Open Access Open Badges Research article

Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle

Shinichiro Ogawa1*, Hirokazu Matsuda1, Yukio Taniguchi1, Toshio Watanabe2, Shota Nishimura3, Yoshikazu Sugimoto3 and Hiroaki Iwaisaki1

Author Affiliations

1 Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan

2 National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan

3 Shirakawa Institute of Animal Genetics, Nishigo, Fukushima 961-8061, Japan

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BMC Genetics 2014, 15:15  doi:10.1186/1471-2156-15-15

Published: 3 February 2014



Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poorly studied. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of equally-spaced single nucleotide polymorphisms (SNPs) density on genomic relationship matrix (G matrix), genetic variance explained and GE were investigated using the genotype data of about 40,000 SNPs and two statistical models.


Using all pairs of two adjacent SNPs in the whole SNP set, the means of LD (r2) at ranges 0–0.1, 0.1–0.2, 0.2–0.5 and 0.5–1 Mb were 0.22, 0.13, 0.10 and 0.08, respectively, and 25.7, 13.9, 10.4 and 6.4% of the r2 values exceeded 0.3, respectively. While about 90% of the genetic variance for carcass weight estimated using all available SNPs was explained using 4,000–6,000 SNPs, the corresponding percentage for marbling score was consistently lower. With the conventional linear model incorporating the G matrix, correlation between the genomic estimated breeding values (GEBVs) obtained using 4,000 SNPs and all available SNPs was 0.99 for carcass weight and 0.98 for marbling score, with an underestimation of the former GEBVs, especially for marbling score.


The Japanese Black is likely to be in a breed group with a relatively high extent of whole genome LD. The results indicated that the degree of marbling is controlled by only QTLs with relatively small effects, compared with carcass weight, and that using at least 4,000 equally-spaced SNPs, there is a possibility of ranking animals genetically for these carcass traits in this breed.

Marbling score; Carcass weight; Japanese black cattle; SNP marker density; Linkage disequilibrium; Genomic evaluation; Genomic relationship matrix; Genetic variance estimation