选择信号分析在家马驯化与选育性状候选基因挖掘中的应用研究进展

doi:10.12160/j.issn.1672-5190.2026.01.010

Abstract

Abstract: Selection signature analysis, as a core analytical approach in population genomics, can identify genomic regions subjected to positive, negative, and balancing selection during long-term natural selection and artificial breeding, providing molecular evidence to elucidate the mechanisms of adaptive evolution and the genetic basis of key traits in animals. This review systematically summarizes the research progress on selection signatures related to important economic and phenotypic traits in domestic horses during domestication and artificial breeding, covering core breeding traits such as body size, athletic performance, and coat color, and also summarizes the characteristics of selection signatures associated with pathological traits retained due to linkage drag. By summarizing the application of selection signature detection techniques and candidate gene screening strategies across diverse horse populations, this review elucidates the pivotal role of this method in revealing population genetic structure, domestication-adaptation mechanisms, and the molecular regulatory mechanisms of economic traits. Finally, in combination with the trends of multi-omics integration and technological development, the review discusses the application prospects of selection signature analysis in equine genomics research, breed improvement, and genetic resource conservation, providing a reference for future molecular breeding and evolutionary studies of domestic horses.

Key words: domestic horse, selection signature analysis, whole-genome resequencing, population genomics, candidate genes

CLC Number:

S821.2

LI Wenbo, Tugeqin, Antana, Manglai. Research Progress on the Application of Selection Signature Analysis in Candidate Gene Mining for Domestication and Breeding Traits of Domestic Horses[J]. Animal Husbandry and Feed Science, 2026, 47(1): 72-82.

