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

摘要/Abstract

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。

关键词: 亲子鉴定, 系谱校正, 遗传标记, 动物育种, IBD片段

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

中图分类号:

S828.2

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.

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.

参考文献 36

[1]	周磊,杨华威,赵祖凯,等.基因组选择在我国种猪育种中应用的探讨[J].中国畜牧杂志,2018,54(3):4-8.ZHOU L,YANG H W,ZHAO Z K,et al.The application of genomic selection in Chinese pig breeding industry[J].Chinese Journal of Animal Science,2018,54(3):4-8.(in Chinese)
[2]	WANG C,WANG H Y,ZHANG Y,et al.Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs[J].Mol Ecol Resour,2015,15(2):414-424.
[3]	王晨,秦珂,薛明,等.全基因组选择在猪育种中的应用[J].畜牧兽医学报,2016,47(1):1-9.WANG C,QIN K,XUE M,et al.Application of genomic selection in swine breeding[J].Acta Veterinaria et Zootechnica Sinica, 2016,47(1):1-9.(in Chinese)
[4]	HILL W G.Applications of population genetics to animal breeding,from wright,fisher and lush to genomic prediction[J]. Genetics, 2014,196(1):1-16.
[5]	丁向东,邱小田,王志刚,等.全国生猪遗传改良计划(2009-2020)给我国生猪种业带来的变化和未来工作建议[J].中国畜牧杂志,2020,56(6):169-174.DING X D,QIU X T,WANG Z G,et al.Changes brought by the national pig genetic improvement plan (2009-2020) to China’s pig breeding industry and suggestions for future work[J].Chinese Journal of Animal Science,2020,56(6):169-174.(in Chinese)
[6]	RADKO A,SMOUCHA G,KOSENIUK A.Microsatellite DNA analysis for diversity study,individual identification and parentage control in pig breeds in Poland[J].Genes (Basel),2021,12(4):595.
[7]	张哲,罗元宇,李晴晴,等.一种基于高密度遗传标记的亲子鉴定方法及其应用[J].遗传,2014,36(8):835-841.ZHANG Z,LUO Y Y,LI Q Q,et al.Developing and applying of a parentage identification approach based on high density genetic markers[J].Hereditas (Beijing),2014,36(8):835-841.(in Chinese)
[8]	谢苏,沈永巧,陈焱森,等.利用微卫星标记进行猪亲子鉴定[J].中国兽医学报,2019,39(8):1596-1603.XIE S,SHEN Y Q,CHEN Y S,et al.Pigs paternity testing by using microsatellite markers analysis[J].Chinese Journal of Veterinary Science,2019,39(8):1596-1603.(in Chinese)
[9]	胡明月,刘正喜,赵中利,等.绵羊(ATAG)n四碱基微卫星位点的筛选及其在亲子鉴定中的应用[J].中国畜牧兽医,2021,48(7):2484-2494.HU M Y,LIU Z X,ZHAO Z L,et al.Isolation of (ATAG)n tetrameric microsatellite loci and its application on paternity analysis in sheep[J].China Animal Husbandry & Veterinary Medicine,2021,48(7):2484-2494.(in Chinese)
[10]	张金鑫,唐韶青,宋海亮,等.北京地区大白猪基因组联合育种研究[J].中国农业科学,2019,52(12):2161-2170.ZHANG J X,TANG S Q,SONG H L,et al.Joint Genomic selection of Yorkshire in Beijing[J].Scientia Agricultura Sinica,2019,52(12):2161-2170.(in Chinese)
[11]	VAN BA N,NAM L Q,DO D N,et al.An assessment of genetic diversity and population structures of fifteen Vietnamese indigenous pig breeds for supporting the decision making on conservation strategies[J].Trop Anim Health Prod,2020,52(3): 1033-1041.
[12]	NECHTELBERGER D,KALTWASSER C,STUR I,et al.DNA microsatellite analysis for parentage control in Austrian pigs[J]. Anim Biotechnol,2001,12(2):141-144.
[13]	余国春.微卫星与SNP标记技术在猪亲子鉴定中的有效性研究[D].雅安:四川农业大学,2014.YU G C.Study on the validity of microsatellite and SNP marker technology in pig parentage identification[D].Ya’an:Sichuan Agricultural University,2014.(in Chinese)
[14]	MANICHAIKUL A,MYCHALECKYJ J C,RICH S S,et al.Robust relationship inference in genome-wide association studies[J]. Bioinformatics,2010,26(22):2867-2873.
[15]	DIMITROMANOLAKIS A,PATERSON A D,SUN L.Fast and accurate shared segment detection and relatedness estimation in un-phased genetic data via TRUFFLE[J].Am J Hum Genet,2019,105(1):78-88.
[16]	GALVÁN-FEMENÍA I,BARCELÓ-VIDAL C,SUMOY L,et al.A likelihood ratio approach for identifying three-quarter siblings in genetic databases[J].Heredity (Edinb),2021,126(3):537-547.
[17]	NASERI A,SHI J J,LIN X H,et al.RAFFI:Accurate and fast familial relationship inference in large scale biobank studies using RaPID[J].PLoS Genet,2021,17(1):e1009315.
