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

Open Access
|Oct 2022

References

  1. 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: 229–246.10.1111/j.1420-9101.2012.02599.x
  2. Adavoudi R., Pilot M. (2022). Consequences of hybridization in mammals: A systematic review. Genes, 13: 50.10.3390/genes13010050
  3. 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: 20200690.10.1098/rspb.2020.0690
  4. 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: 158–168.10.1111/j.1365-2052.2012.02376.x
  5. Behjati S., Tarpey P.S. (2013). What is next generation sequencing? Arch. Dis. Child. Educ. Pract. Ed., 98: 236–238.10.1136/archdischild-2013-304340
  6. 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: 1073–1081.10.1534/genetics.112.147710
  7. 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: 1486.10.3390/genes12101486
  8. 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: 1–18.10.3390/genes12020291
  9. 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: 1–12.10.1186/s12862-020-01621-8
  10. 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: 499–510.10.1038/nrg3012
  11. 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: 62137.10.1371/journal.pone.0062137
  12. Deschamps S., Llaca V., May G.D. (2012). Genotyping-by-sequencing in plants. Biology, 1: 460–483.10.3390/biology1030460
  13. 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: e63390.10.7554/eLife.63390
  14. 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: 289–292.10.1016/j.legalmed.2011.08.001
  15. 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: 158–168.10.1016/j.ympev.2017.04.001
  16. 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: 106921.10.1016/j.ympev.2020.106921
  17. Echalar J., Barreta J. (2022). Introgression in domestic camelid productive systems in Bolivia. Small Rumin. Res., 214: 106742.10.1016/j.smallrumres.2022.106742
  18. 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: 106137.10.1016/j.smallrumres.2020.106137
  19. Ellegren H. (2014). Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol., 29: 51–63.10.1016/j.tree.2013.09.008
  20. 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: e19379.10.1371/journal.pone.0019379
  21. 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: 1–26.10.1186/s13059-020-02080-6
  22. 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: e01681.10.1016/j.gecco.2021.e01681
  23. 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: 403–415.10.2478/aoas-2020-0082
  24. Germain E., Benhamou S., Poulle M.L. (2008). Spatio-temporal sharing between the European wildcat, the domestic cat and their hybrids. J. Zool., 276: 195–203.10.1111/j.1469-7998.2008.00479.x
  25. 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: 965–982.10.1111/eva.13174
  26. 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.2018.02.00229427639
  27. 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
  28. 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: 2575–2584.10.1098/rspb.2001.1774
  29. 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: 14–22.10.1016/j.plantsci.2015.04.016
  30. 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: 591–595.10.1111/age.12570
  31. Marques D.A., Meier J.I., Seehausen O. (2019). A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol., 34: 531–544.10.1016/j.tree.2019.02.008
  32. 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: 123–129.10.1016/j.smallrumres.2006.04.016
  33. 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: 765–767.10.1111/j.1471-8286.2004.00744.x
  34. McFarlane S.E., Pemberton J.M. (2019). Detecting the true extent of introgression during anthropogenic hybridization. Trends Ecol. Evol., 34: 315–326.10.1016/j.tree.2018.12.013
  35. 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. 87–91.10.3920/978-90-8686-727-1_10
  36. 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: 361.10.3389/fgene.2019.00361
  37. 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: 107313.10.1016/j.ympev.2021.107313
  38. 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: 2841–2847.10.1111/mec.12350
  39. 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: 138.10.3389/fevo.2018.00138
  40. 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: 119–127.10.1016/j.ympev.2019.04.013
  41. Pfennig K.S. (2021). Biased hybridization and its impact on adaptive introgression. Trends Ecol. Evol., 36: 488–497.10.1016/j.tree.2021.02.010
  42. 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: 106690.10.1016/j.smallrumres.2022.106690
  43. Podbielska A., Piórkowska K., Szmatoła T. (2021). Microsatellite-based genetic structure and hybrid detection in alpacas bred in poland. Animals, 11: 2193.10.3390/ani11082193
  44. 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
  45. Poland J.A., Rife T.W. (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant Genome, 5.10.3835/plantgenome2012.05.0005
  46. 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: 106880.10.1016/j.ympev.2020.106880
  47. 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: 586.10.3389/fgene.2019.00586
  48. 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: 887–898.10.1111/jav.00946
  49. 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: e54603.10.1371/journal.pone.0054603
  50. 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: 1–6.10.1098/rspb.1994.0041
  51. Thermes C. (2014). Ten years of next-generation sequencing technology. Trends Genet., 30: 418–426.10.1016/j.tig.2014.07.001
  52. 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: 0161333.10.1371/journal.pone.0161333
  53. 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: 104249.10.1016/j.jaridenv.2020.104249
  54. 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
  55. 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
  56. Wheeler J.C. (2012). South American camelids – past, present and future. J. Camelid Sci., 5: 1–24.
  57. 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.
  58. Yue G.H., Wang L. (2017). Current status of genome sequencing and its applications in aquaculture. Aquaculture, 468: 337–347.10.1016/j.aquaculture.2016.10.036
DOI: https://doi.org/10.2478/aoas-2022-0063 | Journal eISSN: 2300-8733 | Journal ISSN: 1642-3402
Language: English
Page range: 1185 - 1192
Submitted on: Mar 3, 2022
Accepted on: Aug 29, 2022
Published on: Oct 29, 2022
Published by: National Research Institute of Animal Production
In partnership with: Paradigm Publishing Services
Publication frequency: 4 times per year

© 2022 Angelika Podbielska, Katarzyna Piórkowska, published by National Research Institute of Animal Production
This work is licensed under the Creative Commons Attribution 4.0 License.