1. bookVolume 22 (2022): Issue 4 (October 2022)
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eISSN
2300-8733
First Published
25 Nov 2011
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4 times per year
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English
Open Access

Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection

Published Online: 29 Oct 2022
Volume & Issue: Volume 22 (2022) - Issue 4 (October 2022)
Page range: 1185 - 1192
Received: 03 Mar 2022
Accepted: 29 Aug 2022
Journal Details
License
Format
Journal
eISSN
2300-8733
First Published
25 Nov 2011
Publication timeframe
4 times per year
Languages
English

Abbott R., Albach D., Ansell S., Arntzen J.W., Baird S.J.E., Bierne N., Boughman J., Brelsford A., Buerkle C.A., Buggs R., Butlin R.K., Dieckmann U., Eroukhmanoff F., Grill A., Cahan S.H., Hermansen J.S., Hewitt G., Hudson A.G., Jiggins C., Jones J., Keller B., Marczewski T., Mallet J., Martinez-Rodriguez P., Möst M., Mullen S., Nichols R., Nolte A.W., Parisod C., Pfennig K., Rice A.M., Ritchie M.G., Seifert B., Smadja C.M., Stelkens R., Szymura J.M., Väinölä R., Wolf J.B.W., Zinner D. (2013). Hybridization and speciation. J. Evol. Biol., 26: 229–246. Search in Google Scholar

Adavoudi R., Pilot M. (2022). Consequences of hybridization in mammals: A systematic review. Genes, 13: 50. Search in Google Scholar

Allen R., Ryan H., Davis B.W., King C., Frantz L., Irving-Pease E., Barnett R., Linderholm A., Loog L., Haile J., Lebrasseur O., White M., Kitchener A.C., Murphy W.J., Larson G. (2020). A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc. R. Soc. B Biol. Sci., 287: 20200690. Search in Google Scholar

Barreta J., Gutiérrez-Gil B., Iñiguez V., Saavedra V., Chiri R., Latorre E., Arranz J.J. (2013). Analysis of mitochondrial DNA in Bolivian llama, alpaca and vicuna populations: A contribution to the phylogeny of the South American camelids. Anim. Genet., 44: 158–168. Search in Google Scholar

Behjati S., Tarpey P.S. (2013). What is next generation sequencing? Arch. Dis. Child. Educ. Pract. Ed., 98: 236–238. Search in Google Scholar

Beissinger T.M., Hirsch C.N., Sekhon R.S., Foerster J.M., Johnson J.M., Muttoni G., Vaillancourt B., Robin Buell C., Kaeppler S.M., de Leon N. (2013). Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics, 193: 1073–1081. Search in Google Scholar

Berbel-Filho W.M., Tatarenkov A., Pacheco G., Espírito-Santo H.M.V., Lira M.G., de Leaniz C.G., Avise J.C., Lima S.M.Q., Rodríguez-López C.M., Consuegra S. (2021). Against the odds: Hybrid zones between mangrove killifish species with different mating systems. Genes, 12: 1486. Search in Google Scholar

Calderon M., More M.J., Gutierrez G.A., Abel Ponce de León F. (2021). Development of a 76K alpaca (Vicugna pacos) single nucleotide polymorphisms (SNPs) microarray. Genes, 12: 1–18. Search in Google Scholar

Cordeiro E.M.G., Pantoja-Gomez L.M., De Paiva J.B., Nascimento A.R.B., Omoto C., Michel A.P., Correa A.S. (2020). Hybridization and introgression between Helicoverpa armigera and H. zea: An adaptational bridge. BMC Evol. Biol., 20: 1–12. Search in Google Scholar

Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet., 12: 499–510. Search in Google Scholar

De Donato M., Peters S.O., Mitchell S.E., Hussain T., Imumorin I.G. (2013). Genotyping-by-Sequencing (GBS): A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing. PLoS ONE, 8: 62137. Search in Google Scholar

Deschamps S., Llaca V., May G.D. (2012). Genotyping-by-sequencing in plants. Biology, 1: 460–483. Search in Google Scholar

Díaz-Maroto P., Rey-Iglesia A., Cartajena I., Núñez L., Westbury M.V., Varas V., Moraga M., Campos P.F., Orozco-terWenge P., Marín J.C., Hansen A.J. (2021). Ancient DNA reveals the lost domestication history of south american camelids in Northern Chile and across the andes. eLife, 10: e63390. Search in Google Scholar

Di Rocco F., Posik D.M., Ripoli M.V., Díaz S., Maté M.L., Giovambattista G., Vidal-Rioja L. (2011). South American camelid illegal traffic detection by means of molecular markers. Leg. Med., 13: 289–292. Search in Google Scholar

Dupuis J.R., Brunet B.M.T., Bird H.M., Lumley L.M., Fagua G., Boyle B., Levesque R., Cusson M., Powell J.A., Sperling F.A.H. (2017). Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol. Phylogenet. Evol., 111: 158–168. Search in Google Scholar

