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Home / Equine Research Bank / Anim Genet / A genome-wide association study indicates LCORL/NCAPG as a c...
Animal genetics2013; 44(4); 467-471; doi: 10.1111/age.12031

A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in German Warmblood horses.

Abstract: A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human height in several large meta-analyses. Furthermore, a mutation within the NCAPG gene was found to affect growth and body frame size in cattle. Together with the results of this study in German Warmbloods, these findings strongly indicate LCORL/NCAPG as a candidate locus for withers height in horses. Further studies are, however, needed to confirm this.
© 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics.
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Publication Date: 2013-02-18 PubMed ID: 23418885DOI: 10.1111/age.12031Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research focuses on finding genetic influences on the height of German Warmblood stallions. A major gene location (LCORL/NCAPG) was identified that could be responsible for 18% of the height variance observed in these horses.

Research Methodology

  • The researchers conducted a genome-wide association scan on 782 German Warmblood stallions to find genes affecting their withers height (height at the base of the neck).
  • The horses were genotyped using the Illumina EquineSNP50 Bead Chip, a technology that allows for comprehensive genomic coverage.
  • To correct for population structure, a principal components approach was applied – a statistical method that transforms possible correlated variables into uncorrelated variables called principal components.

Findings

  • The analysis led to the identification of a major Quantitative Trait Locus (QTL) on ECA3. QTL is a region in the DNA which correlates with variation in a phenotype (in this case, the height of the horse). The ECA3 refers to a specific location in the horse’s chromosomes.
  • This QTL explains about 18% of the phenotypic difference in height between the horses.
  • The identified gene location – LCORL/NCAPG – is a strong candidate gene for this QTL. This gene locus has been consistently found to influence human height in several large meta-analyses.
  • A mutation within the NCAPG gene is found to affect growth and body frame size in cattle, supporting the premise that LCORL/NCAPG could influence height in horses as well.

Implications and Future Research

  • This study provides strong evidence that the LCORL/NCAPG gene locus may influence withers height in German Warmblood horses.
  • This finding could be helpful for breeders focusing on withers height in their breeding programs.
  • Further studies are needed to confirm the role of this gene location on withers height in horses.

Cite This Article

APA
Tetens J, Widmann P, Kühn C, Thaller G. (2013). A genome-wide association study indicates LCORL/NCAPG as a candidate locus for withers height in German Warmblood horses. Anim Genet, 44(4), 467-471. https://doi.org/10.1111/age.12031

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 44
Issue: 4
Pages: 467-471

Researcher Affiliations

Tetens, J
  • Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Str. 6, D-24118 Kiel, Germany. jtetens@tierzucht.uni-kiel.de
Widmann, P
    Kühn, C
      Thaller, G

        MeSH Terms

        • Animals
        • Biometry
        • Breeding
        • Chromosome Mapping / veterinary
        • Chromosomes, Mammalian / genetics
        • Genetic Loci
        • Genome-Wide Association Study / methods
        • Genome-Wide Association Study / veterinary
        • Genotype
        • Horses / anatomy & histology
        • Horses / genetics
        • Horses / growth & development
        • Male
        • Mutation
        • Polymorphism, Single Nucleotide
        • Quantitative Trait Loci / genetics

