Volume 13, Issue 37 (11-2022)
rap 2022, 13(37): 175-186 |
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Biabani P, Mehrbani Yeganeh H, Moradi shahr babak H, Mokhber M. (2022). Detection of Genetic Differences between Holstein and Iranian North-West Indigenous Hybrid Cattles using Genomic Data. rap. 13(37), 175-186. doi:10.52547/rap.13.37.175
URL: http://rap.sanru.ac.ir/article-1-1294-en.html
URL: http://rap.sanru.ac.ir/article-1-1294-en.html
Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Tehran, Iran.
Abstract: (1430 Views)
Extended Abstract
Introduction and Objective: Selection to increase the frequency of new mutations useful only in some subpopulations leaves markers at the genome level. Most of these regions are related to genes and QTLs controlling significant economic traits.
Material and Methods: In order to detection of genetic differences between Iranian northwestern crossbred and Holstein cattle breed, respectively number of 100 and 60 sample from Iranian north-west hybrid and Holstein populations were used. After ensuring the distinct structure of the studied populations, FST, XP_EHH and Rsb statistics were used to identify the selection signatures and 21, 16 and 24 regions exceeding the threshold were identified as signatures of selection respectively. These selected genomic regions were surveyed and 104 and 135 genes were extracted from the corresponding areas in ARS-UCD1.2 Bos Taurus Genome Assembly for FST and LD based methods, respectively.
Results: Some of detected genes in regions under selection were involved in metabolic pathways related to taste, smell, fat metabolic pathways, resistance to disease and reproduction performance. Some of detected genes were involved with milk production by involving in WNT (Wingless-type) signaling pathway. The selected genomic regions were further examined for further analysis and finding of gene networks. These analyzes were performed by online software related to the genomic database (DAVID). Only one significant network was identified (p<4.5×10-9). This gene network communicates with taste receptors and specially detection of bitter tastes.
Conclusion: In addition to better understanding about natural and artificial selection effects on the Holstein breed and Iraniannorth-west indigenous hybrid, the selected regions can helpus to detecte QTLs and regions associated with important economic traits. In any case, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.
Introduction and Objective: Selection to increase the frequency of new mutations useful only in some subpopulations leaves markers at the genome level. Most of these regions are related to genes and QTLs controlling significant economic traits.
Material and Methods: In order to detection of genetic differences between Iranian northwestern crossbred and Holstein cattle breed, respectively number of 100 and 60 sample from Iranian north-west hybrid and Holstein populations were used. After ensuring the distinct structure of the studied populations, FST, XP_EHH and Rsb statistics were used to identify the selection signatures and 21, 16 and 24 regions exceeding the threshold were identified as signatures of selection respectively. These selected genomic regions were surveyed and 104 and 135 genes were extracted from the corresponding areas in ARS-UCD1.2 Bos Taurus Genome Assembly for FST and LD based methods, respectively.
Results: Some of detected genes in regions under selection were involved in metabolic pathways related to taste, smell, fat metabolic pathways, resistance to disease and reproduction performance. Some of detected genes were involved with milk production by involving in WNT (Wingless-type) signaling pathway. The selected genomic regions were further examined for further analysis and finding of gene networks. These analyzes were performed by online software related to the genomic database (DAVID). Only one significant network was identified (p<4.5×10-9). This gene network communicates with taste receptors and specially detection of bitter tastes.
Conclusion: In addition to better understanding about natural and artificial selection effects on the Holstein breed and Iraniannorth-west indigenous hybrid, the selected regions can helpus to detecte QTLs and regions associated with important economic traits. In any case, it will be necessary to carry out more association and functional studies to demonstrate the implication of these genes.
Keywords: Holstein cattle breed, Iranian northwestern native crossbred cattle, Population differentiation index, Signatures of selection
Type of Study: Research |
Subject:
ژنتیک و اصلاح نژاد دام
Received: 2022/04/13 | Revised: 2022/11/19 | Accepted: 2022/08/16 | Published: 2022/11/19
Received: 2022/04/13 | Revised: 2022/11/19 | Accepted: 2022/08/16 | Published: 2022/11/19
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