Institute of Animal Husbandry and Breeding, University of Hohenheim, 70593 Stuttgart, Germany.
G3 (Bethesda). 2013 Jul 8;3(7):1085-93. doi: 10.1534/g3.113.006536.
Genotype-by-environment interaction (GxE) has been widely reported in dairy cattle. One way to analyze GxE is to apply reaction norm models. The first derivative of a reaction norm is the environmental sensitivity (ES). In the present study we conducted a large-scale, genome-wide association analysis to identify single-nucleotide polymorphisms (SNPs) that affect general production (GP) and ES of milk traits in the German Holstein population. Sire estimates for GP and for ES were calculated from approximately 13 million daughter records by the use of linear reaction norm models. The daughters were offspring from 2297 sires. Sires were genotyped for 54k SNPs. The environment was defined as the average milk energy yield performance of the herds at the time during which the daughter observations were recorded. The sire estimates were used as observations in a genome-wide association analysis, using 1797 sires. Significant SNPs were confirmed in an independent validation set (500 sires of the same population). To separate GxE scaling and other GxE effects, the observations were log-transformed in some analyses. Results from the reaction norm model revealed GxE effects. Numerous significant SNPs were validated for both GP and ES. Many SNPs that affect GP also affect ES. We showed that ES of milk traits is a typical quantitative trait, genetically controlled by many genes with small effects and few genes with larger effect. A log-transformation of the observation resulted in a reduced number of validated SNPs for ES, pointing to genes that not only caused scaling GxE effects. The results will have implications for breeding for robustness in dairy cattle.
基因型与环境互作（GxE）在奶牛中已被广泛报道。分析 GxE 的一种方法是应用反应规范模型。反应规范的一阶导数是环境敏感性（ES）。本研究中，我们进行了一项大规模的全基因组关联分析，以鉴定影响德国荷斯坦牛群体中一般生产性能（GP）和牛奶性状 ES 的单核苷酸多态性（SNP）。通过使用线性反应规范模型，从大约 1300 万头母畜记录中计算了 sire 对 GP 和 ES 的估计值。这些母畜是 2297 头 sire 的后代。 sire 对 54kSNP 进行了基因分型。环境定义为母畜记录时的牛群平均牛奶能量产量表现。 sire 估计值作为全基因组关联分析的观察值，使用了 1797 头 sire。在独立验证集（相同群体的 500 头 sire）中对显著 SNP 进行了验证。为了分离 GxE 缩放和其他 GxE 效应，在一些分析中对观察值进行了对数转换。反应规范模型的结果揭示了 GxE 效应。对 GP 和 ES 都验证了许多显著的 SNP。许多影响 GP 的 SNP 也影响 ES。我们表明，牛奶性状的 ES 是一种典型的数量性状，受许多具有较小效应的基因和少数具有较大效应的基因遗传控制。对观察值进行对数转换会导致 ES 的验证 SNP 数量减少，这表明不仅存在引起缩放 GxE 效应的基因。这些结果将对奶牛的稳健性育种产生影响。
