen. Americans’ Attitudes on Individual or Racially Inflected Genetic Inheritance. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190465285.003.0003.

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This chapter proffers a political science perspective on how Americans view the ways in which genetics affect identity. It lays the groundwork for exploring possible relationships in the eyes of the public between genetics and race, by developing hypotheses based mainly on extrapolations from popular media or American history. Next the chapter introduces a 2011 public opinion survey of approximately 4,000 US adults. The Genomics Knowledge, Attitudes, and Politics Survey includes questions designed to reveal Americans' views about the importance of genetics in explaining various traits, behaviors, and diseases. The chapter then shows that respondents' understanding of the relationships among race, genes, and phenotypes is coherent and sensible (regardless of whether it is right or wrong).

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42

Stotz, Karola, and Paul Griffiths. A Developmental Systems Account of Human Nature. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198823650.003.0004.

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We argue here that to understand human nature is to understand the plastic process of human development and the diversity it produces. Drawing on the framework of developmental systems theory and the idea of developmental niche construction, we argue that human nature is not embodied in only one input to development, such as the genome, and that it should not be confined to universal or typical human characteristics. Both similarities and certain classes of differences are explained by a human developmental system that reaches well out into the ‘environment’. We point to a significant overlap between our account and the ‘life history trait cluster’ account of Grant Ramsey, and defend the developmental systems account against the accusation that trying to encompass developmental plasticity and human diversity leads to an unmanageably complex account of human nature.

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43

Kan, Carol, and Ma-Li Wong. Genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198789284.003.0004.

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An association between type 2 diabetes mellitus (T2DM) and depression has been reported in epidemiological studies. Finding a genetic overlap between T2DM and depression will provide evidence to support a common biological pathway to both disorders. Genetic correlations observed from twin studies indicate that a small magnitude of the variance in liability can be attributed to genetic factors. However, no genetic overlap has been observed between T2DM and depression in genome-wide association studies using both the polygenic score and the linkage disequilibrium score regression approaches. Clarifying the shared heritability between these two complex traits is an important next step towards better therapy and treatment. Another area that needs to be explored is gene–environment interaction, since genotypes can affect an individual’s responses to the environment and environment can differentially affect genotypes expression.

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44

Distel, Marijn A., and Marleen H. M. de Moor. Genetic Influences on Borderline Personality Disorder. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199997510.003.0007.

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Borderline personality disorder (BPD) tends to “run in families.” Twin and twin family studies show that BPD is moderately heritable, with some evidence for nonadditive gene action. BPD co-occurs with Axis I and other Axis II disorders, as well as with a certain profile of normal personality traits. Multivariate twin (family) studies have shown that these phenotypic associations are partly due to genetic associations, and this is observed most strongly for BPD and neuroticism. Candidate gene-finding studies for BPD suggest the possible role of genes in the serotonergic and dopaminergic system, but this needs to be confirmed in larger genome-wide studies. Future studies will complement the knowledge described in this chapter to enable us to move toward a comprehensive model of the development of BPD in which biological and environmental influences on BPD are integrated.

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45

Tarr, Anita, and Donna R. White, eds. Posthumanism in Young Adult Fiction. University Press of Mississippi, 2018. http://dx.doi.org/10.14325/mississippi/9781496816696.001.0001.

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Posthumanism in Young Adult Fiction: Finding Humanity in a Posthuman World, edited by Anita Tarr and Donna White, is a collection of twelve essays analyzing young adult science fiction and fantasy in terms of how representative contemporary YA books’ authors describe and their characters portray elements of posthumanist attitudes. The authors give a brief survey of theorists’ discussions of how posthumanism rejects—but does not entirely forsake—liberal humanist tenets. Primarily, posthumanism calls for embracing the Other, eliminating binaries that separate human and nonhuman, human and nature, organic and inorganic, stressing the process of always-becoming. Due to technological enhancements, we should recognize that our species is changing, as it always has, becoming more networked and communal, fluid and changeable. Posthumanism does not mandate cyborgs, cloning, genetic enhancement, animal-human hybrids, mutations, advanced prosthetics, and superhuman strengths—although all of these are discussed in the collected essays. Posthumanism generally upholds liberal humanist values of compassion, fairness, and ethical responsibility, but dismantles the core of anthropocentrism: the notion that humans are superior and dominant over all other species and have the right to control, exploit, destroy, or marginalize those who are not the ideal white, able-bodied male. The more we discover about humans, the more we question our exceptionality; that is, since we co-evolved with many other organisms, especially bacteria, there is no DNA genome that is uniquely human; since we share many traits with animals, there is no single trait that defines us as human or as not human (such as using tools, speaking language, having a soul, expressing emotions, being totally organic, having a sense of wonder). The twelve essayists do not propose that YA fiction should offer guidelines for negotiating posthumanist subjectivity—being fragmented and multiple, networked vulnerable—though many of the novels analyzed actually do this. Other novelists bring their adolescent characters to the brink, but do not allow them to move beyond the familiar structures of society, even if they are rebelling against those very structures. Indeed, adolescence and posthumanism share many elements, especially anxieties about future possibilities, embracing new ideas and new selves, and being in a liminal state of in-between-ness that does not resolve itself. In other words, young adult fiction is the ideal venue to explore how we are now or we might in the future maintain our humanity in a posthuman world.

