上海白猪(上系)基因组遗传变异检测与功能注释分析

doi:10.11843/j.issn.0366-6964.2018.05.003

摘要/Abstract

摘要：

拟通过全基因组范围内遗传变异的检测和注释分析，深入了解上海白猪（上系）群体的遗传现状，以便更好地进行提纯复壮与开发利用。本研究应用基因组简化测序平台—GGRS，对上海白猪（上系）群体（99头）进行基因组测序，并综合实验室前期太湖地方猪种和西方引进品种共计447头测序数据进行SNP和InDel等遗传变异检测和功能注释分析。结果显示，上海白猪基因组测序平均覆盖度为2.87%，平均测序深度为3.9倍，共检测到328 586个SNPs、693 220个InDels。进一步分析表明，SNP和Indel在染色体上的分布相对均一，但在不同染色体上数量和密度的分布存在一定差异。结构注释显示，SNP和InDel对应基因的数量分别为11 496个和13 216个，按照基因的结构区域分类，SNP和InDel在各类功能基因区间的分布特点一致，绝大多数的SNP和InDel变异都分布在基因间区，分别为74.61%和83.38%。内含子中次之，分别为22.76%和14.98%。基因富集分析结果表明，SNP主要与蛋白代谢过程和高分子代谢过程等相关，InDel多在组织、器官发育和疾病相关的通路中发生富集。此外还发现，含有高密度SNP和InDel等遗传变异的QTL主要集中在肉质与胴体性状和健康性状。本研究利用先进的简化基因组测序技术对上海白猪（上系）全基因组范围内的遗传变异进行了普查，并通过对太湖流域地方猪种和西方引进品种的合并比较分析，阐释了这些遗传变异的染色体分布特征，基因区间分布规律和功能注释信息，为后续的开发利用奠定了坚实的基础。

Abstract:

This study intended to understand the genetic status of Shanghai White pig population through detection and annotation analysis of genome-wide genetic variation in order to better purify, rejuvenate and exploit the resource. In this study, genome sequencing was performed on 99 Shanghai White pigs using the genotype by genome simplifying and sequencing platform-GGRS. A total of 447 sequencing data including Taihu local pig breeds and western introduced breeds were collected for SNP and InDel genetic variation detection and functional annotation analysis. The results showed that the average coverage of Shanghai White pig genome was 2.87% and the average sequencing depth was 3.9 times. A total of 328 586 SNPs and 693 220 InDels were detected. Further analysis showed that the distribution of SNP and Indel on chromosomes were relatively uniform, but the distributions of number and density on different chromosomes were different. Structural annotation showed that the corresponding gene number of SNP and InDel were 11 496 and 13 216, respectively. According to the structural region classification of the genes, the distribution characteristics of SNP and InDel were consistent in all kinds of functional gene regions. The most of SNP and InDel variation distributed in the intergenic region, with the ratio of 74.61% and 83.38%, respectively, followed by intron, with 22.76% and 14.98%, respectively. Gene enrichment analysis showed that SNPs were mainly related to protein metabolism and macromolecule metabolism. InDel mostly enriched in tissues, organ development and disease-related pathways. In addition, we also found that the QTLs containing high-density SNP and InDel mainly focused on meat quality, carcass and healthy traits. The whole genome genetic variation of Shanghai White pig was investigated by advanced simplified genomic sequencing. The comparative analysis between Shanghai White pig, Taihu pig breeds and western pig breeds explained the chromosomal distribution characteristics,gene distribution and functional annotation information of these genetic variations, which laid a solid foundation for subsequent exploitation and utilization.

中图分类号:

S828.2

盛中华, 陈国宏, 潘玉春, 王起山, 张哲. 上海白猪(上系)基因组遗传变异检测与功能注释分析[J]. 畜牧兽医学报, 2018, 49(5): 887-896.

SHENG Zhong-hua, CHEN Guo-hong, PAN Yu-chun, WANG Qi-shan, ZHANG Zhe. Identification and Functional Annotation of Genome-wide Genetic Variation in Shanghai White Pigs(Shang)[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2018, 49(5): 887-896.

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https://www.xmsyxb.com/CN/Y2018/V49/I5/887

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