Mitochondrial D-loop Sequences Research Articles

Genetic diversity of mitochondrial DNA D-loop sequence in Bang Troi chicken breed

Bang Troi chicken (GBT) is a local chicken that is free-gardening raised in Quang Ninh province. A 1,268 bp of mitochondrial DNA (mtDNA) D-loop of 17 Bang Troi chicken individuals was sequenced and analyzed. Comparative multiple sequence alignment revealed 17 base substitutions within 17 Bang Troi chicken individuals. Bang Troi chicken had a relatively high level of genetic diversity, expressed in the number of 13 haplotypes, haplotype diversity of 0.949. The Tajima’s test indicated that the analysed population in balancing selection with a D-value of 2.39. A phylogenetic tree based on 455 bp of hypervariable mtD-loop sequence classified 17 Bang Troi chicken individuals into three clades A, B, and E, which are common groups of Vietnamese and Asia indigenous chickens. This result provides the first genetic information and maternal lineages of Bang Troi chickens and it can support for registration of local chicken breeds.

Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences.

The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA) D-loop sequences among 12 Ugandan chicken populations was evaluated. Twenty-eight polymorphic sites, accounting for 4.26% of the total analyzed loci of 658bp, defined 32 haplotypes. The haplotype diversity (Hd) was 0.437, with a nucleotide diversity (π) of 0.0169, while the average number of nucleotide differences (k) was 0.576, indicating a population that is moderately genetically diverse. Analysis of molecular variance found 98.39% (ρ < 0.01) of the total sequence variation among the chicken haplotypes within populations, 1.08% (ρ < 0.05) among populations, and 0.75% (ρ > 0.05) among populations within regions. This revealed subtle genetic differentiation among the populations, which appeared to be influenced by population fragmentation, probably due to neutral mutation, random genetic drift, and/or balancing selection. All the haplotypes showed affinity exclusively to the haplogroup-E mtDNA phylogeny, with haplotype UGA01 signaling an ancestral haplotype in Uganda. Neutrality tests Tajima's D (-2.320) and Fu's Fs (-51.369), augmented with mismatch distribution to measure signatures of recent historical demographic events, supported a population expansion across the chicken populations. The results show one matrilineal ancestry of Ugandan chickens from a lineage widespread throughout the world that began in the Indian subcontinent. The lack of phylogeographic signals is consistent with recent expansion events with extensive within-country genetic intermixing among haplotypes. Thus, the findings in this study hold the potential to guide conservation strategies and breeding programs in Uganda, given that higher genetic diversity comes from within the chicken population.

Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA

Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia–Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.

Contamination acts as a genotype-dependent barrier to gene flow, causing genetic erosion and fine-grained population subdivision in Mussels from the Strait of Istanbul.

This study provides evidence of fine-grained genetic structuring in Mediterranean mussels (Mytilus galloprovincialis) from the Strait of Istanbul, caused by barriers to gene flow via contaminant-mediated selection. In this study, mitochondrial D-loop sequences were analyzed in mussels from 8 localities, all less than 30 kilometers apart, with differing contaminant loads. The results were: 1) Intra-population genetic differentiation (ΦST) between sites with high and low contaminant loads was high (up to 0.459), even at distances of only a few kilometers. 2) Genetic diversity was negatively correlated with the contaminant load ("genetic erosion"). 3) There was evidence of selection, based on haplotype frequencies and neutrality tests (Tajima's D), with purifying selection at the most contaminated site and balancing selection at the least contaminated. 4) Genetic distance was not correlated with geographic distance (no isolation-by-distance), but was correlated with contaminant load at each site. 5) Population dendrograms and Bayesian estimators of migration indicated that gene flow between sites was affected by contamination. For the dendrograms of the sampling sites, the clades clustered according to contaminant load more than geographic distance. Overall, these results suggest that 1) contamination may serve as a genotype-dependent dispersal barrier (i.e., contamination may not affect total number of migrants, just the relative proportions of the haplotypes in the established immigrants), leading strong population differentiation over short distances, and 2) genetic erosion may occur by a combination of selection and altered patterns of haplotype-specific gene flow. These effects may be more pronounced in the Strait of Istanbul than in other locations because of the riverine nature and strong, uni-directional current of the strait.

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Phylogenetic evolution of Egyptian goat breeds “Capra hircus” based on Mitochondrial DNA D-loop sequence.

Phylogenetic evolution of Egyptian goat breeds “Capra hircus” based on Mitochondrial DNA D-loop sequence.

Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses.

Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin culture. To that end, we collected 211 hair samples from stud farms renowned for breeding Arabian show horses from Nejd KSA, Bahrain, Egypt, Qatar, Morocco, UAE, and Poland. The phylogenetic and network analyses of the whole mitochondrial DNA D-loop sequence highlighted a great genetic diversity among the Arabian horse populations, in which about 75% of variance was assigned to populations and 25% to strains. The discriminant analysis of principal components illustrated a relative distinction between those populations. A clear subdivision between traditional strains was found in PL, in contrast to the situation of DB and EG populations. However, several Polish horse individuals could not be traced back to the Bedouin tribes by historical documentation and were shown to differ genetically from other studied Bedouin strains, hence motivating extended investigations.

Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken.

Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.

Genetic diversity of mitochondrial DNA D-loop in wild and domestic pigs (Sus scrofa) in East Asia

Chinese domestic pig breeds have abundant genetic resources, but definite information about the geographic specificity and genetic structure is lacking. In this study, we analysed 359 mitochondrial D-loop sequences, including 86 sequences from Chinese domestic pigs and the rest downloaded from GenBank. The haplotype and nucleotide diversity indices ranged from 0.467 ±0.132 (Duroc) to 1.000 ±0.500 (Thailand, North Korea and Cambodia) and 0.00067 ±0.00019 (Duroc) to 0.02000 ±0.01000 (Thailand), respectively. The neighbour-joining tree revealed two clads in the individual pigs, with a Chinese domestic breed distributed discontinuously among several breeds. The network data indicated that the gene pools of Chinese domestic pigs are likely related to Chinese, Japanese and some other Southeast Asian wild boars.

Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling.

Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.

Pilot study of a comprehensive resource estimation method from environmental DNA using universal D-loop amplification primers

Many studies have investigated the ability of environmental DNA (eDNA) to identify the species. However, when individual species are to be identified, accurate estimation of their abundance using traditional eDNA analyses is still difficult. We previously developed a novel analytical method called HaCeD-Seq (haplotype count from eDNA by sequencing), which focuses on the mitochondrial D-loop sequence for eels and tuna. In this study, universal D-loop primers were designed to enable the comprehensive detection of multiple fish species by a single sequence. To sequence the full-length D-loop with high accuracy, we performed nanopore sequencing with unique molecular identifiers (UMI). In addition, to determine the D-loop reference sequence, whole genome sequencing was performed with thin coverage, and complete mitochondrial genomes were determined. We developed a UMI-based Nanopore D-loop sequencing analysis pipeline and released it as open-source software. We detected 5 out of 15 species (33%) and 10 haplotypes out of 35 individuals (29%) among the detected species. This study demonstrates the possibility of comprehensively obtaining information related to population size from eDNA. In the future, this method can be used to improve the accuracy of fish resource estimation, which is currently highly dependent on fishing catches.

Matrilineal Composition of the Reconstructed Stock of the Szekler Horse Breed

The Szekler horse was a small-sized mountain horse of the Carpathian Mountains whose official stud book ceased to exist after WWII. Despite that, individual horses preserving all the characteristics of the Szekler horse remained scattered in remote areas. This study aims to evaluate the mitochondrial D-loop sequence (608 bp) of the founder population (n = 59) in 2021 of a breed reconstruction project started in 2012. D-loop showed 68 polymorphic sites. The number of haplotypes was 34, with haplotype diversity (Hd) 0.966 and nucleotide diversity (π) 0.02232. The value of Fu’s Fs statistic (−6.566) was significant (p &lt; 0.001), which rejects a stable population status. Thirteen haplogroups (HG) were found with a nearly equal number of representatives (HG(n)—A (5), D (1), E (2), G (4), I (4), J–K (1), M (4), N (2), O’P (4), and R (1)). In contrast, the Q, L, and B HGs occurred in more horses (15, 9, and 7, respectively). Based on a large number of polymorphic sites and haplotypes, the founder stock is considered diverse. Since the HG Q is characteristic of Asian horses, the examined stock haplotype distribution reflects the eastern origin of the Hungarian horses brought from the East in 896 AD. It is complemented by the gene pool of horses from Europe (e.g., L) and the Middle East (e.g., B).

Genetic Monitoring of the Last Captive Population of Greater Mouse-Deer on the Thai Mainland and Prediction of Habitat Suitability before Reintroduction

