بررسی ساختار جمعیتی و الگوی عدم تعادل پیوستگی اسب‌های بومی ایران با استفاده از نشانگرهای SNP

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی، دانشکده کشاورزی، دانشگاه زنجان، زنجان، ایران.

2 گروه علوم دامی، دانشکده کشاورزی، دانشگاه زنجان، زنجان. ایران.

چکیده

هدف این پژوهش، بررسی ساختار و فواصل ژنتیکی، هم‌خونی و الگوی عدم تعادل پیوستگی (LD) و درک روابط بین نژادهای اسب بومی ایران بود. در مجموع از 167 راس اسب که شامل 24 راس از نژاد عرب (اصیل)، 24 راس نژاد کاسپین، 15 راس نژاد دره‌شوری، 66 راس نژاد کرد و 40 راس ترکمن بودند، استفاده شد. نمونه‌ها با استفاده از تراشه (Illumina 70k SNP equine bead chip) ژنوتایپ شدند. در پالایش داده‌ها، جایگاه‌هایی با MAF کمتر از 2 درصد، Mind  کمتر از 5 درصد، HWE کمتر از  و ژنوتاپت‌های کمتر از 01/0 حذف شدند و 45270 جایگاه SNP در 159 راس اسب برای آنالیزهای بررسی ساختار ژنتیکی اسب‌های بومی ایران به کار گرفته شد. تجزیه‌ ساختار ژنتیکی نشان داد که در K=5 نژادهای کاسپین و کرد در یک خوشه مشترک قرار گرفتند و نژادهای ترکمن، دره‌شوری و عرب (اصیل) نیز خوشه‌های متمایزی تشکیل دادند. فاز LD در بین تمام نژادها در فاصله زیر bp400 کاهش معناداری داشت. نژاد کاسپین و دره‌شوری به ترتیب کم‌ترین و بیش‌ترین LD و بیش‌ترین و کم‌ترین اندازه موثر جمعیت را تجربه کردند. کم‌ترین و بیش‌ترین ضریب هم‌خونی براساس رشته‌های هموزیگوت ژنومی (ROH) نیز به ترتیب در نژادهای عرب اصیل و کاسپین دیده شد. نتایج نشان داد نژادهای بومی اسب ایران به خوبی با نشانگرهای (SNP) شناسایی شدند که این موضوع می‌تواند در تشکیل پایه‌های ژنومی نژادها (Data Base) و با صحت بالا مورد استفاده قرار گیرد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Study of population structure and linkage disequilibrium pattern of Iranian native horse breeds by SNP markers

نویسندگان [English]

  • Mohammad Abdoli 1
  • Mohammad Bagher Zandi baghcheh maryam 1
  • Taher Harkinezhad 2
  • Moein Taned 2
1 Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran.
2 Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran.
چکیده [English]

The aim of this study was to investigate the structure and genetic distances, inbreeding, and linkage disequilibrium (LD) in Iranian native horse breeds. Samples on 167 horses including Arabian Asil (24), Caspian (22), Dareshouri (15), Kurdish (66), and Turkmen (40) breeds were used. The samples were genotyped using Illumina 70k SNP equine bead chip. Data quality control was applied and loci with MAF < 2%, Mind < 5%, HWE (<10-6), and genotype call rate < 1% were removed. Finally, 159 horses with 45,270 SNP loci were reminded for the genetic structure analyse. Clustering analyse showed that in K=5 Caspian and Kurdish breeds were placed in a common cluster, and Turkmen, Dareshouri, and Arabian Asil breeds were also located in distinct clusters. The LD decay among all breeds showed a significant decrease below 400 bp. Caspian and Dareshouri breeds experienced the lowest and highest LD and the highest and lowest effective population size, respectively. The inbreeding value based on the runs of homozygosity (ROH) were highest and lowest for Arabian Asil and Caspian breeds, respectively. The results showed that the Iranian native horse breeds were well identified by SNP markers, which can be used for stud base foundations of breeds with more accuracy.

