Open Access

The Use of SNP Microarrays for Biodiversity Studies of Sheep – A Review


Cite

Anderson R., Mc Ewan J., Brauning R. (2014). Development ofahigh density (600K) Illumina Ovine SNPchip and its use to fine map the yellow fat locus. Plant and Animal Genome XXII. San Diego, C.A. https://pag.confex.com/pag/xxii/webprogram/Paper10725.html.Search in Google Scholar

Auvray B., Mc Ewan C., Newman S.-A.N., Lee M., Dodds K.G. (2014). Genomic prediction of breeding values in the New Zealand sheep industry usinga50K SNPchip. J. Anim. Sci., 92: 4375-4389.Search in Google Scholar

Baloche B., Legarra A., Sallé G., Larroque H., Astruc J.-M., Robert - Granié C., Barillet F. (2014). Assessment of accuracy of genomic prediction for French Lacaune dairy sheep. J. Dairy Sci., 97: 1107-1116.Search in Google Scholar

Beynon S., Slavov G.T., Farré M., Sunduimijid B., Waddams K., Davies B., Ha- resign W., Kijas J., Mac Leod J., Newbold J., Davies L., Larkin D.M. (2015). Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics, 16, p. 65.10.1186/s12863-015-0216-x447458126091804Search in Google Scholar

Blackburn H.D., Toishibekov Y., Toishibekov M., Welsh C.S., Spiller S.F., Brown M., Paiva S.R. (2011). Genetic diversity of Ovis aries populations near domestication centers and in the New World. Genetica, 139: 1169-1178.Search in Google Scholar

Burren A., Signer - Hasler H., Neuditschko M., Tetens J., Kijas J., Drögemüller C., Flury C. (2014). Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNPdata. Anim. Genet. Res., 55: 67-76.Search in Google Scholar

Ciani E., Crepaldi P., Nicoloso L., Lasagna E., Sarti F.M., Moioli B., Napolita - no F., Carta A., Usai G., D’ Andrea M., Marletta D., Ciampolini R., Riggio V., Occidente M., Matassino D., Kompan D., Modesto P., Macciot- ta N., Ajmone - Marsan P., Pilla F. (2014). Genome-wide analysis of Italian sheep diversity revealsastrong geographic pattern and cryptic relationships between breeds. Anim. Genet., 45: 256-266.Search in Google Scholar

Ciani E., Lasagna E., D ’ Andrea M., Alloggio I., Marroni F., Ceccobelli S., Del- gado Bermejo J., Sarti F.M., Kijas J., Lenstra J.A., Pilla F., The International Sheep Genomics Consortium (2015). Merino and Merino-derived sheep breeds:agenome-wide intercontinental study. Genet. Sel. Evol., 47, p. 64.Search in Google Scholar

FAO (2004). Secondary Guidelines for Development of National Animal Genetic Resources Management Plans. Measurement of Domestic Animal Diversity (Mo DAD): Recommended Microsatellite Markers. FAO, Rome.Search in Google Scholar

FAO (2007). The state of the world’s animal genetic resources for food and agriculture. Rome, Italy, www.fao.org/docrep/010/a1250e/a1250e00.html.Search in Google Scholar

Fariello M.I., Servin B., Tosser - Klopp G., Rupp R., Moreno C., International Sheep Genomics Consortium, San Cristobal M., Boitard S. (2014). Selection Signatures in Worldwide Sheep Populations. PLo S ONE 9(8): e103813.Search in Google Scholar

Ferrando A., Goyache F. , Parés P.-M., Carrión C., Miró J., Jordana J. (2014). Genetic relationships between six eastern Pyrenean sheep breeds assessed using microsatellites. Span. J. Agric. Res., 12: 1029-1037.Search in Google Scholar

Gill P. (2011). An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int. J. Legal. Med., 114: 204-210.Search in Google Scholar

Glowatzki- Mullis M.L., Muntwyler J., B äumle E., Gaillard C. (2009). Genetic diversity of Swiss sheep breeds in the focus of conservation research. J. Anim. Breed. Genet., 126: 164-175.Search in Google Scholar

Gurgul A., Rubiś D., Z ąbek T., Zukowski K., Pawlina K., Semik E., Bugno- Po- niewierska M. (2013). The evaluation of the usefulness of pedigree verification-dedicated SNPs for breed assignment in three Polish cattle populations. Mol. Biol. Rep., 40: 6803-6809; doi: 10.1007/s11033-013-2797-7.Search in Google Scholar

Gurgul A., Pawlina K., Frys- Żurek M., Bugno- Poniewierska M. (2015). Identification of differential selection traces in two Polish cattle breeds. Anim. Sci. J., 86: 17-24. doi: 10.1111/ asj.12242.Search in Google Scholar

Heaton M.P., Leymaster K.A., Kalbfleisch T.S., Kijas J.W., Clarke S.M., Mc Ewan J. (2014). SNPs for parentage testing and traceability in globally diverse breeds of sheep. PLo S ONE 9(4): e94851.Search in Google Scholar

