全基因组关联分析的扩展方法及其在畜禽中应用的研究进展

doi:10.16431/j.cnki.1671-7236.2024.04.006

Abstract

Abstract: Genome-wide association studies (GWAS) is a method of comparing genotype and phenotype data on a large sample set to identify genetic variations associated with specific traits.With the continuous development of high-throughput sequencing technology,bioinformatics technology,and statistical methods,some genetic variations or small molecular substances with lower frequencies can be detected more accurately and economically.The extension method of GWAS derived from technological progress provides new ideas for precision breeding and genetic improvement of livestock and poultry,including GWAS based on copy number variation (CNV),structural variation (SV),and tandem repeats (TR),and GWAS based on haplotypes,gene expression,and metabolomics.Researchers hope to use different molecular markers to provide more comprehensive and detailed genetic variation information to enhance the interpretability and accuracy of GWAS,or further explain and deepen the results of GWAS by combining other types of data,in order to deeply study the relationship between genetic variation and traits and identify key genes that affect complex traits.The author introduces the application of GWAS based on different molecular markers in livestock and poultry research and discusses its results.The advantages and feasibility of different methods are analyzed,providing more ideas and support for further promoting the application of GWAS in livestock and poultry research,precision breeding,and genetic improvement.

Key words: genome-wide association studies (GWAS); livestock and poultry; molecular markers

CLC Number:

S813.3

XIE Xinfeng, WANG Ziyi, ZHONG Ziqi, PAN Deyou, NI Shiheng, XIAO Qian. Advances in Extended Methods of Genome-Wide Association Studies and Their Applications in Livestock and Poultry[J]. China Animal Husbandry & Veterinary Medicine, 2024, 51(4): 1382-1389.

