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Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds

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journal contribution
posted on 2023-05-03, 18:04 authored by Mohammad Moradi, Amir Khaltabadi-Farahani, Mahdi Khodaei-Motlagh, Mehdi Kazemi-Bonchenari, John McEwanJohn McEwan
the assignment of an individual to the true population of origin is one of the most important appli-cations of genomic data for practical use in animal breeding. the aim of this study was to develop a statistical method and then, to identify the minimum number of informative snP markers from high-throughput genotyping data that would be able to trace the true breed of unknown samples in indigenous sheep breeds. the total numbers of 217 animals were genotyped using illumina ovinesnP50k beadchip in Zel, lori-bakhtiari, afshari, moqani, Qezel and a wild-type iranian sheep breed. after snP quality check, the principal component analysis (Pca) was used to deter-mine how the animals allocated to the groups using all genotyped markers. the results revealed that the first principal component (PC1) separated out the two domestic and wild sheep breeds, and all domestic breeds were separated from each other for Pc2. the genetic distance between different breeds was calculated using fst and reynold methods and the results showed that the breeds were well differentiated. a statistical method was developed using the stepwise discrimi-nant analysis (sda) and the linear discriminant analysis (lda) to reduce the number of snPs for discriminating 6 different iranian sheep populations and k-fold cross-validation technique was employed to evaluate the potential of a selected subset of snPs in assignment success rate. the procedure selected reduced pools of markers into 201 snPs that were able to exactly discriminate all sheep populations with 100% accuracy. moreover, a discriminate analysis of principal compo-nents (daPc) developed using 201 linearly independent snPs revealed that these markers were able to assign all individuals into true breed. Finally, these 201 identified SNPs were successfully used in an independent out-group breed consisting of 96 samples of baluchi sheep breed and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. in general, the results of this study indicated that the combined use of the SDA and LDA techniques represents an efficient strategy for selecting a reduced pool of highly discriminant markers.


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© 2021 Mohammad Hossein Moradi et al., published by Sciendo This work is licensed under the Creative Commons Attribution 4.0 International License.


  • English

Does this contain Māori information or data?

  • No


De Gruyter

Journal title

Annals of Animal Science




Moradi, M. H., Khaltabadi-Farahani, A. H., Khodaei-Motlagh, M., Kazemi-Bonchenari, M., & McEwan, J. (2021). Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds. Annals of Animal Science, 21(3), 807–831. doi:10.2478/aoas-2020-0097