Hoda A., Ajmone - Marsan P., Dobi P., Bozgo V., Consortium E. (2010). Genetic diversity in Albanian sheep breeds estimated by AFLPmarkers. Alb. J. Agric. Sci., 9: 23-29.Search in Google Scholar

Johnson N., Fletcher O., Palles C., Rudd M., Webb E., Sellick G., Silva I.D.S., Mc Cormack V., Gibson L., Fraser A. (2007). Counting potentially functional variants in BRCA1, BRCA2 and ATMpredicts breast cancer susceptibility. Hum. Mol. Genet., 16: 1051-1057.Search in Google Scholar

Karlsson S., Moen T., Lien S., Glover K., Hindar K. (2011). Generic genetic differences between farmed and wild Atlantic salmon identified froma7K SNP-chip. Mol. Ecol. Res., 11 (Suppl. 1): 236-242.Search in Google Scholar

Kijas J.W., Townley D., Dalrymple B.P., Heaton M.P., Maddox J.F., Mc Grath A., Wilson P., Ingersoll R.G., Mc Culloch R., Mc William S., Tang D., Mc Ewan J., Cockett N., Oddy V.H., Nicholas F.W., Raadsma H., International Sheep Genomics Consortium (2009). Agenome wide survey of SNPvariation reveals the genetic structure of sheep breeds. PLo S ONE 4(3): e4668.Search in Google Scholar

Kijas J.W., Lenstra J.A., Hayes B., Boitard S., Porto Neto L.R., San Cristo - bal M. et al. (2012). Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLo S Biol. 10(2): e1001258.Search in Google Scholar

Kijas J.W., Hadfield T., Naval Sanchez M., Cockett N. (2016). Genome-wide association reveals the locus responsible for four-horned ruminant. Anim. Genet., doi: 10.1111/age.12409.Search in Google Scholar

Kong F.R., Tong Z.S., Chen X.Y., Sorrell T., Wang B., Wu Q.X., Ellis D., Chen S. (2008). Rapid identification and differentiation of Trichophyton species, based on sequence polymorphisms of the ribosomal internal transcribed spacer regions, by rolling-circle amplification. J. Clin. Microbiol., 46: 1192-1199.Search in Google Scholar

Koseniuk A., Rychlik T. (2013). Mitochondrial DNA - characteristics and potential practical applications in sheep breeding (in Polish). Wiad. Zoot., 4: 65-69.Search in Google Scholar

Kusza S., Nagy I., Sasvári Z., Stágel A., N émeth T., Molnár A., Kume K., Bősze Z., Jávor A., Kukovics S. (2008). Genetic diversity and population structure of Tsigai and Zackel type of sheep breeds in the Central-, Eastern- and Southern-European regions. Small Rumin. Res., 78: 1-3, 13-23.10.1016/j.smallrumres.2008.04.002Search in Google Scholar

Lao O.,van Duijn K., Kersbergen P.,de Knijff P., Kayser M. (2006). Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry. Am. J. Hum. Genet., 78: 680-690.Search in Google Scholar

Lenstra J.A., Groeneveld L.F., Eding H., Kantanen J., Williams J.L., Taberlet P., Nicolazzi E.L., S ölkner J., Simianer H., Ciani E., Garcia J.F., Bruford M.W., Ajmone - Marsan P., Weigend S. (2012). Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim. Genet., 43: 483-502.Search in Google Scholar

Liu N., Chen L., Wang S., Oh C., Zhao H. (2005). Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genetics, 6 (Suppl. 1): S26.Search in Google Scholar

Macedo F., Navajas E.A., Aguilar I., Grasso A.N., Pieruccioni F., Ciappesoni G. (2014). New parentage testing SNPpanel for commercial breeds will beauseful tool for conservation of Creole sheep, Proceedings, 10th World Congress of Genetics Applied to Livestock Production, http://www.geneticaovina.com.uy/archivos/F_Macedo_etal_2014_10-WCGALP.pdf Search in Google Scholar

Martyniuk E., Krupiński J., Chełmińska A. (eds) (2013). National strategy for sustainable use and conservation of genetic resources of farm animals (in Polish), Warszawa, 170 pp.Search in Google Scholar

Meadows J.R., Cemal I., Karaca O., Gootwine E., Kijas J.W. (2007). Five ovine mitochondrial lineages identified from sheep breeds of the Near East. Genetics, 175: 1371-1379.Search in Google Scholar

Miller J.M., Poissant J., Kijas J.W. et al. (2011). Agenome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Mol. Ecol. Resour., 11: 314-322.Search in Google Scholar

Morin P.A., Mc Carthy M. (2007). Highly accurate SNPgenotyping from historical and low-quality samples. Mol. Ecol. Notes, 7: 937-946.Search in Google Scholar

Mucha S., Bunger L., Conington J. (2015). Genome-wide association study of footrot in Texel sheep. Genet. Sel. Evol. 47, p. 35; doi: 10.1186/s12711-015-0119-3.Search in Google Scholar

Namroud M.C., Beaulieu J., Juge N., Laroche J., Bousquet J. (2008). Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol. Ecol., 17: 3599-3613.Search in Google Scholar

