Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
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Abstract
Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream of the KIT gene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white-head-associated locus for the first time based on long-read sequencing data and pangenome analyses. We introduce a pangenome-wide association mapping approach that examines assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant (SV) 66 kb upstream of KIT and facial depigmentation. The complex SV contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the SV segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome, which had fewer copies. Our work shows that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex SVs.
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A complex SV situated 66 kb upstream of the KIT gene, a variable number of tandemly duplicated 14.3 kb repeats, has been identified as the causal mutation for the white-head phenotype.
“A striking example is the complex SV situated 66 kb upstream of the KIT gene: a variable number of tandemly duplicated 14.3 kb repeats has been identified as the causal mutation for the white-head phenotype, a trait whose heritability was previously difficult to pinpoint using standard SNP arrays [187].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [187]
The Results (pages unavailable in our copy) locate the complex SV 66 kb upstream of KIT and describe a variable number of 14.3 kb duplication units in white-headed cattle. The Discussion calls it a promising SV associated with the phenotype and treats its functional mechanism as speculative, so the claim that it was identified as the causal mutation overstates the evidence. The paper discusses earlier mapping difficulties but does not establish the sentence’s specific claim about standard SNP arrays. (LLM, conf=0.88)
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Cites
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0686-2 · Cited by 38,430 · see citing works
fastp: an ultra-fast all-in-one FASTQ preprocessor
(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works
Twelve years of SAMtools and BCFtools
Danecek, P., Bonfield, J., Liddle, J., Marshall, J., Ohan, V., Pollard, M., Whitwham, A., Keane, T., McCarthy, S., Davies, R. M., et al. (2021) · GigaScience · doi:10.1093/gigascience/giab008 · Cited by 15,314 · see citing works
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works
Second-generation PLINK: rising to the challenge of larger and richer datasets
Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015) · Gigascience · doi:10.1186/s13742-015-0047-8 · Cited by 12,709 · see citing works
Principal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248 · see citing works
GCTA: a tool for genome-wide complex trait analysis
Yang, J., Lee, S. H., Goddard, M. E., & Visscher, P. M. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.11.011 · Cited by 8,279 · see citing works
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2021) · Nature Methods · doi:10.1038/s41592-020-01056-5 · Cited by 5,859 · see citing works
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643 · see citing works
Mash: fast genome and metagenome distance estimation using MinHash
(2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373 · see citing works
Bandage: interactive visualization of de novo genome assemblies
Wick, R. R., Schultz, M. B., Zobel, J., & Holt, K. E. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv383 · Cited by 3,067 · see citing works
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378 · see citing works
A universal SNP and small-indel variant caller using deep neural networks
Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4235 · Cited by 1,840 · see citing works
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
Alonge, M., Lebeigle, L., Kirsche, M., Jenike, K., Ou, S., Aganezov, S. S., Wang, X., Lippman, Z. B., Schatz, M. C., & Soyk, S. (2022) · Genome biology · doi:10.1186/s13059-022-02823-7 · Cited by 980 · see citing works
Evidence for Two Independent Domestications of Cattle
Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2757 · Cited by 812 · see citing works
<i>De novo</i> assembly of the cattle reference genome with single-molecule sequencing
Rosen, B. D., Bickhart, D. M., Schnabel, R. D., Koren, S., Elsik, C. G., Tseng, E., Rowan, T. N., Low, W. Y., Zimin, A., Couldrey, C., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa021 · Cited by 802 · see citing works
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary
Brynildsrud, O. B., Bohlin, J., Scheffer, L., & Eldholm, V. (2016) · Genome biology · doi:10.1186/s13059-016-1108-8 · Cited by 702 · see citing works
Strong signatures of selection in the domestic pig genome
Rubin, C.-J., Megens, H.-J., Barrio, A. M., Maqbool, K., Sayyab, S., Schwochow, D., Wang, C., Carlborg, Ö., Jern, P., Jørgensen, C. B., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217149109 · Cited by 652 · see citing works
Progressive Cactus is a multiple-genome aligner for the thousand-genome era
Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature · doi:10.1038/s41586-020-2871-y · Cited by 586 · cited 1× · see citing works
“There are several approaches to constructing pange-nomes, using reference-backed (Li et al. 2020), phylogeny-guided (Armstrong et al. 2020), or all-to-all (Garrison et al. 2023) alignments.”
