芯片技术在畜禽育种中的应用研究进展

doi:10.16431/j.cnki.1671-7236.2020.01.012

Abstract

Abstract: There are abundant resources of livestock and poultry breeds in China,and there are many good trait genes.Unfortunately,these fine trait genes have not been fully utilized.Therefore,the development and utilization of genetics and resources at the genetic level is an important direction for improving economic traits of domestic animal genetics resources.The traditional pedigree selection method played a vital role in breeding while it also has shortcomings such as low accuracy and long breeding cycle.With the rapid development of molecular biology,advanced genome sequencing and gene typing technology have pushed the innovation of livestock and poultry breeding methods.The efficiency of genetic detection has been dramatically improved from the low-throughput,time-consuming restriction fragment polymorphism (RFLP) markers in the past to the single nucleotide polymorphism (SNP) with high-throughput and high density.Genotyping based on chip was widely used in research and breeding practice,becoming a new technology and hotspot in livestock and poultry breeding.In this review,the research and application of SNP chip technology in livestock and poultry breeding,its technical advantages,existing problems,challenges and application prospects are summarized.The paper showed that gene chip technology would become an important basic technology in molecular breeding of livestock and poultry,and play an important role in the rapid development of livestock and poultry breeding industry,promoting the genetics progress of livestock and poultry breeding in China,and enhancing the scientific and technological competiveness of livestock and poultry breeding industry in China.

Key words: chip technology; SNP; high-throughput sequencing; animal breeding

CLC Number:

S813.3

MA Lina, LIU Yongjin, WANG Jin, ZHAO Zhengwei, MA Qing. Research Advance on Application of Chip Technology in Livestock and Poultry Breeding[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(1): 98-106.

