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

Kawęcka, Aldona; Gurgul, Artur; Miksza-Cybulska, Anna

doi:10.1515/aoas-2016-0017

Abstract

The conservation of farm animal genetic resources and their protection against genetic erosion requires knowledge of biodiversity status. Genetic variation in populations can be estimated using both traditional pedigree-based methods and molecular techniques. SNP microarrays are a new generation of molecular genetic tools, which have found application in analysis of biodiversity in populations of domestic and wild sheep, in studies of resistance to intestinal parasites and foot rot, and in searching for markers associated with meat and milk yield, or colour inheritance traits. The aim of the study is the review of recent literature on the biodiversity and the use of molecular markers for population genetics in different breeds and populations of sheep.

References

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 Back to article
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 Back to article
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 Back to article
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-x447458126091804
Search in Google Scholar Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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.
Open DOI Search in Google Scholar Back to article
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.
Open DOI Search in Google Scholar Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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.
Open DOI Search in Google Scholar Back to article
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 Back to article
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 Back to article
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.2008.04.002
Search in Google Scholar Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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.
Open DOI Search in Google Scholar Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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.2007.06.00117629419
Search in Google Scholar Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
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 Back to article
Scherf B. (ed.) (2000). World Watch List for Domestic Animal Diversity, 3rd edn. FAO, Rome.
Search in Google Scholar Back to article
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 Back to article
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 Back to article
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 Back to article
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.
Open DOI Search in Google Scholar Back to article
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 Back to article
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.
Open DOI Search in Google Scholar Back to article
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.
Open DOI Search in Google Scholar Back to article
www.dad.fao.org
Search in Google Scholar Back to article
www.econogene.eu
Search in Google Scholar Back to article
www.illumina.com/documents/products/datasheets/datasheet_ovinesnp50.pdf
Search in Google Scholar Back to article

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

Abstract

Paradigm

My account