Use of Molecular Markers in Parentage Testing, Genetic Diversity, Marker-Assisted Breeding and Disease Identification

Main Article Content

Mubeen ul Hasan
Ayhan Ceyhan


Conventional breeding programs have limitations while working with the quantitative traits and traits with low heritability. Furthermore, the identification of defective genes that can cause the development of a disease cannot be identified through conventional strategies until the development of the disease. The Discovery of molecular markers has made it easier for animal breeders and animal geneticists to enhance the productivity of animal breeding programs. Different kinds of molecular markers, RAPDs, SNPs, AFLPs, QTLs, and SSR are being used in animal breeding for gene mapping, phylogenetic studies, disease resistance studies, genetic conservation, and genetic diversity.  Molecular markers also provide the advantage of working with low heritability and complex quantitative traits. QTL markers are being used for quantitative traits like milk production meat production because they are linked to quantitative trait genes. Marker-assisted breeding has helped the breeding programs to increase the efficiency of the breeding programs. Molecular markers like SNPs can be used to detect the mutation in genes at an early age. Microsatellites have been used at a very large scale for phylogenetic identification. In this review, we will discuss the importance and application of molecular markers in animal breeding and genetics.

Article Details

How to Cite
ul Hasan, M. ., & Ceyhan, A. (2021). Use of Molecular Markers in Parentage Testing, Genetic Diversity, Marker-Assisted Breeding and Disease Identification . Journal of Agriculture, Food, Environment and Animal Sciences, 2(1), 70-84. Retrieved from


Alsayed O, Erkunt-Alak S, Un C., 2019. Analysis of prion protein coding gene polymorphisms in Palestinian native sheep breeds. Ankara Üniversitesi Veteriner Fakültesi Dergisi, 66(3): pp.261-266.

Barillet F. 2007. Genetic improvement for dairy production in sheep and goats. Small Ruminant Research, 70(1): pp.60-75.

Baron EE, Martinez ML, Verneque, RS, and Coutinho LL., 2002. Parentage testing and effect of misidentification on the estimation of breeding value in Gir cattle. Genetics and Molecular Biology, 25(4), pp:389-394.

Baumung R, Simianer H, and Hoffmann I., 2004. Genetic diversity studies in farm animals?a survey. Journal of Animal Breeding and Genetics, 121(6), pp:361-373.

Bell AM, Henshall JM, Gill S, Gore K, Kijas JW, and Villalobos N., 2013. Success rates of commercial SNP based parentage assignment in sheep. In Proc Assoc Advmt Anim Breed Genet (Vol. 20, pp: 278-281).

Berthouly C, Bed'Hom B, Tixier?Boichard M, Chen CF, Lee YP, Laloë D, Legros H, Verrier E, and Rognon X., 2008. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Animal genetics, 39(2), pp:121-129.

Beuzen ND, Stear MJ, and Chang KC., 2000. Molecular markers and their use in animal breeding. The Veterinary Journal, 160(1), pp:42-52.

Bidinost F, Roldan DL, Dodero AM, Cano EM, Taddeo HR, Mueller JP, and Poli, MA., 2008. Wool quantitative trait loci in Merino sheep. Small Ruminant Research, 74(1-3), pp:113-118.

Bjørnstad G, and Røed KH., 2002. Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses. Animal Genetics, 33(4), pp:264-270.

Blott SC, Williams JL, and Haley CS., 1999. Discriminating among cattle breeds using genetic markers. Heredity, 82(6), pp:613-619.

Bruford MW, Bradley DG, and Luikart G., 2003. DNA markers reveal the complexity of livestock domestication. Nature Reviews Genetics, 4(11), pp:900-910.

Carlson GA, Kingsbury DT, Goodman PA, Coleman S, Marshall ST, DeArmond S, Westaway D, and Prusiner SB., 1986. Linkage of prion protein and scrapie incubation time genes. Cell, 46(4), pp:503-511.

Clarke SM, Henry HM, Dodds KG, Jowett TW, Manley TR, Anderson RM, and McEwan JC., 2014. A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep. PLoS One, 9(4), p:e93392.

Deb R, and Chakraborty S., 2012. Trends in veterinary diagnostics. Journal of Veterinary Science and Technology, 3(1).

