Müller M-P, Rothammer S, Seichter D, Russ I, Hinrichs D, Tetens J, Thaller G, Medugorac I
Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586 Poing, Germany; Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität Munich, Veterinärstr. 13, 80539 Munich, Germany.
Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität Munich, Veterinärstr. 13, 80539 Munich, Germany.
J Dairy Sci. 2017 Mar;100(3):1987-2006. doi: 10.3168/jds.2016-11506. Epub 2017 Jan 18.
Over the last decades, a dramatic decrease in reproductive performance has been observed in Holstein cattle and fertility problems have become the most common reason for a cow to leave the herd. The premature removal of animals with high breeding values results in both economic and breeding losses. For efficient future Holstein breeding, the identification of loci associated with low fertility is of major interest and thus constitutes the aim of this study. To reach this aim, a genome-wide combined linkage disequilibrium and linkage analysis (cLDLA) was conducted using data on the following 10 calving and fertility traits in the form of estimated breeding values: days from first service to conception of heifers and cows, nonreturn rate on d 56 of heifers and cows, days from calving to first insemination, days open, paternal and maternal calving ease, paternal and maternal stillbirth. The animal data set contained 2,527 daughter-proven Holstein bulls from Germany that were genotyped with Illumina's BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). For the cLDLA, 41,635 sliding windows of 40 adjacent single nucleotide polymorphisms (SNP) were used. At each window midpoint, a variance component analysis was executed using ASReml. The underlying mixed linear model included random quantitative trait locus (QTL) and polygenic effects. We identified 50 genome-wide significant QTL. The most significant peak was detected for direct calving ease at 59,179,424 bp on chromosome 18 (BTA18). Next, a mixed-linear model association (MLMA) analysis was conducted. A comparison of the cLDLA and MLMA results with special regard to BTA18 showed that the genome-wide most significant SNP from the MLMA was associated with the same trait and located on the same chromosome at 57,589,121 bp (i.e., about 1.5 Mb apart from the cLDLA peak). The results of 5 different cLDLA and 2 MLMA models, which included the fixed effects of either SNP or haplotypes, suggested that the cLDLA method outperformed the MLMA in accuracy and precision. The haplotype-based cLDLA method allowed for a more precise mapping and the definition of ancestral and derived QTL alleles, both of which are essential for the detection of underlying quantitative trait nucleotides.
在过去几十年中，荷斯坦奶牛的繁殖性能显著下降，繁殖问题已成为奶牛被淘汰出牛群的最常见原因。具有高育种价值的动物被过早淘汰会导致经济和育种损失。为了未来高效的荷斯坦育种，识别与低繁殖力相关的基因座具有重大意义，因此构成本研究的目标。为实现这一目标，利用以下10个产犊和繁殖性状的估计育种值数据进行了全基因组连锁不平衡与连锁分析（cLDLA）：小母牛和母牛从首次输精到受孕的天数、小母牛和母牛第56天的不返情率、从产犊到首次输精的天数、空怀天数、父系和母系产犊难易度、父系和母系死胎率。动物数据集包含来自德国的2527头经女儿验证的荷斯坦公牛，这些公牛使用Illumina公司的牛50K单核苷酸多态性（SNP）芯片（Illumina公司，加利福尼亚州圣地亚哥）进行了基因分型。对于cLDLA，使用了41635个由40个相邻单核苷酸多态性（SNP）组成的滑动窗口。在每个窗口中点，使用ASReml执行方差成分分析。基本的混合线性模型包括随机数量性状基因座（QTL）和多基因效应。我们鉴定出50个全基因组显著的QTL。在18号染色体（BTA18）上59179424 bp处检测到直接产犊难易度的最显著峰值。接下来，进行了混合线性模型关联（MLMA）分析。对cLDLA和MLMA结果，特别是关于BTA18的比较表明，MLMA中全基因组最显著的SNP与相同性状相关，位于57589121 bp的同一染色体上（即与cLDLA峰值相距约1.5 Mb）。5种不同的cLDLA和2种MLMA模型的结果（包括SNP或单倍型的固定效应）表明，cLDLA方法在准确性和精确性方面优于MLMA。基于单倍型 的cLDLA方法允许更精确的定位以及祖先和衍生QTL等位基因的定义，这两者对于检测潜在的数量性状核苷酸都是必不可少的。
