BACKGROUND Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. RESULTS In this study, 9102 ROH were identified, with an average number of 21.2 ± 13.1 and 33.2 ± 15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8 ± 120.3 Mb), and in KHZ, 5.96% (149.1 ± 107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P ≤ 0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). CONCLUSION The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

中文翻译：

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伊朗河水牛（Bubalus bubalis）的纯合子岛的近交系数的基因组测量和全基因组扫描。

背景技术由后代从共同祖先遗传的基因组的连续纯合片段被称为纯合运行（ROH）。ROH可用于计算基因组近交和识别可能处于历史选择压力下的基因组区域。我们的研究数据集由254个Azeri（AZ）和115个Khuzestani（KHZ）河水牛的基因型组成，具有约65,000个SNP，用于以下两个目的：1）估算和比较使用ROH（FROH）计算的近交，纯合度（FHOM） ），联合配子（FUNI）与基因组关系矩阵（FGRM）的对角元素之间的相关性；2）为我们的选择签名和基因富集研究确定频繁发生的ROH（即ROH岛）。结果在本研究中，鉴定出9102 ROH，平均数为21.2±13.1和33.2±15。AZ和KHZ品种中每只动物分别有9个片段。平均而言，AZ中的基因组是4.35％（108.8±120.3 Mb），而在KHZ中，基因组的5.96％（149.1±107.7 Mb）是自交的。基于FHOM，FUNI和FGRM的近交估计值在AZ高于在KHZ中，这与FROH估计相反。我们确定了11个ROH岛（四个在AZ，七个在KHZ）。在KHZ品种中，位于ROH岛上的基因被丰富用于多个基因本体论（GO）项（P≤0.05）。位于ROH岛上的基因与多种生物学功能和性状相关，例如体重和肌肉发育（BMP2），免疫应答（CYP27B1），产奶量和成分（MARS，ADRA1A和KCTD16），外皮颜色和色素沉着（PMEL）和MYO1A），生殖性状（INHBC，INHBE，STAT6和PCNA）和骨骼发育（SUOX）。结论由于KHZ的有效种群较小，因此计算出的FROH与KHZ中比AZ高的预期近交相符。因此，我们发现FROH可以用作基因组近交的可靠估计。此外，大多数ROH峰与先前报道的具有选择特征的基因组区域重叠或非常接近。这告诉我们，ROH岛中的基因可能已经过人工或自然选择。大多数ROH峰与先前报道的具有选择标志的基因组区域重叠或非常接近。这告诉我们，ROH岛中的基因可能已经过人工或自然选择。大多数ROH峰与先前报道的具有选择标志的基因组区域重叠或非常接近。这告诉我们，ROH岛中的基因可能已经过人工或自然选择。