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Publisher: John Wiley and Sons   (Total: 1582 journals)

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Showing 1 - 200 of 1582 Journals sorted alphabetically
Abacus     Hybrid Journal   (Followers: 11, SJR: 0.48, h-index: 22)
About Campus     Hybrid Journal   (Followers: 5)
Academic Emergency Medicine     Hybrid Journal   (Followers: 53, SJR: 1.385, h-index: 91)
Accounting & Finance     Hybrid Journal   (Followers: 42, SJR: 0.547, h-index: 30)
ACEP NOW     Free  
Acta Anaesthesiologica Scandinavica     Hybrid Journal   (Followers: 50, SJR: 1.02, h-index: 88)
Acta Archaeologica     Hybrid Journal   (Followers: 131, SJR: 0.101, h-index: 9)
Acta Geologica Sinica (English Edition)     Hybrid Journal   (Followers: 3, SJR: 0.552, h-index: 41)
Acta Neurologica Scandinavica     Hybrid Journal   (Followers: 5, SJR: 1.203, h-index: 74)
Acta Obstetricia et Gynecologica Scandinavica     Hybrid Journal   (Followers: 15, SJR: 1.197, h-index: 81)
Acta Ophthalmologica     Hybrid Journal   (Followers: 5, SJR: 0.112, h-index: 1)
Acta Paediatrica     Hybrid Journal   (Followers: 54, SJR: 0.794, h-index: 88)
Acta Physiologica     Hybrid Journal   (Followers: 7, SJR: 1.69, h-index: 88)
Acta Polymerica     Hybrid Journal   (Followers: 9)
Acta Psychiatrica Scandinavica     Hybrid Journal   (Followers: 35, SJR: 2.518, h-index: 113)
Acta Zoologica     Hybrid Journal   (Followers: 5, SJR: 0.459, h-index: 29)
Acute Medicine & Surgery     Hybrid Journal   (Followers: 2)
Addiction     Hybrid Journal   (Followers: 32, SJR: 2.086, h-index: 143)
Addiction Biology     Hybrid Journal   (Followers: 12, SJR: 2.091, h-index: 57)
Adultspan J.     Hybrid Journal   (SJR: 0.127, h-index: 4)
Advanced Energy Materials     Hybrid Journal   (Followers: 24, SJR: 6.411, h-index: 86)
Advanced Engineering Materials     Hybrid Journal   (Followers: 25, SJR: 0.81, h-index: 81)
Advanced Functional Materials     Hybrid Journal   (Followers: 47, SJR: 5.21, h-index: 203)
Advanced Healthcare Materials     Hybrid Journal   (Followers: 13, SJR: 0.232, h-index: 7)
Advanced Materials     Hybrid Journal   (Followers: 247, SJR: 9.021, h-index: 345)
Advanced Materials Interfaces     Hybrid Journal   (Followers: 6, SJR: 1.177, h-index: 10)
Advanced Optical Materials     Hybrid Journal   (Followers: 4, SJR: 2.488, h-index: 21)
Advanced Science     Open Access   (Followers: 4)
Advanced Synthesis & Catalysis     Hybrid Journal   (Followers: 17, SJR: 2.729, h-index: 121)
Advances in Polymer Technology     Hybrid Journal   (Followers: 13, SJR: 0.344, h-index: 31)
Africa Confidential     Hybrid Journal   (Followers: 19)
Africa Research Bulletin: Economic, Financial and Technical Series     Hybrid Journal   (Followers: 12)
Africa Research Bulletin: Political, Social and Cultural Series     Hybrid Journal   (Followers: 9)
African Development Review     Hybrid Journal   (Followers: 33, SJR: 0.275, h-index: 17)
African J. of Ecology     Hybrid Journal   (Followers: 14, SJR: 0.477, h-index: 39)
Aggressive Behavior     Hybrid Journal   (Followers: 15, SJR: 1.391, h-index: 66)
Aging Cell     Open Access   (Followers: 9, SJR: 4.374, h-index: 95)
Agribusiness : an Intl. J.     Hybrid Journal   (Followers: 6, SJR: 0.627, h-index: 14)
Agricultural and Forest Entomology     Hybrid Journal   (Followers: 14, SJR: 0.925, h-index: 43)
Agricultural Economics     Hybrid Journal   (Followers: 44, SJR: 1.099, h-index: 51)
AIChE J.     Hybrid Journal   (Followers: 28, SJR: 1.122, h-index: 120)
Alcoholism and Drug Abuse Weekly     Hybrid Journal   (Followers: 7)
Alcoholism Clinical and Experimental Research     Hybrid Journal   (Followers: 7, SJR: 1.416, h-index: 125)
Alimentary Pharmacology & Therapeutics     Hybrid Journal   (Followers: 33, SJR: 2.833, h-index: 138)
Alimentary Pharmacology & Therapeutics Symposium Series     Hybrid Journal   (Followers: 3)
Allergy     Hybrid Journal   (Followers: 50, SJR: 3.048, h-index: 129)
Alternatives to the High Cost of Litigation     Hybrid Journal   (Followers: 3)
American Anthropologist     Hybrid Journal   (Followers: 127, SJR: 0.951, h-index: 61)
American Business Law J.     Hybrid Journal   (Followers: 24, SJR: 0.205, h-index: 17)
American Ethnologist     Hybrid Journal   (Followers: 89, SJR: 2.325, h-index: 51)
American J. of Economics and Sociology     Hybrid Journal   (Followers: 28, SJR: 0.211, h-index: 26)
American J. of Hematology     Hybrid Journal   (Followers: 30, SJR: 1.761, h-index: 77)
American J. of Human Biology     Hybrid Journal   (Followers: 12, SJR: 1.018, h-index: 58)
American J. of Industrial Medicine     Hybrid Journal   (Followers: 16, SJR: 0.993, h-index: 85)
American J. of Medical Genetics Part A     Hybrid Journal   (Followers: 15, SJR: 1.115, h-index: 61)
American J. of Medical Genetics Part B: Neuropsychiatric Genetics     Hybrid Journal   (Followers: 3, SJR: 1.771, h-index: 107)
American J. of Medical Genetics Part C: Seminars in Medical Genetics     Partially Free   (Followers: 5, SJR: 2.315, h-index: 79)
American J. of Orthopsychiatry     Hybrid Journal   (Followers: 4, SJR: 0.756, h-index: 69)
American J. of Physical Anthropology     Hybrid Journal   (Followers: 35, SJR: 1.41, h-index: 88)
American J. of Political Science     Hybrid Journal   (Followers: 235, SJR: 5.101, h-index: 114)
American J. of Primatology     Hybrid Journal   (Followers: 14, SJR: 1.197, h-index: 63)
American J. of Reproductive Immunology     Hybrid Journal   (Followers: 3, SJR: 1.347, h-index: 75)
American J. of Transplantation     Hybrid Journal   (Followers: 15, SJR: 2.792, h-index: 140)
American J. on Addictions     Hybrid Journal   (Followers: 9, SJR: 0.843, h-index: 57)
Anaesthesia     Hybrid Journal   (Followers: 117, SJR: 1.404, h-index: 88)
Analyses of Social Issues and Public Policy     Hybrid Journal   (Followers: 11, SJR: 0.397, h-index: 18)
Analytic Philosophy     Hybrid Journal   (Followers: 15)
Anatomia, Histologia, Embryologia: J. of Veterinary Medicine Series C     Hybrid Journal   (Followers: 3, SJR: 0.295, h-index: 27)
Anatomical Sciences Education     Hybrid Journal   (Followers: 1, SJR: 0.633, h-index: 24)
Andrologia     Hybrid Journal   (Followers: 2, SJR: 0.528, h-index: 45)
Andrology     Hybrid Journal   (Followers: 2, SJR: 0.979, h-index: 14)
Angewandte Chemie     Hybrid Journal   (Followers: 154)
Angewandte Chemie Intl. Edition     Hybrid Journal   (Followers: 204, SJR: 6.229, h-index: 397)
