Download or read book Quantitative and Genomic Analyses of Inbreeding in Dairy Cattle Populations written by Bayode Makanjuola and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The overall objective of this thesis was to assess the loss of genetic diversity, estimate the adverse effects of increasing homozygosity on economically important traits and investigate at the genomic level the unique location causing the detrimental effects. To understand the pattern of genetic diversity losses, we investigated the rate of inbreeding (∆F), rate of coancestry (∆f) and effective population size (N_e) as important quantitative indicators of genetic diversity and evaluated the effect of the recent implementation of genomic selection on the loss of genetic diversity in Holstein and Jersey dairy cattle. The rate of inbreeding and coancestry were calculated using both the traditional pedigree method and genomic methods estimated from segment and marker-based approaches. The ∆F and ∆f per generation ranged from 0.62 to 1.16%. Therefore, the N_e ranged from 43 to 85 for the two breeds. This result suggests the need to implement measures and means for controlling the rate of inbreeding, which will help to manage and maintain farm animal genetic resources. Following the assessment of genetic diversity loss, the negative effects of the accumulation of inbreeding expected from the reducing N_e was investigated. More specifically, we investigated the effect of recent and ancient inbreeding on production and fertility traits in Holsteins. In general, negative effects of inbreeding were found on production and fertility traits with production traits having more significant negative effects. Interestingly, ancient inbreeding had no significant negative impact on traits analysed; however, recent inbreeding showed more adverse and significant impact on analysed traits. This result indicates that more attention should be focused on recent inbreeding. Furthermore, we sought to identify unique homozygous genomic regions (ROH) showing negative associations with production and fertility traits as well as investigating their effects. Unique ROH regions with unfavorable effects were identified for both production and fertility traits. These unique homozygous regions with negative effects on production and fertility traits were identified within and across multiple traits in almost all chromosomes. The identified harmful regions could be advantageously used in mate selection pipelines for minimizing their frequency in future generations.
Download or read book Mason s World Encyclopedia of Livestock Breeds and Breeding 2 Volume Pack written by Valerie Porter and published by CABI. This book was released on 2016-03-09 with total page 1109 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mason's World Encyclopedia of Livestock Breeds and Breeding describes breeds of livestock worldwide as well as a range of breed-related subjects such as husbandry, health and behaviour. This definitive and prestigious reference work presents easily accessible information on domestication (including wild ancestors and related species), genetics and breeding, livestock produce and markets, as well as breed conservation and the cultural and social aspects of livestock farming. Written by renowned livestock authorities, these volumes draw on the authors' lifelong interest and involvement in livestock breeds of the world, presenting a unique, comprehensive and fully cross-referenced guide to cattle, buffalo, horses, pigs, sheep, asses, goats, camelids, yak and other domesticants.
