Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Ünal, Emel Özkan; Özdil, Fulya; Kaplan, Selçuk; Gürcan, Eser Kemal; Genç, Serdar; Arat, Sezen; Soysal, M. I.

doi:10.3390/ani10111970

Cited by 6 publications

(10 citation statements)

References 44 publications

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“…The mtDNA genome of donkeys is 16 670 bp, of which the D-loop region is 1 207 bp (Xu et al, 1996). As reported in previous genetic studies on donkeys (Lopez et al, 2005;Ma et al, 2020;Ozkan Unal et al, 2020), the D-loop region of ancestral mtDNA supplies adequate information to assess genetic variation, evolutionary relationships, and matrilineal genetic origins.…”

Section: Discussionmentioning

confidence: 79%

“…DNAsp v6 (Rozas et al, 2017) was used to calculate the nucleotide diversity, polymorphic sites, and haplotype diversity of the most variable region in the HGD mtDNA D-loop region. Genetic relationships among populations were determined using median-joining networks (MJN) using Network v.10.1.0.0 software (Bandelt et al, 1999), the MJN was constructed from 11 haplotypes found in this study and 60 reference sequences found previously (Ozkan Unal et al, 2020;Xia et al, 2019), the 15 sequences including Hap4,Hap6,Hap7,and Hap10,Hap12,Hap16,Hap18,Hap20,Hap22,Hap23,Hap24,Hap25,Hap26,Hap27, Hap29 belonged to Clade I. Reference mtDNA D-loop region sequences of wild and domestic donkey were obtained from GenBank and used as comparators of HGDs to build phylogenetic trees and speculate their origin (Han et al, 2014;Ivankovic et al, 2002;Kimura et al, 2011;Oakenfull et al, 2000;Ozkan Unal et al, 2020).…”

Section: Sequence Assembly and Sequence Analysismentioning

confidence: 99%

“…Studies of donkey mitochondrial sequences have suggested that there were two highly differentiated maternal lineages (Clade I and Clade II) during donkey domestication (Equus asinus ), Clade I clustered clearly with the Nubian wild ass (E. africanus africanus ); Clade II originated from the Somali wild ass (E. africanus somaliensis ) which was probably on the verge of extinction (Beja-Pereira et al, 2004;Chen et al, 2006;Kimura et al, 2011). In recent years, an increasing number of studies on donkeys' mtDNA have assessed the evolutionary relationship, variation and genetic diversity among Asian, European, and African breeds (Gan et al, 2011;Han et al, 2014;Lei et al, 2007;Ma et al, 2020;Ozkan Unal et al, 2020;Perez-Pardal et al, 2014).…”

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confidence: 99%

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The complete mtDNA genome of Huaibei Grey donkey: genome characterization and phylogenetic analysis

Xia

Chang

et al. 2022

Preprint

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To investigate the conservation and phylogenetic relationship with other breeds of the local Anhui Province Huaibei Grey donkey (HGD), the complete mitochondrial DNA (mtDNA) was sequenced and de novo assembled using deep sequencing data from total genomic DNA. The final size of mtDNA was 16 670 bp (NCBI submission number: MZ911746), including 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one non-coding control region. The PCGs region consisted of 5 559 codons. Most of the PCGs had ATG and TAA as the start and stop codons, respectively. Then we analyzed the proximal part of the D-loop region (418 bp, between 15 419 bp to 15 836 bp) from HGDs, using DNAsp v6 software. We identified 23 polymorphic nucleotide sites and found that the A, C, G, and T bases comprised 30.4%, 34.9%, 13.1%, 21.6%, respectively, of the mtDNA D-loop sequence. The haplotype and nucleotide diversity were 0.87000 and 0.02115, correspondingly. Altogether, the 60 sequences displayed 11 different haplotypes, the most frequent haplotype was H9 (23.33%), followed by H4 (21.67%). MJ network analysis indicated that all haplotypes were clearly divided into Clade Ⅰ and Ⅱ lineages, which indicates that HGD may have two maternal lineages. Phylogeographic analysis indicates that the Somali lineage could be the most probable domestication center for HGD. Our study provides an empirical basis for the characterization, conservation, and management of HGD genetic resources.