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46

Jex, Aaron R., Rachel M. Chalmers, Huw V. Smith, Giovanni Widmer, Vincent McDonald, and Robin B. Gasser. Cryptosporidiosis. Oxford University Press, 2011. http://dx.doi.org/10.1093/med/9780198570028.003.0053.

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Cryptosporidium species represent a genus of parasitic protozoa (Apicomplexa) that are transmitted via the faecal-oral route and commonly infect the epithelial tissues of the gastric or intestinal (or sometimes the respiratory) tract of many vertebrates, including humans. Infection occurs following the ingestion of viable and resistant oocysts, through direct host-to-host contact or in contaminated food, drinking or recreational water. Infection can be transmitted via anthroponotic (human-to-human, human-to-animal) or zoonotic (animal-to-human or animal-to-animal) pathways, depending upon the species of Cryptosporidium. Although infection can be asymptomatic, common symptoms of disease (cryptosporidiosis) include diarrhoea, colic (abdominal pain), nausea or vomiting, dehydration and/or fever. In humans, cryptosporidial infection in immunocompetent patients is usually short-lived (days to weeks) and eliminated following the stimulation of an effective immune response. However, infection in immunodeficient individuals (e.g., those with HIV/AIDS) can be chronic and fatal (in the absence of immunotherapy), as there are few effective anti-cryptosporidial drugs and no vaccines available. The present chapter provides an account of the history, taxonomy and biology, genomics and genetics of Cryptosporidium, the epidemiology, pathogenesis, treatment and control of cryptosporidiosis and the advances in tools for the identification and characterisation of Cryptosporidium species and the diagnosis of cryptosporidiosis.

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47

MacGregor, Alex, Ana Valdes, and Frances M. K. Williams. Genetics of osteoarthritis. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0044.

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In this chapter we outline the approaches which have been adopted to identify genetic variants predisposing to osteoarthritis (OA), a condition long recognized as having a heritable component. Such routes to their identification include examining mendelian traits in which OA is a feature, candidate gene studies based on knowledge of OA pathobiology, linkage analysis in related individuals, and, more recently, genome-wide association studies in large samples of unrelated individuals. It is increasingly evident that the main symptom deriving from OA—notably joint pain—also has a genetic basis but this is differs from that underlying OA. Variants convincingly shown to predispose to OA lie in the GDF5 and MCF2L genes and in the chr7 cluster mapping to the COG5 gene, in addition to the ASPN gene in Asian populations. Those associated with pain in OA include TRPV1 and PACE4. Epigenetic influences are also being explored in both the pathogenesis of OA and the variation of pain processing.

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48

(Editor), Jeffrey C. Hall, Jay C. Dunlap (Editor), Theodore Friedmann (Editor), and Francesco Giannelli (Editor), eds. Advances in Genetics, Volume 41 (Advances in Genetics). Academic Press, 1999.

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49

Holroyd, Christopher R., Nicholas C. Harvey, Mark H. Edwards, and Cyrus Cooper. Environment. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0038.

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Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.

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50

Holroyd, Christopher R., Nicholas C. Harvey, Mark H. Edwards, and Cyrus Cooper. Environment. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199642489.003.0038_update_001.

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Musculoskeletal disease covers a broad spectrum of conditions whose aetiology comprises variable genetic and environmental contributions. More recently it has become clear that, particularly early in life, the interaction of gene and environment is critical to the development of later disease. Additionally, only a small proportion of the variation in adult traits such as bone mineral density has been explained by specific genes in genome-wide association studies, suggesting that gene-environment interaction may explain a much larger part of the inheritance of disease risk than previously thought. It is therefore critically important to evaluate the environmental factors which may predispose to diseases such as osteorthritis, osteoporosis, and rheumatoid arthritis both at the individual and at the population level. In this chapter we describe the environmental contributors, across the whole life course, to osteoarthritis, osteoporosis and rheumatoid arthritis, as exemplar conditions. We consider factors such as age, gender, nutrition (including the role of vitamin D), geography, occupation, and the clues that secular changes of disease pattern may yield. We describe the accumulating evidence that conditions such as osteoporosis may be partly determined by the early interplay of environment and genotype, through aetiological mechanisms such as DNA methylation and other epigenetic phenomena. Such studies, and those examining the role of environmental influences across other stages of the life course, suggest that these issues should be addressed at all ages, starting from before conception, in order to optimally reduce the burden of musculoskeletal disorders in future generations.

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