SNP芯片技术原理及其在鸡遗传育种中的应用

doi:10.11843/j.issn.0366-6964.2025.09.004

摘要/Abstract

摘要： 单核苷酸多态性(SNP)芯片作为高效的基因分型工具，具有分型准确率高、检测速度快、分析流程简单和检测成本低等优势，已被广泛应用于分子遗传学研究和基因组育种等领域。特别是对家禽遗传育种，SNP芯片技术的应用极大地提升了育种效率和准确性。本文旨在全面剖析SNP芯片技术，从固相芯片与液相芯片两大类出发，深入探讨各自的技术原理及其独特优点。同时，本文总结了SNP芯片技术在鸡遗传育种领域的最新研究进展，详细阐述了其在商业育种、重要经济性状相关位点挖掘、抗病育种、品种鉴定以及种质资源保护等方面的应用与贡献。研究结果表明，SNP芯片技术不仅在推动鸡遗传改良方面发挥了重要作用，还为品种多样性的保护提供了有力的工具。未来，随着技术的进一步发展，SNP芯片在鸡遗传育种中的应用潜力将更加广阔。

关键词: 鸡, SNP, 固相芯片, 液相芯片, 育种

Abstract: Single nucleotide polymorphism (SNP) chips, as highly efficient genotyping tools, offer advantages such as high genotyping accuracy, fast detection speed, simple analysis workflows, and low detection costs. These chips have been widely applied in molecular genetics research and genomic breeding. Particularly in avian genetic breeding, the application of SNP chip technology has significantly enhanced breeding efficiency and accuracy. This article aims to provide a comprehensive analysis of SNP chip technology, focusing on the two major categories: solid-phase chips and liquid-phase chips. The technical principles and unique advantages of each category are thoroughly explored. Additionally, the article summarizes the latest research advancements of SNP chip technology in chicken genetic breeding, detailing its applications and contributions in commercial breeding, identification of important economic trait loci, disease resistance breeding, breed identification, and germplasm resource protection. The findings indicate that SNP chip technology has played a crucial role in promoting genetic improvement in chickens and has provided a powerful tool for the protection of breed diversity. Looking ahead, with further technological advancements, the potential applications of SNP chips in chicken genetic breeding are expected to be even more extensive.

Key words: chicken, SNP, solid-phase chips, liquid-phase chips, breeding

中图分类号:

S831.2

王有栋, 曹志平, 李玉茂, 栾鹏, 李辉, 白雪. SNP芯片技术原理及其在鸡遗传育种中的应用[J]. 畜牧兽医学报, 2025, 56(9): 4165-4175.

WANG Youdong, CAO Zhiping, LI Yumao, LUAN Peng, LI Hui, BAI Xue. The Principle of SNP Chip Technology and Its Application in Chicken Genetic Breeding[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(9): 4165-4175.