Detection of mosaic and population-level structural variants with Sniffles2
Smolka, M., Paulin, L. F., Grochowski, C. M., Horner, D. W., Mahmoud, M., Behera, S., Kalef-Ezra, E., Gandhi, M., Hong, K., Pehli̇van, D., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-02024-y · Cited by 526 · see citing works
Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle
Decker, J. E., McKay, S. D., Rolf, M. M., Kim, J., Molina Alcalá, A., Sonstegard, T. S., Hanotte, O., Götherström, A., Seabury, C. M., Praharani, L., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004254 · Cited by 521 · see citing works
De novo assembly of haplotype-resolved genomes with trio binning
Koren, S., Rhie, A., Walenz, B. P., Dilthey, A., Bickhart, D. M., Kingan, S. B., Hiendleder, S., Williams, J. L., Smith, T. P. L., & Phillippy, A. M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4277 · Cited by 494 · see citing works
Hayes, B. J., & Daetwyler, H. D. (2018) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-020518-115024 · Cited by 467 · see citing works
The design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455 · see citing works
Hayes, B. J., Pryce, J. E., Chamberlain, A. J., Bowman, P. J., & Goddard, M. E. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001139 · Cited by 406 · see citing works
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., et al. (2021) · Science · doi:10.1126/science.abg8871 · Cited by 400 · see citing works
compleasm: a faster and more accurate reimplementation of BUSCO
Huang, N., & Li, H. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad595 · Cited by 342 · see citing works
S weep F inder 2: increased sensitivity, robustness and flexibility
DeGiorgio, M., Huber, C. D., Hubisz, M. J., Hellmann, I., & Nielsen, R. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw051 · Cited by 322 · see citing works
Mash Screen: high-throughput sequence containment estimation for genome discovery
Ondov, B., Starrett, G. J., Sappington, A., Kostic, A. M., Koren, S., Buck, C. B., & Phillippy, A. M. (2019) · Genome biology · doi:10.1186/s13059-019-1841-x · Cited by 306 · see citing works
Cieslak, M., Reißmann, M., Hofreiter, M., & Ludwig, A. (2011) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2011.00177.x · Cited by 283 · see citing works
Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, L., Hagmann, J., Vorbrugg, S., Marco-Sola, S., Kubica, C., et al. (2024) · Nature Methods · doi:10.1038/s41592-024-02430-3 · Cited by 277 · see citing works
Population structure in genetic studies: Confounding factors and mixed models
Sul, J. H., Martin, L. S., & Eskin, E. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007309 · Cited by 264 · see citing works
GraphAligner: rapid and versatile sequence-to-graph alignment
Rautiainen, M., & Marschall, T. (2020) · Genome Biology · doi:10.1186/s13059-020-02157-2 · Cited by 242 · see citing works
Classic Selective Sweeps Revealed by Massive Sequencing in Cattle
Qanbari, S., Pausch, H., Jansen, S., Somel, M., Strom, T. M., Fries, R., Nielsen, R., & Simianer, H. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004148 · Cited by 233 · see citing works
Self-citationResolving the evolution of extant and extinct ruminants with high-throughput phylogenomics
Decker, J. E., Pires, J. C., Conant, G. C., McKay, S., Heaton, M. P., Chen, K., Cooper, A., Vilkki, J., Seabury, C. M., Caetano, A. R., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904691106 · Cited by 224 · see citing works
ODGI: understanding pangenome graphs
