Beef cattle

Genomic autosomal contribution to total additive and non-additive genetic effects for carcass weight and beef marbling in Japanese Black cattle

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Abstract

Using single nucleotide polymorphism (SNP) information from animal-parents trios enables the construction of genomic relationship matrices corresponding to additive genetic (A) and non-additive genetic effects such as dominance (D) and genomic imprinting (I) effects. In addition, since variance components can now be estimated for each individual chromosome, it is possible to estimate the genetic contribution of each chromosome to a trait. In this study, we utilized these methods to estimate the additive and non-additive genetic effects per chromosome for carcass weight (CW) and beef marbling score (BMS) in Japanese Black cattle. The total number of 1,908 Japanese Black beef steers and heifers with the records and their parents were genotyped. Finally, 34,481 SNPs on the 29 bovine autosomes were used in this analysis. Based on the SNP information of the animal-parents trios, paternal and maternal SNPs were determined, and genomic relationship matrices corresponding to A, D, and I were constructed. In addition, we constructed the three (A, D, and I) genomic relationship matrices for each of the 29 autosomes (AUT), as well as the matrices for the remaining 28 autosomes excluding the corresponding autosome. Each variance component was estimated employing a model based on the three (A, D, and I) genomic relationship matrices constructed from all autosomes (Model 1) and a model including two sets of the three genomic relationship matrices: one for each autosome and the remaining 28 autosomes (Model 2), e.g. y = fixed effects + A (AUT 1) + A (AUT 2-29) + D (AUT 1) + D (AUT 2-29) + I (AUT 1) + I (AUT 2-29) + e. The D and I variance components for the traits estimated from the all autosomes (Model 1) were small. The proportions of the D and I variance to the phenotypic variance (s.e.) were also small, being 0.08 (0.02) and 0.06 (0.01) for CW and 0.09 (0.03) and 0.05 (0.01) for BMS, respectively. In the results by Model 2, A variances of CW in each autosome were relatively large for chromosomes 6, 7, 8, and 14. In addition, the proportion of individual autosome variance within the total genetic variance is also substantial at around 10%, reflecting the influence of the CW-2 (chromosome 6), CW-3 (chromosome 8), and CW-1 (chromosome 14) genes. In BMS, no chromosome-specific characteristics were observed in A variance. In the D and I variances, no clear chromosome-specific characteristics were observed for either trait. However, both variances showed a tendency to decrease in size along chromosome length (number of SNPs), from chromosome 1 to chromosome 29. These results suggest that different polygenic function may be at work between additive and non-additive genetic effects.

Keywords: 2026

How to Cite:

Inoue, K., Nishio, M., Takeda, M., Kishida, Y. & Hirooka, H., (2026) “Genomic autosomal contribution to total additive and non-additive genetic effects for carcass weight and beef marbling in Japanese Black cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285374. doi: https://doi.org/10.31274/wcgalp.23664

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