Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.
Associazione Nazionale Coniglicoltori Italiani (ANCI), Contrada Giancola Snc, Volturara Appula, Italy.
Anim Genet. 2022 Dec;53(6):849-862. doi: 10.1111/age.13264. Epub 2022 Sep 8.
Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (150) and the lowest in Italian Silver (106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.
纯合区域（ROH）定义为在每个多态性位置都纯合的长 DNA 片段。ROH 覆盖的基因组比例及其长度是衡量近交程度和近交来源的指标。在这项研究中，我们分析了来自 12 个观赏品种和 4 个肉用品种的 702 只兔子的 SNP 芯片数据集（使用 Axiom OrcunSNP Array 获得），采用不同的方法识别 ROH，并计算了几个基因组近交参数。每只动物的 ROH 数量最高的是比利时野兔（150 个），最低的是意大利银兔（106 个）。ROH 的平均长度范围从意大利白兔的 4.001 ± 0.556 Mb 到雪兔的 6.268 ± 1.355 Mb。这两个品种的所有 ROH 片段总和的平均值最低（427.9 ± 86.4 Mb，意大利白兔），最高（921.3 ± 179.8 Mb，雪兔）。与肉用品种相比，更多的观赏品种具有更高的基因组近交水平（由 ROH 定义）。几个 ROH 岛屿包含参与体型、体长、色素沉着过程、胴体性状、生长和繁殖性状的基因（例如：AOX1、GPX5、IFRD1、ITGB8、NELL1、NR3C1、OCA2、TRIB1、TRIB2）。基因组近交参数可用于弥补兔子遗传资源管理信息的不足。ROH 提供了一些信息，有助于在一定程度上了解兔子品种的遗传历史，并识别兔子基因组中的选择特征。
