Department of Agricultural Sciences, University of Sassari, Sassari, Italy.
Department of Agricultural, Forest and Food Sciences, University of Torino, Torino, Italy.
J Anim Breed Genet. 2021 Nov;138(6):708-718. doi: 10.1111/jbg.12637. Epub 2021 Jun 28.
Genomic information allows for a more accurate calculation of relationships among animals than the pedigree information, leading to an increase in accuracy of breeding values. Here, we used pedigree-based and single-step genomic approaches to estimate variance components and breeding values for β-hydroxybutyrate milk content (BHB). Additionally, we performed a genome-wide association study (GWAS) to depict its genetic architecture. BHB concentrations within the first 90 days of lactation, estimated from milk medium infrared spectra, were available for 30,461 cows (70,984 records). Genotypes at 42,152 loci were available for 9,123 animals. Low heritabilities were found for BHB using pedigree-based (0.09 ± 0.01) and genomic (0.10 ± 0.01) approaches. Genetic correlation between BHB and milk traits ranged from -0.27 ± 0.06 (BHB and protein percentage) to 0.13 ± 0.07 (BHB and fat-to-protein ratio) using pedigree and from -0.26 ± 0.05 (BHB and protein percentage) to 0.13 ± 0.06 (BHB and fat-to-protein ratio) using genomics. Breeding values were validated for 344 genotyped cows using linear regression method. The genomic EBV (GEBV) had greater accuracy (0.51 vs. 0.45) and regression coefficient (0.98 vs. 0.95) compared to EBV. The correlation between two subsequent evaluations, without and with phenotypes for validation cows, was 0.85 for GEBV and 0.82 for EBV. Predictive ability (correlation between (G)EBV and adjusted phenotypes) was greater when genomic information was used (0.38) than in the pedigree-based approach (0.31). Validation statistics in the pairwise two-trait models (milk yield, fat and protein percentage, urea, fat/protein ratio, lactose and logarithmic transformation of somatic cells count) were very similar to the ones highlighted for the single-trait model. The GWAS allowed discovering four significant markers located on BTA20 (57.5-58.2 Mb), where the ANKH gene is mapped. This gene has been associated with lactose, alpha-lactalbumin and BHB. Results of this study confirmed the usefulness of genomic information to provide more accurate variance components and breeding values, and important insights about the genomic determination of BHB milk content.
基因组信息比谱系信息更能准确地计算动物之间的关系，从而提高了繁殖值的准确性。在这里，我们使用基于系谱和单步基因组的方法来估计β-羟基丁酸（BHB）的变异分量和繁殖值。此外，我们进行了全基因组关联研究（GWAS）以描绘其遗传结构。泌乳早期（90 天内）的 BHB 浓度可以通过牛奶中红外光谱来估算，共有 30461 头奶牛（70984 条记录）的数据可用。对于 9123 头动物，可用 42152 个基因座的基因型。使用基于系谱（0.09±0.01）和基因组（0.10±0.01）的方法，发现 BHB 的遗传力较低。使用系谱，BHB 与乳性状的遗传相关系数范围为-0.27±0.06（BHB 与蛋白质百分比）至 0.13±0.07（BHB 与脂肪-蛋白质比），而使用基因组学则为-0.26±0.05（BHB 与蛋白质百分比）至 0.13±0.06（BHB 与脂肪-蛋白质比）。使用线性回归法对 344 头已鉴定基因型的奶牛进行了繁殖值验证。与 EBV 相比，基因组 EBV（GEBV）具有更高的准确性（0.51 比 0.45）和回归系数（0.98 比 0.95）。在没有和验证牛的表型的情况下，两次后续评估之间的相关性分别为 0.85 用于 GEBV 和 0.82 用于 EBV。当使用基因组信息时，预测能力（（G）EBV 与调整后的表型之间的相关性）更高（0.38），而在基于系谱的方法中（0.31）则较低。在两性状模型（产奶量、脂肪和蛋白质百分比、尿素、脂肪/蛋白质比、乳糖和体细胞计数的对数转换）中的验证统计数据与单性状模型中的非常相似。GWAS 允许发现四个位于 BTA20 上的显著标记（57.5-58.2 Mb），ANKH 基因映射在该位置。该基因与乳糖、α-乳白蛋白和 BHB 有关。本研究结果证实了基因组信息在提供更准确的变异分量和繁殖值方面的有用性，并且为 BHB 牛奶含量的基因组决定因素提供了重要的见解。