References

[1] FORDOR S P,READ J L,PIRNING M C.Light-directed spatially addressable parallel chemical synthesis[J].Science,1991,251(4995):762-773.
[2] FORDOR S P,RAVA R P,HUANG X C.Multiplexed biochemical assays with biological chip[J].Nature,1993,364:555-556.
[3] 张于光,李迪强,肖启明,等.基因芯片及其在环境微生物研究中的应用[J].微生物学报,2004,44(3):406-410. ZHANG Y G,LI D Q,XIAO Q M,et al.Microarrays and their application to environmental microorganisms[J].Acta Microbiological Sinica,2004,44(3):406-410.(in Chinese)
[4] 邢婉丽,程京.生物技术芯片[M].北京:清华大学出版社,2004. XING W L,CHENG J.Biological Chip Technology[M].Beijing:Tsinghua University Press,2004.(in Chinese)
[5] 于文静.我国诞生全球首张水稻全基因组育种芯片[J].北京农业,2012,17:5. YU W J.The world’s first rice genome breeding chip was born in China[J].Beijing Agriculture,2012,17:5.(in Chinese)
[6] DAVEY J W,HOHENLOHE P A,ETTER P D,et al.Genome-wide genetic marker discovery and genotyping using next-generation sequencing[J].Nature Reviews Genetics,2011,12(7):499-510.
[7] GUPTA P K,RUSTGI S,MIR R R.Array-based high-throughput DNA markers for crop improvement[J].Heredity,2008,101(1):5-18.
[8] TOSSER-KLOPP G,BARDOU P,BOUCHEZ O,et al.Design and characterization of a 52K SNP chip for goats[J].PLoS One,2014,9(1):e86227.
[9] 宣苏哲.我国研制出首款鸡55K SNP芯片[J].家禽科学,2017,19:12. XUAN S Z.China developed the first chicken 55K SNP chip[J].Poultry Science,2017,19:12.(in Chinese)
[10] DE ROOS A P,HAYES B J,SPELMAN R J,et al.Linkage disequilibrium and persistence of phase in Holstein-Frie-sian,Jersey and Angus cattle[J].Genetics,2008,179(3):1503-1512.
[11] DE LOS C G,VAZQUEZ A I,FERNANDO R,et al.Prediction of complex human traits using the genomic best linear unbiased predictor[J].PLoS Genetics,2013,9(7):e1003608.
[12] CAÑAS-ÁLVAREZ J,GONZALEZ-RODRIGUEZ A,MUNILLA S,et al.Genetic diversity and divergence among Spanish beef cattle breeds assessed by a bovine high-density SNP chip[J].Journal of Animal Science,2015,93(11):5164-5174.
[13] DA SILVA V H,LAEIN V N,BOSSE M,et al.CNVs are associated with genomic architecture in a songbird[J].BMC Genomics,2018,19(1):195.
[14] 袁泽湖,王慧华,胡师金,等.利用50K芯片数据分析中国11个地方绵羊群体的遗传结构[J].畜牧兽医学报,2016,47(5):899-908. YUAN Z H,WANG H H,HU S J,et al.Population structure analysis of Chine indigenous sheep by 50K chip data[J].Acta Veterinaria et Zootechnica Sinica,2016,47(5):899-908.(in Chinese)
[15] 兰蓉,朱兰,杨红远,等.基于SNP芯片的云上黑山羊遗传结构分析[J].中国畜牧兽医,2019,46(2):480-488. LAN R,ZHU L,YANG H Y,et al.Analysis of genetic structure of Yunshang Black goat based on SNP chip[J].China Animal Husbandry & Veterinary Medicine,2019,46(2):480-488.(in Chinese)
[16] MARTIN P,PALHIERE I,TOSSER K G,et al.Heritability and genome-wide association mapping for supernumerary teats in French Alpine and Saanen dairy goats[J].Journal of Dairy Science,2016,99(11):8891-8900.
[17] 兰蓉,朱兰,姚新荣,等.山羊产羔数全基因组关联分析[J].畜牧兽医学报,2015,46(4):549-554. LAN R,ZHU L,YAO X R,et al.Genome-wide association analysis of lambing number in goat[J].Acta Veterinaria et Zootechnica Sinica,2015,46(4):549-554.(in Chinese)
[18] YI G,QU L,CHEN S,et al.Genome-wide copy number profiling using high-density SNP array in chickens[J].Animal Genetics,2015,46(2):148-157.
[19] 刘澳星,郭刚,王雅春,等.中国荷斯坦牛初产日龄遗传评估及全基因组关联分析[J].畜牧兽医学报,2015,46(3):373-381. LIU A X,GUO G,WANG Y C,et al.Genetic analysis and genome wide association studies for age at first calving in Chinese Holsteins[J].Acta Veterinaria et Zootechnica Sinica,2015,46(3):373-381.(in Chinese)
[20] DAHLGREN S,ZIENER M L,LINGAAS F.A genome-wide association study identifies a region strongly associated with symmetrical onychomadesis on chromosome 12 in dogs[J].Animal Genetics, 2016,47(6):708-716.
[21] ZHU B,LI Q H,LIU R R,et al.Genome-wide association study of H/L traits in chicken[J].Animals(Basel),2019,9(5):E260.
[22] JUNQUEIRA V S,CARDOSO F F,OLIVEIRA M M,et al.Use of molecular markers to improve relationship information in the genetic evaluation of beef cattle tick resistance under pedigree-based models[J].Journal of Animal Breeding and Genetics,2017,134(1):14-26.