Download or read book Genomic Selection in Small Dairy Cattle Populations written by Jørn Rind Thomasen and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genetic and Genomic Analyses of Fertility and Production Traits in Dairy Cattle written by Wen Huang, 1984- and published by . This book was released on 2011 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genomic Prediction Across Dairy Cattle Populations and Breeds written by Lei Zhou and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Genomic Analysis of Male Fertility in Brown Swiss Cattle written by Hendyel Aparecida Pacheco and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation investigated bull fertility in Brown Swiss cattle. Chapter One offers an overview and an outline for the contents of the dissertation. Chapter Two provides a literature review on topics such as the importance of reproduction performance in dairy cattle, the importance of dairy bull fertility, and different genetic analyses. Chapter Three focuses on the evaluation of dairy bull fertility using confirmed pregnancy records. The analysis included both factors related to the bull under evaluation and factors associated with the cow that receives the unit of semen. The results showed that there is a substantial variation in conception rate among bulls, and the prediction of service sire fertility is feasible. These findings represent the foundation for the development of novel tools that will allow the dairy industry to make enhanced management and selection decisions on Brown Swiss male fertility. Chapter Four focuses on understanding the genetic basis of male fertility in Italian Brown Swiss dairy cattle. The analyses included whole-genome scans and gene-set analyses to identify genomic regions, individual genes, and genetic mechanisms affecting Brown Swiss bull fertility. These analyses identified genomic regions, individual genes, and gene-set related to male fertility. Additionally, the results showed genomic regions with marked non-additive effects associated with bull fertility. This comprehensive study contributes to a better understanding of the genetic basis of male fertility in cattle. Chapter Five aims to assess the feasibility of predicting male fertility in Brown Swiss cattle using genomic data under different scenarios, including within-country, across-country, and incorporating markers with large effect. The analyses included the use of linear kernel-based regression models fitting all SNPs or incorporating markers with large effect, using five-fold cross-validation. The findings showed that the prediction of service sire fertility using genomic data achieves moderate to high accuracy and the inclusion of markers with large effect is a promising alternative to the standard approach. However, the use of an across-country reference population did not outperform the standard within-country approach. Genomic predictions of service sire fertility can help Brown Swiss breeders make accurate genome-guided selection and management decisions. Chapter Six evaluates the presence of homozygosity in Italian Brown Swiss dairy cattle and assesses its association with bull fertility. The findings showed that inbreeding and increased homozygosity have a negative impact on male fertility in Italian Brown Swiss cattle. The quantification of homozygosity can contribute to minimizing the inbreeding rate and avoid its negative effect on fitness-related traits, such as male fertility. Lastly, a final Chapter is provided with some concluding remarks.
Download or read book Outlier Analysis written by Charu C. Aggarwal and published by Springer. This book was released on 2016-12-10 with total page 481 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides comprehensive coverage of the field of outlier analysis from a computer science point of view. It integrates methods from data mining, machine learning, and statistics within the computational framework and therefore appeals to multiple communities. The chapters of this book can be organized into three categories: Basic algorithms: Chapters 1 through 7 discuss the fundamental algorithms for outlier analysis, including probabilistic and statistical methods, linear methods, proximity-based methods, high-dimensional (subspace) methods, ensemble methods, and supervised methods. Domain-specific methods: Chapters 8 through 12 discuss outlier detection algorithms for various domains of data, such as text, categorical data, time-series data, discrete sequence data, spatial data, and network data. Applications: Chapter 13 is devoted to various applications of outlier analysis. Some guidance is also provided for the practitioner. The second edition of this book is more detailed and is written to appeal to both researchers and practitioners. Significant new material has been added on topics such as kernel methods, one-class support-vector machines, matrix factorization, neural networks, outlier ensembles, time-series methods, and subspace methods. It is written as a textbook and can be used for classroom teaching.