References

[1] RISCH N,MERIKANGAS K.The future of genetic studies of complex human diseases[J].Science,1996,273(5281):1516-1517.
[2] HIRSCHHORN J N,DALY M J.Genome-wide association studies for common diseases and complex traits[J].Nature Reviews Genetics,2005,6(2):95-108.
[3] MATUKUMALLI L K,LAWLEY C T,SCHNABEL R D,et al.Development and characterization of a high density SNP genotyping assay for cattle[J].PLoS One,2009,4(4):e5350.
[4] GROENEN M A,MEGENS H J,ZARE Y,et al.The development and characterization of a 60K SNP chip for chicken[J].BMC Genomics,2011,12(1):1471-2164.
[5] RAMOS A M,CROOIJMANS R P,AFFARA N A,et al.Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology[J].PLoS One,2009,4(8):e6524.
[6] QIAO X,SU R,WANG Y,et al.Genome-wide target enrichment-aided chip design:A 66K SNP chip for cashmere goat[J].Scientific Reports,2017,7(1):8621.
[7] MCCARROLL S A.Extending genome-wide association studies to copy-number variation[J].Human Molecular Genetics,2008,17(R2):R135-42.
[8] 王继英,王海霞,迟瑞宾,等.全基因组关联分析在畜禽中的研究进展[J].中国农业科学,2013,46(4):819-829. WANG J Y,WANG H X,CHI R B,et al.Research progress of genome-wide association analysis in livestock and poultry[J].Scientia Agriculturae Sinica,2013,46(4):819-829.(in Chinese)
[9] LI Y,CHEN L.Big biological data:Challenges and opportunities[J].Genomics Proteomics Bioinformatics,2014,12(5):187-189.
[10] ZHANG Z,BUCKLER E S,CASSTEVENS T M,et al.Software engineering the mixed model for genome-wide association studies on large samples[J].Briefings in Bioinformatics,2009,10(6):664-675.
[11] HU L,ZHANG L,LI Q,et al.Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing[J].Frontiers in Genetics,2022,13:971464.
[12] FEUK L,CARSON A R,SCHERER S W.Structural variation in the human genome[J].Nature Reviews Genetics,2006,7(2):85-97.
[13] ZARREI M,MACDONALD J R,MERICO D,et al.A copy number variation map of the human genome[J].Nature Reviews Genetics,2015,16(3):172-183.
[14] MACDONALD J R,ZIMAN R,YUEN R K,et al.The database of genomic variants:A curated collection of structural variation in the human genome[J].Nucleic Acids Research,2014,42:D986-92.
[15] MAHMOUD M,GOBET N,CRUZ-DÁVALOS D I,et al.Structural variant calling:The long and the short of it[J].Genome Biology,2019,20(1):246.
[16] REDON R,ISHIKAWA S,FITCH K R,et al.Global variation in copy number in the human genome[J].Nature,2006,444(7118):444-454.
[17] STANKIEWICZ P,LUPSKI J R.Structural variation in the human genome and its role in disease[J].Annual Review of Medicine,2010,61:437-455.
[18] COOPER G M,NICKERSON D A,EICHLER E E.Mutational and selective effects on copy-number variants in the human genome[J].Nature Genetics,2007,39(7 Suppl):S22-S29.
[19] SAITOU M,GOKCUMEN O.An evolutionary perspective on the impact of genomic copy number variation on human health[J].Journal of Molecular Evolution,2020,88(1):104-119.
[20] ZHENG X,ZHAO P,YANG K,et al.CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits[J].Journal of Animal Science and Biotechnology,2020,11:42.
[21] BAI H,SUN Y,LIU N,et al.Genome-wide detection of CNVs associated with beak deformity in chickens using high-density 600K SNP arrays[J].Animal Genetics,2018,49(3):226-236.
[22] GORLA E,COZZI M C,ROMÁN-PONCE S I,et al.Genomic variability in Mexican chicken population using copy number variants[J].BMC Genetics,2017,18(1):61.
[23] QIU Y,DING R,ZHUANG Z,et al.Genome-wide detection of CNV regions and their potential association with growth and fatness traits in Duroc pigs[J].BMC Genomics,2021,22(1):332.
[24] FERNANDES A C,DA SILVA V H,GOES C P,et al.Genome-wide detection of CNVs and their association with performance traits in broilers[J].BMC Genomics,2021,22(1):354.
[25] HANNAN A J.Tandem repeats mediating genetic plasticity in health and disease[J].Nature Reviews Genetics,2018,19(5):286-298.
[26] GYMREK M,WILLEMS T,GUILMATRE A,et al.Abundant contribution of short tandem repeats to gene expression variation in humans[J].Nature Genetics,2016,48(1):22-29.
[27] QUILEZ J,GUILMATRE A,GARG P,et al.Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans[J].Nucleic Acids Research,2016,44(8):3750-3762.
[28] ŻMIEŃKO A,SAMELAK A,KOZȽOWSKI P,et al.Copy number polymorphism in plant genomes[J].Theoretical and Applied Genetics,2014,127(1):1-18.
[29] GAUT B S,SEYMOUR D K,LIU Q,et al.Demography and its effects on genomic variation in crop domestication[J].Nature Plants,2018,4(8):512-520.
[30] HO S S,URBAN A E,MILLS R E.Structural variation in the sequencing era[J].Nature Reviews Genetics,2020,21(3):171-189.
[31] CHIANG C,SCOTT A J,DAVIS J R,et al.The impact of structural variation on human gene expression[J].Nature Genetics,2017,49(5):692-699.
[32] DU H,ZHENG X,ZHAO Q,et al.Analysis of structural variants reveal novel selective regions in the genome of Meishan pigs by whole genome sequencing[J].Frontiers in Genetics,2021,12:550676.
