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

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

Size of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus,...

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Published in:BMC genomics Vol. 22; no. 1; pp. 1 - 799
Main Authors: 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
Format: Journal Article
Language:English
Published: London BioMed Central Ltd 06-11-2021
BioMed Central
BMC
Subjects:
Accuracy
Accuracy of genomic prediction
Animal populations
Animals
Arrays
Beef cattle
Breeding
Carcasses
Cattle
Chromosomes
Empirical analysis
Gene mapping
Genetic aspects
Genetic testing
Genomics
Heritability
Independent chromosome segments
Methods
Polygenic inheritance
Population
Population genetics
Predictions
Progeny
Quantitative trait loci
Simulation
Simulation analysis
Size of reference population
Software
Statistics
Japan
United States > US
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Summary:Size of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus, extent to which traits of interest affect accuracy of genomic prediction in Japanese Black cattle remains obscure. This study aimed to explore the size of reference population for expected accuracy of genomic prediction for simulated and carcass traits in Japanese Black cattle using a large amount of samples. A simulation analysis showed that heritability and size of reference population substantially impacted the accuracy of GEBV, whereas the number of quantitative trait loci did not. The estimated numbers of independent chromosome segments (M.sub.e) and the related weighting factor (w) derived from simulation results and a maximum likelihood (ML) approach were 1900-3900 and 1, respectively. The expected accuracy for trait with heritability of 0.1-0.5 fitted well with empirical values when the reference population comprised > 5000 animals. The heritability for carcass traits was estimated to be 0.29-0.41 and the accuracy of GEBVs was relatively consistent with simulation results. When the reference population comprised 7000-11,000 animals, the accuracy of GEBV for carcass traits can range 0.73-0.79, which is comparable to estimated breeding value obtained in the progeny test. Our simulation analysis demonstrated that the expected accuracy of GEBV for a polygenic trait with low-to-moderate heritability could be practical in Japanese Black cattle population. For carcass traits, a total of 7000-11,000 animals can be a sufficient size of reference population for genomic prediction.
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content type line 23
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-021-08121-z