Dupuis J.R., Sperling F.A.H. (2020). Phylogenomic test of mitochondrial clues to archaic ancestors in a group of hybridizing swallowtail butterflies. Mol. Phylogenet. Evol., 152: 106921. Search in Google Scholar

Echalar J., Barreta J. (2022). Introgression in domestic camelid productive systems in Bolivia. Small Rumin. Res., 214: 106742. Search in Google Scholar

Echalar J., Barreta J., Iniguez V., Romero F., Callisaya A.M., Saavedra V. (2020). Intraspecific genetic analysis of Bolivian alpacas and interspecific relationship with llamas and vicunas. Small Rumin. Res., 189: 106137. Search in Google Scholar

Ellegren H. (2014). Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol., 29: 51–63. Search in Google Scholar

Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S., Mitchell S.E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6: e19379. Search in Google Scholar

Fan R., Gu Z., Guang X., Marín J.C., Varas V., González B.A., Wheeler J.C., Hu Y., Li E., Sun X., Yang X., Zhang C., Gao W., He J., Munch K., Corbett-Detig R., Barbato M., Pan S., Zhan X., Bruford M.W., Dong C. (2020). Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. Genome Biol., 21: 1–26. Search in Google Scholar

Forsdick N.J., Martini D., Brown L., Cross H.B., Maloney R.F., Steeves T.E., Knapp M. (2021). Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob. Ecol. Conserv., 28: e01681. Search in Google Scholar

Gabryś J., Kij B., Kochan J., Bugno-Poniewierska M. (2021). Interspecific hybrids of animals in nature, breeding and science – a review. Ann. Anim. Sci., 21: 403–415. Search in Google Scholar

Germain E., Benhamou S., Poulle M.L. (2008). Spatio-temporal sharing between the European wildcat, the domestic cat and their hybrids. J. Zool., 276: 195–203. Search in Google Scholar

Graham C.F., Eberts R.L., Goncin U., Somers C.M. (2021). Spontaneous hybridization and introgression between walleye (Sander vitreus) and sauger (Sander canadensis) in two large reservoirs: Insights from genotyping by sequencing. Evol. Appl., 14: 965–982. Search in Google Scholar

Gurgul A., Miksza-Cybulska A., Szmatoła T., Jasielczuk I., Piestrzyńska-Kajtoch A., Fornal A., Semik-Gurgul E., Bugno-Poniewierska M. (2019 a). Genotyping-by-sequencing performance in selected livestock species. Genomics, 111: 186–195.10.1016/j.ygeno.2018.02.002 Search in Google Scholar

Gurgul A., Miksza-Cybulska A., Szmatoła T., Semik-Gurgul E., Jasielczuk I., Bugno-Poniewierska M., Figarski T., Kajtoch Ł. (2019 b). Evaluation of genotyping by sequencing for population genetics of sibling and hybridizing birds: an example using Syrian and Great Spotted Woodpeckers. J. Ornithol., 160: 287–294.10.1007/s10336-018-1601-9 Search in Google Scholar

Kadwell M., Fernandez M., Stanley H.F., Baldi R., Wheeler J.C., Rosadio R., Bruford M.W. (2001). Genetic analysis reveals the wild ancestors of the llama and the alpaca. Proc. R. Soc. B Biol. Sci., 268: 2575–2584. Search in Google Scholar

Kim C., Guo H., Kong W., Chandnani R., Shuang L.S., Paterson A.H. (2016). Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Sci., 242: 14–22. Search in Google Scholar

Marín J.C., Romero K., Rivera R., Johnson W.E., González B.A. (2017). Y-chromosome and mtDNA variation confirms independent domestications and directional hybridization in South American camelids. Anim. Genet., 48: 591–595. Search in Google Scholar

Marques D.A., Meier J.I., Seehausen O. (2019). A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol., 34: 531–544. Search in Google Scholar

Maté M.L., Di Rocco F., Zambelli A., Vidal-Rioja L. (2007). Mitochondrial heteroplasmy in Control Region DNA of South American camelids. Small Rumin. Res., 71: 123–129. Search in Google Scholar

Maté M.L., Di Rocco F., Zambelli A., Vidal-Rioja L. (2004). Mitochondrial DNA structure and organization of the control region of South American camelids. Mol. Ecol. Notes, 4: 765–767. Search in Google Scholar

McFarlane S.E., Pemberton J.M. (2019). Detecting the true extent of introgression during anthropogenic hybridization. Trends Ecol. Evol., 34: 315–326. Search in Google Scholar

Melo C., Manunza A., Melo M., Olivera L., Amills M. (2012). Analysis of the mitochondrial diversity of alpacas in eight farming areas of the south of Peru, in: Fibre Production in South American Camelids and Other Fibre Animals. Wageningen Academic Publishers, pp. 87–91. Search in Google Scholar

More M., Gutiérrez G., Rothschild M., Bertolini F., Abel Ponce De León F. (2019). Evaluation of SNP genotyping in alpacas using the bovine HD genotyping beadchip. Front. Genet., 10: 361. Search in Google Scholar

