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Detecting and Managing Suspected Admixture and Genetic Drift in Domestic Livestock: Modern Dexter Cattle - a Case Study
Detecting and managing suspected admixture and genetic drift in domestic livestock: modern Dexter cattle - a case study Timothy C Bray Cardiff University C a r d if f UNIVERSITY PRIFYSCOL C a e RDY|§> A dissertation submitted to Cardiff University in candidature for the degree of Doctor of Philosophy UMI Number: U585124 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. Dissertation Publishing UMI U585124 Published by ProQuest LLC 2013. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Table of Contents Page Number Abstract I Declaration II Acknowledgements III Table of Contents IV Chapter 1. Introduction 1 1. introduction 2 1.1. Molecular genetics in conservation 2 1.2. Population genetic diversity 3 1.2.1. Microsatellites 3 1.2.2. Within-population variability 4 1.2.3. Population bottlenecks 5 1.2.4. Population differentiation 6 1.3. Assignment of conservation value 8 1.4. Genetic admixture 10 1.4.1. Admixture affecting conservation 12 1.5. Quantification of admixture 13 1.5.1. Different methods of determining admixture proportions 14 1.5.1.1. Gene identities 16 1.5.1.2. -
Wagyu from Kyoto to the World
About Our New Facilities Wagyu from Kyoto to the World Kyoto City Central Wholesale Meat Market & Market History Slaughterhouse Kyoto City Central Wholesale Meat Market & The new facilities are the latest among the 10 national Slaughterhouse was established as a central wholesale central wholesale markets managed by municipal market specifically for fresh meat in October 1969 governments in Japan, and the most advanced taking over its function from the Kyoto Municipal equipment is installed. Also, owing to the streamlined Slaughterhouse which was founded in 1909. process including slaughtering, dressing and It has been fully renovated in order to provide facilities processing, we are able to produce beef in higher designed for exporting Japanese beef overseas and it quality than ever and export it overseas. has been in operation since April 2018. Main Distribution Channels for Kyoto City Central Wholesale Meat Market & Slaughterhouse ※The ovals in the chart below reflect the status at that point in time Kyoto City Central Wholesale Meat Market & Slaughterhouse Consumer Producer Kyoto Meat Market Co., Ltd (wholesalers) Meat Buyer processing Meat processing Dressed carcass and and (slaughtering) edible offal meats Sellers Carcass Retailers and caterers Auction or relative Skin and inedible transaction offal meats Meat portion processing Sales by consignment Meat portion which include processing viscera,byproducts,etc. Research and development agencies, Skin and fat processors including universities TEL: +81-75-681-5791 FAX: +81-75-681-5793 Kyoto City Central Wholesale Meat Market & Slaughterhouse 2 Higashinokuchi, Kisshoin Ishihara, Minami-Ku, Kyoto City 601-8361 Issued on January, 2019 【Homepage】http://www.city.kyoto.lg.jp/menu2/category/34-0-0-0-0-0-0-0-0-0.html Kyoto City Printing Number 303191 Wagyu Dishes About Wagyu “Sukiyaki” One of the most famous Japanese dishes known worldwide is Sukiyaki. -
Comparison on the Growth Characteristics Between Calves of Two Different Japanese Beef Breeds Suckled by Japanese Shorthorn Dams
Comparison on Growth between Two Different Japanese Beef Calves JARQ 54 (1), 93-100 (2020) https://www.jircas.go.jp Comparison on Growth between Two Different Japanese Beef Calves Comparison on the Growth Characteristics between Calves of Two Different Japanese Beef Breeds Suckled by Japanese Shorthorn Dams Manabu YAMAGUCHI1*, Akira WATANABE2, Naoki TAKENOUCHI3, Hiroyuki SUZUKI4 and Masatoshi MATSUZAKI4 1 Division of Japanese Black Cattle Production and Wildlife Management Research, Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Ohda, Japan 2 Livestock and Forage Research Division, Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, Morioka, Japan 3 Division of Livestock and Grassland Research, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Japan 4 Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan Abstract The growth characteristics of five male Japanese Black calves that were produced by embryo transfer to, born from, and nursed by Japanese Shorthorn surrogate dams (BS-group) were compared with those of five male Japanese Shorthorn calves that were delivered from dams of the same breed after natural mating (SS-group). The birth weights of the BS-group calves were lower (P < 0.01) than those of the SS-group calves. During the first two months, the daily weight gain of the SS-group calves was greater (P < 0.05) than that of the BS-group calves. However, between the third and fourth months, the daily weight gain of the BS-group calves was greater (P > 0.05). During the first two months, the chest girth was smaller (P < 0.05) in the BS-group calves than in the SS-group calves, but was similar in both groups by the age of four months. -
Cattle Genetic Resources in Japan: One Successful Crossbreeding Story and Genetic Diversity Erosion
