基于SNP芯片分析新浦东鸡的遗传多样性和遗传结构

doi:10.11843/j.issn.0366-6964.2023.12.008

摘要/Abstract

摘要： 旨在探究新浦东鸡群体的遗传多样性、亲缘关系及家系结构。本研究采用"京芯一号"SNP芯片对368只新浦东鸡全基因组范围内的SNPs进行检测,对新浦东鸡的遗传结构、亲缘关系和近交系数进行了分析,以期揭示个体之间的亲缘关系。结果共得到55 023个SNPs,通过Plink软件质控,剩余42 267个有效SNPs,其中78%的SNPs具有多态性;各位点平均有效等位基因数为1.552,PIC为0.237,MAF为0.226,Ho为0.355,H_E为0.353。新浦东鸡群体的平均IBS遗传距离为0.280 9,110只公鸡的平均IBS遗传距离为0.280 1。通过聚类分析(标准为亲缘关系系数大于等于0.1)构建新浦东鸡家系,110只公鸡被划分为32个家系。新浦东鸡个体ROH长度在0~350 Mb之间,其中,个体ROH长度在100~150 Mb内的个体数比例最大,基于ROH值计算的群体平均近交系数为0.155,近交程度较高。综上,本研究从基因组水平揭示了新浦东鸡的种群遗传结构和遗传多样性,可为后续的种群选育及开发利用工作提供参考。

关键词: 新浦东鸡, SNP芯片, 遗传多样性, 群体遗传结构

Abstract: The study aimed to explore the genetic diversity, relationship and family structure of the New Pudong chickens population. In order to reveal the genetic relationship between individuals, "Jingxin No.1" SNP chip was used to detect the SNPs in the whole genome of 368 New Pudong chickens. The genetic structure, genetic relationship and inbreeding coefficient of New Pudong chickens were also analyzed. The result showed that a total of 55 023 SNPs were obtained. According to the quality control of Plink (V1.90) software, there were 42 267 remaining SNPs, among which 78% were polymorphic. The effective allele number was 1.552, the PIC was 0.237, the MAF was 0.226, the H_O was 0.355, and the H_E was 0.353. The average IBS genetic distance of New Pudong chickens was 0.280 9. The average IBS genetic distance of 110 roosters was 0.280 1. According to the cluster analysis (the standard is that the coefficient of genetic relationship was greater than or equal to 0.1), 110 roosters were divided into 32 families. The ROH length of each New Pudong chicken were 0-350 Mb, and the proportion of individuals with ROH length of 100-150 Mb was the largest. The average inbreeding coefficient calculated based on ROH value was 0.155, indicating a high degree of inbreeding. According to these results, this study reveals the population genetic structure and genetic diversity of New Pudong chickens at the genomic level, which can provide reference for future breeding and utilization.

Key words: New Pudong chicken, SNP chip, genetic diversity, population genetic structure

中图分类号:

S831.2

齐丽娜, 陆雪林, 杨凯旋, 周瑾, 李先玉, 刘珂, 张文刚, 顾欣, 章伟建. 基于SNP芯片分析新浦东鸡的遗传多样性和遗传结构[J]. 畜牧兽医学报, 2023, 54(12): 4962-4971.

QI Lina, LU Xuelin, YANG Kaixuan, ZHOU Jin, LI Xianyu, LIU Ke, ZHANG Wengang, GU Xin, ZHANG Weijian. Analysis of Genetic Diversity and Genetic Structure of New Pudong Chicken Based on SNP Chips[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4962-4971.

