Productive life (PL) of a cow is the time the cow remains in the milking herd from first calving to exit from the herd due to culling or death and is an important economic trait in U.S. Holstein cattle. The large samples of Holstein genomic evaluation data that have become available recently provided unprecedented statistical power to identify genetic factors affecting PL in Holstein cows using the approach of genome-wide association study (GWAS). The GWAS analysis used 1,103,641 Holstein cows with phenotypic observations on PL and genotypes of 75,282 single nucleotide polymorphism (SNP) markers. The statistical tests and estimation of SNP additive and dominance effects used the approximate generalized least squares method implemented by the EPISNPmpi computer program. The GWAS detected 5390 significant additive effects of PL distributed over all 29 autosomes and the X–Y nonrecombining region of the X chromosome (Chr31). Two chromosome regions had the most significant and largest cluster of additive effects, the SLC4A4-GC-NPFFR2 (SGN) region of Chr06 with pleiotropic effects for PL, fertility, somatic cell score and milk yield; and the 32–52 Mb region of Chr10 with peak effects for PL in or near RASGRP1 with many important immunity functions. The dominance tests detected 38 significant dominance effects including 12 dominance effects with sharply negative homozygous recessive genotypes on Chr18, Chr05, Chr23 and Chr24. The GWAS results showed that highly significant genetic effects for PL were in chromosome regions known to have highly significant effects for fertility and health and a chromosome region with multiple genes with reproductive and immunity functions. SNPs with rare but sharply negative homozygous recessive genotypes for PL existed and should be used for eliminating heifers carrying those homozygous recessive genotypes.

中文翻译：

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一项针对美国荷斯坦奶牛生产生活的百万头奶牛全基因组关联研究


奶牛的生产寿命（PL）是指奶牛从第一次产犊到因扑杀或死亡而退出奶牛群的时间，是美国荷斯坦牛的重要经济性状。最近可用的荷斯坦奶牛基因组评估数据的大样本提供了前所未有的统计能力，可以使用全基因组关联研究（GWAS）方法来识别影响荷斯坦奶牛 PL 的遗传因素。 GWAS 分析使用了 1,103,641 头荷斯坦奶牛，对 PL 和 75,282 个单核苷酸多态性 (SNP) 标记的基因型进行了表型观察。 SNP 加性和显性效应的统计测试和估计使用由 EPISNPmpi 计算机程序实现的近似广义最小二乘法。 GWAS 检测到 PL 的 5390 个显着加性效应分布在所有 29 个常染色体和 X 染色体 (Chr31) 的 X-Y 非重组区域。两个染色体区域具有最显着和最大的加性效应簇，即 Chr06 的 SLC4A4-GC-NPFFR2 (SGN) 区域，对 PL、生育力、体细胞评分和产奶量具有多效性效应； Chr10 的 32-52 Mb 区域对 RASGRP1 内或附近的 PL 具有峰值作用，具有许多重要的免疫功能。显性测试检测到 38 个显着的显性效应，其中 12 个显性效应在 Chr18、Chr05、Chr23 和 Chr24 上具有显着负纯合隐性基因型。 GWAS结果表明，PL的高度显着遗传效应位于已知对生育和健康具有高度显着影响的染色体区域以及具有生殖和免疫功能的多个基因的染色体区域。 PL 存在罕见但明显阴性的纯合隐性基因型的 SNP，应该用于消除携带这些纯合隐性基因型的小母牛。