利用猪1.4M高密度SNP芯片检测巴马香猪全基因组拷贝数变异

doi:10.11843/j.issn.0366-6964.2020.09.005

Abstract

Abstract: The aim of this study was to detect the copy number variation (CNV) in the genome of Bama Xiang pigs and investigate the effect of marker density on the efficiency and accuracy of CNV detection. PennCNV and R-Gada were employed to detect CNVs using the 1.4M high-density SNP chip data of 319 (160 hogs and 159 gilts) Bama Xiang pigs, and the CNV region (CNVR) was constructed by merging overlapping CNVs. Only the CNVR with higher frequency than 5% was verified by the genome-wide association study (GWAS). Finally, according to the marker densities, a certain number of SNPs were evenly extracted, and the effect of marker density on CNV detection efficiency and accuracy was explored. There were 6 327 CNVs detected by PennCNV and 3 489 CNVs detected by R-Gada, which made up of 795 and 340 CNVRs, respectively, including 226 CNVRs identified by both programs. Among the 226 CNVRs, the shortest was 3.98 kb, the longest was 1 297.78 kb, and their total length was 33.27 Mb, of which 102 (45%) overlapped the CNVRs reported previously. Among the 795 CNVRs detected by PennCNV, 135 had a higher frequency than 5%, 20 of which had been verified by GWAS, and the verification rate was 15%. With the SNP density increasing, the efficiency and accuracy of CNV detection were increased, especially for the small size CNVs. A CNVR sketch of Bama Xiang pigs had been drawn using 1.4M SNP chips, which was helpful to identify CNVRs associated with important economic traits in the future. At the same time, we revealed the positive effect of marker density on the efficiency and accuracy of CNV detection, and the results provided a reference of choosing marker density for the follow-up research of CNV detection.

Key words: Bama Xiang pig, copy number variation, 1.4M high-density SNP chip

CLC Number:

S828.2

QIU Hengqing, XIAO Shijun, GUO Yuanmei. Detection of Genome-wide Copy Number Variation Using Porcine 1.4M High-density SNP Chips in Bama Xiang Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(9): 2079-2088.

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Detection of Genome-wide Copy Number Variation Using Porcine 1.4M High-density SNP Chips in Bama Xiang Pigs

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