Abstract
BackgroundJapanese 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.ResultsUsing all pairs of two adjacent SNPs in the whole SNP set, the means of LD (r 2 ) 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 r 2 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.ConclusionsThe 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.
Highlights
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
Genomic evaluation (GE) and selection (GS), as proposed by Meuwissen et al [1], is expected to chase the Quantitative trait loci (QTLs) simultaneously using single nucleotide polymorphism (SNP) markers, given that at least one single nucleotide polymorphisms (SNPs) is in linkage disequilibrium (LD) with each QTL
The mean r2 for pairs of two adjacent SNPs, ≤ 1 kb–≤ 2 Mb apart, was 0.81–0.20, and most of the average r2 values obtained using all the SNPs in each given distance range were higher than those reported for the eight breeds
Summary
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. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of -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. Most economically important traits in beef cattle, including carcass traits, are controlled by many quantitative trait loci (QTLs), which usually have relatively small individual effects For such traits, genomic evaluation (GE) and selection (GS), as proposed by Meuwissen et al [1], is expected to chase the QTLs simultaneously using single nucleotide polymorphism (SNP) markers, given that at least one SNP is in linkage disequilibrium (LD) with each QTL. On the other hand, its adoption has been slower, because the accuracy of the genomic estimated breeding value (GEBV) is much lower because of less availability of sires with highly accurate results in progeny tests
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