参考文献

[1] 张丽娟,杨长锁,严华祥,等.新浦东鸡DNA指纹的随机扩增多态分析[J].中国家禽,2003,7(1):36-38.ZHANG L J,YANG C S,YAN H X,et al.RAPD analysis of DNA fingerprinting on NewPudong chicken[J].Chinese Poultry Science,2003,7(1):36-38.(in Chinese)
[2] 屠云洁,唐燕飞,蒋华莲,等.利用基因芯片开展广西麻鸡2个群体亲缘关系的遗传分析[J].中国畜牧杂志,2021,57(8):143-146.TU Y J,TANG Y F,JIANG H L,et al.Genetic analysis of the relationship between two populations of Guangxi ma chicken was carried out by using gene chip[J].Chinese Journal of Animal Science,2021,57(8):143-146.(in Chinese)
[3] 刘冉冉,赵桂苹,文杰.鸡基因组育种和保种用SNP芯片研发及应用[J].中国家禽,2018,40(15):1-6.LIU R R,ZHAO G P,WEN J.Development of genome-wide SNP genotyping arrays for chicken breeding and conservation[J]. China Poultry,2018,40(15):1-6.(in Chinese)
[4] 唐立群,肖层林,王伟平.SNP分子标记的研究及其应用进展[J].中国农学通报,2012,28(12):154-158.TANG L Q,XIAO C L,WANG W P.Research and application progress of SNP markers[J].Chinese Agricultural Science Bulletin,2012,28(12):154-158.(in Chinese)
[5] 陶璇,杨雪梅,梁艳,等.基于SNP芯片的丫杈猪保种群体遗传结构研究[J].畜牧兽医学报,2023,54(6):2308-2319.TAO X,YANG X M,LIANG Y,et al.Analysis of genetic structure of conservation population in Yacha pig based on SNP chip[J].Acta Veterinaria et Zootechnica Sinica,2023,54(6):2308-2319.(in Chinese)
[6] 周隽,覃星文,吴细波,等.基于SNP芯片对陆川猪进行遗传多样性与遗传结构分析的研究[J].中国畜牧杂志,2023, 59(8): 257-263.ZHOU J,QIN X W,WU X B,et al.Analysis of genetic diversity and genetic structure of Luchuan pig based on SNP chip[J]. Chinese Journal of Animal Science,2023,59(8):257-263.(in Chinese)
[7] 张任豹,周东辉,周李生,等.基于70 K SNP芯片分析济宁青山羊保种群体的遗传结构[J].畜牧兽医学报,2023, 54(7):2836-2847.ZHANG R B,ZHOU D H,ZHOU L S,et al.Analysis of genetic structure of conservation population in Jining gray goats based on 70 K SNP Chip[J].Acta Veterinaria et Zootechnica Sinica,2023,54(7):2836-2847.(in Chinese)
[8] 王振宇,张赛博,刘文慧,等.基于SNP芯片数据分析不同奶牛场基因组近交系数及筛选功能性基因[J].畜牧兽医学报,2023,54(7):2848-2857.WANG Z Y,ZHANG S B,LIU W H,et al.Genomic inbreeding coefficient analysis and functional gene screening in different dairy farms based on SNP chip data[J].Acta Veterinaria et Zootechnica Sinica,2023,54(7):2848-2857.(in Chinese)
[9] 史露露,胡明月,赖伟宁,等.基于50K SNP芯片的夏洛来羊遗传结构及选择信号分析[J].黑龙江畜牧兽医,2023(6): 49-53,59,139-140.SHI L L,HU M Y,LAI W N,et al.Genetic structure and selection signal analysis of Charolais sheep based on 50K SNP chip[J]. Heilongjiang Animal Science and Veterinary Medicine,2023(6):49-53,59,139-140.(in Chinese)
[10] 时坤鹏,刘莹,张志勇,等.基于SNP芯片分析安庆六白猪群体遗传结构[J].中国畜牧杂志,2022,58(8):136-140.SHI K P,LIU Y,ZHANG Z Y,et al.Analysis of genetic structure of Anqing liubai pig population based on SNP chip[J].Chinese Journal of Animal Science,2022,58(8):136-140.(in Chinese)
[11] 束婧婷,屠云洁,唐燕飞,等.基于SNP芯片分析瑶鸡2个群体亲缘关系[J].中国家禽,2021,43(9):23-28.SHU J T,TU Y J,TANG Y F,et al.Genetic relationship analysis of two populations of Yao chicken based on SNP chip[J].China Poultry,2021,43(9):23-28.(in Chinese)
[12] 李凯航,赵乐乐,陆雪林,等.基于SNP芯片的浦东鸡保种分析[J].中国家禽,2020,42(6):31-36.LI K H,ZHAO L L,LU X L,et al.Analysis of conservation effect in Pudong chicken based on SNP chip[J].China Poultry, 2020,42(6):31-36.(in Chinese)
