基于高密度SNP标记重构猪多品种群体系谱

doi:10.11843/j.issn.0366-6964.2022.12.006

Abstract

Abstract: Pedigree is an important information source for animal breeding. This experiment was conducted to study the effect of high-density SNP markers on reconstructing genealogy in production populations and to fill the gap of using high-density SNP information to reconstruct multi-breed, large-scale realistic production pig populations. In this study, 1 471 great-grandparent purebred Duroc (n=986) and Landrace (n=485) pigs born from 2017 to 2021 in a pig farm in Sichuan province were genotyped by Illumina GeneSeek GGP Porcine 50K chip. Genomic relationship between the two populations was analysed and reconstructed using the common ancestor fragment method, and genomic relationship was used to reconstruct the genealogy of the two populations. At the same time, to measure the accuracy of the common ancestor fragment method,115 breeding pigs with individual chip genotype information and pedigree records were selected, and their pedigree records were ensured by strictly controlling the production operation process. The results showed that the identity by descent(IBD)-based method could use genomic information to simultaneously infer the distribution and proportion of common ancestral fragment among individual pairs in a multi-generational, breed-mixed true production population, and could more accurately differentiate kinship between individuals than identical by state(IBS), thereby determining inter-individual relatedness and further inferring lineage structure. A total of 702 kinship pairs were inferred in the validation population of 115 pigs, including all parent-offspring pairs (n=184), full sibling pairs (n=175), half sibling pairs (n=109) and grandparent and grandchild pairs (n=18) recorded in the pedigree. It was also possible to infer additional unrecorded 3rd (n=8) kinship and 4th (n=18) kinship between individuals than that with recorded genealogies. The reconstructed genealogy provides a clearer picture of kinship relationships between individuals within the family line than the common three-generation genealogy. In this study, the method of reconstructing the pedigree of a multi-variety population based on the analysis of high-density SNP markers by the IBD fragment method can quickly and easily judge the correctness of the pedigree of a multi-variety mixed population, and reconstruct the genealogy of individuals with missing genealogies, which provides a basis for breeding work such as selection and matching, calculation of breeding value and GWAS mining.

Key words: parentage identification, pedigree correction, genetic marker, animal breeding, identity by descent segments

CLC Number:

S828.2

YANG Yuting, ZHANG Xing, NIU Anran, YAN Zhichun, GONG Huazhong, DING Ruonan, MA Li. Rebuilding Multi-species Population Genealogies Based on High-density SNP Markers in Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12): 4183-4196.

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Rebuilding Multi-species Population Genealogies Based on High-density SNP Markers in Pigs

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