References

[1] 冯韶华,李尚,刘刁,等.基于基因组重测序的地方畜禽选择信号研究进展[J].中国畜牧杂志,2020,56(9):41-45.
[2] QANBARI S,SIMIANER H.Mapping signatures of positive selection in the genome of livestock[J].Livestock Science,2014,166:133-143.
[3] DE SIMONI GOUVEIA J J,DA SILVA M V G B,PAIVA S R,et al. Identification of selection signatures in livestock species[J].Genetics and Molecular Biology,2014,37(2):330-342.
[4] AMARAL A J,FERRETTI L,MEGENS H J,et al.Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA[J].PLoS One,2011,6(4):e14782.
[5] LIPPOLD S,MATZKE N J,REISSMANN M,et al.Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication[J].BMC Evolutionary Biology,2011,11:328.
[6] LUDWIG A,PRUVOST M,REISSMANN M,et al.Coat color variation at the beginning of horse domestication[J].Science,2009,324(5926):485.
[7] OUTRAM A K,STEAR N A,BENDREY R,et al.The earliest horse harnessing and milking[J].Science,2009,323(5919):1332-1335.
[8] PENNINGS P S,HERMISSON J.Soft sweeps Ⅱ:molecular population genetics of adaptation from recurrent mutation or migration[J].Molecular Biology and Evolution,2006,23(5):1076-1084.
[9] HERMISSON J,PENNINGS P S.Soft sweeps:molecular population genetics of adaptation from standing genetic variation[J].Genetics,2005,169(4):2335-2352.
[10] BARRETT R D H,SCHLUTER D. Adaptation from standing genetic variation[J].Trends in Ecology and Evolution,2008,23(1):38-44.
[11] SUZUKI Y.Statistical methods for detecting natural selection from genomic data[J].Genes and Genetic Systems,2010,85(6):359-376.
[12] NIELSEN R.Molecular signatures of natural selection[J].Annual Review of Genetics,2005,39:197-218.
[13] LOHMUELLER K E,BUSTAMANTE C D,CLARK A G.Detecting directional selection in the presence of recent admixture in African-Americans[J].Genetics,2011,187(3):823-835.
[14] PERSI E,WOLF Y I,KOONIN E V.Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins[J].Nature Communications,2016,7:13570.
[15] FIJARCZYK A,BABIK W.Detecting balancing selection in genomes:limits and prospects[J].Molecular Ecology,2015,24(14):3529-3545.
[16] 薛周舣源,宋显威,吴林慧,等.畜禽选择信号检测方法及其统计学问题[J].畜牧兽医学报,2018,49(06):1099-1107.
[17] LEWONTIN R C,KRAKAUER J.Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms[J].Genetics,1973,74(1):175-195.
[18] WRIGHT S.Genetical structure of populations[J].Nature,1950,166(4215):247-249.
[19] SHRIVER M D,KENNEDY G C,PARRA E J,et al.The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs[J].Human Genomics,2004,1(4):274-286.
[20] AKEY J M,RUHE A L,AKEY D T,et al.Tracking footprints of artificial selection in the dog genome[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(3):1160-1165.
[21] ZHU L,BUSTAMANTE C D.A composite-likelihood approach for detecting directional selection from DNA sequence data[J].Genetics,2005,170(3):1411-1421.
[22] TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[23] FAY J C,WU C I.Hitchhiking under positive Darwinian selection[J].Genetics,2000,155(3):1405-1413.
[24] SABETI P C,REICH D E,HIGGINS J M,et al.Detecting recent positive selection in the human genome from haplotype structure[J].Nature,2002,419(6909):832-837.
[25] SABETI P C,VARILLY P,FRY B,et al.Genome-wide detection and characterization of positive selection in human populations[J].Nature,2007,449(7164):913-918.
[26] VOIGHT B F,KUDARAVALLI S,WEN X Q,et al.A map of recent positive selection in the human genome[J].PLoS Biology,2006,4(3):e72.
[27] PAN Z Y,HE X Y,WANG X Y,et al.Selection signature in domesticated animals[J].Hereditas,2016,38(12):1069-1080.
[28] FARIELLO M I,BOITARD S,NAYA H,et al.Detecting signatures of selection through haplotype differentiation among hierarchically structured populations[J].Genetics,2013,193(3):929-941.
[29] BONHOMME M,CHEVALET C,SERVIN B,et al.Detecting selection in population trees:the Lewontin and Krakauer test extended[J].Genetics,2010,186(1):241-262.
[30] GROSSMAN S R,SHLYAKHTER I,KARLSSON E K,et al.A composite of multiple signals distinguishes causal variants in regions of positive selection[J].Science,2010,327(5967):883-886.
[31] RANDHAWA I A S,KHATKAR M S,THOMSON P C,et al. Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep[J].BMC Genetics,2014,15:34.
[32] MA Y,DING X,QANBARI S,et al.Properties of different selection signature statistics and a new strategy for combining them[J].Heredity,2015,115(5):426-436.
[33] GURGUL A,JASIELCZUK I,SEMIK-GURGUL E,et al.A genome-wide scan for diversifying selection signatures in selected horse breeds[J].PLoS One,2019,14(1):e0210751.
[34] ASADOLLAHPOUR NANAEI H,ESMAILIZADEH A,AYATOLLAHI MEHRGARDI A,et al.Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony[J].BMC Genomics,2020,21(1):496.
