SHORT COMMUNICATION
doi: 10.1111/age.12300
Whole-genome prediction of fatty acid composition in meat of Japanese Black cattle A. Onogi*, A. Ogino†, T. Komatsu‡, N. Shoji‡, K. Shimizu†, K. Kurogi†, T. Yasumori§, K. Togashi§ and H. Iwata* *Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan. †Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan. ‡ Agricultural Research Center, Ipponmatsu, Torigoe, Shinjo, Yamagata 996-0041, Japan. §Cattle Breeding Department (beef), Livestock Improvement Association of Japan, Inc., Tokyo 135-0041, Japan.
Summary
Because fatty acid composition influences the flavor and texture of meat, controlling it is particularly important for cattle breeds such as the Japanese Black, characterized by high meat quality. We evaluated the predictive ability of single-step genomic best linear unbiased prediction (ssGBLUP) in fatty acid composition of Japanese Black cattle by assessing the composition of seven fatty acids in 3088 cattle, of which 952 had genome-wide marker genotypes. All sires of the genotyped animals were genotyped, but their dams were not. Cross-validation was conducted for the 952 animals. The prediction accuracy was higher with ssGBLUP than with best linear unbiased prediction (BLUP) for all traits, and in an empirical investigation, the gain in accuracy of using ssGBLUP over BLUP increased as the deviations in phenotypic values of the animals increased. In addition, the superior accuracy of ssGBLUP tended to be more evident in animals whose maternal grandsire was genotyped than in other animals, although the effect was small. Keywords beef cattle, blupf90, genomic selection, prediction error
Fatty acid composition influences the flavor and texture of meat. Because Japanese Black cattle are characterized by high meat quality, the control of fatty acid composition is important to improve and maintain this attribute. In this study, we evaluated the usefulness of whole-genome marker information to predict breeding values for fatty acid composition in meat. We used single-step genomic best linear unbiased prediction (ssGBLUP) (Legarra et al. 2009; Aguilar et al. 2010) because only a few animals had both marker genotypes and phenotypic records. In addition, reliable breeding value estimates were known for only a few bulls. These constraints hampered the application of methods that require large training sets. ssGBLUP has been previously shown to be useful for the prediction of carcass traits of Japanese Black cattle (Onogi et al. 2014). We collected the phenotypic records of the composition of seven fatty acids (C14:0, C14:1, C16:0, C16:1, C18:0, C18:1 and C18:2) and of three carcass traits (beef marbling score, carcass weight and rib eye area) for 3088 Japanese
Address for correspondence A. Onogi, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. E-mail: [email protected] Accepted for publication 21 March 2015
Black cattle. These animals had been fattened in Yamagata prefecture, Japan, and had been slaughtered between 2006 and 2010. All animals were cared for and slaughtered according to Japanese rules and regulations for animal care. Fatty acid composition was measured in tissues from musculus trapezius as described by Inoue et al. (2011), with some modifications (Appendix S1). The composition of monounsaturated fatty acids (MUFA) was calculated by summing those of C14:1, C16:1 and C18:1. Beef marbling score, carcass weight and rib eye area were measured as described in Onogi et al. (2014). Among the 3088 animals, 952 were genotyped using the Illumina BovineLD BeadChip version 1 (Illumina). In addition, 616 bulls, including the 61 sires of the 952 animals, were genotyped with Illumina BovineSNP50 BeadChip version 1 or 2. After pruning markers as described by Onogi et al. (2014), 38755 marker genotypes were obtained for the bulls. The genotypes of ungenotyped markers in the 952 animals were imputed using BEAGLE (Browning & Browning 2009). We fitted a single-trait mixed model to the full data for each trait to estimate variance components and fixed effects. The model included sex, slaughter month and year, farm, and linear and quadratic deviations of slaughter age as fixed effects and additive genetic effects as random effects. The numerator relationship matrix (A) was calculated from
© 2015 Stichting International Foundation for Animal Genetics, 46, 557–559
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558
Onogi et al. pedigrees traced back five generations. Parameters were inferred using AIREMLF90 software (Misztal et al. 2002). We adjusted the phenotypic values using the fixed effects estimated. The estimated heritability for the fatty acid compositions presented in Table 1 was largely consistent with previous estimates in this breed (Inoue et al. 2011; Nogi et al. 2011). However, for C14:0, C16:0 and MUFA, the heritability was estimated to be considerably higher than in previous reports [e.g. 0.82 for C14:0, 0.65 for C16:0 and 0.66 for MUFA, as reported by Inoue et al. (2011)].
Table 1 Comparison of realized prediction accuracy1.
C14:0 C14:1 C16:0 C16:1 C18:0 C18:1 C18:2 MUFA BMS CW REA
h2
ssGBLUP
BLUP
Gain2
0.98 0.56 0.83 0.59 0.67 0.73 0.55 0.88 0.70 0.48 0.42
0.66 0.70 0.51 0.72 0.58 0.65 0.56 0.55 0.44 0.69 0.50
0.59 0.52 0.39 0.61 0.50 0.52 0.52 0.45 0.31 0.60 0.36
1.11 1.34 1.30 1.18 1.15 1.25 1.07 1.23 1.44 1.15 1.37
h2, heritability. C14:0 to C18:2, fatty acids; MUFA, monounsaturated fatty acids; BMS, beef marbling score; CW, carcass weight; REA, rib eye area. 1 Fivefold cross-validation was repeated five times. Standard deviations of accuracy were
doi: 10.1111/age.12300
Whole-genome prediction of fatty acid composition in meat of Japanese Black cattle A. Onogi*, A. Ogino†, T. Komatsu‡, N. Shoji‡, K. Shimizu†, K. Kurogi†, T. Yasumori§, K. Togashi§ and H. Iwata* *Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan. †Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi 371-0121, Japan. ‡ Agricultural Research Center, Ipponmatsu, Torigoe, Shinjo, Yamagata 996-0041, Japan. §Cattle Breeding Department (beef), Livestock Improvement Association of Japan, Inc., Tokyo 135-0041, Japan.