ᙾ㉏ᵩả 2003/8/15 ֏ૌ 01:38 C:\Documents Cattleand Settings\Administrator\ Genetic Resources ோ૿ in Japan\ᄅངᏺᅃ \05_Japan_cattle_edited(4).doc Cattle Genetic Resources in Japan: One Successful Crossbreeding Story and Genetic Diversity Erosion Mitsuru MINEZAWA Animal Genetic Resources Laboratory, Genebank, National Institute of Agrobiological Sciences, Japan Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan I. Beef cattle production background I-1. Historical features influencing cattle production Besides pigs and ducks, Sus scrofa and Anas sp., no ancestral domesticated animals naturally inhabited Japan. Domestic animals, such as pigs, cattle and chickens were introduced in the late Jomon (~ B.C. 500) to Yayoi Eras (B.C. 500 – A.D. 300). A Chinese historical book (~ A.D. 250) described that there were no cattle, horses or sheep in Japan. Because no descriptions of pigs and chickens were found in the book, the possibility of their existence could not be denied. Several books written in the mid 7th century referred to cow’s milk. Engishiki (A.D. 927), written in the Heian Era, is a description of the milk product, “So”, surmised as condensed milk for medical purposes. A reference to a presentation of “So” to the government is made in this book. However, this habit was abolished at the beginning of the 12th century. The government banned the slaughtering of animals, cattle, horses, dogs, monkeys and chickens in A.D. 675. Cattle and horse slaughtering were abolished again in A.D. 742. This suggested that the people of this period ate meat. After the prohibitory edict, meat and milk became less common. -
Random Regression Analysis of Calving Interval of Japanese Black Cows
animals Article Random Regression Analysis of Calving Interval of Japanese Black Cows Shinichiro Ogawa * and Masahiro Satoh Graduate School of Agricultural Science, Tohoku University, Sendai 980-8572, Miyagi, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-22-757-4114 Simple Summary: Genetic parameters for the calving interval of Japanese Black cows were estimated by using a random regression model and a repeatability model. Legendre polynomials based on age at previous calving, ranging from 18 to 120 months, were used as sub-models for random regression analysis. The estimated heritability for the calving interval was low and was similar between the models. The estimated genetic correlation between ages was always higher than >0.8. Spearman’s rank correlation of the estimated breeding values between the two models was ≥0.97 for cows with their own records and ≥0.94 for sires of these cows. Therefore, this study supports the validity of fitting a repeatability model to the records of the calving interval of Japanese Black cows for breeding value evaluation. Our results could contribute to determining strategies for selection and management of Japanese Black cattle. Abstract: We estimated genetic parameters for the calving interval of Japanese Black cows using a random regression model and a repeatability model. We analyzed 92,019 calving interval records of 36,178 cows. Pedigree data covered 390,263 individuals. Age of cow at previous calving for each record ranged from 18 to 120 months. We used up to the second-order Legendre polynomials based on age at previous calving as sub-models for random regression analysis, and assumed a constant error variance across ages. -
Animal Genetic Resources Information Bulletin
The designations employed and the presentation of material in this publication do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Les appellations employées dans cette publication et la présentation des données qui y figurent n’impliquent de la part de l’Organisation des Nations Unies pour l’alimentation et l’agriculture aucune prise de position quant au statut juridique des pays, territoires, villes ou zones, ou de leurs autorités, ni quant au tracé de leurs frontières ou limites. Las denominaciones empleadas en esta publicación y la forma en que aparecen presentados los datos que contiene no implican de parte de la Organización de las Naciones Unidas para la Agricultura y la Alimentación juicio alguno sobre la condición jurídica de países, territorios, ciudades o zonas, o de sus autoridades, ni respecto de la delimitación de sus fronteras o límites. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying or otherwise, without the prior permission of the copyright owner. Applications for such permission, with a statement of the purpose and the extent of the reproduction, should be addressed to the Director, Information Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00100 Rome, Italy. Tous droits réservés. Aucune partie de cette publication ne peut être reproduite, mise en mémoire dans un système de recherche documentaire ni transmise sous quelque forme ou par quelque procédé que ce soit: électronique, mécanique, par photocopie ou autre, sans autorisation préalable du détenteur des droits d’auteur. -
WAGYU BREEDERS HANDBOOK an Introduction to Wagyu
