基于高密度SNP标记重构猪多品种群体系谱

系谱是动物育种的重要信息来源，本研究旨在探究高密度SNP标记重构系谱在生产群体中的效果，填补使用高密度SNP信息重构多品种、大规模真实生产猪群的空白。本研究利用Illumina GeneSeek GGP Porcine 50K芯片对四川某猪场2017—2021年出生的1 471头曾祖代纯种杜洛克猪(n=986)和长白猪(n=485)进行分型，通过共祖片段法(common ancestor fragment method)分析上述两个品种群体内基因组亲缘关系，由此分别重构两品种群体系谱。同时选取有个体芯片分型信息及系谱记录的115头种猪，通过严格控制生产操作流程保证其系谱记录准确无误，用以评价准确性。结果表明，基于共祖片段法利用基因组信息可以同时推断多代次、品种混合的真实生产群体内个体对间的共祖片段分布情况及比例，且较状态相同片段(identical by state,IBS)能更准确的区分个体间亲缘关系，借此判断个体间亲缘关系并进一步推断家系结构。同时该方法在115头种猪的验证群体中共推断出702对亲缘关系，包括系谱记录的全部亲子关系对(n=184)、全同胞对(n=175)、半同胞关系对(n=109)和祖孙关系对(n=18)，同时较记录系谱能额外推断出个体间未记录的三级亲缘关系(n=8)和四级亲缘关系(n=18)。其重构的系谱较常见三代系谱能更清晰地体现家系内个体间亲缘关系。本研究所用基于血缘同源(identity by descent,IBD)片段法(即共祖片段法)分析高密度SNP标记重构多品种群体系谱的方法可快速、简便的判断多品种混合群体的系谱正确性，可对丢失系谱的个体重构系谱，为选种选配、计算育种值及GWAS挖掘等育种工作提供基础。

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

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.