Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy
Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy
复制标题
DOI：
10.1111/age.12259
复制
发表时间：
2015-04-01
期刊：
影响因子：
2.4
通讯作者：
Macciotta, Nicolo P. P.
中科院分区：
文献类型：
--
作者：
Marras, Gabriele;Gaspa, Giustino;Macciotta, Nicolo P. P.
近亲交配的增加是牲畜种群选择的必然结果。对高密度单核苷酸多态(SNPs)的分析有助于识别长而不间断的纯合性(ROH)，可用于识别因血统而相同的染色体区域。在这项工作中，描述了不同长度的ROH在五个意大利黄牛品种中的分布。对2093头意大利荷斯坦牛、749头意大利布朗牛、364头皮埃蒙特牛、410头马尔奇吉亚纳牛和479头意大利西门塔尔牛共4095头公牛进行了54K SNP位点的基因分型。将分子近交系数(F-ROH)与根据系谱信息估计的近交系数(F-PED)和利用基因组关系矩阵(F-GRM)估计的近交系数进行比较。平均每只动物的ROH数量从皮埃蒙特的54+/-7.2到意大利布朗的94.6+/-11.6不等。皮埃蒙特人的短ROH(与远古血缘有关)的数量最多，其次是西门塔尔人。意大利棕牛和荷斯坦牛的ROH较长的比例较高，分布在整个基因组中，这揭示了最近的近亲交配。F-PED与F-ROH和Gt；1Mb呈中度相关(意大利布朗、意大利荷斯坦和意大利西门塔尔分别为0.662、0.700和0.669)，但与F-GRM相关性较差(意大利布朗、意大利荷斯坦和意大利西门塔尔分别为0.134、0.128和0.448)。将ROH>；8Mb纳入近交计算，提高了F-ROH与F-PED和F-GRM的相关性。ROH是DNA水平上的自合性的直接测量，可以克服由不完整的系谱数据引起的近似和误差。在具有高度连锁不平衡(LD)和最近近亲交配的群体(例如意大利荷斯坦和意大利布朗)中，一个中等密度的标记面板，如这里使用的，可能提供一个很好的近亲繁殖估计。然而，在低LD和古老近亲交配的群体中，必须增加标记密度，以更准确地识别血统相同的短ROH。
Increased inbreeding is an inevitable consequence of selection in livestock populations. The analysis of high-density single nucleotide polymorphisms (SNPs) facilitates the identification of long and uninterrupted runs of homozygosity (ROH) that can be used to identify chromosomal regions that are identical by descent. In this work, the distribution of ROH of different lengths in five Italian cattle breeds is described. A total of 4095 bulls from five cattle breeds (2093 Italian Holstein, 749 Italian Brown, 364 Piedmontese, 410 Marchigiana and 479 Italian Simmental) were genotyped at 54K SNP loci. ROH were identified and used to estimate molecular inbreeding coefficients (F-ROH), which were compared with inbreeding coefficients estimated from pedigree information (F-PED) and using the genomic relationship matrix (F-GRM). The average number of ROH per animal ranged from 54 +/- 7.2 in Piedmontese to 94.6 +/- 11.6 in Italian Brown. The highest number of short ROH (related to ancient consanguinity) was found in Piedmontese, followed by Simmental. The Italian Brown and Holstein had a higher proportion of longer ROH distributed across the whole genome, revealing recent inbreeding. The F-PED were moderately correlated with F-ROH>1Mb (0.662, 0.700 and 0.669 in Italian Brown, Italian Holstein and Italian Simmental respectively) but poorly correlated with F-GRM (0.134, 0.128 and 0.448 for Italian Brown, Italian Holstein and Italian Simmental respectively). The inclusion of ROH>8Mb in the inbreeding calculation improved the correlation of F-ROH with F-PED and F-GRM. ROH are a direct measure of autozygosity at the DNA level and can overcome approximations and errors resulting from incomplete pedigree data. In populations with high linkage disequilibrium (LD) and recent inbreeding (e.g. Italian Holstein and Italian Brown), a medium-density marker panel, such as the one used here, may provide a good estimate of inbreeding. However, in populations with low LD and ancient inbreeding, marker density would have to be increased to identify short ROH that are identical by descent more precisely.