Cole J B, Waurich B, Wensch-Dorendorf M, Bickhart D M, Swalve H H
Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350.
Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Theodor-Lieser-Str. 11, D-06120 Halle / Saale, Germany.
J Dairy Sci. 2014 May;97(5):3156-72. doi: 10.3168/jds.2013-7409. Epub 2014 Mar 5.
Previous research has found that a quantitative trait locus exists affecting calving and conformation traits on Bos taurus autosome 18 that may be related to increased calf birth weights, which are not routinely recorded in the United States. Birth weight data from large, intensively managed dairies in eastern Germany with management systems similar to those commonly found in the United States were used to develop a selection index predictor for predicted transmitting ability (PTA) of birth weight. The predictor included body depth, rump width, sire calving ease, sire gestation length, sire stillbirth, stature, and strength. Genetic and phenotypic correlations and heritabilities from the United States were substituted for the German values, and birth weight PTA predicted for 31,984 bulls with US genetic evaluations. A genome-wide association study was conducted on the predicted birth weight PTA with the 2-step genomic BLUP procedure used for routine evaluations in the United States. Allele substitution effects were predicted for 43,188 single nucleotide polymorphisms (SNP). Genotypes were available for 53,644 predictor animals. Gene set enrichment analysis was performed on the 100 SNP that had the largest effects expressed in additive genetic standard deviations. Several SNP related to growth and development were found among the 25 SNP with the largest effects, including markers located within or near (≤ 100 kbp) ABCA12, FLRT2, LHX4, MAP3K5, NRAC, NTNG1, PIGN, and ZNF75A. The gene set enrichment analysis identified the Kyoto Encyclopedia of Genes and Genomes "Regulation of actin cytoskeleton" pathway (bta04810) as being enriched. That pathway includes the ROCK gene, which is involved in placental function in the human, as well as other developmental genes (e.g., FAK and PAK). Prediction equations derived from one population are useful for identifying genes and gene networks associated with phenotypes that are not directly measured in a second population. This approach will identify only genes associated with the traits used to construct the birth weight predictor, and not loci that affect only birth weight.
先前的研究发现,在牛的18号常染色体上存在一个影响产犊和体型性状的数量性状基因座,这可能与犊牛出生体重增加有关,而美国通常不记录出生体重。利用德国东部大型集约化管理奶牛场的出生体重数据(其管理系统与美国常见的管理系统相似),开发了一个用于预测出生体重预测传递能力(PTA)的选择指数预测器。该预测器包括体深、臀宽、父本产犊难易度、父本妊娠期长度、父本死产情况、身高和力量。用美国的遗传和表型相关性及遗传力替代德国的值,并对31984头具有美国遗传评估的公牛预测出生体重PTA。采用美国常规评估中使用的两步基因组最佳线性无偏预测(BLUP)程序,对预测出生体重PTA进行全基因组关联研究。预测了43188个单核苷酸多态性(SNP)的等位基因替代效应。有53644头预测动物的基因型数据可用。对在加性遗传标准差中影响最大的100个SNP进行了基因集富集分析。在影响最大的25个SNP中发现了几个与生长发育相关的SNP,包括位于ABCA12、FLRT2、LHX4、MAP3K5、NRAC、NTNG1、PIGN和ZNF75A基因内部或附近(≤100千碱基对)的标记。基因集富集分析确定京都基因与基因组百科全书“肌动蛋白细胞骨架调控”途径(bta04810)被富集。该途径包括ROCK基因,其与人的胎盘功能有关,以及其他发育基因(如FAK和PAK)。从一个群体得出的预测方程有助于识别与在第二个群体中未直接测量的表型相关的基因和基因网络。这种方法只会识别与用于构建出生体重预测器的性状相关的基因,而不会识别仅影响出生体重的基因座。