Guarracino, A., Heumos, S., Nahnsen, S., Prins, P., & Garrison, E. P. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac308 · Cited by 193 · see citing works
Serial translocation by means of circular intermediates underlies colour sidedness in cattle
Durkin, K., Coppieters, W. R., Drögemüller, C., Ahariz, N., Cambisano, N., Druet, T., Fasquelle, C., Haile, A., Hořín, P., Huang, L., et al. (2012) · Nature · doi:10.1038/nature10757 · Cited by 179 · see citing works
Fast gap-affine pairwise alignment using the wavefront algorithm
Marco‐Sola, S., Moure, J. C., Moretó, M., & Espinosa, A. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa777 · Cited by 165 · see citing works
Giuffra, E., Törnsten, A., Marklund, S. L., Bongcam‐Rudloff, E., Chardon, P., Kijas, J. M. H., Anderson, S. I., Archibald, A. L., & Andersson, L. (2002) · Mammalian Genome · doi:10.1007/s00335-002-2184-5 · Cited by 157 · see citing works
Red coat color in Holstein cattle is associated with a deletion in the MSHR gene
Joerg, H., Fries, H. R., Meijerink, E., & Stranzinger, G. (1996) · Mammalian Genome · doi:10.1007/s003359900090 · Cited by 143 · see citing works
The challenges and importance of structural variation detection in livestock
Bickhart, D. M., & Liu, G. E. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00037 · Cited by 143 · see citing works
Allelic Heterogeneity at the Equine KIT Locus in Dominant White (W) Horses
Haase, B., Brooks, S. A., Schlumbaum, A., Azor, P. J., Bailey, E., Alaeddine, F., Mevissen, M., Burger, D., Poncet, P.-A., Rieder, S., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030195 · Cited by 143 · see citing works
Pausch, H., MacLeod, I. M., Fries, R., Emmerling, R., Bowman, P. J., Daetwyler, H. D., & Goddard, M. E. (2017) · Genetics Selection Evolution · doi:10.1186/s12711-017-0301-x · Cited by 124 · see citing works
Seven novel KIT mutations in horses with white coat colour phenotypes
Haase, B., Brooks, S. A., Tozaki, T., Burger, D., Poncet, P. A., Rieder, S., Hasegawa, T., Penedo, C., & Leeb, T. (2009) · Animal Genetics · doi:10.1111/j.1365-2052.2009.01893.x · Cited by 111 · see citing works
A super-pangenome of the North American wild grape species
Cochetel, N., Minio, A., Guarracino, A., García, J. F., Figueroa-Balderas, R. E., Massonnet, M., Kasuga, T., Londo, J. P., Garrison, E. P., Gaut, B. S., et al. (2023) · Genome biology · doi:10.1186/s13059-023-03133-2 · Cited by 105 · see citing works
A chromosome inversion near the KIT gene and the Tobiano spotting pattern in horses
Brooks, S. A., Lear, T. L., Adelson, D. L., & Bailey, E. (2007) · Cytogenetic and Genome Research · doi:10.1159/000112065 · Cited by 101 · see citing works
Henkel, J., Saif, R., Jagannathan, V., Schmocker, C., Zeindler, F., Bangerter, E., Herren, U., Posantzis, D., Bulut, Z., Ammann, P., et al. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008536 · Cited by 92 · see citing works
Garrison, E. P., & Guarracino, A. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac743 · Cited by 92 · see citing works
Strobealign: flexible seed size enables ultra-fast and accurate read alignment
Sahlin, K. (2022) · Genome biology · doi:10.1186/s13059-022-02831-7 · Cited by 90 · see citing works
Rice, E. S., Koren, S., Rhie, A., Heaton, M. P., Kalbfleisch, T., Hardy, T., Hackett, P. H., Bickhart, D. M., Rosen, B. D., Ley, B. L. V., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa029 · Cited by 82 · see citing works
Endogenous Retrovirus Insertion in theKITOncogene DeterminesWhiteandWhite spottingin Domestic Cats
