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Scientific reports2023; 13(1); 11592; doi: 10.1038/s41598-023-38601-z

Detecting SNP markers discriminating horse breeds by deep learning.

Abstract: The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead chip were used in the current study and principal component analysis (PCA), log-likelihood ratios (LLR) and Neighbor-Joining (NJ) were applied to assess the performance of different assignment methods. The results revealed that the DNN, Garson, and Olden methods are able to assign individuals to true populations with 4270, 4937, and 7999 SNP markers, respectively. The PCA was used to determine how the animals allocated to the groups using all genotyped markers available on 50k Bead chip and the subset of SNP markers identified with different methods. The results indicated that all SNP panels are able to assign individuals into their true breeds. The success percentage of genetic assignment for different methods assessed by different levels of LLR showed that the success rate of 70% in the analysis was obtained by three methods with the number of markers of 110, 208, and 178 tags for DNN, Garson, and Olden methods, respectively. Also the results showed that DNN performed better than other two approaches by achieving 93% accuracy at the most stringent threshold. Finally, the identified SNPs were successfully used in independent out-group breeds consisting 120 individuals from eight breeds and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. Furthermore, the NJ tree of allele-sharing distances on the validation dataset showed that the DNN has a high potential for feature selection. In general, the results of this study indicated that the DNN technique represents an efficient strategy for selecting a reduced pool of highly discriminant markers for assigning individuals to the true population of origin.
© 2023. The Author(s).
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Publication Date: 2023-07-18 PubMed ID: 37464049PubMed Central: PMC10354035DOI: 10.1038/s41598-023-38601-zGoogle Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research study seeks to accurately identify the breed of horses through the use of genomic data and machine learning models like Deep Neural Networks. The studies offers details on the efficiency of these models in selecting relevant SNP markers that can be used for precise breed identification.

Study Objective and Data

  • The goal of this research was to assess the capabilities of various Artificial Neural Networks (ANNs), specifically Deep Neural Networks (DNN), Garson and Olden methods, in selecting relevant SNP (Single Nucleotide Polymorphisms) markers from comprehensive genotyping data.
  • A total of 795 horses from 37 different breeds were genotyped using the Illumina SNP 50k Bead chip for this investigation.

Implementation and Results

  • The researchers applied Principal Component Analysis (PCA), log-likelihood ratios (LLR), and Neighbor-Joining (NJ) to examine the efficiency of the different assignment methods.
  • These methods showed that there are a possible 4270, 4937, and 7999 SNP markers for the DNN, Garson, and Olden methods respectively that could accurately assign individuals to true populations.
  • The effectiveness of genetic assignment for different methods was gauged at different LLR levels, with a 70% success rate achieved with SNP markers of 110, 208, and 178 for the DNN, Garson, and Olden methods respectively.
  • The DNN method outperformed the others, achieving a 93% accuracy rate at the most stringent threshold.

Conclusion and Further Applications

  • The discovered SNPs were successfully applied to independent out-group breeds consisting of 120 individuals from eight breeds, effectively confirming their potential in correctly allocating all unknown samples to their true origin population.
  • From the validation dataset, it was also found that the DNN model has a high potential for feature selection as highlighted in the NJ tree of allele-sharing distances.
  • In conclusion, the study showed that the DNN technique serves as an efficient strategy in selecting a reduced highly discriminant set of markers for assigning individuals to their correct population of origin.

Cite This Article

APA
Manzoori S, Farahani AHK, Moradi MH, Kazemi-Bonchenari M. (2023). Detecting SNP markers discriminating horse breeds by deep learning. Sci Rep, 13(1), 11592. https://doi.org/10.1038/s41598-023-38601-z

Publication

Scientific reports
ISSN: 2045-2322
NlmUniqueID: 101563288
Country: England
Language: English
Volume: 13
Issue: 1
Pages: 11592

Researcher Affiliations

Manzoori, Siavash
  • Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.
Farahani, Amir Hossein Khaltabadi
  • Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran. a-farahani@araku.ac.ir.
Moradi, Mohammad Hossein
  • Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.
Kazemi-Bonchenari, Mehdi
  • Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

MeSH Terms

  • Horses / genetics
  • Animals
  • Polymorphism, Single Nucleotide
  • Deep Learning
  • Plant Breeding
  • Genotype
  • Alleles

Conflict of Interest Statement

The authors declare no competing interests.

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Citations

This article has been cited 3 times.
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  2. Kanaka KK, Ganguly I, Singh S, Kuralkar SV, Dixit S, Sukhija N, Goli RC. RASEL: An Ensemble Model for Selection of Core SNPs and Its Application for Identification and Classification of Cattle Breeds. Biochem Genet 2025 Aug 22;.
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