Marras Gabriele, Gaspa Giustino, Sorbolini Silvia, Dimauro Corrado, Ajmone-Marsan Paolo, Valentini Alessio, Williams John L, Macciotta Nicolò P P
Dipartimento di Agraria-Sezione Scienze Zootecniche, Università di Sassari, Sassari, 07100, Italy; Parco Tecnologico Padano, Lodi, 26900, Italy.
Anim Genet. 2015 Apr;46(2):110-21. doi: 10.1111/age.12259. Epub 2014 Dec 22.
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 (FROH ), which were compared with inbreeding coefficients estimated from pedigree information (FPED ) and using the genomic relationship matrix (FGRM ). 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 FPED were moderately correlated with FROH > 1 Mb (0.662, 0.700 and 0.669 in Italian Brown, Italian Holstein and Italian Simmental respectively) but poorly correlated with FGRM (0.134, 0.128 and 0.448 for Italian Brown, Italian Holstein and Italian Simmental respectively). The inclusion of ROH > 8 Mb in the inbreeding calculation improved the correlation of FROH with FPED and FGRM . 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.
近亲繁殖增加是家畜群体选择的必然结果。对高密度单核苷酸多态性（SNP）的分析有助于识别长且不间断的纯合子片段（ROH），这些片段可用于识别同源的染色体区域。在本研究中，描述了五个意大利牛品种中不同长度ROH的分布情况。对来自五个牛品种的4095头公牛（2093头意大利荷斯坦牛、749头意大利褐牛、364头皮埃蒙特牛、410头马尔凯牛和479头意大利西门塔尔牛）在54K SNP位点进行了基因分型。识别出ROH并用于估计分子近亲繁殖系数（FROH），将其与根据系谱信息估计的近亲繁殖系数（FPED）以及使用基因组关系矩阵估计的系数（FGRM）进行比较。每头动物的ROH平均数量从皮埃蒙特牛的54±7.2个到意大利褐牛的94.6±11.6个不等。在皮埃蒙特牛中发现的短ROH（与古代近亲繁殖有关）数量最多，其次是西门塔尔牛。意大利褐牛和荷斯坦牛在全基因组中分布的较长ROH比例较高，表明近期存在近亲繁殖。FPED与长度大于1 Mb的FROH中度相关（意大利褐牛、意大利荷斯坦牛和意大利西门塔尔牛分别为0.662、0.700和0.669），但与FGRM相关性较差（意大利褐牛、意大利荷斯坦牛和意大利西门塔尔牛分别为0.134、0.128和0.448）。在近亲繁殖计算中纳入长度大于8 Mb的ROH可提高FROH与FPED和FGRM的相关性。ROH是DNA水平上纯合性的直接度量，可克服因系谱数据不完整导致的近似值和误差。在连锁不平衡（LD）高且近期存在近亲繁殖的群体（如意大利荷斯坦牛和意大利褐牛）中，此处使用的中等密度标记面板可能能很好地估计近亲繁殖情况。然而，在LD低且存在古代近亲繁殖的群体中，必须提高标记密度才能更精确地识别同源的短ROH。