David, V. A., Menotti-Raymond, M. A., Wallace, A. C., Roelke, M. E., Kehler, J., Leighty, R. M., Eduardo Eizirik, C., Hannah, S. S., Nelson, G. W., Schäffer, A. A., et al. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.013425 · Cited by 78 · see citing works
Leonard, A. S., Crysnanto, D., Fang, Z., Heaton, M. P., Ley, B. L. V., Herrera, C., Bollwein, H., Bickhart, D. M., Kuhn, K. L., Smith, T. P. L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30680-2 · Cited by 76 · see citing works
Fontanesi, L., Tazzoli, M., Russo, V. C., & Beever, J. E. (2009) · Animal Genetics · doi:10.1111/j.1365-2052.2009.02007.x · Cited by 71 · see citing works
Berrozpe, G., Timokhina, I., Yukl, S. A., Tajima, Y., Ono, M., Zelenetz, A. D., & Besmer, P. (1999) · Blood · doi:10.1182/blood.v94.8.2658.420k23_2658_2666 · Cited by 62 · see citing works
Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
Trigo, B. B., Utsunomiya, A. T. H., Fortunato, A. A. A. D., Milanesi, M., Torrecilha, R. B. P., Lamb, H. J., Nguyen, L. T., Ross, E. M., Hayes, B. J., Padula, R. C. M., et al. (2021) · Genetics Selection Evolution · doi:10.1186/s12711-021-00633-2 · Cited by 61 · see citing works
Pausch, H., Wang, X., Jung, S., Krogmeier, D., Edel, C., Emmerling, R., Götz, K., & Fries, R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036346 · Cited by 58 · see citing works
Nagle, D. L., Kozak, C. A., Mano, H., Chapman, V. M., & Bućan, M. (1995) · Human Molecular Genetics · doi:10.1093/hmg/4.11.2073 · Cited by 57 · see citing works
Zinovieva, N. A., Dotsev, A. V., Sermyagin, А. А., Deniskova, T. E., Abdelmanova, A. S., Kharzinova, V. R., Sölkner, J., Reyer, H., Wimmers, K., & Brem, G. (2020) · PLoS ONE · doi:10.1371/journal.pone.0242200 · Cited by 57 · see citing works
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Leonard, A. S., Crysnanto, D., Mapel, X. M., Bhati, M., & Pausch, H. (2023) · Genome biology · doi:10.1186/s13059-023-02969-y · Cited by 57 · see citing works
Smith, T. P. L., Bickhart, D. M., Boichard, D., Chamberlain, A. J., Djikeng, A., Jiang, Y., Low, W. Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02975-0 · Cited by 57 · see citing works
Dog colour patterns explained by modular promoters of ancient canid origin
Bannasch, D. L., Kaelin, C. B., Letko, A., Loechel, R., Hug, P., Jagannathan, V., Henkel, J., Roosje, P. J., Hytönen, M. K., Lohi, H., et al. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01524-x · Cited by 53 · see citing works
Chin, C.-S., Behera, S., Khalak, A., Sedlazeck, F. J., Sudmant, P. H., Wagner, J., & Zook, J. M. (2023) · Nature Methods · doi:10.1038/s41592-023-01914-y · Cited by 53 · see citing works
A Reference Genome Assembly of Simmental Cattle, <i>Bos taurus taurus</i>
Heaton, M. P., Smith, T. P. L., Bickhart, D. M., Vander Ley, B. L., Kuehn, L. A., Oppenheimer, J., Shafer, W. R., Schuetze, F. T., Stroud, B., McClure, J. C., et al. (2021) · Journal of Heredity · doi:10.1093/jhered/esab002 · Cited by 52 · see citing works
Berrozpe, G., Agosti, V., Tucker, C., Blanpain, C., Manova, K., & Besmer, P. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01854-05 · Cited by 42 · see citing works
Brief communication. The 'spotted' locus maps to bovine chromosome 6 in Hereford-cross population
Grosz, M. D. (1999) · Journal of Heredity · doi:10.1093/jhered/90.1.233 · Cited by 41 · see citing works
Dürig, N., Jude, R., Holl, H. M., Brooks, S. A., Lafayette, C., Jagannathan, V., & Leeb, T. (2017) · Animal Genetics · doi:10.1111/age.12556 · Cited by 41 · see citing works