2018 WAGYU BREEDERS HANDBOOK An introduction to Wagyu. Pamela Armstrong, LVT Maple Row Stock Farm [email protected] www.Wagyupedia.com FOREWARD Many people consider Wagyu beef to be the most tender and flavorful beef in the World. The cattle used to make this beef are docile with good temperaments, and they are known for their intense intramuscular marbling, high fertility rates and calving ease traits. Why wouldn’t a cattle farmer want to raise Wagyu? The internet is flush with information about Wagyu, some of it is accurate and some of it is misleading. This handbook is designed to help breeders decide whether or not raising this breed is the right choice for them. Peer-reviewed journals and academic textbooks were used to create this handbook, and world-renowned Wagyu experts were consulted. There are good opportunities for producers who are informed, careful and realistic. There are many variances within the Wagyu breeds and bloodlines; as well as differences in short and long-fed animals, and results of feeding protocols. Wagyu are very special animals, they are considered a national treasure in Japan. I hope you enjoy and appreciate them as much as I do. Pam Armstrong, LVT © 2018 Pamela Armstrong, LVT Page 2 Table of Contents FOREWARD ................................................................................................................................................... 2 ORIGIN OF WAGYU ...................................................................................................................................... -
The Genetic Diversity of Japanese Wagyu Using Molecular Markers
Journal of Animal Breeding and Genomics JABG. 2017 Sep, 1(1): 17-22 https://doi.org/10.12972/jabng.20170002 Review OPEN ACCESS The genetic diversity of Japanese Wagyu using molecular markers Hideyuki MANNEN1* 1Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Nada, Kobe 657-8501, Japan ABSTRACT We have investigated the genetic diversity and structure using several DNA markers, such as mtDNA, Sry gene in Y chromosome and autosomal SNPs for Japanese Wagyu and native cattle in the North Eastern Asia. Most of Japanese cattle mtDNA belonged to Bos taurus mtDNA haplogroups T1, T2, T3 and T4. All Japanese populations included Asian unique mtDNA haplogroup T4 with high frequencies (0.43 – 0.81). The predominant T4 haplogroup may be a result of founder effect when ancestral cattle were introduced to Japan Islands at the immigration. We found that Mongolian cattle have Bos indicus mtDNA with the genetic frequency of 0.20, but no Bos indicus Y chromosome. No Bos indicus mtDNA in both Japanese and Korean samples suggested that the introgression may be a secondary phenomenon, with the earlier cattle in the region being purely Bos taurus. We analyzed 117 SNPs to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations. The results could suffi ciently explain the genetic construction of Asian cattle populations. These results reflected to the geographical and historical background in each population. The genetic information would contribute to understanding origin of North Asian native cattle, in addition to the origin of Japanese Wagyu cattle. Keywords: Genetic diversity, mtDNA, molecular markers, origin, Wagyu Introduction The Wagyu generally refers to four Japanese native breeds bred in Japan, but nowadays the famous brand name Wagyu includes not only Japanese native cattle produced in Japan, but also animals or even crossbred Japanese native cattle produced in foreign countries such as Australia or the United States. -
PDF Livestock Production
Livestock production Hiroki Nakatsuji Laboratory of Animal Production System Research Faculty of Agriculture Hokkaido University Email:[email protected] Chapter 5 Livestock Production Hiroki Nakatsuji Hokkaido is a major area of livestock production in Japan. According to Statistics on Agriculture, Forestry and Fisheries (Table 5-1), in 2006, the livestock production of Hokkaido was of 502 billion yen, accounting for 18.6% of the total livestock output of Japan, and was the highest among Japan’s 47 prefectures. Dairy farming holds a dominant position in Japan’s livestock production. There is a large area of grasslands in Hokkaido, accounting 72.7% of the national area of grasslands. In 2006, the number of dairy farmers was 8,590 and there were 859,100 dairy cattle, which meant 100 cows per farm. Dairy farms in Hokkaido are shipping 3,798,123 metric tons of milk (Table 5-2), that is, 46.7% of Japan’s total milk production (Table 5-1). 1. Dairy It is said that dairy farming in Hokkaido began with the milking of “Nanbu Cattle” in Hakodate city in 1857. In 1873, Mr. Edwin Dan, an agricultural expert from United States, arrived as an advisor with commissioner Capron. He taught the system of livestock production to Hokkaido’s people for 9 years. He laid the foundation for dairy farming by introducing “Durham“ (Shorthorn) cows, which were used for both milk and beef in the United States. In 1878, the Sapporo Agricultural College imported “Ayrshire” milking cows. In 1889, for the first time in Japan, the college imported “Holstein” cattle (3 females, “Shikishima”, “Sazanami” and “Chidori”; 2 males, “Akitsushima” and “Yamato”: as named in Japanese). -
Japanese Agricultural Standard for Organic Livestock