Myers E.A. (2021). Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol. Phylogenet. Evol., 165: 107313. Search in Google Scholar

Narum S.R., Buerkle C.A., Davey J.W., Miller M.R., Hohenlohe P.A. (2013). Genotyping-by-sequencing in ecological and conservation genomics. Mol. Ecol., 22: 2841–2847. Search in Google Scholar

Pacheco-Sierra G., Vázquez-Domínguez E., Pérez-Alquicira J., Suárez-Atilano M., Domínguez-Laso J. (2018). Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums. Front. Ecol. Evol., 6: 138. Search in Google Scholar

Pazmiño D.A., van Herderden L., Simpfendorfer C.A., Junge C., Donnellan S.C., Hoyos-Padilla E.M., Duffy C.A.J., Huveneers C., Gillanders B.M., Butcher P.A., Maes G.E. (2019). Introgressive hybridisation between two widespread sharks in the east Pacific region. Mol. Phylogenet. Evol., 136: 119–127. Search in Google Scholar

Pfennig K.S. (2021). Biased hybridization and its impact on adaptive introgression. Trends Ecol. Evol., 36: 488–497. Search in Google Scholar

Podbielska A., Piórkowska K. (2022). Examination of D-loop region and DBY gene as tools for identifying hybridisation in alpacas (Vicugna pacos) based on Polish populations. Small Rumin. Res., 211: 106690. Search in Google Scholar

Podbielska A., Piórkowska K., Szmatoła T. (2021). Microsatellite-based genetic structure and hybrid detection in alpacas bred in poland. Animals, 11: 2193. Search in Google Scholar

Poland J., Endelman J., Dawson J., Rutkoski J., Wu S., Manes Y., Dreisigacker S., Crossa J., Sánchez-Villeda H., Sorrells M., Jannink J.-L. (2012). Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome, 5.10.3835/plantgenome2012.06.0006 Search in Google Scholar

Poland J.A., Rife T.W. (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant Genome, 5.10.3835/plantgenome2012.05.0005 Search in Google Scholar

Ramírez-Reyes T., Blair C., Flores-Villela O., Piñero D., Lathrop A., Murphy R. (2020). Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico. Mol. Phylogenet.Evol., 150: 106880. Search in Google Scholar

Richardson M.F., Munyard K., Croft L.J., Allnutt T.R., Jackling F., Alshanbari F., Jevit M., Wright G.A., Cransberg R., Tibary A., Perelman P., Appleton B., Raudsepp T. (2019). Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids. Front. Genet., 10: 586. Search in Google Scholar

Seneviratne S.S., Davidson P., Martin K., Irwin D.E. (2016). Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers). J. Avian Biol., 47: 887–898. Search in Google Scholar

Sonah H., Bastien M., Iquira E., Tardivel A., Légaré G., Boyle B., Normandeau É., Laroche J., Larose S., Jean M., Belzile F. (2013). An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE, 8: e54603. Search in Google Scholar

Stanley H.F., Kadwell M., Wheeler J.C. (1994). Molecular evolution of the family Camelidae: A mitochondrial DNA study. Proc. R. Soc. B Biol. Sci., 256: 1–6. Search in Google Scholar

Thermes C. (2014). Ten years of next-generation sequencing technology. Trends Genet., 30: 418–426. Search in Google Scholar

Torkamaneh D., Laroche J., Belzile F. (2016). Genome-wide SNP calling from genotyping by sequencing (GBS) data: A comparison of seven pipelines and two sequencing technologies. PLoS ONE, 11: 0161333. Search in Google Scholar

Varas V., Vásquez J.P., Rivera R., Longo A., Valdecantos P.A., Wheeler J.C., Johnson W.E., Marín J.C. (2020). Interbreeding among South American camelids threatens species integrity. J. Arid Environ., 181: 104249. Search in Google Scholar

Wheeler J.C. (1995 a). Evolution and present situation of the South American camelidae. Biol. J. Linn. Soc., 54: 271–295.10.1016/0024-4066(95)90021-7 Search in Google Scholar

Wheeler J.C., Russel A.J.F., Redden H. (1995 b). Llamas and Alpacas: Pre-conquest breeds and post-conquest hybrids. J. Archaeol. Sci., 22: 833–840.10.1016/0305-4403(95)90012-8 Search in Google Scholar

Wheeler J.C. (2012). South American camelids – past, present and future. J. Camelid Sci., 5: 1–24. Search in Google Scholar

Yadav A.D., Sahu J.D., Dubey A.D., Gadpayle R.D., Kiran Barwa D., Kashyap K., Yadav A., Jain A., Sahu J., Dubey A., Gadpayle R., Kiran Barwa D., Verma U. (2019). An overview on species hybridization in animals. Int. J. Fauna Biol. Stud., 6: 36–42. Search in Google Scholar

Yue G.H., Wang L. (2017). Current status of genome sequencing and its applications in aquaculture. Aquaculture, 468: 337–347. Search in Google Scholar

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