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Asian-Australas J Anim Sci > Accepted Articles
DOI: https://doi.org/10.5713/ajas.19.0380    [Accepted] Published online November 12, 2019.
Investigating population structure and genetic diversity of some Iranian native cattle breeds using SNP markers
Zahra Jafari1  , Ali Akbar Masoudi1,*  , Hossein Moradi Shahrbabak2,* 
1Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, PO Box 14115–336, Pajoohesh Blvd, 149771311 Tehran, Iran
2Department of Animal Science, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources, University of Tehran, Postal code 31587-11167, PO Box 4111, Karaj, Iran
Correspondence:  Ali Akbar Masoudi, Tel: +98-48292353, Fax: +98-48292200, Email: masoudia@modares.ac.ir
Hossein Moradi Shahrbabak,Email: hmoradis@ut.ac.ir
Received: 7 May 2019   • Revised: 31 July 2019   • Accepted: 8 November 2019
Abstract
Objective
Reliable information about the demographics and population structure of endangered species is important for conservation strategies. In this regard, the population structure and genetic diversity of three Iranian cattle breeds were investigated.
Methods
The samples included Sarabi (n = 213), Taleshi (n = 81), and Nejdi (n = 211). They were genotyped using BovineSNP40 BeadChip. In addition, 45 Holstein (Bos taurus) and 46 Brahman (Bos indicus) out-group samples were used. Principal component analysis (PCA) and discriminant analysis of principal components (DAPC) were used to study the population structure.
Results
Based on Bayesian information criterion (BIC), the optimal number of clusters for DAPC method was obtained equal to seven. The populations were separated based on this clustering. The highest value of markers with minor allele frequency (MAF) ≥ 0.05 was observed in the Nejdi population (94.24%). The lowest FST (0.053) and the lowest Nei's genetic distance (0.037) in the indigenous cattle were observed between Taleshi and Nejdi breeds, which were also consistent with the results of the phylogenetic analysis. Moreover, phylogenetic tree showed that Iranian cattle breeds are admixture breeds from varying degrees of Bos indicus and Bos taurus. The results of AMOVA revealed 36.62 % genetic variation between cattle breeds (P < 0.001).
Conclusions
This study showed that the value of FST was low between the Taleshi and Nejdi breeds, which is due to their common ancestry. Within breed genetic diversity was high in Sarabi, Taleshi, and Nejdi breeds. Significant levels of genetic diversity in these breeds can be applied to conserve these cattle and increase their reproduction through suitable breeding programs.
Keywords: Conservation; DAPC Analysis; Biodiversity; SNP chip; Bos taurus and Bos indicus


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