Japanese Agricultural Standard for Organic Livestock Products (Notification No.1608 of the Ministry of Agriculture, Forestry and Fisheries of October 27, 2005) (Provisional Translation) Established: October 27, 2005 (Purpose) Article 1. The purpose of this standard is to define the criteria of production methods for the organic livestock products. (Principles of Production of Organic Livestock Products) Article 2. Organic livestock products are, in principle, manufactured from organic livestock raised in deference to their physiological and behavioral needs, on the basis of provision of providing the feeds produced by reducing pressure on the environment as much as possible and the avoidance of use of veterinary drugs, to sustain and enhance the natural cyclical function of agriculture. (Definition) Article 3. In this standard, terms listed on the left side of the table below are defined on the right side. Terms Definitions Organic Livestock produced by the criteria in the next Article. Livestock products Domestic Bovine, equine, ovine, caprine, and porcine animals. animals Poultry Chickens, quails, ducks, and wild ducks (including crossbreeds with ducks as wild duck; the same hereafter). Organic feeds Limited to those with the grading labels on the products produced in accordance with the Japanese Agricultural Standard of Organic Agricultural Products (Notification No.59 of the Ministry of Agriculture, Forestry and Fisheries of October 27, 2005; hereinafter referred to as the Standard for Organic agricultural products,) the Japanese -
![Japanese Beef Cattle - Wa Means Japan[Ese] and Gyu Means Cow](https://docslib.b-cdn.net/cover/7126/japanese-beef-cattle-wa-means-japan-ese-and-gyu-means-cow-1567126.webp)
Japanese Beef Cattle - Wa Means Japan[Ese] and Gyu Means Cow
Definition and breed makeup Origins Meat Quality Breed Register and its Structure Wagyu is the name of Japanese beef cattle - wa means Japan[ese] and gyu means cow. There are four(4) types of Wagyu Cattle in Japan; Japanese Black Japanese Brown or Red (also known as Akaushi) Japanese Shorthorn Japanese Poll Japanese Beef cattle Japanese Black Japanese Brown (Wagyu) (Red Wagyu) Native Cattle Japanese Shorthorn Japanese Poll These breed have been established by cross between Japanese native cattle and western breeds. The Japanese Black, called “Wagyu”, is the most popular beef cattle in Japan, and this breed was established by cross between Japanese native cattle and several European breeds, including Brown Swiss, Devon, and Ayrshire Japanese Brown, known as “Red Wagyu”, was established by cross with Korean originated cattle and Simmental breed. We have also Japanese shorthorn and Japanese polled, but the population of these two breeds has recently significantly reduced in recent times • For centuries Buddhism was predominant in Japan and meat consumption was prohibited. The utilization of animal products did not become popular until the Meiji restoration in 1868 In the Meiji era many foreign breeds were introduced to Japan and initially crossbred with the native cattle under the direction of the government. Through this, the gene pool for Japanese breed had diluted but the population had expanded. After the initial frenzy of crossbreeding was over, cattle breeders began to improve and promote their own breeds without further crossbreeding within the prefectures. Meat has been consumed in Japan for only about 140 years. Meat eating has only reached widespread popularity in the last 40 years after the “Law for Improvement and Increased Livestock Production” was enacted in 1950s. -
Oita Bank Ltd. by Hugh Patrick Chairman, Center on Japanese Economy and Business R
Oita Bank Ltd. By Hugh Patrick Chairman, Center on Japanese Economy and Business R. D. Calkins Professor of International Business Emeritus Columbia Business School Oita Bank is the leading regional bank in Oita Prefecture. Established in 1893, its headquarters are in Oita City, and it has 94 branches throughout the prefecture. It is a successful, profitable bank, though its profits have been under pressure due to the Bank of Japan’s sustained low interest rate policy. The bank has the highest (A+) rating for its long-term preferred debt from the Japan Credit Rating Agency. Oita Prefecture, like Japan overall, is experiencing population decline, and prefectural economic growth is slow. Because lending is not profitable and demand growth is limited, the bank is placing emphasis on increasing its fees and services business, as well as creating, investing in, and lending to, new companies. One is Oita Made Company, for which there is a separate report. The Bank’s shares are listed. They are owned by a life insurance company and other (primarily regional) institutional investors; 18 percent are foreign-owned. Total equity as of March 31, 2018 was ¥196.4 billion ($1.755 billion at the 106.24 yen/dollar exchange rate used in the bank’s 2018 annual report), with paid-in capital of ¥19.6 billion ($184.5 million). Accordingly, the capital adequacy ratio was a healthy 10.8 percent, far above the domestic standard minimum of 4 percent. Deposits were ¥2,918 billion ($27.5 billion). Loans and discounted bills were only 61 percent of its deposits, ¥1,792 billion ($16.9 billion).