参考文献

[1] 王紫嫣, 吴琳, 张钰晗, 等. 单核苷酸多态性检测技术研究进展[J]. 生命的化学, 2025, 45(5): 885-896.
WANG Z Y, WU L, ZHANG Y H, et al. Research progress on single nucleotide polymorphism detection technology[J]. Chem Life, 2025, 45(5): 885-896. (in Chinese)
[2] WONG G K, LIU B, WANG J, et al. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms[J].Nature, 2004, 432(7018): 717-722.
[3] MOUSTAFA H A M, EL-DAKROURY W A, ASHRAF A, et al. SNP use as a potential chemotoxicity stratification tool in breast cancer: from bench to clinic[J].Funct Integr Genomics, 2025, 25(1): 93.
[4] GUL H, HABIB G, KHAN I M, et al. Genetic resilience in chickens against bacterial, viral and protozoal pathogens[J]. Front Vet Sci, 2022, 9: 1032983.
[5] 汪佳豪, 赵卿尧, 周月玲,等. 基因芯片在畜禽遗传育种中的应用及展望[J]. 遗传, 2023, 45(12): 1114-1127.
WANG J H, ZHAO Q Y, ZHOU Y L, et al. Application and prospect of gene chip in livestock and poultry genetic breeding[J]. Hereditas(Beijing), 2023, 45(12): 1114-1127. (in Chinese)
[6] GHILDIYAL K, NAYAK S S, RAJAWAT D, et al. Genomic insights into the conservation of wild and domestic animal diversity: A review[J]. Gene, 2023, 886: 147719.
[7] ALEMU A, ÅSTRAND J, MONTESINOS-LÓPEZ O A, et al. Genomic selection in plant breeding: Key factors shaping two decades of progress[J]. Mol Plant, 2024, 17(4): 552-578.
[8] 王新越, 乔贤, 李祥龙. 坝上长尾鸡HNF1A基因多态性及其与腿肌脂肪酸、肌苷酸性状关联分析[J]. 中国畜牧杂志, 2025. 10.19556/j.0258-7033.20241129-03.
WANG X Y, QIAO X, LI X L. Polymorphism of HNF1A gene and its association analysis with leg muscle fatty acid and inosinic acid traits in Bashang long-tailed chicken[J]. Chinese Journal of Animal Science, 2025. 10.19556/j.0258-7033.20241129-03. (in Chinese)
[9] FODOR S P, READ J L, PIRRUNG M C, et al. Light-directed, spatially addressable parallel chemical synthesis[J]. Science, 1991, 251(4995): 767.
[10] NICKERSON D A, TAYLOR S L, WEISS K M, et al. DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene[J]. Nat Genet, 1998, 19(3): 233-240.
[11] GUO Z, WANG H, TAO J, et al. Development of multiple SNP marker panels affordable to breeders through genotyping by target sequencing (GBTS) in maize[J]. Mol Breeding, 2019, 39(3): 37.
[12] 姚丽, 张伟, 王妹妹, 等. 液相芯片技术原理及应用简介[J]. 现代肿瘤医学, 2008, 16(12): 2196-2198.
YAO L, ZHANG W, WANG M M, et al. Principle and application of liquid phase chip technology[J]. Journal of Modern Oncology, 2008, 16(12): 2196-2198. (in Chinese)
[13] 李军玲, 刘燕清, 崔中秋, 等. 水稻重要农艺性状控制基因GBTS液相芯片开发及应用[J]. 分子植物育种，2023， 1-19.
LI J L, LIU Y Q, CUI Z Q, et al. Development and application of the liquid-phase chip for GBTS gene controlling important agronomic traits in rice[J]. Molecular Plant Breeding, 2023, 1-19. (in Chinese)
[14] 王攀. 植物分子标记高通量快速检测技术的研究进展[J]. 中国种业, 2024(7): 17-22.
WANG P. Research progress on high-throughput rapid detection technology of plant molecular markers[J]. China Seed Industry, 2024, 7(7): 17-22. (in Chinese)
[15] 李欢, 张文洋, 田志强, 等. 高通量分子标记检测方法的研究进展[J]. 玉米科学, 2022, 30(3): 1-9.
LI H, ZHANG W Y, TIAN Z Q, et al. Research progress on high-throughput molecular marker detection methods[J]. Journal of Maize Sciences, 2022, 30(3): 1-9. (in Chinese)
[16] 徐云碧, 杨泉女, 郑洪建, 等. 靶向测序基因型检测(GBTS)技术及其应用[J]. 中国农业科学, 2020, 53(15): 2983-3004.
XU Y B, YANG Q N, ZHENG H J, et al. Genotyping by target sequencing (GBTS) technology and its application[J]. Scientia Agricultura Sinica, 2020, 53(15): 2983-3004. (in Chinese)
[17] SAMORODNITSKY E, DATTA J, JEWELL B M, et al. Comparison of custom capture for targeted next-generation DNA sequencing[J]. J Mol Diagn, 2015, 17(1): 64-75.
[18] MUIR W M, WONG G K, ZHANG Y, et al. Review of the initial validation and characterization of a 3K chicken SNP array[J]. World’s Poult Sci J, 2008, 64(2): 219-226.
[19] GROENEN M A M, MEGENS H J, ZARE Y, et al. The development and characterization of a 60K SNP chip for chicken[J]. BMC Genomics, 2011, 12(1): 274.
[20] KRANIS A, GHEYAS A A, BOSCHIERO C, et al. Development of a high density 600K SNP genotyping array for chicken[J]. BMC Genomics, 2013, 14(1): 59.
[21] LIU R, XING S, WANG J, et al. A new chicken 55K SNP genotyping array[J]. BMC Genomics, 2019, 20(1): 410.
