芯片和重测序在猪遗传结构研究中的应用比较

doi:10.11843/j.issn.0366-6964.2023.07.011

Abstract

Abstract: This study aimed to compare the effects of SNP genotyping techniques (array and sequencing) and marker densities on the analysis results of genetic diversity, phylogenetic tree and genomic inbreeding coefficient, and explore low-cost and efficient genotyping method and appropriate SNP density in genetic structure study. The data of the CAUPorcine SNP50 array and the resequencing data of 35 Zaozhuang Heigai pigs were used in this study. In this study, using resequencing data as "raw materials", 4 SNP panels of random 34K, even 34K, even 340K and even 3 400K were constructed. The genetic diversity, phylogenetic tree and genomic inbreeding coefficient of Zaozhuang Heigai pigs were analyzed using SNP data of CAUPorcine SNP50 array and several sequencing panels. The results showed that:1) The index values of genetic diversity, including observed heterozygosity (H_O) (0.385 9 vs. 0.320 0-0.324 1), expected heterozygosity (H_E) (0.381 3 vs. 0.333 5-0.334 6), and genetic distance (0.305 7 vs. 0.279 8-0.280 6), estimated by array SNPs were higher than those by the SNPs of sequencing panels, and the phylogenetic tree constructed by array SNPs was of much difference from those by the SNPs of sequencing panels. These may be caused by the tendency of choosing higher minor allele frequency (MAF) SNPs in array design. 2) All sequencing panels had small impact on the analysis results of H_O (0.320 0-0.324 1), H_E (0.333 5-0.334 6), genetic distance (0.279 8-0.280 6) and phylogenetic tree, but had great impact on the number (784-106 547) and length (0.20-13.51 Mb) of runs of homozygosity (ROH) and genomic inbreeding coefficient (F_ROH) (0.127-0.263). Currently used 50 K genome-wide SNP arrays in the analysis of inbreeding coefficient of livestock and poultry is good at detection of large fragments of ROHs, but weak in identification small and medium ones. So the genomic inbreeding coefficient estimated by them may be lower than the actual value. In summary, different SNP genotyping techniques have a significant impact on the analysis results of genetic diversity, phylogenetic tree, and ROH. In the sequencing group, different SNP densities had a small impact on genetic diversity and phylogenetic tree analysis results, but had a significant impact on ROH and F_ROH analysis results.

Key words: SNP array, resequencing, genetic diversity, phylogenetic tree, genomic inbreeding coefficient

CLC Number:

S828.2

YANG Qing, GONG Jing, ZHAO Xueyan, ZHU Xiaodong, GENG Liying, ZHANG Chuansheng, WANG Jiying. Comparison of Array and Resequencing in Pig Genetic Structure Studies[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2772-2782.

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Comparison of Array and Resequencing in Pig Genetic Structure Studies

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