Animal Conservation     Hybrid Journal   (Followers: 34, SJR: 1.576, h-index: 62)
Animal Genetics     Hybrid Journal   (Followers: 8, SJR: 0.957, h-index: 67)
Animal Science J.     Hybrid Journal   (Followers: 5, SJR: 0.569, h-index: 24)
Annalen der Physik     Hybrid Journal   (Followers: 5, SJR: 1.46, h-index: 40)
Annals of Anthropological Practice     Partially Free   (Followers: 2, SJR: 0.187, h-index: 5)
Annals of Applied Biology     Hybrid Journal   (Followers: 8, SJR: 0.816, h-index: 56)
Annals of Clinical and Translational Neurology     Open Access   (Followers: 1)
Annals of Human Genetics     Hybrid Journal   (Followers: 9, SJR: 1.191, h-index: 67)
Annals of Neurology     Hybrid Journal   (Followers: 42, SJR: 5.584, h-index: 241)
Annals of Noninvasive Electrocardiology     Hybrid Journal   (Followers: 2, SJR: 0.531, h-index: 38)
Annals of Public and Cooperative Economics     Hybrid Journal   (Followers: 9, SJR: 0.336, h-index: 23)
Annals of the New York Academy of Sciences     Hybrid Journal   (Followers: 5, SJR: 2.389, h-index: 189)
Annual Bulletin of Historical Literature     Hybrid Journal   (Followers: 12)
Annual Review of Information Science and Technology     Hybrid Journal   (Followers: 14)
Anthropology & Education Quarterly     Hybrid Journal   (Followers: 24, SJR: 0.72, h-index: 31)
Anthropology & Humanism     Hybrid Journal   (Followers: 16, SJR: 0.137, h-index: 3)
Anthropology News     Hybrid Journal   (Followers: 14)
Anthropology of Consciousness     Hybrid Journal   (Followers: 11, SJR: 0.172, h-index: 5)
Anthropology of Work Review     Hybrid Journal   (Followers: 11, SJR: 0.256, h-index: 5)
Anthropology Today     Hybrid Journal   (Followers: 93, SJR: 0.545, h-index: 15)
Antipode     Hybrid Journal   (Followers: 45, SJR: 2.212, h-index: 69)
Anz J. of Surgery     Hybrid Journal   (Followers: 6, SJR: 0.432, h-index: 59)
Anzeiger für Schädlingskunde     Hybrid Journal   (Followers: 1)
Apmis     Hybrid Journal   (Followers: 1, SJR: 0.855, h-index: 73)
Applied Cognitive Psychology     Hybrid Journal   (Followers: 66, SJR: 0.754, h-index: 69)
Applied Organometallic Chemistry     Hybrid Journal   (Followers: 6, SJR: 0.632, h-index: 58)
Applied Psychology     Hybrid Journal   (Followers: 125, SJR: 1.023, h-index: 64)
Applied Psychology: Health and Well-Being     Hybrid Journal   (Followers: 47, SJR: 0.868, h-index: 13)
Applied Stochastic Models in Business and Industry     Hybrid Journal   (Followers: 5, SJR: 0.613, h-index: 24)
Aquaculture Nutrition     Hybrid Journal   (Followers: 13, SJR: 1.025, h-index: 55)
Aquaculture Research     Hybrid Journal   (Followers: 31, SJR: 0.807, h-index: 60)
Aquatic Conservation Marine and Freshwater Ecosystems     Hybrid Journal   (Followers: 34, SJR: 1.047, h-index: 57)
Arabian Archaeology and Epigraphy     Hybrid Journal   (Followers: 11, SJR: 0.453, h-index: 11)
Archaeological Prospection     Hybrid Journal   (Followers: 12, SJR: 0.922, h-index: 21)
Archaeology in Oceania     Hybrid Journal   (Followers: 13, SJR: 0.745, h-index: 18)
Archaeometry     Hybrid Journal   (Followers: 27, SJR: 0.809, h-index: 48)
Archeological Papers of The American Anthropological Association     Hybrid Journal   (Followers: 14, SJR: 0.156, h-index: 2)
Architectural Design     Hybrid Journal   (Followers: 24, SJR: 0.261, h-index: 9)
Archiv der Pharmazie     Hybrid Journal   (Followers: 4, SJR: 0.628, h-index: 43)
Archives of Drug Information     Hybrid Journal   (Followers: 4)
Archives of Insect Biochemistry and Physiology     Hybrid Journal   (SJR: 0.768, h-index: 54)
Area     Hybrid Journal   (Followers: 12, SJR: 0.938, h-index: 57)
Art History     Hybrid Journal   (Followers: 203, SJR: 0.153, h-index: 13)
Arthritis & Rheumatology     Hybrid Journal   (Followers: 48, SJR: 1.984, h-index: 20)
Arthritis Care & Research     Hybrid Journal   (Followers: 24, SJR: 2.256, h-index: 114)
Artificial Organs     Hybrid Journal   (Followers: 1, SJR: 0.872, h-index: 60)
ASHE Higher Education Reports     Hybrid Journal   (Followers: 13)
Asia & the Pacific Policy Studies     Open Access   (Followers: 15)
Asia Pacific J. of Human Resources     Hybrid Journal   (Followers: 318, SJR: 0.494, h-index: 19)
Asia Pacific Viewpoint     Hybrid Journal   (SJR: 0.616, h-index: 26)
Asia-Pacific J. of Chemical Engineering     Hybrid Journal   (Followers: 7, SJR: 0.345, h-index: 20)
Asia-pacific J. of Clinical Oncology     Hybrid Journal   (Followers: 6, SJR: 0.554, h-index: 14)
Asia-Pacific J. of Financial Studies     Hybrid Journal   (SJR: 0.241, h-index: 7)
Asia-Pacific Psychiatry     Hybrid Journal   (Followers: 3, SJR: 0.377, h-index: 7)
Asian Economic J.     Hybrid Journal   (Followers: 8, SJR: 0.234, h-index: 21)
Asian Economic Policy Review     Hybrid Journal   (Followers: 3, SJR: 0.196, h-index: 12)
Asian J. of Control     Hybrid Journal   (SJR: 0.862, h-index: 34)
Asian J. of Endoscopic Surgery     Hybrid Journal   (SJR: 0.394, h-index: 7)
Asian J. of Organic Chemistry     Hybrid Journal   (Followers: 4, SJR: 1.443, h-index: 19)
Asian J. of Social Psychology     Hybrid Journal   (Followers: 5, SJR: 0.665, h-index: 37)
Asian Politics and Policy     Hybrid Journal   (Followers: 13, SJR: 0.207, h-index: 7)
Asian Social Work and Policy Review     Hybrid Journal   (Followers: 5, SJR: 0.318, h-index: 5)
Asian-pacific Economic Literature     Hybrid Journal   (Followers: 5, SJR: 0.168, h-index: 15)
Assessment Update     Hybrid Journal   (Followers: 4)
Astronomische Nachrichten     Hybrid Journal   (Followers: 2, SJR: 0.701, h-index: 40)
Atmospheric Science Letters     Open Access   (Followers: 29, SJR: 1.332, h-index: 27)
Austral Ecology     Hybrid Journal   (Followers: 12, SJR: 1.095, h-index: 66)
Austral Entomology     Hybrid Journal   (Followers: 10, SJR: 0.524, h-index: 28)
Australasian J. of Dermatology     Hybrid Journal   (Followers: 7, SJR: 0.714, h-index: 40)
Australasian J. On Ageing     Hybrid Journal   (Followers: 7, SJR: 0.39, h-index: 22)
Australian & New Zealand J. of Statistics     Hybrid Journal   (Followers: 13, SJR: 0.275, h-index: 28)
Australian Accounting Review     Hybrid Journal   (Followers: 3, SJR: 0.709, h-index: 14)
Australian and New Zealand J. of Family Therapy (ANZJFT)     Hybrid Journal   (Followers: 3, SJR: 0.382, h-index: 12)
Australian and New Zealand J. of Obstetrics and Gynaecology     Hybrid Journal   (Followers: 42, SJR: 0.814, h-index: 49)
Australian and New Zealand J. of Public Health     Hybrid Journal   (Followers: 11, SJR: 0.82, h-index: 62)