کلیدواژه‌ها [English]

  • Iranian native horses
  • Genetic diversity
  • linkage disequilibrium
  • Runs of homozygosity
  • single nucleotide polymorphism markers

Extended Abstract

Introduction

    Horse (Equus ferus caballus) has been one of the oldest animals domesticated by humans. In terms of geographical distribution, this animal is also present in all the lands, and horses are included as the most popular domesticated animals in human societies (Jun et al., 2014; Mahrous et al., 2011 and Petersen et al., 2013). At present, the populations of Iranian native horse breeds include Turkmen, Caspian, Kurdish, Dareshouri, and Arabian (Asil) (Rafeie et al., 2011). From the five official registered horse breeds of Iran, Turkmen and Asil horses had the greatest impact on the breeding program and foundation of many breeds. So, most bloodlines of stallions from other breeds originate from these two horse breeds (Wallner et al. 2017). Therefore, based on archaeological findings, the early stages of the establishment of most European horse breeds originated from the bloodline of Iranian horses and these breeds played a significant role in the development of horse breeds in globe (Fages et al., 2019). So, this research was carried out to investigate and genomic scan of the structure, genetic diversity, linkage disequilibrium (LD), and estimate the level of inbreeding by Illumina 70k SNP Equine bead chip to determine the distances and genetic structure related to the mentioned populations, to identify some conservation strategies for further investigations.

 

Material and methods

   In this study, the genotype dataset of 167 horses including Turkmen (40), Caspian (22), Kurdish (66), Dareshouri (15), and Arabian Asil (24) from the Equestrian federation of Iran databases were used. It was tried to ensure that none of the horses have family relationships in the pedigree for the analysis of genomic data. The hair samples were sent to the Geneseek laboratory in the United States and were genotyped using Illumina 70k SNP Equine bead chip. Data quality control was applied by PLINK v 1.9 (Purcell et al., 2007) software, and loci with MAF < 2%, Mind < 5%, HWE (<10-6), and genotype call rate < 1% were removed. Finally, 159 horses with 45,270 SNP loci were reminded for further analysis. Principal component analysis (PCA) was performed on SNP data using the "Prcomp" function in R v 4.2.1 (R Development Core Team, 2022). Finally, to examine the population structure, the assignment test, also determines the genomic kinship relationships between individuals in order to distinguish populations and identify outliners, we used adegenet v 2.0.0 package (Jombart et al., 2018) in R. Assigning of individual into their genetic groups was examined using the Structure v 2.3.4 (Pritchard et al., 2000) assuming K=2 to 8. The Structure algorithm included the admixture model and correlated allele frequencies.

 

Results and discussion

   Data quality control was applied and loci with MAF < 2%, Mind < 5%, HWE (<10-6), and genotype call rate < 1% were removed. Finally, 159 horses with 45,270 SNP loci were reminded. The results of PCA analysis showed that the populations were separated based on PC1 and based on PC2 geographic regions of all samples were separated into five main components. According to the PCA analysis, it can be seen that Dareshouri breed has a slight genomic admixture with Arabian Asil and Kurdish horses, while Arabian Asil, Turkmen, and Caspian were well differentiated from each other, which is close with results of Babayi et al., (2021). Similar to such grouping with a little admixture was also observed in Yousefi Mashouf et al., (2021) and Maghsoudi et al., (2017). In this research, both PCA and DAPC methods correctly separated the population of Iranian native horse breeds. The analysis of the genetic structure within the whole sample of Iranian horses with the admixture algorithm confirmed lack of differentiation between Caspian and Kurdish, Arabian Asil, and Dareshouri breeds at K=2, then we select different K from 2 to 5 as the optimal structure. The further results for K from 5 to 8 did not add information about genetic differentiation between populations. The LD decay among all breeds showed a significant decrease below 400 bp. Caspian and Dareshouri breeds experienced the lowest and highest LD and the highest and lowest effective population size, respectively. The low level of LD of the Caspian breed indicates that the effective size of this population is greater than that of other breeds. The inbreeding value based on runs of homozygosity (ROH) were highest and lowest for Arabian Asil and Caspian breeds, respectively. The results of this study showed that the Iranian native horse breeds were well defined by SNP markers, which can be used for stud base foundations of breeds with more accuracy.