Developing successful conservation programs for genetically depleted species is challenging. Survival and adaptive potential are related to genetic and habitat factors; therefore, conservation programs are designed to minimize risks associated with inbreeding and loss of genetic diversity. The greater mouse-deer (Tragulus napu) is a true forest species that contributes to seed distribution dynamics in forests. However, with continuous demographic decline over the last century in the wild, only captive populations of the greater mouse-deer remain on the Thai mainland. A restoration program initiated 20 years ago has increased their population to more than 100 individuals but maintaining high genetic diversity in a small captive population is crucial for successful recovery. Microsatellite genotyping and mitochondrial D-loop and SRY gene sequence analyses were performed to examine the genetic diversity and population structure in 123 greater mouse-deer (64 females and 59 males). Highly reduced effective captive population size with trends of inbreeding were observed. No historical bottleneck was observed. These conditions have reduced their reproductive fitness and ability to adapt to environmental change, increasing the risk of population decline and eventual extinction. Demographic analyses suggested a recent captive population expansion due to effective animal welfare and reproduction. The results also suggested that population size at equilibrium is the main factor of allelic diversity (number of alleles). Large habitat carrying capacity, representing each fixed captive population size can support the genetic diversity of greater mouse-deer. We also identified suitable habitat areas for reintroduction and long-term in situ conservation of greater mouse-deer using maximum entropy modeling. Based on the environmental variables, species distribution modeling for greater mouse-deer indicated lowland tropical forest regions in the Khlong Saeng-Khao Sok forest complexes as most suitable and requiring urgent habitat improvement. These findings highlight the relevance of careful genetic monitoring and habitat suitability for the long-term conservation of greater mouse-deer and enhance the success of future conservation plans.

Large-scale genetic surveys for main extant population of wild giant panda (Ailuropoda melanoleuca) reveals an urgent need of human management.

There are only six isolated living giant panda populations, and a comprehensive understanding of their genetic health status is crucial for the conservation of this vulnerable species. Liangshan Mountains is one of the main distribution areas of living giant pandas and is outside the newly established Giant panda national park. In this study, 971 giant panda fecal samples were collected in the heartland of Liangshan Mountains (Mabian Dafengding Nature Reserve: MB; Meigu Dafengding Nature Reserve: MG; and Heizhugou Nature Reserve: HZG). Microsatellite markers and mitochondrial D-loop sequences were used to estimate population size and genetic diversity. We identified 92 individuals (MB: 27, MG: 22, HZG: 43) from the three reserves. Our results showed that: (1) genetic diversity of three giant panda populations was moderate; (2) several loci deviated significantly from the Hardy-Weinberg equilibrium and almost all these deviated loci showed significant heterozygote deficiencies and inbreeding; (3) three giant panda populations have substantial genetic differentiation with the most differentiation between MB and the two other populations; and (4) a large amount of giant panda feces outside the three reserves were found, implying the existence of protection gap. These results indicated that under stochastic events, the giant panda populations in Liangshan Mountains are at risk of genetic decline or extinction and urgent need of human management. This study revealed that high attention should be paid to the protection of these giant panda populations outside the Giant panda national park, to ensure their survival in their distribution areas.

Mitochondrial DNA D-Loop Amplification and Sequencing for Species Differentiation in Milk.

Adulteration of dairy products, mainly through the substitution of high-quality milk for lower-quality milk, results in the production of low-value products, raising health, social, and economic concerns. As such, the development of methods to ensure dairy products' safety and quality is of great concern for governments and consumers. Although several methods have been developed for species differentiation in dairy products, their application and the establishment of reliable molecular markers for authentication purposes still need to be improved. In this chapter, we describe a low-cost, sensitive, fast, and reliable PCR-based method for mitochondrial D-loop DNA amplification for efficient detection of cattle milk in binary mixtures with sheep milk, thereby allowing the authentication of processed dairy products.

Phylogenetic analysis of mitochondrial D-loop sequence of Mongolian wild boars

Genomic DNA was extracted from tissue specimens of wild boars (Sus scrofa) in 10 different locations Mongolia. D-loop part of genome was amplified by PCR and was subjected to DNA sequencing. Determined sequences from 18 specimens were registered with the GenBank and accession numbers were obtained. A total of 54 complete mitochondrial D-loop sequences of wild boars available with NCBI GenBank were taken as a reference for comparison with that of Mongolian wild boars. Sequence alignment, detection of parsimonious informative sites, model selection, calculation of nucleotide distances, and Maximum Likelihood (ML) phylogenetic tree construction with 1000 bootstrapped replications were conducted using MEGA X software. Maximum Likelihood trees were constructed by the Hasegawa-Kishino-Yano (HKY) model. The results of the study showed that geographic location played an important role in sequence divergence between wild boars from various locations. Most of them were grouped together according to their respective geographic locations, except for several individuals. It is highly likely that the Mongolian subpopulation of wild boars, such as S. scrofa raddianus and S. scrofa nigripes, have had the same ancestor. In order to fully evaluate the distribution, ecology, and biology of Mongolian wild boars, it is essential to compare supplemental gene sequences that can reveal phylogenetic differences from the populations in the neighboring areas, such as Russia, northeast China, and Kazakhstan. The results of this study will be useful and informative for the protecting and conserving of wild boars in Mongolia.