[33] MULLE J G.Genomic structural variation and schizophrenia[J].Current Psychiatry Reports,2008,10(2):171-177.
[34] RUCKER J J H,MCGUFFIN P.Genomic structural variation in psychiatric disorders[J].Development and Psychopathology,2012,24(4):1335-1344.
[35] SULLIVAN P F,GESCHWIND D H.Defining the genetic,genomic,cellular,and diagnostic architectures of psychiatric disorders[J].Cell,2019,177(1):162-183.
[36] KADRI N K,SAHANA G,CHARLIER C,et al.A 660-kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle:Additional evidence for the common occurrence of balancing selection in livestock[J].PLoS Genetics,2014,10(1):e1004049.
[37] LI W,CHEN S,LI H,et al.A new insertion/deletion fragment polymorphism of inhibin-α gene associated with follicular cysts in Large White sows[J].Journal of Veterinary Medical Science,2016,78(3):473-476.
[38] FLISIKOWSKI K,VENHORANTA H,NOWACKA-WOSZUK J,et al.A novel mutation in the maternally imprinted PEG3 domain results in a loss of MIMT1 expression and causes abortions and stillbirths in cattle (Bos taurus)[J].PLoS One,2010,5(11):e15116.
[39] FALKER-GIESKE C,BENNEWITZ J,TETENS J.Structural variation and eQTL analysis in two experimental populations of chickens divergently selected for feather-pecking behavior[J].Neurogenetics,2023,24(1):29-41.
[40] BLAJ I,TETENS J,BENNEWITZ J,et al.Structural variants and tandem repeats in the founder individuals of four F(2) pig crosses and implications to F(2) GWAS results[J].BMC Genomics,2022,23(1):631.
[41] CALUS M P,MEUWISSEN T H,DE ROOS A P,et al.Accuracy of genomic selection using different methods to define haplotypes[J].Genetics,2008,178(1):553-561.
[42] VILLUMSEN T M,JANSS L,LUND M S.The importance of haplotype length and heritability using genomic selection in dairy cattle[J].Journal of Animal Breeding and Genetics,2009,126(1):3-13.
[43] CHEN Z,YAO Y,MA P,et al.Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins[J].PLoS One,2018,13(2):e0192695.
[44] WANG F,MEYER N J,WALLEY K R,et al.Causal genetic inference using haplotypes as instrumental variables[J].Genetic Epidemiology,2016,40(1):35-44.
[45] WANG Y T,SUNG P Y,LIN P L,et al.A multi-SNP association test for complex diseases incorporating an optimal P-value threshold algorithm in nuclear families[J].BMC Genomics,2015,16(1):381.
[46] ZHANG H,SHEN L Y,XU Z C,et al.Haplotype-based genome-wide association studies for carcass and growth traits in chicken[J].Poultry Science,2020,99(5):2349-2361.
[47] SRIVASTAVA S,SRIKANTH K,WON S,et al.Haplotype-based genome-wide association study and identification of candidate genes associated with carcass traits in Hanwoo cattle[J].Genes (Basel),2020,11(5):551.
[48] BALLESTER M,RAMAYO-CALDAS Y,REVILLA M,et al.Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs[J].Scientific Reports,2017,7:46539.
[49] 卜李那,赵毅强.全基因组关联分析及其扩展方法的研究进展[J].农业生物技术学报,2019,27(1):150-158. PU L N,ZHAO Y Q,Research progress of genome-wide association analysis and its extension methods[J].Chinese Journal of Agricultural Biotechnology,2019,27(1):150-158.(in Chinese)
[50] CRIADO-MESAS L,BALLESTER M,CRESPO-PIAZUELO D,et al.Identification of eQTLs associated with lipid metabolism in longissimus dorsi muscle of pigs with different genetic backgrounds[J].Scientific Reports,2020,10(1):9845.
[51] WANG J,JIANG S,XI Y,et al.Integration of GWAS and eGWAS to screen candidate genes underlying green head traits in male ducks[J].Animal Genetics,2023,54(4):500-509.
[52] KARISA B K,THOMSON J,WANG Z,et al.Plasma metabolites associated with residual feed intake and other productivity performance traits in beef cattle[J].Livestock Science,2014,165:200-211.
[53] WIDMANN P,REVERTER A,FORTES M R,et al.A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle[J].BMC Genomics,2013,14(798):1471-2164.
[54] MONTGOMERY S P,SINDT J J,GREENQUIST M A,et al.Plasma metabolites of receiving heifers and the relationship between apparent bovine respiratory disease,body weight gain,and carcass characteristics[J].Journal of Animal Science,2009,87(1):328-333.
[55] SHI T,ZHU A,JIA J,et al.Metabolomics analysis and metabolite-agronomic trait associations using kernels of wheat (Triticum aestivum) recombinant inbred lines[J].The Plant Journal,2020,103(1):279-292.
[56] TOHGE T,FERNIE A R.Combining genetic diversity,informatics and metabolomics to facilitate annotation of plant gene function[J].Nature Protocols,2010,5(6):1210-1227.
[57] LIU D,ZHANG H,YANG Y,et al.Metabolome-based genome-wide association study of duck meat leads to novel genetic and biochemical insights[J].Advanced science (Weinheim,Baden-Wurttemberg,Germany),2023,10(18):e2300148.
[58] TIAN J,ZHU X,WU H,et al.Serum metabolic profile and metabolome genome-wide association study in chicken[J].Journal of Animal Science and Biotechnology,2023,14(1):69.

Advances in Extended Methods of Genome-Wide Association Studies and Their Applications in Livestock and Poultry

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