Australian Dental J.     Hybrid Journal   (Followers: 6, SJR: 0.482, h-index: 46)
Australian Economic History Review     Hybrid Journal   (Followers: 4, SJR: 0.171, h-index: 12)
Australian Economic Papers     Hybrid Journal   (Followers: 21, SJR: 0.23, h-index: 9)
Australian Economic Review     Hybrid Journal   (Followers: 6, SJR: 0.357, h-index: 21)
Australian Endodontic J.     Hybrid Journal   (Followers: 3, SJR: 0.513, h-index: 24)
Australian J. of Agricultural and Resource Economics     Hybrid Journal   (Followers: 3, SJR: 0.765, h-index: 36)
Australian J. of Grape and Wine Research     Hybrid Journal   (Followers: 5, SJR: 0.879, h-index: 56)
Australian J. of Politics & History     Hybrid Journal   (Followers: 13, SJR: 0.203, h-index: 14)
Australian J. of Psychology     Hybrid Journal   (Followers: 16, SJR: 0.384, h-index: 30)
Australian J. of Public Administration     Hybrid Journal   (Followers: 380, SJR: 0.418, h-index: 29)
Australian J. of Rural Health     Hybrid Journal   (Followers: 4, SJR: 0.43, h-index: 34)
Australian Occupational Therapy J.     Hybrid Journal   (Followers: 64, SJR: 0.59, h-index: 29)
Australian Psychologist     Hybrid Journal   (Followers: 11, SJR: 0.331, h-index: 31)
Australian Veterinary J.     Hybrid Journal   (Followers: 19, SJR: 0.459, h-index: 45)
Autism Research     Hybrid Journal   (Followers: 31, SJR: 2.126, h-index: 39)
Autonomic & Autacoid Pharmacology     Hybrid Journal   (SJR: 0.371, h-index: 29)
Banks in Insurance Report     Hybrid Journal   (Followers: 1)
Basic & Clinical Pharmacology & Toxicology     Hybrid Journal   (Followers: 9, SJR: 0.539, h-index: 70)
Basic and Applied Pathology     Open Access   (Followers: 2, SJR: 0.113, h-index: 4)
Basin Research     Hybrid Journal   (Followers: 3, SJR: 1.54, h-index: 60)
Bauphysik     Hybrid Journal   (Followers: 2, SJR: 0.194, h-index: 5)
Bauregelliste A, Bauregelliste B Und Liste C     Hybrid Journal  
Bautechnik     Hybrid Journal   (Followers: 1, SJR: 0.321, h-index: 11)
Behavioral Interventions     Hybrid Journal   (Followers: 7, SJR: 0.297, h-index: 23)
Behavioral Sciences & the Law     Hybrid Journal   (Followers: 21, SJR: 0.736, h-index: 57)
Berichte Zur Wissenschaftsgeschichte     Hybrid Journal   (Followers: 9, SJR: 0.11, h-index: 5)
Beton- und Stahlbetonbau     Hybrid Journal   (Followers: 2, SJR: 0.493, h-index: 14)
Biochemistry and Molecular Biology Education     Hybrid Journal   (Followers: 6, SJR: 0.311, h-index: 26)
Bioelectromagnetics     Hybrid Journal   (Followers: 1, SJR: 0.568, h-index: 64)
Bioengineering & Translational Medicine     Open Access  
BioEssays     Hybrid Journal   (Followers: 10, SJR: 3.104, h-index: 155)
Bioethics     Hybrid Journal   (Followers: 14, SJR: 0.686, h-index: 39)
Biofuels, Bioproducts and Biorefining     Hybrid Journal   (Followers: 1, SJR: 1.725, h-index: 56)
Biological J. of the Linnean Society     Hybrid Journal   (Followers: 14, SJR: 1.172, h-index: 90)
Biological Reviews     Hybrid Journal   (Followers: 2, SJR: 6.469, h-index: 114)
Biologie in Unserer Zeit (Biuz)     Hybrid Journal   (Followers: 44, SJR: 0.12, h-index: 1)
Biology of the Cell     Full-text available via subscription   (Followers: 9, SJR: 1.812, h-index: 69)
Biomedical Chromatography     Hybrid Journal   (Followers: 6, SJR: 0.572, h-index: 49)
Biometrical J.     Hybrid Journal   (Followers: 5, SJR: 0.784, h-index: 44)
Biometrics     Hybrid Journal   (Followers: 37, SJR: 1.906, h-index: 96)
Biopharmaceutics and Drug Disposition     Hybrid Journal   (Followers: 10, SJR: 0.715, h-index: 44)
Biopolymers     Hybrid Journal   (Followers: 18, SJR: 1.199, h-index: 104)
Biotechnology and Applied Biochemistry     Hybrid Journal   (Followers: 45, SJR: 0.415, h-index: 55)
Biotechnology and Bioengineering     Hybrid Journal   (Followers: 133, SJR: 1.633, h-index: 146)
Biotechnology J.     Hybrid Journal   (Followers: 13, SJR: 1.185, h-index: 51)
Biotechnology Progress     Hybrid Journal   (Followers: 38, SJR: 0.736, h-index: 101)
Biotropica     Hybrid Journal   (Followers: 17, SJR: 1.374, h-index: 71)
Bipolar Disorders     Hybrid Journal   (Followers: 10, SJR: 2.592, h-index: 100)
Birth     Hybrid Journal   (Followers: 33, SJR: 0.763, h-index: 64)
Birth Defects Research Part A : Clinical and Molecular Teratology     Hybrid Journal   (Followers: 2, SJR: 0.727, h-index: 77)
Birth Defects Research Part B: Developmental and Reproductive Toxicology     Hybrid Journal   (Followers: 5, SJR: 0.468, h-index: 47)
Birth Defects Research Part C : Embryo Today : Reviews     Hybrid Journal   (SJR: 1.513, h-index: 55)

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Journal Cover Animal Genetics
  [SJR: 0.957]   [H-I: 67]   [8 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 0268-9146 - ISSN (Online) 1365-2052
   Published by John Wiley and Sons Homepage  [1582 journals]
  • First study of mtDNA (D-loop) in Brazilian Caipira chickens
    • Authors: M. E. Herkenhoff; F. M. Salzano, C. A. V. Lima-Rosa
      PubDate: 2017-05-16T02:40:36.743517-05:
      DOI: 10.1111/age.12562
  • Detecting selection signatures between Duroc and Duroc synthetic pig
           populations using high-density SNP chip
    • Authors: Z. Edea; J.-K. Hong, J.-H. Jung, D.-W. Kim, Y.-M. Kim, E.-S. Kim, S. S. Shin, Y. C. Jung, K.-S. Kim
      Abstract: The development of high throughput genotyping techniques has facilitated the identification of selection signatures of pigs. The detection of genomic selection signals in a population subjected to differential selection pressures may provide insights into the genes associated with economically and biologically important traits. To identify genomic regions under selection, we genotyped 488 Duroc (D) pigs and 155 D × Korean native pigs (DKNPs) using the Porcine SNP70K BeadChip. By applying the FST and extended haplotype homozygosity (EHH-Rsb) methods, we detected genes under directional selection associated with growth/stature (DOCK7, PLCB4, HS2ST1, FBP2 and TG), carcass and meat quality (TG, COL14A1, FBXO5, NR3C1, SNX7, ARHGAP26 and DPYD), number of teats (LOC100153159 and LRRC1), pigmentation (MME) and ear morphology (SOX5), which are all mostly near or at fixation. These results could be a basis for investigating the underlying mutations associated with observed phenotypic variation. Validation using genome-wide association analysis would also facilitate the inclusion of some of these markers in genetic evaluation programs.