[23] 田佳,李委奇,刘丽元,等.宁夏地区青年荷斯坦母牛基因组育种值分析[J].中国奶牛,2018,2:15-19. TIAN J,LI W Q,LIU L Y,et al.Analysis on genome breeding value of young Holstein cows in Ningxia area[J].China Dairy Cattle,2018,2:15-19.(in Chinese)
[24] MARCHINI J,HOWIE B.Genotype imputation for genome-wide association studies[J].Nature Reviews Genetics,2010,11(7):499-511.
[25] YE S P,YUAN X L,LIN X R,et al.Imputation from SNP chip to sequence:A case study in a Chinese indigenous chicken population[J].Journal of Livestock and Biotechnology,2018,2:294-305.
[26] VAN DEN BERG I,GULDBRANDTSEN B,HOZE C,et al.Across breed QTL detection and genomic prediction in French and Danish dairy cattle breeds[A].10th World Congress of Genetics Applied to Livestock Production[C].2014.
[27] VANRADEN P M,OCONNELL J R,WIGGANS G R,et al.Genomic evaluations with many more genotypes[J].Genetics Selection Evolution,2011,43:10.
[28] MEUWISSEN T,GODDARD M.Accurate prediction of genetic values for complex traits by whole-genome re-sequencing[J].Genetics, 2010,185(2):623-631.
[29] NAJ A C.Genotype imputation in genome-wide association studies[J].Current Protocols in Human Genetics,2019,102(1):e84.
[30] HULSEGGE B,CALUS M P,WINDIG J J,et al.Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle[J].Journal of Animal Science,2013,91(11):5128-5134.
[31] GUNIA M,SAINTILAN R,VENOT E,et al.Genomic prediction in French Charolais beef cattle using high-density single nucleotide polymorphism markers[J].Journal of Animal Science,2014,92(8):3258-3269.
[32] BOLORMAA S,GORE K,HAYAYES B J,et al.Design of a low-density SNP chip for the main Australian sheep breeds and its effect on imputation and genomic prediction accuracy[J].Animal Genetics,2015,46(5):544-556.
[33] OGAWA S,MATSUDA H,TANIGUCHI Y,et al.Accuracy of imputation of single nucleotide polymorphism marker genotypes from low-density panels in Japanese Black cattle[J].Journal of Animal Science,2015,87(1):3-12.
[34] AUVUVRAY B,MCEWAN J C,NEWMAN S A,et al.Genomic prediction of breeding values in the New Zealand sheep industry using a 50K SNP chip[J].Journal of Animal Science,2014,92(10):4375-4389.
[35] LOPES F B,WU X L,LI H,et al.Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes[J].Journal of Animal Breeding and Genetics,2018,135(1):14-27.
[36] LIACA V.Sequencing Technologies and Their Use in Plant Biotechnology and Breeding[M].DNA Sequencing:Methods and Applications.In Tech,2012.
[37] PEREZ-ENCISO M,RINCON J C,LEGARRA A,et al.Sequence-vs.chip-assisted genomic selection:Accurate biological information is advised[J].Genetics Selection Evolution,2015,47:43.
[38] JAMI A I,ANDREA S P,ASAKO Y N,et al.Applying SNP-derived molecular coancestry estimates to captive breeding programs[J].Journal of Heredity,2016,107(5):403-412.
[39] 林彭.几种基因组评估方法选择效率的比较研究[D].雅安:四川农业大学,2013. LIN P.Comparison of selection efficiency in several genomic evaluating methods[D].Ya’an:Sichuan Agricultural University,2013.(in Chinese)
[40] 李宏伟,王瑞军,王志英,等.家畜基因组选择研究进展[J].遗传,2017,39(5):377-387. LI H W,WANG R J,WANG Z Y,et al.The research progress of genomic selection in livestock[J].Hereditas,2017,39(5):377-387.(in Chinese)
[41] 周立国.水稻水分胁迫相关基因克隆及功能验证[D].武汉:华中农业大学,2010. ZHOU L G.Cloning and functional characterization of genes related to water stress resistance of rice[D].Wuhan:Huazhong Agricultural University,2010.(in Chinese)
[42] 冯政,刘贵生,武华,等.应用基因芯片技术筛选猪抗病相关基因[A].第十二次全国畜禽遗传标记研讨会论文集[C].2010. FENG Z,LIU G S,WU H,et al.Gene chip technology was used to screen genes related to disease resistance in pigs[A].Proceedings of the 12th National Symposium on Genetic Markers of Livestock and Poultry[C].2010.(in Chinese)
[43] 周泉勇.大白猪和二花脸猪妊娠后期胎盘转录谱比较及印记基因鉴定研究[D].武汉:华中农业大学,2009. ZHOU Q Y.Transcriptional analysis of placentas from large white pigs and Erhualian pigs on later gestation and imprinting detection[D].Wuhan:Huazhong Agricultural University,2009.(in Chinese)

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