[35] MOUSAVI S F,RAZMKABIR M,ROSTAMZADEH J,et al.Genetic diversity and signatures of selection in four indigenous horse breeds of Iran[J].Heredity,2023,131(2):96-108.
[36] KADER A,LI Y,DONG K Z,et al.Population variation reveals independent selection toward small body size in Chinese Debao pony[J].Genome Biology and Evolution,2015,8(1):42-50.
[37] METZGER J,SCHRIMPF R,PHILIPP U,et al.Expression levels of LCORL are associated with body size in horses[J].PLoS One,2013,8(2):e56497.
[38] HE S G,ZHANG L H,LI W R,et al.BIEC2-808543 SNP in the LCORL gene is associated with body conformation in the Yili horse[J].Animal Biotechnology,2015,26(4):289-291.
[39] SALEK ARDESTANI S,AMINAFSHAR M,ZANDI BAGHCHE MARYAM M B,et al. Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types[J].Genome,2020,63(8):387-396.
[40] SHEN J F,YU J,DAI X L,et al.Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys[J].Journal of Genetics and Genomics,2021,48(8):737-745.
[41] NAZARI F,SEYEDABADI H R,NOSHARY A,et al.A genome-wide scan for signatures of selection in Kurdish horse breed[J].Journal of Equine Veterinary Science,2022,113:103916.
[42] LI Y,LIU Y,WANG M,et al.Whole-genome sequence analysis reveals the origin of the chakouyi horse[J].Genes,2022,13(12):2411.
[43] SANTOS W B,SCHETTINI G P,MAIORANO A M,et al.Genome-wide scans for signatures of selection in Mangalarga Marchador horses using high-throughput SNP genotyping[J].BMC Genomics,2021,22(1):737.
[44] PETERSEN J L,MICKELSON J R,RENDAHL A K,et al.Genome-wide analysis reveals selection for important traits in domestic horse breeds[J].PLoS Genetics,2013,9(1):e1003211.
[45] SANTOS W B,PEREIRA C B,MAIORANO A M,et al.Genomic inbreeding estimation,runs of homozygosity,and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line[J].Journal of Animal Breeding and Genetics,2023,140(6):583-595.
[46] SRIKANTH K,KIM N Y,PARK W,et al.Comprehensive genome and transcriptome analyses reveal genetic relationship,selection signature,and transcriptome landscape of small-sized Korean native Jeju horse[J].Scientific Reports,2019,9:16672.
[47] CHEN C J,ZHU B,TANG X W,et al.Genome-wide assessment of runs of homozygosity by whole-genome sequencing in diverse horse breeds worldwide[J].Genes,2023,14(6):1211.
[48] SALEK ARDESTANI S,AMINAFSHAR M,ZANDI BAGHCHE MARYAM M B,et al. Whole-genome signatures of selection in sport horses revealed selection footprints related to musculoskeletal system development processes[J].Animals,2020,10(1):53.
[49] NOLTE W,THALLER G,KUEHN C.Selection signatures in four German warmblood horse breeds:tracing breeding history in the modern sport horse[J].PLoS One,2019,14(4):e0215913.
[50] LEE W,PARK K D,TAYE M,et al.Analysis of cross-population differentiation between Thoroughbred and Jeju horses[J].Asian-Australasian Journal of Animal Sciences,2018,31(8):1110-1118.
[51] AVILA F,MICKELSON J R,SCHAEFER R J,et al.Genome-wide signatures of selection reveal genes associated with performance in American quarter horse subpopulations[J].Frontiers in Genetics,2018,9:249.
[52] HAN H G,MCGIVNEY B A,ALLEN L,et al.Common protein-coding variants influence the racing phenotype in galloping racehorse breeds[J].Communications Biology,2022,5:1320.
[53] HAN H G,MCGIVNEY B A,FARRIES G,et al.Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed[J].PLoS One,2020,15(2):e0227212.
[54] GU J J,ORR N,PARK S D,et al.A genome scan for positive selection in thoroughbred horses[J].PLoS One,2009,4(6):e5767.
[55] MCGIVNEY B A,HERNANDEZ B,KATZ L M,et al.A genomic prediction model for racecourse starts in the Thoroughbred horse[J].Animal Genetics,2019,50(4):347-357.
[56] GRILZ-SEGER G,DRUML T,NEUDITSCHKO M,et al.Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size[J].Animal Genetics,2019,50(4):334-346.
[57] GRILZ-SEGER G,NEUDITSCHKO M,RICARD A,et al.Genome-wide homozygosity patterns and evidence for selection in a set of European and near eastern horse breeds[J].Genes,2019,10(7):491.
[58] MOMEN M,BRAUER K,PATTERSON M M,et al.Genetic architecture and polygenic risk score prediction of degenerative suspensory ligament desmitis (DSLD) in the Peruvian Horse[J].Frontiers in Genetics,2023,14:1201628.
[59] GRILZ-SEGER G,DRUML T,NEUDITSCHKO M,et al.High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse[J].BMC Genomics,2019,20(1):174.

Research Progress on the Application of Selection Signature Analysis in Candidate Gene Mining for Domestication and Breeding Traits of Domestic Horses

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