[13] 王继英,成建国,林松,等.枣庄黑盖猪亲缘关系分析及分子系谱构建[J].猪业科学,2019,36(8):136-138.WANG J Y,CHENG J G,LIN S,et al.Genetic relationship analysis and molecular pedigree construction of Zaozhuang Black cover pig[J].Swine Industry Science,2019,36(8):136-138.(in Chinese)
[14] TAMURA K,STECHER G,KUMAR S.MEGA11:molecular evolutionary genetics analysis version 11[J].Mol Biol Evol,2021, 38(7): 3022-3027.
[15] KIRIN M,MCQUILLAN R,FRANKLIN C S,et al.Genomic runs of homozygosity record population history and consanguinity[J]. PLoS One,2010,5(11):e13996.
[16] CEBALLOS F C,JOSHI P K,CLARK D W,et al.Runs of homozygosity:windows into population history and trait architecture[J]. Nat Rev Genet,2018,19(4):220-234.
[17] BERTOLINI F,CARDOSO T F,MARRAS G,et al.Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats[J].Genet Sel Evol,2018,50(1):59.
[18] 高超群,曹然然,杜文苹,等.基于全基因组SNP标记分析中国地方鸡品种的遗传多样性和种群结构[J].畜牧兽医学报,2023,54(2):554-562.GAO C Q,CAO R R,DU W P,et al.Genetic diversity and population structure analysis of chinese native chicken breeds using genome-wide SNPS[J].Acta Veterinaria et Zootechnica Sinica,2023,54(2):554-562.(in Chinese)
[19] PURCELL S,NEALE B,TODD-BROWN K,et al.PLINK:a tool set for whole-genome association and population-based linkage analyses[J].Am J Hum Genet,2007,81(3):559-575.
[20] 李惠龙,刘丽英,吴桂贤,等.应用微卫星标记评估寿光鸡的保种情况[J].家禽科学,2020(5):3-7.LI H L,LIU L Y,WU G X,et al.Evaluation of conservation status of Shouguang chicken using microsatellite markers[J].Poultry Science,2020(5):3-7.(in Chinese)
[21] 陈政昆,韦聪聪,朱雯,等.安徽白山羊保种群微卫星标记遗传多样性分析[J].黑龙江畜牧兽医,2020(9):54-56,63.CHEN Z K,WEI C C,ZHU W,et al.Genetic diversity of Anhui white goat population with microsatellite markers[J]. Heilongjiang Animal Science and Veterinary Medicine,2020(9):54-56,63.(in Chinese)
[22] 邢磊,赵乐乐,袁红艳,等.雉鸡微卫星多态性分析[J].养殖与饲料,2020(2):32-35. XING L,ZHAO L L,YUAN H Y,et al.Microsatellite polymorphism analysis of pheasant[J].Animals Breeding and Feed,2020(2): 32-35.(in Chinese)
[23] 任芳.怒江缺须盆唇鱼种群遗传结构及遗传多样性分析[D].贵阳:贵州大学,2021.REN F.Population genetic diversity and genetic structure analysisof the Placocheilus cryptonemus in the Nujiang river[D]. Guiyang:Guizhou University,2021.(in Chinese)
[24] 李隐侠,牙生江·那斯尔,赛里克·都曼,等.SNP芯片评估柯尔克孜羊群体遗传多样性和遗传结构[J].畜牧兽医学报,2023,54(2):572-583.LI Y X,NASIER Y S,DUMAN S L,et al.Evaluation of genetic diversity and genetic structure in Kirgiz sheep population based on SNPs chip[J].Acta Veterinaria et Zootechnica Sinica,2023,54(2):572-583.(in Chinese)
[25] HAUSER L,BAIRD M,HILBORN R,et al.An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population[J].Mol Ecol Resour,2011,11 Suppl 1:150-161.
[26] 刘继强,郝晓东,武丽娜,等.全基因组SNP分型技术在畜禽遗传育种研究中的应用[J].畜牧兽医学报,2022, 53(12):4123-4137.LIU J Q,HAO X D,WU L N,et al.Application of whole genome SNP genotyping technology in livestock and poultry genetics and breeding[J].Acta Veterinaria et Zootechnica Sinica,2022,53(12):4123-4137.(in Chinese)