      PubDate: 2017-05-16T02:35:30.077181-05:
      DOI: 10.1111/age.12559
  • Frame-shift variant in the CHRNE gene in a juvenile dog with suspected
           myasthenia gravis-like disease
    • Authors: Vanessa Herder; Malgorzata Ciurkiewicz, Wolfgang Baumgärtner, Vidhya Jagannathan, Tosso Leeb
      PubDate: 2017-05-16T02:30:32.52574-05:0
      DOI: 10.1111/age.12558
  • Isolation of subtelomeric sequences of porcine chromosomes for
           translocation screening reveals errors in the pig genome assembly
    • Authors: R. E. O'Connor; G. Fonseka, R. Frodsham, A. L. Archibald, M. Lawrie, G. A. Walling, D. K. Griffin
      Abstract: Balanced chromosomal aberrations have been shown to affect fertility in most species studied, often leading to hypoprolificacy (reduced litter size) in domestic animals such as pigs. With an increasing emphasis in modern food production on the use of a small population of high quality males for artificial insemination, the potential economic and environmental costs of hypoprolific boars, bulls, rams etc. are considerable. There is therefore a need for novel tools to facilitate rapid, cost-effective chromosome translocation screening. This has previously been achieved by standard karyotype analysis; however, this approach relies on a significant level of expertise and is limited in its ability to identify subtle, cryptic translocations. To address this problem, we developed a novel device and protocol for translocation screening using subtelomeric probes and fluorescence in situ hybridisation. Probes were designed using BACs (bacterial artificial chromosomes) from the subtelomeric region of the short (p-arm) and long (q-arm) of each porcine chromosome. They were directly labelled with FITC or Texas Red (p-arm and q-arm respectively) prior to application of a ‘Multiprobe’ device, thereby enabling simultaneous detection of each individual porcine chromosome on a single slide. Initial experiments designed to isolate BACs in subtelomeric regions led to the discovery of a series of incorrectly mapped regions in the porcine genome assembly (from a total of 82 BACs, only 45 BACs mapped correctly). Our work therefore highlights the importance of accurate physical mapping of newly sequenced genomes. The system herein described allows for robust and comprehensive analysis of the porcine karyotype, an adjunct to classical cytogenetics that provides a valuable tool to expedite efficient, cost effective food production.
      PubDate: 2017-05-12T05:06:47.457164-05:
      DOI: 10.1111/age.12548
  • A novel mutation in the TYRP1 gene associated with brown coat colour in
           the Australian Shepherd Dog Breed
    • Authors: Evelina Hrckova Turnova; Zuzana Majchrakova, Marcela Bielikova, Katarina Soltys, Jan Turna, Andrej Dudas
      PubDate: 2017-05-12T05:06:22.921621-05:
      DOI: 10.1111/age.12563
  • A survey of single nucleotide polymorphisms identified from whole-genome
           sequencing and their functional effect in the porcine genome,
    • Authors: B. N. Keel; D. J. Nonneman, G. A. Rohrer
      Abstract: Genetic variants detected from sequence have been used to successfully identify causal variants and map complex traits in several organisms. High and moderate impact variants, those expected to alter or disrupt the protein coded by a gene and those that regulate protein production, likely have a more significant effect on phenotypic variation than do other types of genetic variants. Hence, a comprehensive list of these functional variants would be of considerable interest in swine genomic studies, particularly those targeting fertility and production traits. Whole-genome sequence was obtained from 72 of the founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC). These animals included all 24 of the founding boars (12 Duroc and 12 Landrace) and 48 Yorkshire–Landrace composite sows. Sequence reads were mapped to the Sscrofa10.2 genome build, resulting in a mean of 6.1 fold (×) coverage per genome. A total of 22 342 915 high confidence SNPs were identified from the sequenced genomes. These included 21 million previously reported SNPs and 79% of the 62 163 SNPs on the PorcineSNP60 BeadChip assay. Variation was detected in the coding sequence or untranslated regions (UTRs) of 87.8% of the genes in the porcine genome: loss-of-function variants were predicted in 504 genes, 10 202 genes contained nonsynonymous variants, 10 773 had variation in UTRs and 13 010 genes contained synonymous variants. Approximately 139 000 SNPs were classified as loss-of-function, nonsynonymous or regulatory, which suggests that over 99% of the variation detected in our pigs could potentially be ignored, allowing us to focus on a much smaller number of functional SNPs during future analyses.
      PubDate: 2017-05-08T22:25:26.593719-05:
      DOI: 10.1111/age.12557
  • An evaluation of the International Society for Animal Genetics recommended
           parentage and identification panel for the domestic pigeon (Columba livia
    • Authors: M. Groot; W. A. Haeringen
      Abstract: In this study, the International Society for Animal Genetics (ISAG) recommended panel for the identification of the domestic pigeon (Columba livia domestica) is characterized based on commonly used statistical parameters. The marker panel is based on 16 short tandem repeat (STR) loci (PIGN15, PIGN10, PIGN57, PIGN26, CliμD16, CliμD19, PIGN12, CliμD17, CliμT17, PIGN04, CliμD01, CliμD11, CliμD35, CliμT02, CliμT13, CliμT43). The alleles of the 16 loci consist of a mixture of tri-, tetra-, penta- and hexameric repeat patterns. A sex determination marker was included in the multiplex for quality control. The repeat sequence of the PIGN markers was previously unpublished and therefore sequenced to reveal the sequence pattern. In total, 1421 pigeons were genotyped on 16 STR loci to generate allele frequency data for each locus. For all 16 markers combined, a PE1 (combined non-exclusion probability, first parent) of 0.9986 and PE2 (combined non-exclusion probability, second parent) of >0.9999 was observed. Comparing the alleged father and mother, a PE value of >0.9999 was observed. Two of the markers, CliμD19 and PIGN12, were found to have relatively high Hardy–Weinberg equilibrium and F(null) values. Therefore these markers may be considered to be replaced by other STRs. Another point of discussion may be to add a gender identification marker to the recommended ISAG panel. Not only can this serve as an extra identification marker, but this can also confirm the sex of a sample, because it is challenging to determine the sex based on phenotypical characteristics, especially for chicks. In conclusion, the set of 16 STR markers can be used in routine parentage verification and the identification of individuals.
      PubDate: 2017-04-27T13:26:23.027856-05:
      DOI: 10.1111/age.12555
  • Whole genome sequencing reveals a novel deletion variant in the KIT gene
           in horses with white spotted coat colour phenotypes
    • Authors: N. Dürig; R. Jude, H. Holl, S. A. Brooks, C. Lafayette, V. Jagannathan, T. Leeb
      Abstract: White spotting phenotypes in horses can range in severity from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for such phenotypes in horses. For the present study, we re-investigated a large horse family segregating a variable white spotting phenotype, for which conventional Sanger sequencing of the candidate genes’ individual exons had failed to reveal the causative variant. We obtained whole genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~1.9-kb deletion spanning exons 10–13 of the KIT gene (chr3:77,740,239_77,742,136del1898insTATAT). In continuity with previously named equine KIT variants we propose to designate the newly identified deletion variant W22. We had access to 21 horses carrying the W22 allele. Four of them were compound heterozygous W20/W22 and had a completely white phenotype. Our data suggest that W22 represents a true null allele of the KIT gene, whereas the previously identified W20 leads to a partial loss of function. These findings will enable more precise genetic testing for depigmentation phenotypes in horses.
      PubDate: 2017-04-26T06:35:36.306242-05:
      DOI: 10.1111/age.12556
  • Haplotype structure and copy number polymorphism of the beta-defensin 7
           genes in diverse chicken breeds
    • Authors: M. O. Lee; M. N. Romanov, K. V. Plemyashov, N. V. Dementieva, O. V. Mitrofanova, O. Y. Barkova, J. E. Womack
      Abstract: Beta-defensins is a family of avian peptides related to the innate immune system. Copy number variation was recently reported for the avian beta-defensin 7 gene (AvBD7) between the highly inbred Leghorn and Fayoumi lines. Here, we examined copy number variants in 35 different chicken breeds and found that 31 of them have at least the same representation of the duplicated AvBD7 allele. We also found haplotypes upstream of the AvBD6 regions that are strongly linked to the AvBD7 duplication. We observed a strong linkage disequilibrium spanning of the upstream region of the AvBD6 gene, with two SNPs being flanking markers to detect duplication of the AvBD7.