Dekkers JC., 2004. Commercial application of marker-and gene-assisted selection in livestock: strategies and lessons. Journal of animal science, 82(suppl_13), pp:E313-E328.

Demir E, and Balcioğlu MS, 2019. Genetic diversity and population structure of four cattle breeds raised in Turkey using microsatellite markers. Czech Journal of Animal Science, 64(10), pp:411-419.

Erhardt G, and Weimann C., 2007. Use of molecular markers for evaluation of genetic diversity and in animal production. Archivos Latinoamericanos de Producción Animal, 15(5).

Fernández ME, Goszczynski DE, Lirón JP, Villegas-Castagnasso EE, Carino MH, Ripoli MV, Rogberg-Muñoz A, Posik DM, Peral-García P, and Giovambattista G., 2013. Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genetics and molecular biology, 36(2), pp:185-191.

Fisher PJ, Malthus B, Walker MC, Corbett G, and Spelman RJ., 2009. The number of single nucleotide polymorphisms and on-farm data required for whole-herd parentage testing in dairy cattle herds. Journal of dairy science, 92(1), pp:369-374.

Gianola D, Perez-Enciso M, and Toro MA, 2003. On marker-assisted prediction of genetic value: beyond the ridge. Genetics, 163(1), pp:347-365.

Goldmann W., 2008. PrP genetics in ruminant transmissible spongiform encephalopathies. Veterinary research, 39(4), pp:1-14.

Hayes BJ, and Goddard ME., 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), pp:1819-1829.

Heaton MP, Leymaster KA, Kalbfleisch TS, Kijas JW, Clarke SM, McEwan J, Maddox JF, Basnayake V, Petrik DT, Simpson B, and Smith TP., 2014. SNPs for parentage testing and traceability in globally diverse breeds of sheep. PloS one, 9(4), p:e94851.

Henderson CR., 1984. Applications of linear models in animal breeding (University of Guelph, Guelph, ON, Canada). Applications of linear models in animal breeding. University of Guelph, Guelph, ON, Canada.

Hiendleder S, Thomsen H, Reinsch N, Bennewitz J, Leyhe-Horn B, Looft C, Xu N, Medjugorac I, Russ I, Kühn C, and Brockmann GA., 2003. Mapping of QTL for body conformation and behavior in cattle. Journal of Heredity, 94(6), pp:496-506.

Hunter N, Foster JD, Dickinson AG, and Hope J., 1989. Linkage of the gene for the scrapie-associated fibril protein (PrP) to the Sip gene in Cheviot sheep. The Veterinary Record, 124(14), pp:364-366.

Israel C, and Weller JI., 2000. Effect of misidentification on genetic gain and estimation of breeding value in dairy cattle populations. Journal of Dairy Science, 83(1), pp:181-187.

Kijas JW, Lenstra JA, Hayes B, Boitard S, Neto LRP, San Cristobal M, Servin B, McCulloch R, Whan V, Gietzen K, and Paiva S., 2012. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol, 10(2), p:e1001258.

Kiplagat SK, Limo MK, and Kosgey IS., 2012. Genetic improvement of livestock for milk production. Milk Production-Advanced Genetic Traits, Cellular Mechanism, Animal Management and Health (N. Chaiyabutr, ed.). Intech Publishers, Rijeka, pp:77-96.

Kumar S, Singh U, Deb R, and Sharma A., 2012. Biomarkers for semen quality in bull. Advances in Cattle Research. New Delhi: Satish Serial Publishing House, 65, p:e86.

Lahav T, Atzmon G, Blum S, Ben?Ari G, Weigend S, Cahaner A, Lavi U, and Hillel, J., 2006. Marker?assisted selection based on a multi?trait economic index in chicken: experimental results and simulation. Animal genetics, 37(5), pp:482-488.

Lindhe B, and Philipsson J., 1998. resistance to animal diseases. Rev. sci. tech. Off. int. Epiz, 17(1), pp:291-301.

Mirkena T, Duguma G, Haile A, Tibbo M, Okeyo AM, Wurzinger M, and Sölkner J., 2010. Genetics of adaptation in domestic farm animals: A review. Livestock Science, 132(1-3), pp:1-12.

Moniruzzaman M, Khatun R, and Mintoo AA., 2014. Application of marker assisted selection for livestock improvement in Bangladesh. Bangladesh Veterinarian, 31(1), pp:1-11.