        Citations

        This article has been cited 50 times.
        1. Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids.. PLoS One 2023;18(6):e0286861.
          doi: 10.1371/journal.pone.0286861pubmed: 37289743google scholar: lookup
        2. Zhi Y, Wang D, Zhang K, Wang Y, Geng W, Chen B, Li H, Li Z, Tian Y, Kang X, Liu X. Genome-Wide Genetic Structure of Henan Indigenous Chicken Breeds.. Animals (Basel) 2023 Feb 19;13(4).
          doi: 10.3390/ani13040753pubmed: 36830540google scholar: lookup
        3. Silva FA, Souza ÉMS, Ramos E, Freitas L, Nery MF. The molecular evolution of genes previously associated with large sizes reveals possible pathways to cetacean gigantism.. Sci Rep 2023 Jan 19;13(1):67.
          doi: 10.1038/s41598-022-24529-3pubmed: 36658131google scholar: lookup
        4. Finno CJ. Science-in-brief: Genomic and transcriptomic approaches to the investigation of equine diseases.. Equine Vet J 2022 Mar;54(2):444-448.
          doi: 10.1111/evj.13549pubmed: 35133024google scholar: lookup
        5. Vosgerau S, Krattenmacher N, Falker-Gieske C, Seidel A, Tetens J, Stock KF, Nolte W, Wobbe M, Blaj I, Reents R, Kühn C, von Depka Prondzinski M, Kalm E, Thaller G. Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses.. J Appl Genet 2022 May;63(2):369-378.
          doi: 10.1007/s13353-021-00681-wpubmed: 35028913google scholar: lookup
        6. Sheet S, Kim JS, Ko MJ, Kim NY, Lim YJ, Park MR, Lee SJ, Kim JM, Oh SI, Choi BH. Insight into the Candidate Genes and Enriched Pathways Associated with Height, Length, Length to Height Ratio and Body-Weight of Korean Indigenous Breed, Jindo Dog Using Gene Set Enrichment-Based GWAS Analysis.. Animals (Basel) 2021 Nov 2;11(11).
          doi: 10.3390/ani11113136pubmed: 34827868google scholar: lookup
        7. Bolormaa S, Swan AA, Stothard P, Khansefid M, Moghaddar N, Duijvesteijn N, van der Werf JHJ, Daetwyler HD, MacLeod IM. A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits.. Genet Sel Evol 2021 Jul 8;53(1):58.
          doi: 10.1186/s12711-021-00651-0pubmed: 34238208google scholar: lookup
        8. Sousa MAP, de Athayde FRF, Maldonado MBC, Lima AO, Fortes MRS, Lopes FL. Single nucleotide polymorphisms affect miRNA target prediction in bovine.. PLoS One 2021;16(4):e0249406.
          doi: 10.1371/journal.pone.0249406pubmed: 33882076google scholar: lookup
        9. Rosengren MK, Sigurðardóttir H, Eriksson S, Naboulsi R, Jouni A, Novoa-Bravo M, Albertsdóttir E, Kristjánsson Þ, Rhodin M, Viklund Å, Velie BD, Negro JJ, Solé M, Lindgren G. A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.. BMC Genomics 2021 Apr 14;22(1):267.
          doi: 10.1186/s12864-021-07454-zpubmed: 33853519google scholar: lookup
        10. Kvist L, Honka J, Niskanen M, Liedes O, Aspi J. Selection in the Finnhorse, a native all-around horse breed.. J Anim Breed Genet 2021 Mar;138(2):188-203.
          doi: 10.1111/jbg.12524pubmed: 33226152google scholar: lookup
        11. Asadollahpour Nanaei H, Esmailizadeh A, Ayatollahi Mehrgardi A, Han J, Wu DD, Li Y, Zhang YP. Comparative population genomic analysis uncovers novel genomic footprints and genes associated with small body size in Chinese pony.. BMC Genomics 2020 Jul 20;21(1):496.
          doi: 10.1186/s12864-020-06887-2pubmed: 32689947google scholar: lookup
        12. Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A. Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data.. Animals (Basel) 2020 Jun 8;10(6).
          doi: 10.3390/ani10061005pubmed: 32521830google scholar: lookup