[22] LIU Z, SUN C, YAN Y, et al. Design and evaluation of a custom 50K Infinium SNP array for egg-type chickens[J]. Poult Sci, 2021, 100(5): 101044.
[23] 王梦燏, 周成浩, 薛倩, 等. “酉芯一号”在地方鸡遗传多样性和结构分析中的应用效力研究[J]. 遗传, 2024, 46(8): 640-648.
WANG M Y, ZHOU C H, XUE Q, et al. Research on the application efficacy of "Youxin-1" in the analysis of genetic diversity and structure of local chicken breeds[J]. Hereditas, 2024, 46(8): 640-648. (in Chinese)
[24] 王杰,周艳,刘杰,等.一种鸡全基因组低密度芯片及其制作方法和应用:202310328998[P]. WANG J, ZHOU Y, LIU J, et al. A low-density whole-genome chip for chickens, its manufacturing method and applications: 202310328998[P].(in Chinese)
[25] 康相涛,李文婷,王克君,等.一种地方鸡40K全基因组SNP液相芯片及其应用:202311218054[P]. KANG X T, LI W T, WANG K J, et al. A 40K whole-genome SNP liquid-phase chip for local chicken breeds and its applications: 202311218054[P].(in Chinese)
[26] 贺喜, 马豪杰, 刘会超,等. “湘芯一号”肉鸡60K液相育种芯片的设计及基因组预测效果[J]. 湖南农业大学学报(自然科学版), 2024, 50(6): 1-9.
HE X, MA H J, LIU H C, et al. Design of "Xiangxin-1" 60K liquid-phase breeding chip for broilers and its genome prediction effect[J]. Journal of Hunan Agricultural University (Natural Sciences), 2024, 50(6): 1-9. (in Chinese)
[27] HILLIER L D W, MILLER W, BIRNEY E, et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution[J]. Nature, 2004, 432(7018): 695-716.
[28] 陈懿, 柳序. 地方鸡遗传资源现状与育种技术的研究进展[J]. 畜牧产业, 2025(5): 32-39.
CHEN Y, LIU X. Research progress on the current situation of local chicken genetic resources and breeding techniques[J]. Animal Husbandry Industry, 2025(5): 32-39. (in Chinese)
[29] 孙研研, 倪爱心, 杨涵涵, 等. 畜禽杂种优势形成机制与预测方法研究进展[J]. 中国农业科学, 2025, 58(5): 1017-1031.
SUN Y Y, NI A X, YANG H H, et al. Research progress on the formation mechanism and prediction methods of heterosis in livestock and poultry[J]. Scientia Agricultura Sinica, 2025, 58(5): 1017-1031.(in Chinese)
[30] 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. Research and application of SNP chips for chicken genomic breeding and conservation[J]. China Poultry, 2018, 40(15): 1-6.(in Chinese)
[31] 石少磊, 武丽娜, 冯羿方, 等. 基因组检测技术在肉鸡遗传育种中的应用[J]. 中国畜禽种业, 2023, 19(12): 122-128.
SHI S L, WU L N, FENG Y F, et al. Application of genomic detection technology in broiler chicken genetic breeding[J]. China Livestock & Poultry Breeding, 2023, 19(12): 122-128.(in Chinese)
[32] 王晓峰. 新形势下我国肉鸡种业高质量发展路径[J]. 中国禽业导刊, 2023, 40(12): 19-23.
WANG X F. Paths to high-quality development of China’s broiler chicken seed industry under the new situation[J]. Guide to Chinese Poultry, 2023, 40(12): 19-23.(in Chinese)
[33] “京芯一号mini”芯片+数字化肉鸡联合育种平台——我国肉鸡育种产业新的里程碑[EB/OL]."Jingxin-1 mini" chip+digital broiler joint breeding platform——a new milestone in China’s broiler breeding industry[EB/OL]. (in Chinese)
[34] 谢华玲, 杨艳萍. 我国白羽肉鸡种源供给能力提升初探[J]. 安徽农业科学, 2024, 52(2): 247-249+256.
XIE H L, YANG Y P. Preliminary study on improving the supply capacity of white feather broiler breeding resources in China[J]. Journal of Anhui Agricultural Sciences, 2024, 52(2): 247-249, 256. (in Chinese)
[35] WOLC A, KRANIS A, ARANGO J, et al. Implementation of genomic selection in the poultry industry[J]. Anim Front, 2016, 6(1): 23-31.
[36] 孙从佼, 于爱芝, 汪洋, 等. 2023年蛋鸡产业发展情况、未来发展趋势及建议[J]. 中国畜牧杂志, 2024, 60(3): 307-311.
SUN C J, YU A Z, WANG Y, et al. Development status, future trends and suggestions of the layer industry in 2023[J]. Chinese Journal of Animal Science, 2024, 60(3): 307-311. (in Chinese)
[37] SEO D, CHO S, MANJULA P, et al. Identification of target chicken populations by machine learning models using the minimum number of SNPs[J]. Animals, 2021, 11(1): 241.
[38] LIU Y, ZHANG M, TU Y, et al. Population structure and genetic diversity of seven Chinese indigenous chicken populations in Guizhou Province[J]. J Poult Sci, 2021, 58(4): 211-215.
[39] CHEN L, WANG X, CHENG D, et al. Population genetic analyses of seven Chinese indigenous chicken breeds in a context of global breeds[J]. Anim Genet, 2019, 50(1): 82-86.
[40] CENDRON F, MASTRANGELO S, TOLONE M, et al. Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds[J]. Poult Sci, 2021, 100(2): 441-451.
