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Abstract
Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.
Highlights
Japanese Black cattle are the main breed in the Japanese native cattle, so-called Wagyu
Single regression coefficients were approximately around 1, or 0.99 to 1.06, and relatively high for the single nucleotide polymorphism (SNP) groups with minor allele frequency (MAF) bins of 0.15 0.20 to 0.45 - 0.50. These results could be mainly due to the distribution of SNP genotypes in the current population and may indicate the possibility of SNPs in different MAF groups to capture a different part of additive genetic variance for a given trait
A smaller sample population size often causes a spurious linkage disequilibrium (LD) structure in the population, which would make the interpretation of the results more difficult. This problem could be mitigated by using more samples. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2
Summary
Japanese Black cattle are the main breed in the Japanese native cattle, so-called Wagyu. Heritability estimates of 6 representative carcass traits including the two traits in the Japanese population of this breed are moderate to high [1], which were obtained using pedigree information. For this breed, 3 candidate regions of major gene quantitative trait loci (QTLs) for carcass weight have been reported (called CW-1, CW-2 and CW-3 [2]-[5]) and Nishimura et al (2012) [5] suggested that one-third of additive genetic variance for this trait is explained by these 3 QTLs. Ogawa et al (2014) [6] stated that degree of marbling in this breed is likely to be controlled by only many polygenes. The whole genetic architectures for these carcass traits are still poorly understood
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