Venhoranta, H., Pausch, H., Wysocki, M., Szczerbal, I., Hänninen, R. L., Taponen, J., Uimari, P., Flisikowski, K., Lohi, H., Fries, R., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0075659 · Cited by 37 · see citing works
Stokstad, E. (2015) · Science · doi:10.1126/science.350.6265.1144 · Cited by 36 · see citing works
Pangenome-genotyped structural variation improves molecular phenotype mapping in cattlePreprint
Leonard, A. S., Mapel, X. M., & Pausch, H. (2024) · Genome Research · doi:10.1101/gr.278267.123 · Cited by 36 · see citing works
Ibsen, H. L. (1933) · Genetics · doi:10.1093/genetics/18.5.441 · Cited by 30 · see citing works
Genome scan for the degree of white spotting in dairy cattle
Liu, L., Harris, B. L., Keehan, M., & Zhang, Y. (2009) · Animal Genetics · doi:10.1111/j.1365-2052.2009.01936.x · Cited by 28 · see citing works
Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle
Mapel, X. M., Kadri, N. K., Leonard, A. S., He, Q., Lloret‐Villas, A., Bhati, M., Hiltpold, M., & Pausch, H. (2024) · Nature Communications · doi:10.1038/s41467-024-44935-7 · Cited by 28 · see citing works
Genetic Study of Eye Cancer in Cattle
Anderson, D. E. (1991) · Journal of Heredity · doi:10.1093/jhered/82.1.21 · Cited by 26 · see citing works
A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern
Küttel, L., Letko, A., Häfliger, I. M., Signer‐Hasler, H., Joller, S., Hirsbrunner, G., Mészáros, G., Sölkner, J., Flury, C., Leeb, T., et al. (2019) · Animal Genetics · doi:10.1111/age.12821 · Cited by 23 · see citing works
Optical mapping compendium of structural variants across global cattle breeds
Talenti, A., Powell, J., Wragg, D., Chepkwony, M. C., Fisch, A., Ferreira, B. R., Mercadante, M. E. Z., Santos, I. K. F. D. M., Ezeasor, C., Obishakin, E., et al. (2022) · Scientific Data · doi:10.1038/s41597-022-01684-w · Cited by 19 · see citing works
The genetic basis for piebald patterns in cattle
Olson, T. A. (1981) · Journal of Heredity · doi:10.1093/oxfordjournals.jhered.a109437 · Cited by 18 · see citing works
Invited review: Genetics and genomics of pigmentation variability in pigs: a review
Fontanesi, L. (2022) · Livestock Science · doi:10.1016/j.livsci.2022.105079 · Cited by 17 · see citing works
Revealing the genetic basis of eyelid pigmentation in Hereford cattle
Jara, E., Peñagaricano, F., Armstrong, E. M., Ciappesoni, G., Iriarte, A., & Navajas, E. A. (2022) · Journal of Animal Science · doi:10.1093/jas/skac110 · Cited by 15 · see citing works
Regulation of a Mammalian Gene Bearing a CpG Island Promoter and a Distal Enhancer
Berrozpe, G., Bryant, G. O., Warpinski, K., & Ptashne, M. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.07.001 · Cited by 14 · see citing works
Jang, J., Jung, J., Lee, Y. H., Lee, S., Baik, M., & Kim, H. (2023) · Scientific Data · doi:10.1038/s41597-023-02453-z · Cited by 13 · see citing works
Dorji, J., Reverter, A., Alexandre, P. A., Chamberlain, A. J., Vander-Jagt, C. J., Kijas, J., & Neto, L. R. P. (2024) · Genetics Selection Evolution · doi:10.1186/s12711-024-00879-6 · Cited by 11 · see citing works
Whitacre, L. K. (2014) · doi:10.32469/10355/44434 · Cited by 10 · see citing works
González-Prendes, R., Ginja, C., Kantanen, J., Ghanem, N., Kugonza, D. R., Makgahlela, M. L., Groenen, M. A. M., & Crooijmans, R. P. M. A. (2022) · PLoS ONE · doi:10.1371/journal.pone.0276309 · Cited by 10 · see citing works
Artesi, M., Tamma, N., Deckers, M., Karim, L., Coppieters, W. R., den Broeke, A. V., Georges, M., Charlier, C., & Durkin, K. (2020) · Animal Genetics · doi:10.1111/age.12932 · Cited by 8 · see citing works
