Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data.
Genome-Wide Detection of Runs of Homozygosity in Laiwu Pigs Revealed by Sequencing Data.
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测序数据揭示莱芜猪纯合性的全基因组检测
DOI：
10.3389/fgene.2021.629966
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发表时间：
2021
影响因子：
3.7
通讯作者：
Pan Y
中科院分区：
文献类型：
--
作者：
Fang Y;Hao X;Xu Z;Sun H;Zhao Q;Cao R;Zhang Z;Ma P;Sun Y;Qi Z;Wei Q;Wang Q;Pan Y
莱芜猪以7-9%的高肌内脂肪为特征，是中国的一个地方猪品种，最近的研究也发现莱芜猪对猪圆环病毒2型具有很高的抗性。然而，随着商业品种的引入，莱芜猪的种群数量下降，一些血统已经消失，这可能导致近交。纯合度（ROH）可以作为衡量个体近交状况的良好指标，通常也用于检测选择特征，从而绘制与重要经济性状相关的候选基因图谱。本研究利用基因组减少和测序的基因分型数据，对93头中国莱芜猪的ROH数量、长度、覆盖范围和分布模式进行了研究，并确定了ROH高频率的基因组区域。由家系计算的平均近交系数为0.021，而所有检测到的ROH片段估计的近交系数为0.133。全长1 Mb以上的ROH片段共7508个，占整个基因组的13.4%，平均长度为3.76 Mb，以短片段（1 - 5 Mb）为主。个体的覆盖率在0.56 ~ 36.86%之间。在染色体上，SSC6的ROH数量最多（n = 688）， SSC12的ROH数量最少（n = 215）。本研究共检测到13个卢岛，在这些区域内共发现86个基因。其中一些基因与重要的经济性状相关，如肉质（ECI1、LRP12、NDUFA4L2、GIL1和LYZ）、免疫能力（IL23A、STAT2、STAT6、TBK1、IFNG和ITH2）、产量（DCSTAMP、RDH16和GDF11）和繁殖（ODF1和CDK2）。共鉴定出6个重要的基因本体术语和9个重要的京都基因与基因组百科全书（KEGG）通路，其中大部分与抗病和生物合成过程相关，1个与脂质代谢相关。此外，我们将所有的ROH岛与猪数量性状位点（QTL）数据库进行比对，最终发现8个与肌内脂肪性状相关的QTL。这些结果有助于我们了解莱芜猪的特点，并为今后的育种策略提供参考。
Laiwu pigs, distinguished by their high intramuscular fat of 7–9%, is an indigenous pig breed of China, and recent studies also found that Laiwu pigs showed high resistance to Porcine circovirus type 2. However, with the introduction of commercial varieties, the population of Laiwu pigs has declined, and some lineages have disappeared, which could result in inbreeding. Runs of homozygosity (ROH) can be used as a good measure of individual inbreeding status and is also normally used to detect selection signatures so as to map the candidate genes associated with economically important traits. In this study, we used data from Genotyping by Genome Reducing and Sequencing to investigate the number, length, coverage, and distribution patterns of ROH in 93 Chinese Laiwu pigs and identified genomic regions with a high ROH frequency. The average inbreeding coefficient calculated by pedigree was 0.021, whereas that estimated by all detected ROH segments was 0.133. Covering 13.4% of the whole genome, a total of 7,508 ROH segments longer than 1 Mb were detected, whose average length was 3.76 Mb, and short segments (1–5 Mb) dominated. For individuals, the coverage was in the range between 0.56 and 36.86%. For chromosomes, SSC6 had the largest number (n = 688), and the number of ROH in SSC12 was the lowest (n = 215). Thirteen ROH islands were detected in our study, and 86 genes were found within those regions. Some of these genes were correlated with economically important traits, such as meat quality (ECI1, LRP12, NDUFA4L2, GIL1, and LYZ), immunity capacity (IL23A, STAT2, STAT6, TBK1, IFNG, and ITH2), production (DCSTAMP, RDH16, and GDF11), and reproduction (ODF1 and CDK2). A total of six significant Gene Ontology terms and nine significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, most of which were correlated with disease resistance and biosynthesis processes, and one KEGG pathway was related to lipid metabolism. In addition, we aligned all of the ROH islands to the pig quantitative trait loci (QTL) database and finally found eight QTL related to the intramuscular fat trait. These results may help us understand the characteristics of Laiwu pigs and provide insight for future breeding strategies.