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STOCK-RAISING AND VETERINARY

STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS

Indira Beishova 1 , Dilyara Gritsenko 2 , Malika Shamekova 2 , Alexandr Pozharskiy 2 , Татьяна Ульянова 1 , Alexandr Kovalchuk 1

1 NJSC «West Kazakhstan Agrarian and Technical University named after Zhangir khan», Uralsk, Kazakhstan; 2 Institute of Plant Biology and Biotechnology, Almaty

doi.org/10.37884/3-2023/05 pp. 48-58 Admitted 15.09.2023 Published 29.09.2023

Abstract

The article presents the results of the study of genetic diversity of traditional horse breeds based on whole  genome analysis of single nucleotide polymorphisms (SNPs) using Equine 80k HTS microarrays (Illumina Inc., USA).

Hair follicle samples from Kazakh horses of the breeds Zhabe (ZHB, n = 631), Adai (ADA, n = 303) and Naiman (NMN, n = 158), Mugalzhar (MUG, n = 584), Kushum (KSH, n = 226) and Kostanay (KOS, n = 116) were used as material for the studies. Quality control of SNP genotyping was performed using PLINK1.9 software, PLINK1.9, R-package, BEAGLE, ADMIXTURE, CLUMPAK, and FigTree software was used for data processing and visualisation. The final set of markers selected by quality control and used for analysis contained 60 987 SNPs.

All horse breeds studied had very close values of expected and observed heterozygosity, with an average of 0,3478 and 0,3443. The degree of observed heterozygosity in the horse breeds studied varied from 0,3402 in the Kazakh breed Adai type and Mugaljar breed to 0,3514 in the Kushum breed. Using Principal Component Analysis (PCA), ADMIXTURE program, expected and observed heterozygosity (He and Ho), and between-group fixation index (Fst), the absence of genetic variability between the studied horse breeds was revealed. Comparison with previously published data on the genetic diversity of horse breeds revealed a relatively high level of individual diversity in traditional horses compared with foreign breeds. At the same time, Mongolian and Tuva breeds were identified as the most closely related horse breeds. This is the first time that we have investigated the genetic diversity of traditional horse breeds using whole genome SNP analysis. These results serve as the beginning of an in-depth study of the gene pool of the breeds and an assessment of their importance for the prospects of agricultural production.

Equus caballus, Kazakh breed Zhabe type, Kazakh breed Adai type, Kazakh breed Naiman type, Mugalzhar breed, Kushum breed, Kostanay breed, SNP

01 Introduction

The full text of the article is available for download in PDF format on the right panel.

02 References

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Citation Links

[1]2023. STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS. Izdenister natigeler. 3 (99) (Sep. 2023), 48–58. DOI:https://doi.org/10.37884/3-2023/05.
(1)STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS. Izdenister natigeler 2023, No. 3 (99), 48-58. https://doi.org/10.37884/3-2023/05.
STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS. (2023). Izdenister Natigeler, 3 (99), 48-58. https://doi.org/10.37884/3-2023/05
STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS. Izdenister natigeler, [S. l.], n. 3 (99), p. 48–58, 2023. DOI: 10.37884/3-2023/05. Disponível em: https://agrosoil.kaznaru.edu.kz/index.php/research/article/view/372. Acesso em: 15 sep. 2026.
“STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS”. 2023. Izdenister Natigeler, no. 3 (99) (September): 48-58. https://doi.org/10.37884/3-2023/05.
“STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS” (2023) Izdenister natigeler, (3 (99), pp. 48–58. doi:10.37884/3-2023/05.
[1]“STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS”, Izdenister natigeler, no. 3 (99), pp. 48–58, Sep. 2023, doi: 10.37884/3-2023/05.
“STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS”. Izdenister Natigeler, no. 3 (99), Sept. 2023, pp. 48-58, https://doi.org/10.37884/3-2023/05.
“STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS”. Izdenister natigeler, no. 3 (99) (September 29, 2023): 48–58. Accessed September 15, 2026. https://agrosoil.kaznaru.edu.kz/index.php/research/article/view/372.
1.STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS. Izdenister natigeler [Internet]. 2023 Sep. 29 [cited 2026 Sep. 15];(3 (99):48-5. Available from: https://agrosoil.kaznaru.edu.kz/index.php/research/article/view/372
1.STUDY OF THE GENETIC DIVERSITY OF TRADITIONAL HORSE BREEDS USING WHOLE GENOME SNP ANALYSIS. Izdenister natigeler. 2023;(3 (99):48-58. doi:10.37884/3-2023/05