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Leonard, A. S., Mapel, X. M., & Pausch, H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.21.545879 · Cited by 7 · see citing works
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Cluster-efficient pangenome graph construction with nf-core/pangenome
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Dynamics of genome evolution in the era of pangenome analysis
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Yang, Q., Sun, J., Wang, X., Wang, J., Liu, Q., Ru, J., Zhang, X., Wang, S., Hao, R., Bian, P., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57756-z · Cited by 9 · see citing works
Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene
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Molecular QTL are enriched for structural variants in a cattle long-read cohort
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Gretl—variation GRaph Evaluation TooLkit
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Furukawa, R., Tozaki, T., Mizukami, K., Iwasaki, Y., Kawate, K., Kikuchi, M., Ishige, T., Momozawa, Y., Fukui, E., & Kakoi, H. (2025) · Journal of Equine Veterinary Science · doi:10.1016/j.jevs.2025.105682 · Cited by 2 · see citing works
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Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
Sorin, V., Besnard, F., Capitan, A., Grohs, C., Naji, M. M., Escouflaire, C., Fritz, S., Lledo, J., Eché, C., Iampietro, C., et al. (2026) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-026-01373-3 · Cited by 3 · see citing works
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Sorin, V., Sanchez, M. P., Drouilhet, L., Tosser‐Klopp, G., Naji, M. M., Boichard, D., Pausch, H., Boussaha, M., & Leonard, A. S. (2026) · Genetics Selection Evolution · doi:10.1186/s12711-026-01037-w
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Bocs, S., Carrette, C., Confais, J., Dubois, S., Duvaux, L., Klopp, C., Lapalu, N., Lasserre‐Zuber, P., Legeai, F., Lemaitre, C., et al. (2026) · Peer Community Journal · doi:10.24072/pcjournal.781
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A Nelore Cattle Structural Variant Catalog
Silva, T. D. L., Leonard, A. S., Fonseca, P. A. D. S., Neves, H. H. D. R., Merlos-Ruiz, A., Andrietta, L. T., Júnior, G. A. F., Balieiro, J. C. D. C., Pausch, H., Carvalheiro, R., et al. (2026) · Animal Genetics · doi:10.1002/age.70225
- Authors
- Milia, S., Leonard, A. S., Mapel, X. M., Bernal Ulloa, S. M., Drögemüller, C., & Pausch, H.
- Affiliations
- ETH Zurich (CH)
- Animal Physiology, ETH Zurich, Zurich 8092, Switzerland;
- University of Bern (CH)
- Corresponding author
- Pausch, Hubert
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2024-12-18
- Volume
- 35
- Issue
- 4
- Pages
- 1041-1052
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC12047182
- OpenAlex
- W4405536335
- Cited by
- 22
- References
- 87
- Citations by year
- 2026: 9 · 2025: 8 · 2024: 5
- Type
- posted content
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Genome Research (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- Funders
- Swiss National Science Foundation (SNSF (204654)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- KIT gene, segmental duplication, structural variants, repetitive elements, lines, coat color inheritance
- MeSH terms
- Animals, Cattle, Hair Color, Haplotypes, Genome, Proto-Oncogene Proteins c-kit, Genome-Wide Association Study, Segmental Duplications, Genomic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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