Download or read book Genomic Inbreeding Estimation and Effective Population Size of Four South African Dairy Breeds written by Janka Limper and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this study 1002 dairy cattle, representing four South African dairy breeds (Ayrshire, Holstein, Jersey and SA Dairy Swiss) were genotyped at the ARC-Biotechnology Platform (Onderstepoort, 0110) with the Infinium Bovine SNP 50-24 V3.0 Beadchip. Genotypes for these animals originated from the Dairy Genomics Program (DGP) as part of an ongoing study aimed at integrating genomic information into the selection of South African dairy cattle. Genotypic data for all registered, genotyped animals participating in Logix Milk Recording was received from SA Stud Book, representing the Ayrshire, Holstein and Jersey breeds. The SA Dairy Swiss had no genotypic data available, thus hair samples from 62 individual animals were collected from three registered breeders to represent this breed. Raw Illumina genotype files were received via a downstream link from the ARC. These files were converted into PLINK (Purcell et al., 2007) files using SNP Convert v1.0 (Nicolazzi et al., 2016) for further analysis. The aim of the study was to estimate genomic inbreeding and effective population sizes for these breeds. The average call rate obtained across the samples was 99%. The observed heterozygosity values obtained for the populations were 0.355, 0.359, 0.340 and 0.345 for the Ayrshire, Holstein, Jersey and SA Dairy Swiss, respectively. Linkage disequilibrium (LD) estimation revealed average r2 values of 0.181 (Ayrshire), 0.311 (Holstein), 0.349 (Jersey) and 0.291 (SA Dairy Swiss). Two different inbreeding estimates were calculated individual inbreeding coefficients (FIS) and runs of homozygosity (FROH) and correlations were estimated between the inbreeding estimates. Pedigree-based inbreeding (FPED) estimates were received from SA Stud Book for the Ayrshire, Holstein and Jersey and compared to the genomic inbreeding estimates. The mean individual inbreeding coefficient (FIS) was -0.039 (Ayrshire), -0.007 (Holstein), -0.010 (Jersey) and -0.019 (SA Dairy Swiss), which indicates effective on farm management against inbreeding in the populations in this study. FROH > 16 Mb ranged from 0.227 to 0.255 (Ayrshire and Holstein). These relatively high FROH values indicate recent inbreeding in these populations. The strongest correlations were observed between FIS and FROH>1 ranging from 0.454 to 0.686 (SA Dairy Swiss and Jersey) respectively, while lower correlations were found between FIS and FROH>16, ranging from 0.071 to 0.377 (SA Dairy Swiss and Jersey) respectively. Very low correlations were found between FPED and FROH, which may have been due to shallow pedigree depth. The highest correlation between FPED and FROH (0.186) was observed for the Holstein at an ROH length of 4000kb. The Ne for the four populations included in the study has decreased to 117, 133, 120 and 112 for the Ayrshire, Holstein, Jersey and SA Dairy Swiss, respectively from approximately five generations ago. The four populations were separated into four separate clusters using principal component analysis (PCA). This corresponded with ADMIXTURE where the populations were also separated into the four respective populations. This indicates that the four populations are genetically distinct and were developed as separate breeds which is also consistent with the history of the four breeds. The high levels of genomic inbreeding could be explained by the increased use of artificial insemination in the populations studied. This is a concern as an increase in inbreeding leads to a reduction in the effective population size which was also evident in the populations included in the study.
Download or read book INTRACELLULAR PANGENESIS written by HUGO DE. VRIES and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mendel s Principles of Heredity written by William Bateson and published by . This book was released on 1902 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bateson named the science "genetics" in 1905-1906. This is the first textbook in English on the subject of genetics.
Download or read book Consanguinity in Context written by Alan H. Bittles and published by Cambridge University Press. This book was released on 2012-05-24 with total page 325 pages. Available in PDF, EPUB and Kindle. Book excerpt: An essential guide to this major contemporary issue, Consanguinity in Context is a uniquely comprehensive account of intra-familial marriage. Detailed information on past and present religious, social and legal practices and prohibitions is presented as a backdrop to the preferences and beliefs of the 1100+ million people in consanguineous unions. Chapters on population genetics, and the role of consanguinity in reproductive behaviour and genetic variation, set the scene for critical analyses of the influence of consanguinity on health in the early years of life. The discussion on consanguinity and disorders of adulthood is the first review of its kind and is particularly relevant given the ageing of the global population. Incest is treated as a separate issue, with historical and present-day examples examined. The final three chapters deal in detail with practical issues, including genetic testing, education and counselling, national and international legislation and imperatives, and the future of consanguineous marriage worldwide.
Download or read book Animal Genomics written by Bhanu P. Chowdhary and published by S. Karger AG (Switzerland). This book was released on 2003 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This publication provides an update on the current status of gene maps in different livestock and pet/companion animal species. The findings summarized in species specific commentaries and original articles testify the rapid advances made in the field of animal genomics. Of significant interest is the fact that current investigations are providing headways for two important and exciting research fronts: targeted high-resolution mapping leading to the application of genomic information in addressing questions of economic and biological significance in animals, and the initiation of whole genome sequencing projects for some of the animal species. Like in humans and mice, this will set the stage for a new level of research and real time complex analysis of the genomes of these species. Animal Genomics signifies the beginning of a new era in this field and celebrates the achievements of the past 20 years of genomics research. It will be of special interest to researchers involved in genome analysis - both gross chromosomal as well as molecular - in various animal species, and to comparative and evolutionary geneticists.
