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

Abstract

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.

Key words: Shanghai White pig(Shang), pig genome, SNP, InDel

CLC Number:

S828.2

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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Identification and Functional Annotation of Genome-wide Genetic Variation in Shanghai White Pigs(Shang)

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