Summary
Because fatty acid composition influences the flavor and texture of meat, controlling it is particularly important for cattle breeds such as the Japanese Black, characterized by high meat quality. We evaluated the predictive ability of single-step genomic best linear unbiased prediction (ssGBLUP) in fatty acid composition of Japanese Black cattle by assessing the composition of seven fatty acids in 3088 cattle, of which 952 had genome-wide marker genotypes. All sires of the genotyped animals were genotyped, but their dams were not. Cross-validation was conducted for the 952 animals. The prediction accuracy was higher with ssGBLUP than with best linear unbiased prediction (BLUP) for all traits, and in an empirical investigation, the gain in accuracy of using ssGBLUP over BLUP increased as the deviations in phenotypic values of the animals increased. In addition, the superior accuracy of ssGBLUP tended to be more evident in animals whose maternal grandsire was genotyped than in other animals, although the effect was small. Keywords beef cattle, blupf90, genomic selection, prediction error
Fatty acid composition influences the flavor and texture of meat. Because Japanese Black cattle are characterized by high meat quality, the control of fatty acid composition is important to improve and maintain this attribute. In this study, we evaluated the usefulness of whole-genome marker information to predict breeding values for fatty acid composition in meat. We used single-step genomic best linear unbiased prediction (ssGBLUP) (Legarra et al. 2009; Aguilar et al. 2010) because only a few animals had both marker genotypes and phenotypic records. In addition, reliable breeding value estimates were known for only a few bulls. These constraints hampered the application of methods that require large training sets. ssGBLUP has been previously shown to be useful for the prediction of carcass traits of Japanese Black cattle (Onogi et al. 2014). We collected the phenotypic records of the composition of seven fatty acids (C14:0, C14:1, C16:0, C16:1, C18:0, C18:1 and C18:2) and of three carcass traits (beef marbling score, carcass weight and rib eye area) for 3088 Japanese
Address for correspondence A. Onogi, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. E-mail: [email protected] Accepted for publication 21 March 2015
Black cattle. These animals had been fattened in Yamagata prefecture, Japan, and had been slaughtered between 2006 and 2010. All animals were cared for and slaughtered according to Japanese rules and regulations for animal care. Fatty acid composition was measured in tissues from musculus trapezius as described by Inoue et al. (2011), with some modifications (Appendix S1). The composition of monounsaturated fatty acids (MUFA) was calculated by summing those of C14:1, C16:1 and C18:1. Beef marbling score, carcass weight and rib eye area were measured as described in Onogi et al. (2014). Among the 3088 animals, 952 were genotyped using the Illumina BovineLD BeadChip version 1 (Illumina). In addition, 616 bulls, including the 61 sires of the 952 animals, were genotyped with Illumina BovineSNP50 BeadChip version 1 or 2. After pruning markers as described by Onogi et al. (2014), 38755 marker genotypes were obtained for the bulls. The genotypes of ungenotyped markers in the 952 animals were imputed using BEAGLE (Browning & Browning 2009). We fitted a single-trait mixed model to the full data for each trait to estimate variance components and fixed effects. The model included sex, slaughter month and year, farm, and linear and quadratic deviations of slaughter age as fixed effects and additive genetic effects as random effects. The numerator relationship matrix (A) was calculated from
© 2015 Stichting International Foundation for Animal Genetics, 46, 557–559
557
558
Onogi et al. pedigrees traced back five generations. Parameters were inferred using AIREMLF90 software (Misztal et al. 2002). We adjusted the phenotypic values using the fixed effects estimated. The estimated heritability for the fatty acid compositions presented in Table 1 was largely consistent with previous estimates in this breed (Inoue et al. 2011; Nogi et al. 2011). However, for C14:0, C16:0 and MUFA, the heritability was estimated to be considerably higher than in previous reports [e.g. 0.82 for C14:0, 0.65 for C16:0 and 0.66 for MUFA, as reported by Inoue et al. (2011)].
Table 1 Comparison of realized prediction accuracy1.
C14:0 C14:1 C16:0 C16:1 C18:0 C18:1 C18:2 MUFA BMS CW REA
h2
ssGBLUP
BLUP
Gain2
0.98 0.56 0.83 0.59 0.67 0.73 0.55 0.88 0.70 0.48 0.42
0.66 0.70 0.51 0.72 0.58 0.65 0.56 0.55 0.44 0.69 0.50
0.59 0.52 0.39 0.61 0.50 0.52 0.52 0.45 0.31 0.60 0.36
1.11 1.34 1.30 1.18 1.15 1.25 1.07 1.23 1.44 1.15 1.37
h2, heritability. C14:0 to C18:2, fatty acids; MUFA, monounsaturated fatty acids; BMS, beef marbling score; CW, carcass weight; REA, rib eye area. 1 Fivefold cross-validation was repeated five times. Standard deviations of accuracy were