        13. He S, Di J, Han B, Chen L, Liu M, Li W. Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino.. Animals (Basel) 2020 Mar 20;10(3).
          doi: 10.3390/ani10030524pubmed: 32245132google scholar: lookup
        14. Doyle JL, Berry DP, Veerkamp RF, Carthy TR, Walsh SW, Evans RD, Purfield DC. Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty.. Front Genet 2020;11:20.
          doi: 10.3389/fgene.2020.00020pubmed: 32117439google scholar: lookup
        15. Hu X, Xing Y, Fu X, Yang Q, Ren L, Wang Y, Li Q, Li J, Zhang L. NCAPG Dynamically Coordinates the Myogenesis of Fetal Bovine Tissue by Adjusting Chromatin Accessibility.. Int J Mol Sci 2020 Feb 13;21(4).
          doi: 10.3390/ijms21041248pubmed: 32070024google scholar: lookup
        16. Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia.. BMC Genomics 2019 May 8;20(Suppl 3):294.
          doi: 10.1186/s12864-019-5537-0pubmed: 32039702google scholar: lookup
        17. Saif R, Henkel J, Jagannathan V, Drögemüller C, Flury C, Leeb T. The LCORL Locus is under Selection in Large-Sized Pakistani Goat Breeds.. Genes (Basel) 2020 Feb 5;11(2).
          doi: 10.3390/genes11020168pubmed: 32033434google scholar: lookup
        18. Doyle JL, Berry DP, Veerkamp RF, Carthy TR, Evans RD, Walsh SW, Purfield DC. Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds.. Genet Sel Evol 2020 Jan 30;52(1):2.
          doi: 10.1186/s12711-020-0523-1pubmed: 32000665google scholar: lookup
        19. Pu Y, Zhang Y, Zhang T, Han J, Ma Y, Liu X. Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds.. Animals (Basel) 2020 Jan 11;10(1).
          doi: 10.3390/ani10010119pubmed: 31940795google scholar: lookup
        20. Qu L, Shen M, Guo J, Wang X, Dou T, Hu Y, Li Y, Ma M, Wang K, Liu H. Identification of potential genomic regions and candidate genes for egg albumen quality by a genome-wide association study.. Arch Anim Breed 2019;62(1):113-123.
          doi: 10.5194/aab-62-113-2019pubmed: 31807621google scholar: lookup
        21. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.. Anim Genet 2019 Dec;50(6):569-597.
          doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
        22. Gmel AI, Druml T, von Niederhäusern R, Leeb T, Neuditschko M. Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of Horses.. Genes (Basel) 2019 May 14;10(5).
          doi: 10.3390/genes10050370pubmed: 31091839google scholar: lookup
        23. Gurgul A, Jasielczuk I, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoła T, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. A genome-wide scan for diversifying selection signatures in selected horse breeds.. PLoS One 2019;14(1):e0210751.
          doi: 10.1371/journal.pone.0210751pubmed: 30699152google scholar: lookup
        24. Dou T, Shen M, Ma M, Qu L, Li Y, Hu Y, Lu J, Guo J, Wang X, Wang K. Genetic architecture and candidate genes detected for chicken internal organ weight with a 600 K single nucleotide polymorphism array.. Asian-Australas J Anim Sci 2019 Mar;32(3):341-349.
          doi: 10.5713/ajas.18.0274pubmed: 30056651google scholar: lookup
        25. Rochus CM, Tortereau F, Plisson-Petit F, Restoux G, Moreno-Romieux C, Tosser-Klopp G, Servin B. Revealing the selection history of adaptive loci using genome-wide scans for selection: an example from domestic sheep.. BMC Genomics 2018 Jan 23;19(1):71.
          doi: 10.1186/s12864-018-4447-xpubmed: 29357834google scholar: lookup
        26. Shen M, Qu L, Ma M, Dou T, Lu J, Guo J, Hu Y, Wang X, Li Y, Wang K, Yang N. A genome-wide study to identify genes responsible for oviduct development in chickens.. PLoS One 2017;12(12):e0189955.