Pariset L., Mariotti M., Gargani M., Joost S., Negrini R., Perez T., Bruford M., Ajmone Marsan P., Valentini A. (2011). Genetic diversity of sheep breeds from Albania, Greece, and Italy assessed by mitochondrial DNAand nuclear polymorphisms (SNPs). Sci. World J., 11: 1641-1659.Search in Google Scholar

Paschou P., Ziv E., Burchard E.G., Choudhry S., Rodriguez- Cintron W., Ma- honey M.W., Drineas P. (2007). PCA-correlated SNPs for structure identification in worldwide human populations. PLo S Genet., 3: 1672-1686.Search in Google Scholar

Peter C., Bruford M., Perez T., Dalamitra S., Hewitt G., Erhardt G. (2007). Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Anim. Genet., 38: 37-44.Search in Google Scholar

Poehlmann A., Kuester D., Meyer F., Lippert H., Roessner A., Schneider- - Stock R. (2007). K-ras mutation detection in colorectal cancer using the Pyrosequencing technique. Pathol. Res. Pract., 203: 489-49710.1016/j.prp.2007.06.00117629419Search in Google Scholar

Radko A., Rychlik T. (2010). Evaluating the usefulness of polymorphism of 7 microsatellite DNA markers for genetic diversity studies of sheep. Ann. Anim. Sci., 10: 373-378.Search in Google Scholar

Riggio V., Pong- Wong R., Sallé G., Usai M.G., Casu S., Moreno C.R., Matika O., Bishop S.C. (2014). Ajoint analysis to identify loci underlying variation in nematode resistance in three European sheep populations. J. Anim. Breed. Genet., 131: 426-436.Search in Google Scholar

Rosenberg N., Li L., Ward R., Pritchard J. (2003). Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet., 73: 1402-1422.Search in Google Scholar

Rychlik T., Krawczyk A. (2007). Use of blood groups and polymorphic proteins to evaluate genetic diversity in Polish conservation breeds (in Polish). Wiad. Zoot., 4: 49-54.Search in Google Scholar

Rychlik T., Duniec M.J., Kościelny M. (2006). Evaluation of changes in the genetic structure of sheep breed Wrzosówka based on the study of blood groups and polymorphic variants of proteins (in Polish). Rocz. Nauk. Zoot., 33: 31-40.Search in Google Scholar

Salamon D., Gutierrez- Gil B., Arranz J., Barreta J., Batinic V., Dzidic A. (2014). Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites. Animal, 8: 200-207.Search in Google Scholar

Scherf B. (ed.) (2000). World Watch List for Domestic Animal Diversity, 3rd edn. FAO, Rome.Search in Google Scholar

Smith M., Pascal C., Grauvogel Z., Habicht C., Seeb J., Seeb L. (2011). Multiplex preamplification PCRand microsatellite validation allows accurate single nucleotide polymorphism (SNP) genotyping of historical fish scales. Mol. Ecol. Resour., 11 (Suppl. 1): 257-266.Search in Google Scholar

Souza C.A., Paiva S.R., Mc Manus C.M., Azevedo H.C., Mariante A.S., Grattapa - glia D. (2012). Genetic diversity and assessment of 23 microsatellite markers for parentage testing of Santa Inês hair sheep in Brazil. Genet. Mol. Res., 11: 1217-1229.Search in Google Scholar

Tapio M., Marzanov N., Ozerov M., Cinkulov M., Gonzarenko G., Kiselyova T., Murawski M., Viinalass H., Kantanen J. (2006). Sheep mitochondrial DNAvariation in European, Caucasian, and Central Asian areas. J. Mol. Biol. Evol., 23: 1776-1783.Search in Google Scholar

Tapio M., Ozerov M., Tapio I., Toro M.A., Marzanov N., Cinkulov M., Goncha - renko G., Kiselyova T., Murawski M., Kantanen J. (2010). Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia. BMC Genet., 11, p. 76; doi: 10.1186/1471-2156-11-76.Search in Google Scholar

Wojciechowska M., Olech W. (2013). The use of DNAmicroarray in the study of the wild animal species (in Polish). Studiai Materiały CEPLw Rogowie, 36: 112-116.Search in Google Scholar

Yamaguchi- Kabata Y., Nakazono K., Takahashi A., Saito S., Hosono N., Ku- bo M., Nakamura Y., Kamatani N. (2008). Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies. Am. J. Hum. Genet., 83: 445-456; doi: 10.1016/j.ajhg.2008.08.019.Search in Google Scholar

Zeder M.A. (2008). Domestication and early agriculture in the Mediterranean Basin: origins, diffusion, and impact. Proc. Natl. Acad. Sci. USA 105: 11597-11604; doi: 10.1073/pnas.0801317105. Search in Google Scholar

www.dad.fao.org Search in Google Scholar

www.econogene.eu Search in Google Scholar

www.illumina.com/documents/products/datasheets/datasheet_ovinesnp50.pdf Search in Google Scholar

eISSN:
2300-8733
Language:
English
Publication timeframe:
4 times per year
Journal Subjects:
Life Sciences, Biotechnology, Zoology, Medicine, Veterinary Medicine