      PubDate: 2017-04-05T05:20:32.700332-05:
      DOI: 10.1111/age.12552
  • A novel splice mutation within equine KIT and the W15 allele in the
           homozygous state lead to all white coat color phenotypes
    • Authors: Heather M. Holl; Samantha A. Brooks, Meredith L. Carpenter, Carlos D. Bustamante, Christa Lafayette
      PubDate: 2017-04-05T05:05:42.95485-05:0
      DOI: 10.1111/age.12554
  • Exclusion of known progressive retinal atrophy genes for blindness in the
           Hungarian Puli
    • Authors: Tracy Chew; Bianca Haase, Cali E. Willet, Claire M. Wade
      PubDate: 2017-04-05T05:05:39.090111-05:
      DOI: 10.1111/age.12553
  • Genotyping by sequencing reveals a new locus for pig teat number
    • Authors: L. Wang; Y. Zhang, T. Zhang, L. Zhang, H. Yan, X. Liu, L. Wang
      Abstract: Teat number is an extremely valuable trait for sow reproduction performance and piglet survival. Here, we used genotyping-by-sequencing and a general liner model to carry out genome-wide analysis of sow total teat number in an Erhualian population. The results indicated that eight SNPs on chromosomes 4, 5, 9 and 10 were significant genome wide (Bonferroni method, P 
      PubDate: 2017-04-03T01:25:46.316234-05:
      DOI: 10.1111/age.12547
  • A novel 14-bp duplicated deletion within goat GHR gene is significantly
           associated with growth traits and litter size
    • Authors: Qing Yang; Hailong Yan, Jie Li, Han Xu, Ke Wang, Haijing Zhu, Hong Chen, Lei Qu, Xianyong Lan
      PubDate: 2017-03-10T10:45:39.458027-05:
      DOI: 10.1111/age.12551
  • Identification of the interaction between bta-miR-370 and OLR1 gene in
           bovine adipocyte
    • Authors: H. F. Li; S. H. Wang, Y. Guo, H. B. Zhao, X. Y. Li, X. Wang
      Abstract: It has been shown that the oxidized low density lipoprotein receptor 1 (OLR1) gene plays an important role in the degradation of oxidized low density lipoprotein. Previous studies found a SNP in the 3′-untranslated region (3′-UTR) of the OLR1 gene associated with milk production traits in different dairy cattle populations and with loin eye area and marbling depth in beef cattle. MicroRNAs can regulate gene expression by binding the 3′-UTR of target genes to degrade or to repress the translation of target genes. Bioinformatics have shown that there is a binding site of bta-miR-370 in the 3′-UTR of the OLR1 gene, and a previous luciferase reporter assay system showed that the A/C mutation occurring in the 3′-UTR of this gene caused the binding sites of bta-miR-370 to disappear in HEK293 cells. To further validate whether OLR1 was the target gene of bta-miR-370, the over-expression and interference expression of bta-miR-370 were determined by transfecting bta-miR-370 mimics and inhibitor supplementations into bovine adipocyte. The qRT-PCR result showed that the relative expression of OLR1 gene significantly decreased in the mimics group compared to the control, whereas the expression level in inhibitor group was higher than its control group. The above results were further verified by a Western blot at the protein level. In addition, lipid formation analysis of bovine adipocytes was performed via oil red O staining, and we found that cytoplasm lipid droplets in the inhibitor group showed a tendency to increase compared to the control group, whereas in the mimics group, we observed an obvious decrease of cytoplasm lipid droplets compared to the control and inhibitor groups. Taken together, our data here suggest that bta-miR-370 has a negative regulation role for OLR1 both at the gene expression and protein levels and bovine adipocytes cytoplasm lipid droplets formation, which provides a reference for illustrating how the OLR1 gene affects milk production and beef quality traits in cattle.
      PubDate: 2017-03-10T10:45:15.700944-05:
      DOI: 10.1111/age.12550
  • An atlas and analysis of bovine skeletal muscle long noncoding RNAs
    • Authors: X. F. Liu; X. B. Ding, X. Li, C. F. Jin, Y. W. Yue, G. P. Li, H. Guo
      Abstract: Long noncoding RNAs (lncRNAs) have various biological functions and have been extensively studied in recent years. However, the identification and characterization of bovine lncRNAs in skeletal muscle has been very limited compared with that of lncRNAs in other model organisms. In this study, 7188 bovine skeletal muscle lncRNAs were identified by RNA-Seq and a stringent screening procedure in four different muscle tissues. These lncRNAs shared many characteristics with other mammalian lncRNAs, such as a shorter open reading frame and lower expression level than for mRNAs. Furthermore, the chromosomal locations and global expression patterns for these lncRNAs are also described in detail. More importantly, we detected the important interaction relationships of lncRNAs–miRNAs–mRNAs related to muscle development among 36 lncRNAs, 62 miRNAs and 12 mRNAs. Our results provide a global expression pattern of lncRNAs specific to bovine skeletal muscle and provide important targets for revealing the function of bovine muscle development by thoroughly studying the interaction relationships of lncRNAs–miRNAs–mRNAs.
      PubDate: 2017-03-06T06:05:55.123278-05:
      DOI: 10.1111/age.12539
  • Identification of a new Y chromosome haplogroup in Spanish native cattle
    • Authors: R. Pelayo; M. C. T. Penedo, M. Valera, A. Molina, L. Millon, C. Ginja, L. J. Royo
      Abstract: The aim of this work was to perform a thorough analysis of the diversity of Y-haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y-specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y-haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle.
      PubDate: 2017-02-27T23:55:25.897878-05:
      DOI: 10.1111/age.12549
  • Sex chromosomal abnormalities associated with equine infertility:
           validation of a simple molecular screening tool in the Purebred Spanish
    • Authors: G. Anaya; A. Molina, M. Valera, M. Moreno-Millán, P. Azor, P. Peral-García, S. Demyda-Peyrás
      Abstract: Chromosomal abnormalities in the sex chromosome pair (ECAX and ECAY) are widely associated with reproductive problems in horses. However, a large proportion of these abnormalities remains undiagnosed due to the lack of an affordable diagnostic tool that allows for avoiding karyotyping tests. Hereby, we developed an STR (single-tandem-repeat)-based molecular method to determine the presence of the main sex chromosomal abnormalities in horses in a fast, cheap and reliable way. The frequency of five ECAX-linked (LEX026, LEX003, TKY38, TKY270 and UCDEQ502) and two ECAY-linked (EcaYH12 and SRY) markers was characterized in 261 Purebred Spanish Horses to determine the efficiency of the methodology developed to be used as a chromosomal diagnostic tool. All the microsatellites analyzed were highly polymorphic, with a sizeable number of alleles (polymorphic information content > 0.5). Based on this variability, the methodology showed 100% sensitivity and 99.82% specificity to detect the most important sex chromosomal abnormalities reported in horses (chimerism, Turner's syndrome and sex reversal syndromes). The method was also validated with 100% efficiency in 10 individuals previously diagnosed as chromosomally aberrant. This STR screening panel is an efficient and reliable molecular–cytogenetic tool for the early detection of sex chromosomal abnormalities in equines that could be included in breeding programs to save money, effort and time of veterinary practitioners and breeders.