مراجع

Abdoli, M. (2019). Genetic structure survey of Iranian horse breeds by SSR and SNP markers. Master Thesis. Department of Animal Science, University of Zanjan, Iran. pp.197. (In Persian).
Alexander, D. H., & Lange, K. (2011). Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC bioinformatics, 12, 1-6.
Almarzook, S., Reissmann, M., Arends, D., & Brockmann, G. A. (2017). Genetic diversity of Syrian Arabian horses. Animal genetics, 48(4), 486-489.
Asadollahpour Nanaei, H., Nosrati, M. and Mohammadabadi, M.R. (2021). Genetic structure analysis of Akhal-Teke horse population and comparison with other horse breeds by using whole genome sequencing data. Modern Genetics Journal. 16(4), pp.299-307. (In Persian).
Babaد yi, N., Rafat, S.A., Moradi, M.H. and Feizi Derakhshi, M.R., 2021. Comparison of principal component analysis (PCA) and discriminant analysis of principal component (DAPC) methods for analysis of population structure in Akhal-Take, Arabian, and Caspian horse breeds using genomic data. Iranian Journal of Animal Science Research, 13(3), pp.453-462. (In Persian).
Biscarini, F., Cozzi, P., Gaspa, G., & Marras, G. (2018). detectRUNS: Detect runs of homozygosity and runs of heterozygosity in diploid genomes.
Bohmanova, J., Sargolzaei, M., & Schenkel, F. S. (2010). Characteristics of linkage disequilibrium in North American Holsteins. BMC genomics, 11(1), 1-11.
Corbin, L. J., Blott, S. C., Swinburne, J. E., Vaudin, M., Bishop, S. C., & Woolliams, J. A. (2010). Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics, 41, 8-15.
Cosgrove, E. J., Sadeghi, R., Schlamp, F., Holl, H. M., Moradi-Shahrbabak, M., Miraei-Ashtiani, S. R., ... & Brooks, S. A. (2020). Genome diversity and the origin of the Arabian horse. Scientific reports, 10(1), 9702.
Eltanany, M., Elfaroug Sidahmed, O., & Distl, O. (2015). Assessment of genetic diversity and differentiation of two major camel ecotypes (Camelus dromedarius) in Sudan using microsatellite markers. Archives Animal Breeding, 58(2), 269-275.
Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin-Orlando, A., Leonardi, M., ... & Orlando, L. (2019). Tracking five millennia of horse management with extensive ancient genome time series. Cell, 177(6), 1419-1435.
Głażewska, I. (2010). Speculations on the origin of the Arabian horse breed. Livestock Science, 129(1-3), 49-55.
Jombart, T., Kamvar, Z. N., Collins, C., Lustrik, R., Beugin, M. P., Knaus, B. J., & Jombart, M. T. (2018). Package ‘adegenet’. Github repository:< https://github. com/thibautjombart/adegenet.
Jun, J., Cho, Y. S., Hu, H., Kim, H. M., Jho, S., Gadhvi, P., ... & Bhak, J. (2014). Whole genome sequence and analysis of the Marwari horse breed and its genetic origin. BMC genomics, 15(9), 1-10.
Ivanković, A., Bittante, G., Konjačić, M., Kelava Ugarković, N., Pećina, M., & Ramljak, J. (2021). Evaluation of the Conservation Status of the Croatian Posavina Horse Breed Based on Pedigree and Microsatellite Data. Animals, 11(7), 2130.
Khalili, M. (2009). Horse and my expertise. Tehran, Nashr-e Zare Publication. pp. 694. (In Persian).
Khalt-Abadi Farahani, A. H., & Moradi, M. H. (2018). Estimation of inbreeding values using genomic run of homozygosity and study of an evolutionary trend for effective population size in some Asian horse breeds. Iranian Journal of Animal Science, 49(3), 381-392. (In Persian).
Khan Ahmadi, A. (2017). Genomic exploration to track selection patterns in Turkmen and Kurdish horses using high-density SNP markers. Ph.D. Thesis, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran, pp. 140. (In Persian).
Mahrous, K. F., Hassanane, M., Mordy, M. A., Shafey, H. I. and Hassan, N. (2011). Genetic variations in horses using microsatellite markers. Journal of Genetic Engineering and Biotechnology. 9:103-9.
Maghsoodi, S. M., Mehrabani Yeganheh, H., Nejati Javaremi, A. and Yousefi Mashouf, N. 2017. Investigating population structure and identifying signatures of selection in Iranian Kurdish and Arabian horses. Iranian Journal of Animal Science, 48(3), 429-438. (In Persian).
