25 (2), 2016. 68 78 Available online at www.jstage.jst.go.jp/ 原著論文 サトウキビ育種のための系譜情報管理システムの開発 * 891-3102 1742-1 要旨 Web キーワード はじめに 2009 12 3 * Corresponding Author E-mail: yusuke@affrc.go.jp 2004 2014 1887 1963 1986 2010 FAO 1 1 3.6 3.5 2.9 0.9 68
25 (2), 2016 2 10 図 1 主要作物の単収の推移 図 2 わが国のサトウキビ単収の推移 69
2003 2011 2012 2003 系譜情報管理システム Breed Mate Tenset Kintraks R Jason 2014 1 Web 2 Pedigree Point Breed Mate <http:// www.pedigreepoint.com/> Pedigree Point 表 1 システム稼働環境 Web Apache 2.4.10 MySQL 5.1.61 PHP 5.3 OS CloudLinux 6.2 1 システムの改良点 Pedigree Point 1 2 3 4 5 Pedigree Point 1 2 3 4 50 データベースの設計 2 8 NiF8 23 25 32 70
25 (2), 2016 表 2 データベース構造 ID Name NiF8 Femal ID Male ID Reg Regist or Not Sex Male or Female Species Spontanium Reg No. :KF81-11 No.30 Smut R < > S Num M < > F Leng L < > S Diam W < > T Suc H < > L Mature E < > L Break R < > S photo KTn03-54 Name ID Female Male ID Name ID Female Male Reg Sex Species 6 2010 5 RR R RS S SS データの作成と管理 Web 600 2 1 CSV 2 Pedigree Point Breed Mate Pedigree Explore Pedigree Explore 系譜システムの利用利用方法 1 21 2 3 3 4 4 NiTn20 NiF4 NiF5 5 5 6 7 6 近交係数の計算方法 (1 + F A ) (1/2) (n+1) F A 71
図 3 一覧表示 図 4 系譜画面 72
25 (2), 2016 図 5 兄弟画面 n 2003 7 20 20 NiF4 2 NCo310 2 NCo310 NCo310 7 A 2 + 2 = 4 A S 19 3 NCo310 Black Cheribon NCo310 Black Cheribon 4 + 3 = 7 2 (1/2) (7+1) 2 0.00781 NCo310 F A 系譜システムを用いた品種分析 1990 8 33 26 6 4 n 2 n 6 126 19 82 47 19 6 73
図 6 近交係数画面 1 9 20 NiF5 5 2 12 22 3 4 26 55 1990 6 0 26 0 4 16 8 8 70 70 70 70 おわりに 2003 58 2015 2011 2012 74
25 (2), 2016 図 7 農林 20 号の全系譜 75
表 3 近交係数の計算元データ NCo310 POJ2364 Co213 EK28 POJ100 POJ213 BlackCheribon A 4 B 8 C 8 D 7 E 10 G 9 N 12 F 10 H 9 O 11 I 10 P 11 J 10 Q 10 K 9 R 13 L 10 S 13 M 10 表 4 近年品種の系譜構造 8 NiF8 50 17 34 1.21 9 Ni9 31 13 42 0.00 10 NiTn10 65 31 48 2.54 11 Ni11 70 53 76 8.87 12 Ni12 58 39 67 0.00 13 Ni13 74 51 69 5.78 14 Ni14 51 32 63 0.00 15 Ni15 57 30 53 2.35 16 Ni16 49 26 53 7.41 17 Ni17 68 38 56 4.12 18 NiTn 18 66 48 73 6.80 19 NiTn19 82 61 74 14.13 20 NiTn20 67 49 73 4.64 21 Ni21 59 37 63 6.90 22 Ni22 28 16 57 0.00 23 Ni23 59 37 63 6.90 24 NiN24 40 8 20 0.59 25 NiH25 51 27 53 1.10 26 Ni26 78 43 55 5.32 27 Ni27 68 36 53 4.12 28 Ni28 70 52 74 26.28 29 Ni29 70 52 74 26.28 30 KN00-114 2 0 0 0.00 31 KY99-176 61 34 56 3.99 32 KTn03-54 28 2 7 0.00 33 RK97-14 68 43 63 5.43 76
25 (2), 2016 図 8 祖父母が把握できる品種の重複率と近交係数 引用文献 2011 NiF8 Ni9 80: 182 183. Jason, P., T. Therneau and D. Schaid (2014) The kinship2 R Package for Pedigree Data, Hum Heredity, 78(2): 91 93. 2014 62: 41 51. 2015 SSR 239: 234. 2009 2(1): 23 26. 2003 47(2): 97 98. 1986 23 28. 2010 2004 73(1): 140 141. 2011 12: 90 93. 2011 2011-15615 2012 2012-235772 2003 72(3): 309 313. 2015 12 8 2016 2 18 77
Agricultural Information Research 25(2) 2016. 68 78 Development of a Sugarcane Pedigree Database for Breeders Yusuke Tarumoto*, Taiichiro Hattori, Minoru Tanaka, Takeo Sakaigaichi and Michiko Hayano NARO Kyushu Okinawa Agricultural Research Center (NARO/KARC), Nishinoomote, Kagoshima 891-3102, Japan Abstract Pedigree information is important for crossing and selection in sugarcane breeding. We developed a sugarcane pedigree database that is a web-based application using PHP and MySQL, which allows breeders anywhere to share pedigree information. For each sugarcane line, it contains data on culm thickness and length, sugar content, maturity, and disease resistance. The database has information on more than 600 sugarcane lines in Japan, providing not only pedigree reports but also offspring and sibling reports. The genetic distance of each line is evaluated based on the inbreeding value calculated using the line s pedigree information. Although ancestor information is lacking in many sugarcane pedigree data, thus limiting the application of inbreeding values, in those lines for which grandparents have been identified, the overlap rate in the pedigree line and inbreeding value provide an efficient way to evaluate the genetic distance. Keywords sugarcane, database, pedigree, inbreeding, breeding * Corresponding Author E-mail: yusuke@affrc.go.jp 78