Tsuruta S, Lourenco D A L, Misztal I, Lawlor T J
Animal and Dairy Science Department, University of Georgia, Athens 30602.
Animal and Dairy Science Department, University of Georgia, Athens 30602.
J Dairy Sci. 2015 Aug;98(8):5796-805. doi: 10.3168/jds.2014-9242. Epub 2015 May 28.
The objective of this study was to investigate genotype by environment interactions for culling rates and milk production in large and small dairy herds in 3 US regions, using genotypes, pedigree, and phenotypes. Single nucleotide polymorphism (SNP) marker variances were also estimated in these different environments. Culling rates including cow mortality were based on 6 Dairy Herd Improvement termination codes reported by dairy producers. Separate data sets for culling rates and 305-d milk yield were created for large and small dairy herds in the US regions of the Southeast (SE), Southwest (SW), and Northeast (NE) for the first 3 lactation cows that calved between 1999 and 2008. Genomic information from 42,503 SNP markers on 34,506 bulls was included in the analysis to predict genomic estimated breeding value (GEBV) of culling rates and 305-d milk yield with a single-step genomic BLUP using a bivariate threshold-linear model. Cow replacement rates in large SE and NE herds were higher. Heritability estimates of culling rates ranged from 0.03 to 0.11, but the differences were small between large and small herds and among the 3 US regions. Genetic correlations between culling rates and 305-d milk yield were medium to high for cows sold for poor production and reproduction problems. Correlations of GEBV for culling rates among the 3 US regions ranged from 0.34 to 0.92 and were lower between the SW and the other regions, especially in small herds. Correlations of GEBV between large and small herds ranged from 0.44 to 0.90 and were lower in the SW. These results indicate genotype by environment interactions of cow culling rate between the US regions and between large and small herds. Correlations of top 30 SNP marker effects for culling rates between 2 US regions ranged from 0.64 to 0.98 and were higher than those of more SNP marker effects except for a culling reason "sold for dairy purpose." Those correlations between large and small herds ranged from 0.67 to 0.98. High correlations of top SNP marker effects on culling reasons between the US regions and between large and small herds suggest that major markers can be useful for selection in different environments. The SNP variance shown in a marker gene segment on chromosome 14 was strongly associated with milk production in large and small herds in the NE but not in the SE and SW. Marker genes on chromosome 14 also showed a strong association with cow culling rates due to poor production and mortality in large herds in the NE.
本研究的目的是利用基因型、系谱和表型，调查美国3个地区大、小型奶牛场淘汰率和产奶量的基因型与环境互作情况。还对这些不同环境下的单核苷酸多态性（SNP）标记方差进行了估计。淘汰率（包括奶牛死亡率）基于奶农报告的6个奶牛群改良终止代码。针对1999年至2008年间产犊的头胎至三胎奶牛，分别为美国东南部（SE）、西南部（SW）和东北部（NE）地区的大、小型奶牛场创建了淘汰率和305天产奶量的数据集。分析纳入了34,506头公牛的42,503个SNP标记的基因组信息，以使用双变量阈值线性模型的单步基因组最佳线性无偏预测法（BLUP）预测淘汰率和305天产奶量的基因组估计育种值（GEBV）。东南部和东北部大型奶牛场的奶牛替换率较高。淘汰率的遗传力估计值在０.０３至０.１１之间，但大、小型奶牛场之间以及美国3个地区之间的差异较小。因生产性能差和繁殖问题而出售的奶牛，其淘汰率与305天产奶量之间的遗传相关性为中等至高。美国3个地区淘汰率的GEBV相关性在0.34至0.92之间，西南部与其他地区之间的相关性较低，尤其是在小型奶牛场。大、小型奶牛场之间GEBV的相关性在0.44至0.90之间，西南部较低。这些结果表明，美国不同地区之间以及大、小型奶牛场之间奶牛淘汰率存在基因型与环境互作。美国两个地区之间淘汰率的前30个SNP标记效应的相关性在0.64至0.98之间，除了“因奶牛场目的出售”这一淘汰原因外，高于更多SNP标记效应的相关性。大、小型奶牛场之间的相关性在0.67至0.98之间。美国不同地区之间以及大、小型奶牛场之间顶级SNP标记对淘汰原因的效应高度相关，表明主要标记可用于不同环境下的选择。14号染色体上一个标记基因片段显示的SNP方差与东北部大、小型奶牛场的产奶量密切相关，但在东南部和西南部则不然。14号染色体上的标记基因还与东北部大型奶牛场因生产性能差和死亡率导致的奶牛淘汰率密切相关。