McCoy, A. M., & McCue, M. E. (2014). Validation of imputation between equine genotyping arrays. Animal genetics, 45(1), 153.
McCue, M. E., Bannasch, D. L., Petersen, J. L., Gurr, J., Bailey, E., Binns, M. M., ... & Mickelson, J. R. (2012). A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS genetics, 8(1), e1002451.
Metzger, J., Karwath, M., Tonda, R., Beltran, S., Águeda, L., Gut, M., ... & Distl, O. (2015). Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC genomics, 16, 1-14.
Mousavi, S. F., Razmkabir, M., Rostamzadeh, J., & Seyedabadi, H. R. (2023). Evaluating of population diversity and detecting of genomic footprints of selection in four main Iranian horse breeds. Agricultural Biotechnology Journal, 15(2), 19-44. (In Persian).
Saghi, D., & Mobaraki, A. (2018). Estimation of inbreeding and survey of the pedigree structure of Iranian Turkmen horses population. Research On Animal Production (Scientific and Research), 9(22), 131-137. (In Persian).
Nasirpour, M., & Moradi Shahr Babak, H. (2024). Analysis of SNP Chip 70k Genomic Data to Identify Loci Related to Differentiation of Caspian and Kurdish Horses using Selection Sweep. Research On Animal Production, 14(39), 154-162. (In Persian).
Ovchinnikov, I. V., Dahms, T., Herauf, B., McCann, B., Juras, R., Castaneda, C., & Cothran, E. G. (2018). Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park. Plos one, 13(8), e0200795.
Pemberton, T. J., Absher, D., Feldman, M. W., Myers, R. M., Rosenberg, N. A., & Li, J. Z. (2012). Genomic patterns of homozygosity in worldwide human populations. The American Journal of Human Genetics, 91(2), 275-292.
Petersen, J. L., Mickelson, J. R., Cothran, E. G., Andersson, L. S., Axelsson, J., Bailey, E., ... & McCue, M. E. (2013). Genetic diversity in the modern horse illustrated from genome-wide SNP data. PloS one, 8(1), e54997.
Pometti, C. L., Bessega, C. F., Saidman, B. O., & Vilardi, J. C. (2014). Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods. Genetics and molecular biology, 37, 64-72.
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.
Purfield, D. C., Berry, D. P., McParland, S., & Bradley, D. G. (2012). Runs of homozygosity and population history in cattle. BMC genetics, 13, 1-11.
Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R., & Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal genetics, 41(4), 346-356.
R Core Team. 2022. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Rafeie, F., Amirinia, C., Javaremi, A. N., Mirhoseini, S. Z., & Amirmozafari, N. (2011). A study of patrilineal genetic diversity in Iranian indigenous horse breeds. African Journal of Biotechnology, 10(75), 17347-17352.
Sadeghi, R., Moradi-Shahrbabak, M., Miraei Ashtiani, S. R., Schlamp, F., Cosgrove, E. J., & Antczak, D. F. (2019). Genetic diversity of Persian Arabian horses and their relationship to other native Iranian horse breeds. Journal of Heredity, 110(2), 173-182.
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., ... & Orlando, L. (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences, 111(52), E5661-E5669.
Wade, C. M., Giulotto, E., Sigurdsson, S., Zoli, M., Gnerre, S., Imsland, F., ... & Lindblad-Toh, K. (2009). Genome sequence, comparative analysis, and population genetics of the domestic horse. Science, 326(5954), 865-867.
Warmuth, V., Eriksson, A., Bower, M. A., Cañon, J., Cothran, G., Distl, O., ... & Manica, A. (2011). European domestic horses originated in two Holocene refugia. PloS one, 6(3), e18194.
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. evolution, 1358-1370.
Yousefi-Mashouf, N., Mehrabani-Yeganeh, H., Nejati-Javaremi, A., Bailey, E., & Petersen, J. L. (2021). Genomic comparisons of Persian Kurdish, Persian Arabian and American thoroughbred horse populations. PLoS One, 16(2), e0247123.
Zandi, M. B. 2014. A study of patrilineal genetic diversity in Iranian indigenous horse breeds. Ph.D. Thesis, University of Tehran, Iran. (In Persian).
علوم دامی ایران
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  • تاریخ دریافت: 16 آبان 1402
  • تاریخ بازنگری: 23 فروردین 1403
  • تاریخ پذیرش: 08 خرداد 1403

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