Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA.
J Dairy Sci. 2013 Jul;96(7):4697-706. doi: 10.3168/jds.2012-6435. Epub 2013 May 16.
The effects of increased pedigree inbreeding in dairy cattle populations have been well documented and result in a negative impact on profitability. Recent advances in genotyping technology have allowed researchers to move beyond pedigree analysis and study inbreeding at a molecular level. In this study, 5,853 animals were genotyped for 54,001 single nucleotide polymorphisms (SNP); 2,913 cows had phenotypic records including a single lactation for milk yield (from either lactation 1, 2, 3, or 4), reproductive performance, and linear type conformation. After removing SNP with poor call rates, low minor allele frequencies, and departure from Hardy-Weinberg equilibrium, 33,025 SNP remained for analyses. Three measures of genomic inbreeding were evaluated: percent homozygosity (FPH), inbreeding calculated from runs of homozygosity (FROH), and inbreeding derived from a genomic relationship matrix (FGRM). Average FPH was 60.5±1.1%, average FROH was 3.8±2.1%, and average FGRM was 20.8±2.3%, where animals with larger values for each of the genomic inbreeding indices were considered more inbred. Decreases in total milk yield to 205d postpartum of 53, 20, and 47kg per 1% increase in FPH, FROH, and FGRM, respectively, were observed. Increases in days open per 1% increase in FPH (1.76 d), FROH (1.72 d), and FGRM (1.06 d) were also noted, as well as increases in maternal calving difficulty (0.09, 0.03, and 0.04 on a 5-point scale for FPH, FROH, and FGRM, respectively). Several linear type traits, such as strength (-0.40, -0.11, and -0.19), rear legs rear view (-0.35, -0.16, and -0.14), front teat placement (0.35, 0.25, 0.18), and teat length (-0.24, -0.14, and -0.13) were also affected by increases in FPH, FROH, and FGRM, respectively. Overall, increases in each measure of genomic inbreeding in this study were associated with negative effects on production and reproductive ability in dairy cows.
奶牛群体中系谱近交的影响已得到充分证实，并对盈利能力产生负面影响。最近基因分型技术的进步使研究人员能够超越系谱分析，从分子水平研究近交。在这项研究中，对 5853 头动物进行了 54001 个单核苷酸多态性（SNP）的基因分型；2913 头奶牛具有表型记录，包括单次泌乳产奶量（第 1、2、3 或 4 次泌乳中的任意一次）、繁殖性能和线性体型特征。在去除了等位基因检出率低、次要等位基因频率低和偏离哈迪-温伯格平衡的 SNP 后，有 33025 个 SNP 用于分析。评估了三种基因组近交程度的度量标准：纯合度百分比（FPH）、基于纯合子连续的近交（FROH）和基于基因组关系矩阵的近交（FGRM）。平均 FPH 为 60.5±1.1%，平均 FROH 为 3.8±2.1%，平均 FGRM 为 20.8±2.3%，每个基因组近交指数较大的动物被认为更近交。观察到每增加 1%的 FPH、FROH 和 FGRM，产后 205d 的总产奶量分别减少 53、20 和 47kg。还观察到 FPH（1.76d）、FROH（1.72d）和 FGRM（1.06d）每增加 1%，空怀天数增加，以及母体产犊难度增加（FPH、FROH 和 FGRM 分别为 0.09、0.03 和 0.04，五分制）。几个线性体型特征，如强度（-0.40、-0.11 和-0.19）、后肢后视图（-0.35、-0.16 和-0.14）、前乳头位置（0.35、0.25 和 0.18）和乳头长度（-0.24、-0.14 和-0.13）也分别受到 FPH、FROH 和 FGRM 增加的影响。总体而言，本研究中每种基因组近交度量的增加都与奶牛生产和繁殖能力的负面影响有关。