Download or read book Economic Aspects of Animal Breeding written by Joel Ira Weller and published by Springer Science & Business Media. This book was released on 1994-02-28 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This important book covers economic evaluation of genetic differences in animals, determination of breeding goals within an economic context and economic evaluation of breeding programs. During the last 50 years there have been great advances made in the breeding of domesticated animal species. Most of this work has been achieved through the efforts of geneticists, and often the economic goals of such advances have not been clearly evaluated. Economic Aspects of Animal Breeding redresses the balance and provides a much needed synthesis of this most important subject. The book is divided into five sections: basic concepts; economic evaluation of genetic differences; advanced topics in selection indices; economic evaluation of breeding programs, including biotechnological aspects; crossbreeding and heterosis.
Download or read book Genetic Improvement of Cattle and Sheep written by Geoff Simm and published by Oxford University Press, USA. This book was released on 2002-11 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: * Outlines the link between genes and performance in farm animals * Shows tools for more effective genetic selection * Highlights the role and ethical implications of new reproductive and molecular genetic technologies The application of scientific methods to animal breeding has led to major improvements in the output, cost and quality of animal products over the last few decades. This book describes the principles of genetic improvement of farm livestock and the practical application of these principles to dairy cattle, beef cattle and sheep breeding. This title has been taken over by CABI Publishing from Farming Press and was originally published in 1998
Download or read book Adaptation and Fitness in Animal Populations written by Julius van der Werf and published by Springer Science & Business Media. This book was released on 2008-10-17 with total page 256 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fitness and adaptation are fundamental characteristics of plant and animal species, enabling them to survive in their environment and to adapt to the inevitable changes in this environment. This is true for both the genetic resources of natural ecosystems as well as those used in agricultural production. Extensive genetic variation exists between varieties/breeds in a species and amongst individuals within breeds. This variation has developed over very long periods of time. A major ongoing challenge is how to best utilize this variation to meet short-term demands whilst also conserving it for longer-term possible use. Many animal breeding programs have led to increased performance for production traits but this has often been accompanied by reduced fitness. In addition, the global use of genetic resources prompts the question whether introduced genotypes are adapted to local production systems. Understanding the genetic nature of fitness and adaptation will enable us to better manage genetic resources allowing us to make efficient and sustainable decisions for the improvement or breeding of these resources. This book had an ambitious goal in bringing together a sample of the world’s leading scientists in animal breeding and evolutionary genetics to exchange knowledge to advance our understanding of these vital issues.
Download or read book Molecular and Quantitative Animal Genetics written by Hasan Khatib and published by John Wiley & Sons. This book was released on 2015-03-02 with total page 336 pages. Available in PDF, EPUB and Kindle. Book excerpt: Animal genetics is a foundational discipline in the fields of animal science, animal breeding, and veterinary sciences. While genetics underpins the healthy development and breeding of all living organisms, this is especially true in domestic animals, specifically with respect to breeding for key traits. Molecular and Quantitative Animal Genetics is a new textbook that takes an innovative approach, looking at both quantitative and molecular breeding approaches. The bookprovides a comprehensive introduction to genetic principles and their applications in animal breeding. This text provides a useful overview for those new to the field of animal genetics and breeding, covering a diverse array of topics ranging from population and quantitative genetics to epigenetics and biotechnology. Molecular and Quantitative Animal Genetics will be an important and invaluable educational resource for undergraduate and graduate students and animal agriculture professionals. Divided into six sections pairing fundamental principles with useful applications, the book's comprehensive coverage will make it an ideal fit for students studying animal breeding and genetics at any level.
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