[27] 宋玉朴,孙永峰,冯自强,等.SNP分型检测技术及其在畜禽遗传和育种中的应用研究进展[J].中国畜牧杂志,2021, 57(7):37-42.SONG Y P,SUN Y F,FENG Z Q,et al.Advances in SNP typing techniques and their application in genetic and breeding of livestock and poultry[J].Chinese Journal of Animal Science,2021,57(7):37-42.(in Chinese)
[28] 熊金珂,鲍晶晶,胡文萍,等.基于SNP芯片的湖羊群体遗传结构分析[J].中国畜牧杂志, doi:10.19556/j.0258-7033.20220927-03.XIONG J K,BAO J J,HU W P,et al.Analysis of genetic structure of Hu sheep population based on SNP chip[J].Chinese Journal of Animal Science,doi:10.19556/j.0258-7033.20220927-03.(in Chinese)
[29] 孙浩,王振,张哲,等.基于基因组测序数据的梅山猪保种现状分析[J].上海交通大学学报:农业科学版,2017,35(4):65-70. SUN H,WANG Z,ZHANG Z,et al.Exploring the current situation of conservation of Meishan pigs based on genome sequencing data[J] Journal of Shanghai Jiaotong University:Agricultural Science,2017,35(4):65-70.(in Chinese)
[30] BARBATO M,OROZCO-TERWENGEL P,TAPIO M,et al.SNeP:a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data[J].Front Genet,2015,6:109.
[31] WANG L,SØRENSEN P,JANSS L,et al.Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds[J].BMC Genet,2013,14:115.
[32] 袁娇,徐国强,周翔,等.基于SNP芯片监测通城猪的保种效果[J].畜牧兽医学报,2022,53(8):2514-2523.YUAN J,XU G Q,ZHOU X,et al.SNP Chip-based monitoring of population conservation effect of Tongcheng pigs[J].Acta Veterinaria et Zootechnica Sinica,2022,53(8):2514-2523.(in Chinese)
[33] EUSEBI P G,MARTINEZ A,CORTES O.Genomic tools for effective conservation of livestock breed diversity[J]. Diversity, 2020,12(1):8.
[34] 邓俊,刘艺端,许文坤,等.基于SNP芯片撒坝猪保种群体的遗传结构分析[J].中国饲料,2022(17):7-11.DENG J,LIU Y D,XU W K,et al.Genetic structure analysis of a conserved population of Saba pigs based on SNP chips[J]. China Feed,2022(17):7-11.(in Chinese)
[35] 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)
[36] 刘晨龙,卢丹,周泉勇,等.利用高密度SNP芯片分析杭猪的群体遗传结构[J].畜牧兽医学报,2022,53(8):2502-2513.LIU C L,LU D,ZHOU Q Y,et al.Analysis of population genetic structure of Hang pigs by high density SNP chip[J].Acta Veterinaria et Zootechnica Sinica,2022,53(8):2502-2513.(in Chinese)
[37] 戴丽荷,褚晓红,陈晓宇,等.利用SNP标记分析淳安花猪群体遗传多样性和群体结构[J].养猪,2021(6):59-64.DAI L H,CHU X H,CHEN X Y,et al.Analysis of genetic diversity and genetic structure in Chun'an spotted pigs conserved population based on SNP chip[J].Swine Production,2021(6):59-64.(in Chinese)
[38] 王晨,马宁,郭春和,等.基于SNP芯片分析的蓝塘猪遗传群体结构[J].广东农业科学,2018,45(6):110-115.WANG C,MA N,GUO C H,et al.Population structure of Lantang pig evaluated using SNP chip[J].Guangdong Agricultural Sciences,2018,45(6):110-115.(in Chinese)
[39] 李正杰,周先坤,王浥尘,等.阿坝藏族羌族自治州若尔盖地区藏猪mtDNA D-Loop的遗传多样性分析[J].畜牧兽医学报, 2019, 50(12):2387-2399. LI Z J,ZHOU X K,WANG Y C,et al.Genetic diversity of Tibetan pig mitochondrial DNA D-loop in Ruoergai area of A’ba Tibetan and Qiang autonomous prefecture[J].Acta Veterinaria et Zootechnica Sinica,2019,50(12):2387-2399.(in Chinese)
[40] 蔡春波,张雪莲,张万峰,等.运用SNP芯片评估马身猪保种群体的遗传结构[J].畜牧兽医学报,2021,52(4):920-931.CAI C B,ZHANG X L,ZHANG W F,et al.Evaluation of genetic structure in Mashen pigs conserved population based on SNP chip[J].Acta Veterinaria et Zootechnica Sinica,2021,52(4):920-931.(in Chinese)