Notter DR., 1999. The importance of genetic diversity in livestock populations of the future. Journal of animal science, 77(1), pp:61-69.

Olesen I, Gjerde B, and Groen AF., 1999. Accommodation and evaluation of ethical, strategic and economic values in animal breeding goals. In Book of Abstracts (No. 5, p:33).

Oner Y, Yesilbag K, Tuncel E, and Elmaci C., 2011. Prion protein gene (PrP) polymorphisms in healthy sheep in Turkey. Animal: an International Journal of Animal Bioscience, 5(11), p:1728.

Özşensoy YUSUF, Kurar E, DOĞAN M, Bulut Z, Nizamlıoğlu M, Işık A, Çamlıdağ A, and Altunok V., 2014. Genetic characterization of Turkish cattle breeds by microsatellite markers: Usefulness for parentage testing. Kafkas Univ Vet Fak Derg, 20(4), pp:521-526.

Pei J, Bao P, Chu M, Liang C, Ding X, Wang H, Wu X, Guo X, and Yan P., 2018. Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens). PeerJ, 6, p:e5946.

Pena GA, Coelho I, Reynoso MM, Soleiro C, and Cavaglieri LR., 2015. Characterization and genetic variability of feed-borne and clinical animal/human Aspergillus fumigatus strains using molecular markers. Medical mycology, 53(7), pp:699-708.

Peter C, Bruford M, Perez T, Dalamitra S, Hewitt G, Erhardt G., and Econogene Consortium, 2007. Genetic diversity and subdivision of 57 European and Middle?Eastern sheep breeds. Animal genetics, 38(1), pp:37-44.

Prusiner SB., 1982. Novel proteinaceous infectious particles cause scrapie. Science, 216(4542), pp:136-144.

Qureshi MI, Sabir JSM, Mutawakil MHZ, El Hanafy AA, Ashmaoui HE, Ramadan H, Anwar Y, Sadek AM, Alsoud MA, Saini KS, and Ahmed MM., 2014. Review of modern strategies to enhance livestock genetic performance: From molecular markers to next-generation sequencing technologies in goats. Journal of Food, Agriculture & Environment, 12(2), pp:752-761.

Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MA, Hillel J, Mäki-Tanila A, Tixier-Boichard M, Vignal A, and Wimmers K., 2001. Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics, 159(2), pp:699-713.

Rout PK, Joshi MB, Mandal A, Laloë D, Singh L, and Thangaraj K., 2008. Microsatellite-based phylogeny of Indian domestic goats. BMC genetics, 9(1), p:11.

Salisu IB, Olawale AS, Jabbar B, Koloko BL, Abdurrahaman SL, Amin AB, and Ali Q., 2018. Molecular markers and their Potentials in Animal Breeding and Genetics. Nigerian J Anim Sci, 20(3), pp:29-48.

Sharma R, Kishore A, Mukesh M, Ahlawat S, Maitra A, Pandey AK, and Tantia MS., 2015. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC genetics, 16(1), p:73.

Singh U, Deb R, Alyethodi RR, Alex R, Kumar S, Chakraborty S, Dhama K, and Sharma A., 2014. Molecular markers and their applications in cattle genetic research: A review. Biomarkers and Genomic Medicine, 6(2), pp:49-58.

Toro MA, Fernández J, and Caballero A., 2009. Molecular characterization of breeds and its use in conservation. Livestock Science, 120(3), pp:174-195.

Werner FAO, Durstewitz G, Habermann FA, Thaller G, Krämer W, Kollers S, Buitkamp J, Georges M, Brem G, Mosner J, and Fries R., 2004. Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds. Animal genetics, 35(1), pp:44-49.

Williams JL., 2005. The use of marker-assisted selection in animal breeding and biotechnology. Revue Scientifique et Technique-Office International des Epizooties, 24(1), p:379.

Yaman Y, Soysal MI, and ÜN C., 2015. Evaluation of the genetic resistance status to classical and atypicalscrapie in Karacabey merino rams. Turkish Journal of Veterinary and Animal Sciences, 39(6), pp:736-740.

Zhao J, Zhu C, Xu Z, Jiang X, Yang S, and Chen A., 2017. Microsatellite markers for animal identification and meat traceability of six beef cattle breeds in the Chinese market. Food Control, 78, pp:469-475.