Additional file 1 of Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle

Takeda, Masayuki; Inoue, Keiichi; Oyama, Hidemi; Uchiyama, Katsuo; Yoshinari, Kanako; Sasago, Nanae; Kojima, Takatoshi; Kashima, Masashi; Suzuki, Hiromi; Kamata, Takehiro; Kumagai, Masahiro; Takasugi, Wataru; Aonuma, Tatsuya; Soma, Yuusuke; Konno, Sachi; Saito, Takaaki; Ishida, Mana; Muraki, Eiji; Inoue, Yoshinobu; Takayama, Megumi; Nariai, Shota; Hideshima, Ryoya; Nakamura, Ryoichi; Nishikawa, Sayuri; Kobayashi, Hiroshi; Shibata, Eri; Yamamoto, Koji; Yoshimura, Kenichi; Matsuda, Hironori; Inoue, Tetsuro; Fujita, Atsumi; Terayama, Shohei; Inoue, Kazuya; Morita, Sayuri; Nakashima, Ryotaro; Suezawa, Ryohei; Hanamure, Takeshi; Zoda, Atsushi; Uemoto, Yoshinobu

doi:10.6084/m9.figshare.16944420.v1

12864_2021_8121_MOESM1_ESM.pptx (362.79 kB)

Additional file 1 of Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle

presentation

posted on 2021-11-07, 04:16 authored by Masayuki Takeda, Keiichi Inoue, Hidemi Oyama, Katsuo Uchiyama, Kanako Yoshinari, Nanae Sasago, Takatoshi Kojima, Masashi Kashima, Hiromi Suzuki, Takehiro Kamata, Masahiro Kumagai, Wataru Takasugi, Tatsuya Aonuma, Yuusuke Soma, Sachi Konno, Takaaki Saito, Mana Ishida, Eiji Muraki, Yoshinobu Inoue, Megumi Takayama, Shota Nariai, Ryoya Hideshima, Ryoichi Nakamura, Sayuri Nishikawa, Hiroshi Kobayashi, Eri Shibata, Koji Yamamoto, Kenichi Yoshimura, Hironori Matsuda, Tetsuro Inoue, Atsumi Fujita, Shohei Terayama, Kazuya Inoue, Sayuri Morita, Ryotaro Nakashima, Ryohei Suezawa, Takeshi Hanamure, Atsushi Zoda, Yoshinobu Uemoto

Additional file 1: Fig. S1. Average linkage disequilibrium (r2) values plotted against intermarker distance for all chromosomes. X axis, distance between single nucleotide polymorphisms (SNPs); Y axis, r2 values between SNPs. Fig. S2. Accuracy of estimated breeding values (EBVs) for carcass traits with heritability estimates. We calculated EBVs according to Mrode (2005). X axis, number of progenies per candidate bull. Y axis, accuracy of EBV calculated from numbers of progenies and heritability. Fig. S3. Expected accuracy of genomic estimated breeding values (GEBVs) for simulated traits based on numbers of independent chromosome segments (Me) estimated from cross-validation findings vs. those from effective population size. X axis, number of animals per reference population. Y axis, expected accuracy of GEBVs for simulated traits with different values of Me per number of QTLs (nQTL) determined using formula developed herein (black, red, and blue curves) and from effective population size (green curve). Heritability: (a), 0.1; (b), 0.3; (c), 0.5. Table S1. The numbers of chromosome segments (Me) estimated by cross-validation from previous studies.