Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs.
Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs.
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DOI：
10.5713/ab.20.0679
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发表时间：
2021-12
影响因子：
2.2
通讯作者：
Ding Y
中科院分区：
文献类型：
--
作者：
Wu X;Zhou R;Zhang W;Cao B;Xia J;Wang C;Zhang X;Chu M;Yin Z;Ding Y
纯合子序列（ROH）是纯合子基因型的连续长度，可以揭示近交水平、选择压力和交配方案。本研究对皖南黑猪进行了ROHs评价，以评估近交水平和ROH高频率的基因组区域。在之前的研究中，我们通过基因组重测序（10x）获得了501.52 GB的原始数据，在20个皖南黑猪样本中鉴定出21,316,754个单核苷酸变异。我们利用重测序数据研究了ROH的数量、长度和频率，以表征皖南黑猪的纯合性，并确定了高ROH频率的基因组区域。在所有样本中共鉴定出1813个ROHs （100 ~ 500 kb 837个，500 ~ 1000 kb 449个，100 ~ 1000 kb 527个），皖南黑猪的平均基因组近交系数（FROH）为0.5234。2、3、7、8、13、15、16号染色体上的61个区域是ROH岛。42个卢武铉岛共鉴定出105个基因，其中部分基因与生产性状有关。这是首次在皖南黑猪基因组中发现ROH。皖南黑猪是中国安徽省的本土品种。总体而言，皖南黑猪的近交水平很高，这是由于古代近交的影响，而最近近交是由于基因组的影响。这些发现为今后的研究提供了可靠的资源，有助于皖南黑猪种质资源的保护和利用。
Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.
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影响因子：
4.5
作者：
Bosse M;Megens HJ;Madsen O;Paudel Y;Frantz LA;Schook LB;Crooijmans RP;Groenen MA
通讯作者：
Groenen MA
影响因子：
2.4
作者：
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通讯作者：
Macciotta, Nicolo P. P.
影响因子：
3
作者：
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通讯作者：
Li, Wenrong
影响因子：
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作者：
Lührig S;Kolb S;Mellies N;Nolte J
通讯作者：
Nolte J
影响因子：
10.7
作者：
Avila-Arcos, Maria C.;McManus, Kimberly F.;Moreno-Estrada, Andres
通讯作者：
Moreno-Estrada, Andres