[18]	管珊珊,张文杰,魏以梁,等.基于IBS算法预测亲缘关系准确性研究[J].生物化学与生物物理进展,2022,49(3):591-599.GUAN S S,ZHANG W J,WEI Y L,et al.Accuracy Research on the kinship relationship prediction by IBS algorithm[J].Progress in Biochemistry and Biophysics,2022,49(3):591-599.(in Chinese)
[19]	高洪梅,王昌,张珊珊,等.多套试剂盒在亲权鉴定特殊案例中的应用[J].法医学杂志,2018,34(4):405-410,416.GAO H M,WANG C,ZHANG S S,et al.Application of multiple kits in special parentage testing cases[J].Journal of Forensic Medicine,2018,34(4):405-410,416.(in Chinese)
[20]	BROWNING S R,BROWNING B L.Probabilistic estimation of identity by descent segment endpoints and detection of recent selection[J].Am J Hum Genet,2020,107(5):895-910.
[21]	RAMSTETTER M D,DYER T D,LEHMAN D M,et al.Benchmarking relatedness inference methods with genome-wide data from thousands of relatives[J].Genetics,2017,207(1):75-82.
[22]	QIAO Y,SANNERUD J G,BASU-ROY S,et al.Distinguishing pedigree relationships via multi-way identity by descent sharing and sex-specific genetic maps[J].Am J Hum Genet,2021,108(1):68-83.
[23]	周子文,王雪,丁向东.基于高密度SNP标记估计群体间遗传关联[J].遗传,2021,43(4):340-349.ZHOU Z W,WANG X,DING X D.Measuring genetic connectedness between herds based on high density SNP markers[J]. Hereditas (Beijing)，2021,43(4):340-349.(in Chinese)
[24]	王海龙,王巧,邢思远,等.基于表型和基因组信息评价北京油鸡保种群保种情况[J].畜牧兽医学报,2021,52(9):2406-2415.WANG H L,WANG Q,XING S Y,et al.Evaluating Beijing You chickens conservation status by phenotype and genome information[J].Acta Veterinaria et Zootechnica Sinica,2021,52(9):2406-2415.(in Chinese)
[25]	刘彬,沈林園,陈映,等.基于SNP芯片分析青峪猪保种群体的遗传结构[J].畜牧兽医学报,2020,51(2):260-269.LIU B,SHEN L Y,CHEN Y,et al.Analysis of genetic structure of conservation population in Qingyu pig based on SNP chip[J]. Acta Veterinaria et Zootechnica Sinica,2020,51(2):260-269.(in Chinese)
[26]	CHAO C H,YEH Y H,CHEN Y M,et al.Sire pedigree error estimation and sire verification of the Taiwan dairy cattle population by using SNP markers[J].Pol J Vet Sci,2022,25(1):61-65.
[27]	殷彬,岳书俭,俞英,等.奶牛分子系谱构建或亲权鉴定的微卫星标记筛选[J].畜牧兽医学报,2017,48(4):595-604.YIN B,YUE S J,YU Y,et al.Selection of microsatellite markers used for pedigree tree construction and/or paternity testing in Chinese Holstein cows[J].Acta Veterinaria et Zootechnica Sinica,2017,48(4):595-604.(in Chinese)
[28]	BJELLAND D W,LINGALA U,PATEL P S,et al.A fast and accurate method for detection of IBD shared haplotypes in genome-wide SNP data[J].Eur J Hum Genet,2017,25(5):617-624.
[29]	FREYMAN W A,MCMANUS K F,SHRINGARPURE S S,et al.Fast and robust identity-by-descent inference with the templated positional burrows-wheeler transform[J].Mol Biol Evol,2021,38(5):2131-2151.
[30]	SEIDMAN D N,SHENOY S A,KIM M,et al.Rapid,phase-free detection of long identity-by-descent segments enables effective relationship classification[J].Am J Hum Genet,2020,106(4):453-466.
[31]	ZHOU Y,BROWNING S R,BROWNING B L.A fast and simple method for detecting identity-by-descent segments in large-scale data[J].Am J Hum Genet,2020,106(4):426-437.
[32]	RAMSTETTER M D,SHENOY S A,DYER T D,et al.Inferring identical-by-descent sharing of sample ancestors promotes high-resolution relative detection[J].Am J Hum Genet,2018,103(1):30-44.
[33]	SEVERSON A L,CARMI S,ROSENBERG N A.The effect of consanguinity on between-individual identity-by-descent sharing[J]. Genetics,2019,212(1):305-316.
[34]	CABALLERO M,SEIDMAN D N,QIAO Y,et al.Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives[J].PLoS Genet,2019,15(12):e1007979.
[35]	初芹,张毅,孙东晓,等.应用微卫星DNA标记分析荷斯坦母牛系谱可靠性及影响因素[J].畜牧兽医学报,2011,42(2): 163-168.CHU Q,ZHANG Y,SUN D X,et al.Pedigree verification of Holstein cows and analysis of factors affecting incorrect paternity based on microsatellite markers[J].Acta Veterinaria et Zootechnica Sinica,2011,42(2):163-168.(in Chinese)
[36]	吴旭东,周忍,章会斌,等.安庆六白猪14个微卫星位点遗传多样性分析[J].中国畜牧杂志,2021,57(S1):181-186.WU X D,ZHOU R,ZHANG H B,et al.Genetic diversity of seven microsatellite markers in Anqing Liubai pigs[J].Chinese Journal of Animal Science,2021,57(S1):181-186.(in Chinese)