      PubDate: 2017-02-22T01:40:44.620824-05:
      DOI: 10.1111/age.12543
  • Relationships between inflammation- and immunity-related transcript
           abundance in the rumen and jejunum of beef steers with divergent average
           daily gain
    • Authors: J. G. Reynolds; A. P. Foote, H. C. Freetly, W. T. Oliver, A. K. Lindholm-Perry
      Abstract: The bovine rumen papillae are in contact with a wide array of microorganisms and the metabolites they produce, which may activate an inflammatory and/or immune response. Cytokines, chemokines and their receptor genes were tested for differential expression in the rumen and jejunum of beef steers with greater and lesser average daily body weight gain (ADG) near the average daily dry matter intake (DMI) for the population. Angus-sired steers (n = 16) were used to represent the greater (ADG = 2.2 ± 0.07 kg/day; DMI = 10.1 ± 0.05 kg/day) and lesser (ADG = 1.7 ± 0.05 kg/day; DMI = 10.1 ± 0.05 kg/day) ADG groups with eight steers each. Rumen epithelium and jejunum mucosal samples were collected at slaughter, and gene expression was evaluated using a commercially available qRT-PCR array containing 84 genes representing chemokines, cytokines and their receptors. None of the genes on the array were differentially expressed in the jejunum of the steers with greater vs. lesser ADG. However, in the rumen, two chemokine genes (CCL11, CXCL5) and one receptor gene (IL10RA) were detected as differentially expressed (P 
      PubDate: 2017-02-21T00:30:22.573568-05:
      DOI: 10.1111/age.12546
  • Genomic prediction of reproduction traits for Merino sheep
    • Authors: S. Bolormaa; D. J. Brown, A. A. Swan, J. H. J. Werf, B. J. Hayes, H. D. Daetwyler
      Abstract: Economically important reproduction traits in sheep, such as number of lambs weaned and litter size, are expressed only in females and later in life after most selection decisions are made, which makes them ideal candidates for genomic selection. Accurate genomic predictions would lead to greater genetic gain for these traits by enabling accurate selection of young rams with high genetic merit. The aim of this study was to design and evaluate the accuracy of a genomic prediction method for female reproduction in sheep using daughter trait deviations (DTD) for sires and ewe phenotypes (when individual ewes were genotyped) for three reproduction traits: number of lambs born (NLB), litter size (LSIZE) and number of lambs weaned. Genomic best linear unbiased prediction (GBLUP), BayesR and pedigree BLUP analyses of the three reproduction traits measured on 5340 sheep (4503 ewes and 837 sires) with real and imputed genotypes for 510 174 SNPs were performed. The prediction of breeding values using both sire and ewe trait records was validated in Merino sheep. Prediction accuracy was evaluated by across sire family and random cross-validations. Accuracies of genomic estimated breeding values (GEBVs) were assessed as the mean Pearson correlation adjusted by the accuracy of the input phenotypes. The addition of sire DTD into the prediction analysis resulted in higher accuracies compared with using only ewe records in genomic predictions or pedigree BLUP. Using GBLUP, the average accuracy based on the combined records (ewes and sire DTD) was 0.43 across traits, but the accuracies varied by trait and type of cross-validations. The accuracies of GEBVs from random cross-validations (range 0.17–0.61) were higher than were those from sire family cross-validations (range 0.00–0.51). The GEBV accuracies of 0.41–0.54 for NLB and LSIZE based on the combined records were amongst the highest in the study. Although BayesR was not significantly different from GBLUP in prediction accuracy, it identified several candidate genes which are known to be associated with NLB and LSIZE. The approach provides a way to make use of all data available in genomic prediction for traits that have limited recording.
      PubDate: 2017-02-17T01:25:39.677657-05:
      DOI: 10.1111/age.12541
  • PCK1 expression is correlated with the plasma glucose level in the duck
    • Authors: L. Chen; T. Zeng, G. Q. Li, R. Liu, Y. Tian, Q. H. Li, L. Z. Lu
      Abstract: Phosphoenolpyruvate carboxykinase 1 (soluble) (PCK1) is a key gene in gluconeogenesis and glyceroneogenesis. Although its functions have been extensively studied in mice, bats and humans, little is known in ducks. Here, PCK1 functions were studied using a duck domestication model and a 48-h fasting experiment. We found PCK1 expression significantly decreased in two breeds of domestic ducks (Jinyun Pockmark ducks and Cherry Valley ducks) as compared with wild ducks (Anas platyrhynchos). Simultaneously, plasma levels of glucose, triglycerides and free fatty acid in domestic ducks were lower than in wild ducks. When compared with fed ducks, the plasma triglyceride level was observed to be significantly decreased, while the glucose and free fatty acid levels remained constant in 48-h fasting ducks. The expression analysis of gluconeogenic genes revealed that fructose-1,6-bisphosphatase genes (FBP1 and FBP2) and the glucose-6-phosphatase gene (G6PC2) were not changed, whereas PCK1 was significantly upregulated. In addition, the reported regulators of PCK1, including forkhead box A2 (FOXA2) gene and orphan nuclear receptor NR4A family genes (NR4A1, NR4A2 and NR4A3), exhibited similar expression levels between 48-h fasting ducks and fed ducks, suggesting that PCK1 is not regulated by these genes in the duck under fasting conditions. In conclusion, PCK1 expression may affect plasma levels of glucose, triglycerides and free fatty acid during the duck domestication process. This work demonstrates for the first time in duck that PCK1 is a key gene in maintaining plasma glucose homeostasis during fasting and that the upregulated expression of PCK1 may be responsible for constant plasma free fatty acid level by the glyceroneogenesis process.
      PubDate: 2017-02-15T02:10:26.012768-05:
      DOI: 10.1111/age.12540
  • ASIP gene variation in Chinese donkeys
    • Authors: Ting Sun; Shiying Li, Xiaoting Xia, Chuanliang Ji, Shanyi Shen, Guoliang Zhang, Jie Yu, Guimiao Jiang, Ruihua Dang, Chuzhao Lei
      PubDate: 2017-02-15T02:05:26.625037-05:
      DOI: 10.1111/age.12530
  • Identification of the crucial genes in the elimination and survival
           process of Salmonella enterica ser. Pullorum in the chicken spleen
    • Authors: T. Ma; L. Xu, H. Wang, X. Guo, Z. Li, F. Wan, J. Chen, L. Liu, X. Liu, G. Chang, G. Chen
      Abstract: Salmonella enterica ser. Pullorum is one of the most easily re-infecting pathogens in poultry production because of its mechanism of escaping from immune elimination. We used the transcriptome method to investigate the variation in gene expression in chicken spleen resulting from the interaction between hosts and S. Pullorum in the survival process. The expression of various genes related to the maturation and activation of B cells was activated before S. Pullorum was eliminated, which might help S. Pullorum escape from the elimination process. The suppression of some genes involved in the fusion of autophagosomes and lysosomes, such as MYO6, was identified and may be regulated by the secretion systems of S. Pullorum. In addition, a large proportion of these differentially expressed genes could be localized in the identified quantitative trait loci regions associated with the antibody response to bacteria. Collectively, these identified genes provided an outline for further understanding the interaction between chicken immune cells and S. Pullorum in chicken spleen.
      PubDate: 2017-02-07T23:51:28.809475-05:
      DOI: 10.1111/age.12533
  • A genome-wide association study for a proxy of intermuscular fat level in
           the Italian Large White breed identifies genomic regions affecting an
           important quality parameter for dry-cured hams
    • Authors: L. Fontanesi; G. Schiavo, G. Galimberti, S. Bovo, V. Russo, M. Gallo, L. Buttazzoni
      Abstract: Intermuscular fat content in protected designations of origin dry-cured hams is a very important meat quality trait that affects the acceptability of the product by the consumers. An excess in intermuscular fat (defined as the level of fat deposition between leg muscles) is a defect that depreciates the final product. In this study we carried out a genome-wide association study for visible intermuscular fat (VIF) of hams in the Italian Large White pig breed. This trait was evaluated on the exposed muscles of green legs in 1122 performance-tested gilts by trained personnel, according to a classification scale useful for routine and cheap evaluation. All animals were genotyped with the Illumina PorcineSNP60 BeadChip. The genome-wide association study identified three QTL regions on porcine chromosome 1 (SSC1; accounting for ~79% of the SNPs below the 5.0E−04 threshold) and SSC2, two on SSC7 and one each on SSC3, SSC6, SSC9, SSC11, SSC13, SSC15, SSC16 and SSC17. The most significant SNP (ALGA0004143 on SSC1 at 77.3 Mb; PFDR 
      PubDate: 2017-02-03T06:25:44.977614-05:
      DOI: 10.1111/age.12542
  • A genome-wide association analysis for carcass traits in a commercial
           Duroc pig population
    • Authors: P. G. Eusebi; R. González-Prendes, R. Quintanilla, J. Tibau, T. F. Cardoso, A. Clop, M. Amills
      Abstract: We performed a genome-wide association study to map the genetic determinants of carcass traits in 350 Duroc pigs typed with the Porcine SNP60 BeadChip. Association analyses were carried out using the gemma software. The proportion of phenotypic variance explained by the SNPs ranged between negligible to moderate (hSNP2= 0.01–0.30) depending on the trait under consideration. At the genome-wide level, we detected one significant association between backfat thickness between the 3rd and 4th ribs and six SNPs mapping to SSC12 (37–40 Mb). We also identified several chromosome-wide significant associations for ham weight (SSC11: 51–53 Mb, three SNPs; 67–68 Mb, two SNPs), carcass weight (SSC11: 66–68 Mb, two SNPs), backfat thickness between the 3rd and 4th ribs (SSC12: 21 Mb, one SNP; 33–40 Mb, 17 SNPs; 51–58 Mb, two SNPs), backfat thickness in the last rib (SSC12: 37 Mb, one SNP; 40–41 Mb, nine SNPs) and lean meat content (SSC13: 34 Mb, three SNPs and SSC16: 45.1 Mb, one SNP; 62–63 Mb, 10 SNPs; 71–75 Mb, nine SNPs). The ham weight trait-associated region on SSC11 contains two genes (UCHL3 and LMO7) related to muscle development. In addition, the ACACA gene, which encodes an enzyme for the catalysis of fatty acid synthesis, maps to the SSC12 (37–41 Mb) region harbouring trait-associated regions for backfat thickness traits. Sequencing of these candidate genes may help to uncover the causal mutations responsible for the associations found in the present study.