Low genetic diversity in a widespread whistling alien: A comparison of Eleutherodactylus johnstonei Barbour, 1914 (Eleutherodactylidae) and congeners in native and introduced ranges

There is no clear empirical evidence to support the general assumption that genetic diversity favours successful invasions. Many invading species disperse and establish successfully despite low genetic diversity, a phenomenon known as the genetic paradox of biological invasion. Model systems that allow comparison of genetic patterns between exotic and native source populations are still scarce. This is particularly true for amphibians. Here we compare genetic patterns of the widely introduced Johnstone’s Whistling Frog, Eleutherodactylus johnstonei, with its successful alien congener E. antillensis and the single island endemic E. portoricensis. Genetic diversity and population differentiation in native and introduced populations of the three taxa were inferred from mitochondrial D-loop sequences (235 bp). Our results reveal that exotic populations of the two alien taxa, E. johnstonei and E. antillensis, are not only genetically impoverished due to founder effects, but that, moreover, their native range source-populations exhibit low genetic diversity and inter-population differentiation in the first place. Populations of the endemic E. portoricensis, on the other hand, are genetically more diverse and show marked inter-population differentiation. These observed genetic patterns are consistent with geological processes and invasion histories. We argue that the establishment success of the alien taxa in our model system is better explained by ecological factors and anthropogenic drivers than by genetic diversity. As these factors provide more parsimonious explanations, they should be given priority in management decisions. However, molecular studies with higher resolution are needed to fully test possible genetic and epigenetic components that could promote the invasion process.

Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle.

Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.

Standard Identification Certificate for Legal Legislation of a Unique Gene Pool of Thai Domestic Elephants Originating from a Male Elephant Contribution to Breeding

Illegal wildlife trade is a major threat to global biodiversity. Asian elephants (Elephas maximus) are highly valued by various cultures as religious symbols and tourist attractions, which has led to a high demand for captive elephants. Owing to the unviability of captive breeding programs, several captive elephant populations are maintained by illegally obtaining wild Asian elephants. Morbidity and mortality rates among captive populations are high, whereas reproduction is low. In this study, we examined the genetic diversity among elephants using microsatellite genotyping and mitochondrial D-loop sequences of three captive elephant populations. The study results showed very low nucleotide diversity D-loop sequences and high variations in microsatellite genotyping, with an extensive variation of the gene pool estimates from different populations. This suggests that the optimal male selection during breeding could aid in maintaining the genetic diversity among captive populations. Forward genetic simulation revealed a decreasing genetic diversity in the fixed state within 50 generations. However, largely different gene pools can be effectively used to infer original elephant sources; this would facilitate the development of an identification certificate integration with machine learning and image processing to prevent illegal legislation owing to registration fraud between wild and domestic elephants. Implementing the proposed approaches and recommendations would aid in the mitigation of the illegal capture and domestic trade of wild elephants in Thailand and contribute to the success of future conservation plans in the blueprint of sustainable development goals.

Mitochondrial D-loop sequences and haplotypes diversity in Egyptian rabbit breeds

Rabbit breeds in Egypt are local and adapted foreign breeds that have been imported since the middle of the last century. Stressful environmental conditions including climatic changes, exposure to diseases and breeding selection have an influence on how gene flow has shaped the genetic diversity of the breeds. Mitochondrial DNA D-loop is a genetic marker used to trace the geographic distribution of genetic variation for the investigation of expansions, migrations and other gene flow patterns. The study aimed to determine the genetic diversity of the mitochondrial DNA D-loop (mtDNA D-loop) in Black Baladi, Red Baladi, Gabali, APRI line and New Zealand breeds to gather the scientific data required to create a proper conservation and sustainable management plan. Blood samples were taken from animals unrelated to each other. A 332-bp of mtDNA D-loop was successfully amplified and alignment sequences were deposited in the GenBank database. The results detected six haplotypes in the five breeds. Haplotype diversity within individual breeds varied from 0 (Red Baladi) to 0.551±0.114 (Gabali). The nucleotide diversity (π) value was relatively low (0.001-0.006), with greater values in APRI and New Zealand. Pairwise distances between breeds yielded varying values ranging from 0 to 0.254, and the values between the Red Baladi and other breeds were comparatively high, with pairwise distances from 0.172 to 0.254. The phylogenetic analysis involved 74 nucleotide sequences of the Egyptian rabbit and thirty-one sequences retrieved from GenBank of the reference samples of different haplogroups. The results of the phylogenetic analysis correlated to the reference mtDNA GenBank database showed that the five Egyptian rabbit breeds were grouped into haplotypes A, B and K. The results of the genetic diversity using mtDNA shed light on the importance of the local breed’s genetic diversity information and revealed unique mtDNA haplotypes, which is an important finding for breeding strategies designed to conserve genetic variants and provide sustainable management.