[41] LI R R, SONG Y F, ZHANG G P, et al. Genome-wide association study identifies loci and candidate genes for body composition and meat quality traits in Beijing-You chickens[J]. PLoS One, 2013, 8(4): e61172.
[42] EMRANI H, MASOUDI A A, TORSHIZI R V, et al. Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population[J]. Anim Genet, 2020, 51(5): 722-730.
[43] LYU S, ARENDS D, NASSAR M K, et al. High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin[J]. Poult Sci, 2023, 102(1): 102303.
[44] MONTEIRO M G C, BOSCHIERO C, MELLO C A S, et al. A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens[J]. BMC Genomics, 2018, 19(1): 374.
[45] ZHANG H, SHEN L Y, XU Z C, et al. Haplotype-based genome-wide association studies for carcass and growth traits in chicken[J]. Poult Sci, 2020, 99(5): 2349-2361.
[46] TREVISOLI P A, MOREIRA G C M, BOSCHIERO C, et al. A missense mutation in the MYBPH gene is associated with abdominal fat traits in meat-type chickens[J]. Front Genet, 2021, 12: 698163.
[47] LI W, ZHENG M, ZHAO G, et al. Identification of QTL regions and candidate genes for growth and feed efficiency in broilers[J]. Genet Sel Evol, 2021, 53(1): 13.
[48] MARCHESI J A P, ONO R K, CANTAO M E, et al. Exploring the genetic architecture of feed efficiency traits in chickens[J]. Sci Rep, 2021, 11(1): 4622.
[49] ZHAO X, NIE C, ZHANG J, et al. Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study[J]. BMC Genomics, 2021, 22(1): 610.
[50] AZMAL S A, BHUIYAN A A, OMAR A I, et al. Novel polymorphisms in RAPGEF6 gene associated with egg-laying rate in Chinese Jing Hong chicken using genome-wide SNP scan[J]. Genes, 2019, 10(5): 384.
[51] TARSANI E, KRANIS A, MANIATIS G, et al. Detection of loci exhibiting pleiotropic effects on body weight and egg number in female broilers[J]. Sci Rep, 2021, 11(1): 7441.
[52] DING J, YING F, LI Q, et al. A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken[J]. J Anim Sci Biotechnol, 2022, 13(1): 96.
[53] ZHUANG L, CONGJIAO S, YIYUAN Y, et al. Genome-Wide Association Analysis of Age-Dependent Egg Weights in Chickens[J]. Front Genet, 2018, 9: 128.
[54] LI Q, DUAN Z, SUN C, et al. Genetic variations for the eggshell crystal structure revealed by genome-wide association study in chickens[J]. BMC Genomics, 2021, 22(1): 1-12.
[55] 张锦. 基于免疫细胞功能解析鸡抗沙门氏菌的作用机制[D]. 北京:中国农业科学院, 2023.
ZHANG J. Mechanism of chicken resistance to Salmonella based on immune cell function analysis[D]. Beijing: Chinese Academy of Agricultural Sciences, 2023. (in Chinese)
[56] ZHU B, LI Q, LIU R, et al. Genome-wide association study of H/L traits in chicken[J]. Animals (Basel), 2019, 9(5): 260.
[57] LEI Z, PENG L, RANRAN L, et al. The identification of loci for immune traits in chickens using a genome-wide association study[J]. PLoS ONE, 2015, 10(3): e0117269.
[58] SUN Y, LI Q, HU Y, et al. Genome-wide association study of immune traits in chicken F2 resource population[J]. J Anim Breed Genet, 2016, 133(3): 197-206.
[59] LI X, NIE C, LIU Y, et al. A genome-wide association study explores the genetic determinism of host resistance to Salmonella pullorum infection in chickens[J]. Genet Sel Evol, 2019, 51(1): 51.
[60] SAELAO P, WANG Y, CHANTHAVIXAY G, et al. Genetics and genomic regions affecting response to newcastle disease virus infection under heat stress in layer chickens[J]. Genes (Basel), 2019, 10(1): 61.
[61] WALUGEMBE M, MUSHI J R, AMUZU-AWEH E N, et al. Genetic analyses of tanzanian local chicken ecotypes challenged with newcastle disease virus[J]. Genes, 2019, 10(7): 546.
[62] 黄嘉源, 张子桦, 吴耀冰, 等. 液相芯片多重检测技术在临床检验应用的研究进展[J]. 齐齐哈尔医学院学报, 2025, 46(2): 159-166.
HUANG J Y, ZHANG Z H, WU Y B, et al. Research progress on the application of liquid chip multiplex detection technology in clinical laboratory tests[J]. Journal of Qiqihar Medical University, 2025, 46(2): 159-166. (in Chinese)
[63] WANG F, GUO Y, LIU Z, et al. New insights into the novel sequences of the chicken pan-genome by liquid chip[J]. J Anim Sci, 2022, 100(12): skac336.