      PubDate: 2017-02-03T06:25:33.039352-05:
      DOI: 10.1111/age.12545
  • A novel VWF variant associated with type 2 von Willebrand disease in
           German Wirehaired Pointers and German Shorthaired Pointers
    • Authors: M. Vos-Loohuis; B. A. Oost, C. Dangel, I. Langbein-Detsch, P. A. Leegwater
      Abstract: Von Willebrand disease (VWD), caused by deficiency of the von Willebrand factor (VWF), is the most common bleeding disorder in humans and dogs. The complete cDNA encoding VWF of a German Wirehaired Pointer with type 2 VWD was sequenced, and we found four variants that alter the amino acid sequence. These variants were: c.1657T>G corresponding to p.Trp553Gly; c.1777G>A (p.Glu593Lys); c.4937A>G (p.Asn1646Ser) and c.5544G>A (p.Met1848Ile). A haplotype of the c.1657G, c.1777A and c.4937G alleles co-segregated with the VWF antigen level in a four-generation pedigree with the disease. Healthy dogs of the breed were found that were homozygous for the c.1777A or the c.5544A allele, indicating that these variants do not cause VWD. Dogs that were homozygous for the c.4937G allele and had no signs of a bleeding disorder were observed in the Chinese Crested dog breed. Thus, only the c.1657G variant was found in the homozygous state exclusively in VWD affecteds, and this variant is the strongest candidate to be the cause of VWD type 2 in the German Wirehaired Pointer breed. A screen of German Shorthaired Pointers indicated that the variant also segregates with VWD in this breed.
      PubDate: 2017-02-03T06:25:31.472668-05:
      DOI: 10.1111/age.12544
  • Fine mapping of a distal chromosome 4 QTL affecting growth and muscle mass
           in a chicken advanced intercross line
    • Authors: S. Lyu; D. Arends, M. K. Nassar, G. A. Brockmann
      Abstract: In our previous research, QTL analysis in an F2 cross between the inbred New Hampshire (NHI) and White Leghorn (WL77) lines revealed a growth QTL in the distal part of chromosome 4. To physically reduce the chromosomal interval and the number of potential candidate genes, we performed fine mapping using individuals of generations F10, F11 and F12 in an advanced intercross line that had been established from the initial F2 mapping population. Using nine single nucleotide polymorphism (SNP) markers within the QTL region for an association analysis with several growth traits from hatch to 20 weeks and body composition traits at 20 weeks, we could reduce the confidence interval from 26.9 to 3.4 Mb. Within the fine mapped region, markers rs14490774, rs314961352 and rs318175270 were in full linkage disequilibrium (D′ = 1.0) and showed the strongest effect on growth and muscle mass (LOD ≥ 4.00). This reduced region contains 30 genes, compared to 292 genes in the original region. Chicken 60 K and 600 K SNP chips combined with DNA sequencing of the parental lines were used to call mutations in the reduced region. In the narrowed-down region, 489 sequence variants were detected between NHI and WL77. The most deleterious variants are a missense variant in ADGRA3 (SIFT = 0.02) and a frameshift deletion in the functional unknown gene ENSGALG00000014401 in NHI chicken. In addition, five synonymous variants were discovered in genes PPARGC1A, ADGRA3, PACRGL, SLIT2 and FAM184B. In our study, the confidence interval and the number of potential genes could be reduced 8- and 10- fold respectively. Further research will focus on functional effects of mutant genes.
      PubDate: 2017-01-26T04:56:30.715408-05:
      DOI: 10.1111/age.12532
  • Novel class II alpha MHC variability in a small peripheral Atlantic salmon
    • Authors: Kate L. Ciborowski; William C. Jordan, Carlos García de Leániz, Sofia Consuegra
      PubDate: 2017-01-24T00:56:06.193729-05:
      DOI: 10.1111/age.12535
  • Limited representation of OMIA causative mutations for cattle in SNP
    • Authors: Aditi Sharma; Yongmin Cho, Bong-Hwan Choi, Han-Ha Chai, Jong-Eun Park, Dajeong Lim
      PubDate: 2017-01-24T00:00:39.591418-05:
      DOI: 10.1111/age.12534
  • Deletion of 2.7 kb near HOXD3 in an Arabian horse with
           occipitoatlantoaxial malformation
    • Authors: M. H. Bordbari; M. C. T. Penedo, M. Aleman, S. J. Valberg, J. Mickelson, C. J. Finno
      Abstract: In the horse, the term occipitoatlantoaxial malformation (OAAM) is used to describe a developmental defect in which the first cervical vertebra (atlas) resembles the base of the skull (occiput) and the second cervical vertebra (axis) resembles the atlas. Affected individuals demonstrate an abnormal posture and varying degrees of ataxia. The homeobox (HOX) gene cluster is involved in the development of both the axial and appendicular skeleton. Hoxd3-null mice demonstrate a strikingly similar phenotype to Arabian foals with OAAM. Whole-genome sequencing was performed in an OAAM-affected horse (OAAM1) and seven unaffected Arabian horses. Visual inspection of the raw reads within the region of HOXD3 identified a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3. A genotyping assay revealed that both parents of OAAM1 were heterozygous for the deletion. Additional genotyping identified two of 162 heterozygote Arabians, and the deletion was not present in 371 horses of other breeds. Comparative genomics studies have revealed that this region is highly conserved across species and that the entire genomic region between Hoxd4 and Hoxd3 is transcribed in mice. Two additional Arabian foals diagnosed with OAAM (OAAM 2 and 3) were genotyped and did not have the 2.7-kb deletion. Closer examination of the phenotype in these cases revealed notable variation. OAAM3 also had facial malformations and a patent ductus arteriosus, and the actual malformation at the craniocervical junction differed. Genetic heterogeneity may exist across the HOXD locus in Arabian foals with OAAM.
      PubDate: 2017-01-23T02:00:27.135192-05:
      DOI: 10.1111/age.12531
  • Development of Diversity Arrays Technology markers as a tool for rapid
           genomic assessment in Nile tilapia, Oreochromis niloticus
    • Authors: C. E. Lind; A. Kilian, J. A. H. Benzie
      Abstract: The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.
      PubDate: 2017-01-17T05:28:13.770155-05:
      DOI: 10.1111/age.12536
  • Deep sequencing of a candidate region harboring the SOX9 gene for the
           canine XX disorder of sex development
    • Authors: J. Nowacka-Woszuk; I. Szczerbal, H. Pausch, S. Hundi, M. K. Hytönen, A. Grzemski, K. Flisikowski, H. Lohi, M. Switonski, M. Szydlowski
      Abstract: A disorder of sex development (DSD) in dogs with female sex chromosomes (78, XX), a lack of the SRY gene and the presence of testes or ovotestes is commonly diagnosed in numerous breeds. The molecular background of DSD is not fully recognized but has been linked to the copy number variation in the region harboring the SOX9 gene. We applied a genome-wide association study and targeted next-generation sequencing techniques to compare DSD and normal female dogs. The genome-wide association study did not indicate a significant chromosome region. Targeted next-generation sequencing of a 1.5-Mb region on canine chromosome 9 harboring the SOX9 gene revealed two putatively DSD-associated copy number variations 355 kb upstream and 691 kb downstream of SOX9, four blocks of low polymorphism and two blocks of an elevated heterozygosity. An initial next-generation sequencing analysis showed an association with two SNPs, but validation in larger cohorts did not confirm this result. We identified a large homologous fragment (over 243.8 kb), named hfMAGI2, located upstream of SOX9, that overlaps a known copy number variation region. It shows a high sequence similarity with the 5′ flanking region of the MAGI2 gene located on canine chromosome 18 that encodes a protein involved in ovary formation during early embryonic development. Our study showed that the identified copy number variation region located upstream of the SOX9 gene contains potential regulatory sequences (long non-coding RNA and hfMAGI2) and led to the assumption that a multiplication of this element may alter expression of the SOX9 gene, triggering the DSD phenotype.
