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Poultry breeding and genetics
01 Jan 1990-Iss: 1
TL;DR: This paper presents new directions in Poultry Genetics, focusing on quantitative and qualitative Genetics of plumage, skin and eye pigmentation in chickens, and Quantitative Genetics and Selection of growth and meat production in chickens.
Abstract: Foreword. Part I. Poultry Biology. Origin and history of poultry species (R.D. Crawford). Poultry genetic resources: evolution, diversity and conservation (R.D. Crawford). Reproductive biology in relation to breeding and genetics (H.P. Van Krey). Preservation of avian cells (M.R. Bakst). II. Qualitative Genetics. Genetics of plumage, skin and eye pigmentation in chickens (J.R. Smyth, Jr.). Mutations and major variants of plumage and skin in chickens (R.G. Somes, Jr.). Mutations and major variants of muscles and skeleton in chickens (R.G. Somes, Jr.). Genetics of biochemical variants in chickens (A.A. Grunder). Mutations and major variants of the nervous system in chickens (R.D. Crawford). Mutations and major variants of other body systems in chickens (R.G. Somes, Jr. et al.). Lethal mutant traits in chickens (R.G. Somes, Jr.). Mutations and major variants in turkeys (T.F. Savage). Mutations and major variants in Japanese quail (K.M. Cheng, M. Kimura). Mutations and major variants in guinea fowl (R.G. Somes, Jr.). Mutations and major variants in ring-necked pheasants (R.G. Somes, Jr.). Mutations and major variants in domestic ducks (F.M. Lancaster). Mutations and major variants in muscovy ducks (C. Fedeli Avanzi, R.D. Crawford). Mutations and major variants in geese (R.O. Hawes). Cytology and cytogenetics (J.J. Bitgood, R.N. Shoffner). Pleiotropic and associated effects of major genes (P. Merat). Linkage relationships and gene mapping (J.J. Bitgood, R.G. Somes, Jr.). III. New Directions in Poultry Genetics. Immunogenetics (S.J. Lamont, R.R. Dietert). Molecular genetics (G. Bulfield). Genetic engineering (R.M. Shuman). IV. Quantitative Genetics and Selection. Genetics of growth and meat production in chickens (J.R. Chambers). Genetics of growth and meat production in turkeys (E.G. Buss). Genetics of growth and meat production in other galliforms (H.L. Marks). Genetics of growth and meat production in waterfowl (H. Pingel). Genetics of egg production in chickens (R.W. Fairfull, R.S. Gowe). Genetics of egg production in other galliforms (H.L. Marks). Genetics of egg production and reproduction in waterfowl (H. Pingel). Genetic variation in egg composition (K.W. Washburn). Disease genetics (J.S. Gavora). Nutritional genetics (R.A.E. Pym). Behavioral genetics (P.B. Siegel, E.A. Dunnington). Genotype x environment interactions (A.K. Sheridan). Heterosis (R.W. Fairfull). Genetic controls in selection (R.S. Gowe, R.W. Fairfull). Inbreeding (H. Abplanalp). V. Applied Breeding and Selection. Industrial breeding and selection (P. Hunton). Breeding and selection by poultry fanciers (W.C. Carefoot). Breeding and selection programs in developing countries (T.K. Mukherjee). Author Index. Subject Index.
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TL;DR: A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
Abstract: We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
2,579 citations
TL;DR: The authors used massively parallel sequencing to identify selective sweeps of favorable alleles and candidate mutations that have had a prominent role in the domestication of domestic chickens and their subsequent specialization into broiler (meat-producing) and layer (egg-consuming) chickens.
Abstract: Domestic animals are excellent models for genetic studies of phenotypic evolution They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens We have generated 445-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research
943 citations
TL;DR: Conceptual issues in evolutionary biology from an endocrinological perspective are approached, noting that single hormones typically act on several target tissues and thereby mediate suites of correlated phenotypic traits.
Abstract: We approach conceptual issues in evolutionary biology from an endocrinological perspective, noting that single hormones typically act on several target tissues and thereby mediate suites of correlated phenotypic traits. When several components of such a suite are beneficial, an important evolutionary question is whether all are adaptations or some are exaptations. The answer may depend on whether the traits arose in response to selection on variation in systemic levels of the hormone on variation in responsiveness of target tissues to invariant levels of the hormone. If the former, selection probably acted directly on fewer than all traits; beneficial traits arising indirectly would be exaptations. In contrast, multiple beneficial traits that arose out of independent changes in target‐tissue sensitivity to invariant hormone levels could all be adaptations. Knowledge of specific hormonal mechanisms as well as of historical selective regimes will be necessary to draw such distinctions. Endocrine c...
588 citations
Zhejiang University1, Beijing Institute of Genomics2, University of Washington3, Peking University4, Chinese Academy of Sciences5, China Agricultural University6, Washington University in St. Louis7, Uppsala University8, Wageningen University and Research Centre9, Lawrence Livermore National Laboratory10, United States Department of Energy11, University of Illinois at Urbana–Champaign12, Iowa State University13, The Roslin Institute14, United States Department of Agriculture15, Swedish University of Agricultural Sciences16, Karolinska Institutet17, National University of Singapore18, University of Oxford19, University of Manchester20, University of Sheffield21
TL;DR: This map is based on a comparison of the sequences of three domestic chicken breeds with that of their wild ancestor, red jungle fowl, and indicates that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds.
Abstract: We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.
406 citations
TL;DR: Different clades may originate from different regions, such as Yunnan, South and Southwest China and/or surrounding areas (i.e., Vietnam, Burma, and Thailand), and the Indian subcontinent, which support the theory of multiple origins in South and Southeast Asia.
401 citations
Cites background from "Poultry breeding and genetics"
...Historically, there have been two hypotheses about chicken domestication: one that defends a monophyletic origin and another that defends multiple origins from several Gallus subspecies (Crawford, 1990, 1995)....
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...…the red jungle fowl—G. g. gallus in Thailand and its adjacent regions, G. g. spadiceus in Burma and Yunnan Province of China, G. g. jabouillei in southern China and Vietnam, G. g. murghi in India, and G. g. bankiva in the Java islands (Crawford, 1990, 1995; Delacour, 1957; Howard and Moore, 1984)....
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...After Fumihito team studies, other scholars suggested the possibility of multiple origins of domestic chicken without providing genetic evidence (Crawford, 1990; Moiseyeva, 1998)....
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