皖岳黑猪基因组遗传变异分析及特征SNPs挖掘

doi:10.11843/j.issn.0366-6964.2023.07.012

Abstract

Abstract: This study aimed to reveal the genome-wide genetic variation of Wangyue black pigs, screen the SNP loci for molecular markers characteristic. Twenty-four Wangyue black pigs weighing 110 kg were randomly selected and re-sequenced at whole-genome level, and genome-wide variation types was detected and population genetic diversity parameters was analyzed; Combined with the public database information, the SNPs informations of Beijing black pigs, Duroc, Large White pigs, Lantang pigs, Min pigs and Shenxian black pigs were downloaded, and the SNPs of 133 individuals of 7 breeds were divided into two datasets by using the method of selecting the maximum classification ability, and the characteristic sites of Wanyue black pigs were selected, and the gene function of the screened SNPs were annotated. The variation information scanning results showed that a total of 315 343 84 SNPs, 43 673 SVs and 3 258 CNVRs were obtained. A feature database of black pigs in Anhui was constructed, and finally 33 specific sites of Wanyue black pigs were screened, and the genes involved in 33 SNPs were functionally enriched, and it was found that these genes were related to growth (SUSD4, NELL1, GPC6), reproduction (KHDRBS2, CRISP1), immunity (NECTIN1), neuromodulation and environmental adaptation (GRIK4); The results of the relevant parameters of the genetic structure of the population showed that the genetic distance between individuals was between 0.157 4-0.287 3, with an average of 0.243 5±0.022 2; the effective population size was 4.2, the expected heterozygosity was 0.320, the observed heterozygosity was 0.328, the polymorphism marker ratio was 0.788, the total individual ROH length was 14.6-178.0Mb, the average ROH length was (61±9.4) Mb, and the inbreeding coefficient of the population was 0.025±0.004, with a low inbreeding coefficient. In summary, the abundant genomic variation resources of Wanyue black pig indicate that Wanyue black pig retains rich genetic diversity in the breeding process, and most of the individuals have a long genetic distance, which is a characteristic and valuable germplasm resource. This study provides scientific reference for the further breeding of Wanyue black pig.

Key words: Wanyue black pig, whole-genome re-sequencing, genome genetic variation, characteristic SNP sites, genetic structure

CLC Number:

S828.2

WANG Jinglin, LIU Yangguang, XU Qilong, CHEN Shuo, DENG Zaishuang, CHENG Shiyu, DING Yueyun, ZHENG Xianrui, YIN Zongjun, ZHANG Xiaodong. Genome Structures Variant Analysis and Feature SNPs Screening of Wanyue Black Pig[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2783-2793.

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Genome Structures Variant Analysis and Feature SNPs Screening of Wanyue Black Pig

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