      PubDate: 2017-01-17T05:28:07.456083-05:
      DOI: 10.1111/age.12538
  • Genetic diversity and patterns of population structure in Creole goats
           from the Americas
    • Authors: C. Ginja; L. T. Gama, A. Martínez, N. Sevane, I. Martin-Burriel, M. R. Lanari, M. A. Revidatti, J. A. Aranguren-Méndez, D. O. Bedotti, M. N. Ribeiro, P. Sponenberg, E. L. Aguirre, L. A. Alvarez-Franco, M. P. C. Menezes, E. Chacón, A. Galarza, N. Gómez-Urviola, O. R. Martínez-López, E. C. Pimenta-Filho, L. L. da Rocha, A. Stemmer, V. Landi, J. V. Delgado-Bermejo
      Abstract: Biodiversity studies are more efficient when large numbers of breeds belonging to several countries are involved, as they allow for an in-depth analysis of the within- and between-breed components of genetic diversity. A set of 21 microsatellites was used to investigate the genetic composition of 24 Creole goat breeds (910 animals) from 10 countries to estimate levels of genetic variability, infer population structure and understand genetic relationships among populations across the American continent. Three commercial transboundary breeds were included in the analyses to investigate admixture with Creole goats. Overall, the genetic diversity of Creole populations (mean number of alleles = 5.82 ± 1.14, observed heterozygosity = 0.585 ± 0.074) was moderate and slightly lower than what was detected in other studies with breeds from other regions. The Bayesian clustering analysis without prior information on source populations identified 22 breed clusters. Three groups comprised more than one population, namely from Brazil (Azul and Graúna; Moxotó and Repartida) and Argentina (Long and shorthair Chilluda, Pampeana Colorada and Angora-type goat). Substructure was found in Criolla Paraguaya. When prior information on sample origin was considered, 92% of the individuals were assigned to the source population (threshold q ≥ 0.700). Creole breeds are well-differentiated entities (mean coefficient of genetic differentiation = 0.111 ± 0.048, with the exception of isolated island populations). Dilution from admixture with commercial transboundary breeds appears to be negligible. Significant levels of inbreeding were detected (inbreeding coefficient > 0 in most Creole goat populations, P 
      PubDate: 2017-01-17T05:27:41.557436-05:
      DOI: 10.1111/age.12529
  • On the origins and genetic diversity of South American chickens: one step
    • Authors: A. Luzuriaga-Neira; G. Villacís-Rivas, F. Cueva-Castillo, G. Escudero-Sánchez, A. Ulloa-Nuñez, M. Rubilar-Quezada, R. Monteiro, M. R. Miller, A. Beja-Pereira
      Abstract: Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.
      PubDate: 2017-01-17T05:27:34.051734-05:
      DOI: 10.1111/age.12537
  • Association analysis of KIT, MITF, and PAX3 variants with white markings
           in Spanish horses
    • Authors: S. Negro; F. Imsland, M. Valera, A. Molina, M. Solé, L. Andersson
      Abstract: Several variants in the KIT, PAX3 and MITF genes have previously been associated with white markings in horses. In this study, we examined eight variants of these genes in 70 Menorca Purebred horses (PRMe, only black solid-coloured horses) and 70 Spanish Purebred horses (PRE, different coat colour patterns) that were scored for the extent of white markings. A maximum-likelihood chi-square test, logistic regression model and ridge regression analyses showed that a missense mutation (p.Arg682His) in KIT was associated with white facial markings (P 
      PubDate: 2017-01-13T06:45:39.820673-05:
      DOI: 10.1111/age.12528
  • Issue Information
    • First page: 253
      PubDate: 2017-04-24T06:58:35.888922-05:
      DOI: 10.1111/age.12499
  • Three intronic lncRNAs with monoallelic expression derived from the MEG8
           gene in cattle
    • Authors: W. Yang; D. Li, G. Wang, C. Zhang, M. Zhang, W. Zhang, S. Li
      Abstract: The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Antisense lncRNAs, intergenetic lncRNAs and enhancer lncRNAs can regulate genomic imprinting, which leads to parent-origin-specific monoalletic expression of genes. However, the function of intronic ncRNAs in genomic imprinting remains unclear. Previously, we obtained the cDNA sequence of cattle MEG8 gene, which is located in the DLK1–DIO3 imprinted clusters of cattle chromosome 21. In this study, we undertook a systematic search for transcripts mapping to the MEG8 intronic region and identified three novel lncRNAs, named MEG8 intronic RNA 1 (MEG8-IT1), MEG8 intronic RNA 2 (MEG8-IT2) and MEG8 intronic RNA 3 (MEG8-IT3) according to the GENCODE annotated bibliography. We characterized the expression pattern of these lncRNAs using RT-PCR in adult cattle tissues, and they were expressed in all tested eight tissues, similar to the expression pattern of MEG8. The allele-specific expression of three novel lncRNAs was assessed using a polymorphism-based sequencing approach. Three single nucleotide polymorphism sites were identified in these three lncRNAs. We found that the three lncRNAs showed monoallelic expression in the analyzed tissues, suggesting that they may be imprinted in cattle. These results expand the number of known monoallelically expressed lncRNAs from the DLK1–DIO3 domain and contribute to further investigation of lncRNA regulatory mechanisms and function.
      PubDate: 2016-12-07T07:49:30.664299-05:
      DOI: 10.1111/age.12527
  • Evidence of a genomic insertion in intron 2 of SOD1 causing allelic
           drop-out during routine diagnostic testing for canine degenerative
    • Authors: M. E. Turba; R. Loechel, E. Rombolà, G. Gandini, F. Gentilini
      Abstract: Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele. To that aim, the genomic context of the causative variant was investigated in two Hovawart dogs. An insertion of 54 nucleotides composed of a poly-T stretch and 15 nucleotides containing the duplication of the exon 2–intron 2 junction was found. The insertion was responsible for the partial mismatch of the reverse primer used for a direct sequencing assay. The mismatch hampered the amplification of the corresponding allele and caused an evident drop-out effect. The insertion is in complete linkage disequilibrium with the c.118G allele. The allele containing the insertion was highly prevalent in Hovawart dogs, accounting for the 26.6% of allele frequency. The insertion was also found in other unrelated breeds such as Rough Collies and Standard Poodles. In conclusion, the study illustrates the importance of correctly designing the primers to avoid inaccurate genotyping of the degenerative myelopathy causative variant in exon 2 of the SOD1 gene.
      PubDate: 2016-12-04T22:50:30.499643-05:
      DOI: 10.1111/age.12525
  • Runs of homozygosity: current knowledge and applications in livestock
    • Authors: E. Peripolli; D. P. Munari, M. V. G. B. Silva, A. L. F. Lima, R. Irgang, F. Baldi
      Abstract: This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome. The frequency, size and distribution of ROH in the genome are influenced by factors such as natural and artificial selection, recombination, linkage disequilibrium, population structure, mutation rate and inbreeding level. Calculating the inbreeding coefficient from molecular information from ROH (FROH) is more accurate for estimating autozygosity and for detecting both past and more recent inbreeding effects than are estimates from pedigree data (FPED). The better results of FROH suggest that FROH can be used to infer information about the history and inbreeding levels of a population in the absence of genealogical information. The selection of superior animals has produced large phenotypic changes and has reshaped the ROH patterns in various regions of the genome. Additionally, selection increases homozygosity around the target locus, and deleterious variants are seen to occur more frequently in ROH regions. Studies involving ROH are increasingly common and provide valuable information about how the genome's architecture can disclose a population's genetic background. By revealing the molecular changes in populations over time, genome-wide information is crucial to understanding antecedent genome architecture and, therefore, to maintaining diversity and fitness in endangered livestock breeds.
      PubDate: 2016-12-01T21:56:16.070089-05:
      DOI: 10.1111/age.12526
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