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Section: Discussionmentioning

confidence: 79%

Section: Sequence Assembly and Sequence Analysismentioning

confidence: 99%

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confidence: 99%

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The complete mtDNA genome of Huaibei Grey donkey: genome characterization and phylogenetic analysis

Xia

Chang

et al. 2022

Preprint

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“…MtDNA contains a non-coding control region, also called the displacement-loop region (Dloop) [23]. Previous studies of donkey mtDNA D-loop (control region) sequences depicted the genetic relationships and origin of worldwide modern donkey breeds well [19,[24][25][26][27][28][29][30][31].…”

Section: Introductionmentioning

confidence: 99%

Genetic and Population Structure of Croatian Local Donkey Breeds

Ivanković

Bittante

Šubara³

et al. 2022

Diversity

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The two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of two donkey breeds, two decades after the start of protection by analyzing their pedigrees and genetic structure. The average generation interval was higher for the Istrian donkey (7.73) than for the Littoral-Dinaric donkey (7.27). The rate of the effective number of founders compared with the effective number of ancestors in the Littoral-Dinaric donkey (1.03; 325/316) and in the Istrian donkey (1.08; 70/65) revealed no evidence of a genetic bottleneck. The inbreeding coefficient (F) and the average relatedness coefficient (AR) was lower in the Littoral-Dinaric donkey population (0.99%; 0.13%) than in the Istrian donkey population (1.77%; 1.10%). Genetic microsatellite analysis showed relatively high genetic diversity in Littoral-Dinaric donkey and Istrian donkey breeds, expressed by mean allele number (5.92; 5.85) and expected heterozygosity (0.650; 0.653). Genetic differentiation between the Littoral-Dinaric donkey and the Istrian donkey has not significantly increased in the last two decades (FST = 0.028). Genetic analysis also showed no evidence of high inbreeding or genetic bottleneck in both breeds. A total of 11 haplotypes including 28 polymorphic sites were found in 30 samples. Analysis of mtDNA has shown that the Littoral-Dinaric donkey and Istrian donkey breeds belong to the Equus asinus africanus group. The study confirms the need to use different analytical approaches to get a regular and complete insight into the situation and trends within and between breeds, so that the existing diversity can be fully preserved.

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“…Turkish indigenous donkey Turkey [50] The Huaibei Grey donkey mitochondrial genome is 16,617 bp long and contains 37 genes, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes [19]. Phylogenetic analysis of 25 Equidae species' complete mitochondrial genomes revealed that the Huaibei Grey donkey is closely related to other domestic donkey breeds, forming a distinct clade.…”

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confidence: 99%

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

Huang,

Khan,

Chai

et al. 2023

Animals

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Donkeys (Equus asinus) play a pivotal role as essential livestock in arid and semi-arid regions, serving various purposes such as transportation, agriculture, and milk production. Despite their significance, donkey breeding has often been overlooked in comparison to other livestock species, resulting in limited genetic improvement programs. Preserving donkey genetic resources within each country necessitates the establishment of breed conservation programs, focusing on managing genetic diversity among populations. In recent years, significant strides have been made in sequencing and analyzing complete mitochondrial DNA (mtDNA) molecules in donkeys. Notably, numerous studies have honed in on the mitochondrial D-loop region, renowned for its remarkable variability and higher substitution rate within the mtDNA genome, rendering it an effective genetic marker for assessing genetic diversity in donkeys. Furthermore, genetic markers at the RNA/DNA level have emerged as indispensable tools for enhancing production and reproduction traits in donkeys. Traditional animal breeding approaches based solely on phenotypic traits, such as milk yields, weight, and height, are influenced by both genetic and environmental factors. To overcome these challenges, genetic markers, such as polymorphisms, InDel, or entire gene sequences associated with desirable traits in animals, have achieved widespread usage in animal breeding practices. These markers have proven increasingly valuable for facilitating the selection of productive and reproductive traits in donkeys. This comprehensive review examines the cutting-edge research on mitochondrial DNA as a tool for assessing donkey biodiversity. Additionally, it highlights the role of genetic markers at the DNA/RNA level, enabling the informed selection of optimal production and reproductive traits in donkeys, thereby driving advancements in donkey genetic conservation and breeding programs.

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Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Cited by 6 publications

References 44 publications

The complete mtDNA genome of Huaibei Grey donkey: genome characterization and phylogenetic analysis

The complete mtDNA genome of Huaibei Grey donkey: genome characterization and phylogenetic analysis

Genetic and Population Structure of Croatian Local Donkey Breeds

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

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