| 基于高密度SNP标记重构猪多品种群体系谱 |
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| 引用本文： | 杨雨婷,张兴,牛安然,闫之春,龚华忠,丁偌楠,马黎. 基于高密度SNP标记重构猪多品种群体系谱[J]. 畜牧兽医学报, 2022, 53(12): 4183-4196. DOI: 10.11843/j.issn.0366-6964.2022.12.006 |
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| 作者姓名： | 杨雨婷 张兴 牛安然 闫之春 龚华忠 丁偌楠 马黎 |
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| 作者单位： | 1. 新希望六和养猪研究院数据与算法实验室, 成都 610095;2. 新希望六和养猪研究院, 青岛 266100;3. 新希望六和育种事业部, 成都 610095;4. 德州市现代生猪养殖技术创新中心, 德州 263000 |
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| 摘 要： | 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...
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| 关 键 词： | 亲子鉴定 系谱校正 遗传标记 动物育种 IBD片段 |
| 收稿时间： | 2022-05-05 |
Rebuilding Multi-species Population Genealogies Based on High-density SNP Markers in Pigs |
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| 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]. Chinese Journal of Animal and Veterinary Sciences, 2022, 53(12): 4183-4196. DOI: 10.11843/j.issn.0366-6964.2022.12.006 |
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| Authors: | YANG Yuting ZHANG Xing NIU Anran YAN Zhichun GONG Huazhong DING Ruonan MA Li |
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| Affiliation: | 1. New Hope Liuhe Academy of Swine Research Data and Algorithm Lab, Chengdu 610095, China;2. New Hope Liuhe Academy of Swine Research, Qingdao 266100, China;3. New Hope Liuhe Breeding Division, Chengdu 610095, China;4. Dezhou Modern Pig Breeding Technology Innovation Center, Dezhou 263000, China |
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| 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. |
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| Keywords: | parentage identification pedigree correction genetic marker animal breeding identity by descent segments |
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