          doi: 10.1371/journal.pone.0189955pubmed: 29281706google scholar: lookup
        27. Gutiérrez-Gil B, Esteban-Blanco C, Wiener P, Chitneedi PK, Suarez-Vega A, Arranz JJ. High-resolution analysis of selection sweeps identified between fine-wool Merino and coarse-wool Churra sheep breeds.. Genet Sel Evol 2017 Nov 7;49(1):81.
          doi: 10.1186/s12711-017-0354-xpubmed: 29115919google scholar: lookup
        28. Bolormaa S, Swan AA, Brown DJ, Hatcher S, Moghaddar N, van der Werf JH, Goddard ME, Daetwyler HD. Multiple-trait QTL mapping and genomic prediction for wool traits in sheep.. Genet Sel Evol 2017 Aug 15;49(1):62.
          doi: 10.1186/s12711-017-0337-ypubmed: 28810834google scholar: lookup
        29. Marchant TW, Johnson EJ, McTeir L, Johnson CI, Gow A, Liuti T, Kuehn D, Svenson K, Bermingham ML, Drögemüller M, Nussbaumer M, Davey MG, Argyle DJ, Powell RM, Guilherme S, Lang J, Ter Haar G, Leeb T, Schwarz T, Mellanby RJ, Clements DN, Schoenebeck JJ. Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2.. Curr Biol 2017 Jun 5;27(11):1573-1584.e6.
          doi: 10.1016/j.cub.2017.04.057pubmed: 28552356google scholar: lookup
        30. Han YJ, Chen Y, Liu Y, Liu XL. Sequence variants of the LCORL gene and its association with growth and carcass traits in Qinchuan cattle in China.. J Genet 2017 Mar;96(1):9-17.
          doi: 10.1007/s12041-016-0732-0pubmed: 28360384google scholar: lookup
        31. Carneiro M, Hu D, Archer J, Feng C, Afonso S, Chen C, Blanco-Aguiar JA, Garreau H, Boucher S, Ferreira PG, Ferrand N, Rubin CJ, Andersson L. Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus.. Genetics 2017 Feb;205(2):955-965.
          doi: 10.1534/genetics.116.196667pubmed: 27986804google scholar: lookup
        32. Zhang W, Li J, Guo Y, Zhang L, Xu L, Gao X, Zhu B, Gao H, Ni H, Chen Y. Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle.. Sci Rep 2016 Nov 28;6:38073.
          doi: 10.1038/srep38073pubmed: 27892541google scholar: lookup
        33. Randhawa IA, Khatkar MS, Thomson PC, Raadsma HW. A Meta-Assembly of Selection Signatures in Cattle.. PLoS One 2016;11(4):e0153013.
          doi: 10.1371/journal.pone.0153013pubmed: 27045296google scholar: lookup
        34. Boitard S, Boussaha M, Capitan A, Rocha D, Servin B. Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds.. Genetics 2016 May;203(1):433-50.
          doi: 10.1534/genetics.115.181594pubmed: 27017625google scholar: lookup
        35. Bolormaa S, Hayes BJ, van der Werf JH, Pethick D, Goddard ME, Daetwyler HD. Detailed phenotyping identifies genes with pleiotropic effects on body composition.. BMC Genomics 2016 Mar 12;17:224.
          doi: 10.1186/s12864-016-2538-0pubmed: 26968377google scholar: lookup
        36. Matika O, Riggio V, Anselme-Moizan M, Law AS, Pong-Wong R, Archibald AL, Bishop SC. Genome-wide association reveals QTL for growth, bone and in vivo carcass traits as assessed by computed tomography in Scottish Blackface lambs.. Genet Sel Evol 2016 Feb 8;48:11.
          doi: 10.1186/s12711-016-0191-3pubmed: 26856324google scholar: lookup
        37. Kader A, Li Y, Dong K, Irwin DM, Zhao Q, He X, Liu J, Pu Y, Gorkhali NA, Liu X, Jiang L, Li X, Guan W, Zhang Y, Wu DD, Ma Y. Population Variation Reveals Independent Selection toward Small Body Size in Chinese Debao Pony.. Genome Biol Evol 2015 Dec 3;8(1):42-50.
          doi: 10.1093/gbe/evv245pubmed: 26637467google scholar: lookup
        38. Frischknecht M, Jagannathan V, Plattet P, Neuditschko M, Signer-Hasler H, Bachmann I, Pacholewska A, Drögemüller C, Dietschi E, Flury C, Rieder S, Leeb T. A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses.. PLoS One 2015;10(10):e0140749.
          doi: 10.1371/journal.pone.0140749pubmed: 26474182google scholar: lookup
        39. Takasuga A. PLAG1 and NCAPG-LCORL in livestock.. Anim Sci J 2016 Feb;87(2):159-67.
          doi: 10.1111/asj.12417pubmed: 26260584google scholar: lookup
        40. Wang H, Zhang L, Cao J, Wu M, Ma X, Liu Z, Liu R, Zhao F, Wei C, Du L. Genome-Wide Specific Selection in Three Domestic Sheep Breeds.. PLoS One 2015;10(6):e0128688.
          doi: 10.1371/journal.pone.0128688pubmed: 26083354google scholar: lookup
        41. Gutiérrez-Gil B, Arranz JJ, Wiener P. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds.. Front Genet 2015;6:167.
          doi: 10.3389/fgene.2015.00167pubmed: 26029239google scholar: lookup
        42. Sahana G, Höglund JK, Guldbrandtsen B, Lund MS. Loci associated with adult stature also affect calf birth survival in cattle.. BMC Genet 2015 May 3;16:47.
          doi: 10.1186/s12863-015-0202-3pubmed: 25935543google scholar: lookup
        43. Randhawa IA, Khatkar MS, Thomson PC, Raadsma HW. Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus.. G3 (Bethesda) 2015 Apr 30;5(7):1391-401.
          doi: 10.1534/g3.115.017772pubmed: 25931611google scholar: lookup
        44. Widmann P, Reverter A, Weikard R, Suhre K, Hammon HM, Albrecht E, Kuehn C. Systems biology analysis merging phenotype, metabolomic and genomic data identifies Non-SMC Condensin I Complex, Subunit G (NCAPG) and cellular maintenance processes as major contributors to genetic variability in bovine feed efficiency.. PLoS One 2015;10(4):e0124574.
          doi: 10.1371/journal.pone.0124574pubmed: 25875852google scholar: lookup
        45. Boyko AR, Brooks SA, Behan-Braman A, Castelhano M, Corey E, Oliveira KC, Swinburne JE, Todhunter RJ, Zhang Z, Ainsworth DM, Robinson NE. Genomic analysis establishes correlation between growth and laryngeal neuropathy in Thoroughbreds.. BMC Genomics 2014 Apr 3;15:259.
          doi: 10.1186/1471-2164-15-259pubmed: 24707981google scholar: lookup
        46. Bolormaa S, Pryce JE, Reverter A, Zhang Y, Barendse W, Kemper K, Tier B, Savin K, Hayes BJ, Goddard ME. A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle.. PLoS Genet 2014 Mar;10(3):e1004198.
          doi: 10.1371/journal.pgen.1004198pubmed: 24675618google scholar: lookup
        47. Signer-Hasler H, Neuditschko M, Koch C, Froidevaux S, Flury C, Burger D, Leeb T, Rieder S. A chromosomal region on ECA13 is associated with maxillary prognathism in horses.. PLoS One 2014;9(1):e86607.
          doi: 10.1371/journal.pone.0086607pubmed: 24466169google scholar: lookup
        48. Cohen-Zinder M, Karasik D, Onn I. Structural maintenance of chromosome complexes and bone development: the beginning of a wonderful relationship?. Bonekey Rep 2013 Aug 7;2:388.
          doi: 10.1038/bonekey.2013.122pubmed: 24422108google scholar: lookup
        49. Lindholm-Perry AK, Kuehn LA, Oliver WT, Sexten AK, Miles JR, Rempel LA, Cushman RA, Freetly HC. Adipose and muscle tissue gene expression of two genes (NCAPG and LCORL) located in a chromosomal region associated with cattle feed intake and gain.. PLoS One 2013;8(11):e80882.
          doi: 10.1371/journal.pone.0080882pubmed: 24278337google scholar: lookup
        50. Widmann P, Reverter A, Fortes MR, Weikard R, Suhre K, Hammon H, Albrecht E, Kuehn C. A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle.. BMC Genomics 2013 Nov 18;14:798.
          doi: 10.1186/1471-2164-14-798pubmed: 24246134google scholar: lookup
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