Genetic Diversity Information Research Articles

Determination of the New SNP g.939A>G of the TYR Gene in Abnormal Coat Color in Bali Cattle

This study aimed to assess the presence of single nucleotide polymorphisms (SNPs) in the exon 1 region of the tyrosinase (TYR) gene in Bali cattle with abnormal coat color. This study analyzed 43 Bali cattle, 26 individuals with typical or standard coat color, and 17 individuals with albinism. The genetic diversity of the TYR gene was determined via direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. The sequence data of the TYR gene were scrutinized using BioEdit and MEGA10 software to detect single nucleotide polymorphisms (SNPs) related to different types of coat color features in Bali cattle. The genetic diversity information was derived from computations performed using PopGen 1.32 software. The results showed that exon 1 of the TYR gene was affected by the new SNP g.939A>G, which is polymorphic in Bali cattle. In conclusion, the SNP c.939A>G can be further analyzed for use as a candidate-assisted selection (MAS) for abnormal coat color in Bali cattle.

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Wild mustard (Sinapis arvensis L.) is a self-fertilizing weed species that exerts negative impacts on wheat production and herbicides are intensively used to manage it. Cross-fertilization may lead to genetic differentiation in this species. Therefore, this study investigated genetic diversity among wild mustard populations collected from wheat fields across various regions in Türkiye. Genetic variation was evaluated using 5 simple sequence repeat (SSR) markers in populations collected from 30 different locations. Populations were analyzed using UPGMA (unweighted pair group method with arithmetic mean) and principal component analysis (PCA). The mean genetic diversity (GD) and polymorphism information content (PIC) values were 0.752 and 0.844, respectively. High genetic variability was recorded among populations within geographic locations. The populations were categorized into two major groups by UPGMA. There was no apparent geographic isolation among tested populations, which displayed a high degree of variability. The primary source of this variability is thought to be the adaptability of wild mustard seeds dispersed through various methods across diverse locations. Despite being a predominantly self-pollinating species, wild mustard may also employ some cross-pollination mechanisms. In conclusion, SSR markers proved useful in determining genetic diversity in outcrossing species, especially where no prior genotypic information is available. The study suggests that genetic diversity is maintained in wild mustard populations even with rotational farming practices and intensive use of herbicides.

Comparison of Genetic Diversity and Core Locus Information of Abies yuanbaoshanensis Natural Population and Progeny

Comparison of Genetic Diversity and Core Locus Information of Abies yuanbaoshanensis Natural Population and Progeny

Integrative Taxonomy Clarifies the Historical Flaws in the Systematics and Distributions of Two Osteobrama Fishes (Cypriniformes: Cyprinidae) in India

The taxonomy and geographical distributions of Osteobrama species have historically posed challenges to ichthyologists, leading to uncertainties regarding their native ranges. While traditional taxonomy has proven valuable in classification, the utility of an integrated approach is restricted for this particular group due to limitations in combining information from biogeography, morphology, and genetic data. This study addresses the taxonomic puzzle arising from the recent identification of Osteobrama tikarpadaensis in the Mahanadi and Godavari Rivers, casting doubt on the actual distribution and systematics of both O. tikarpadaensis and Osteobrama vigorsii. The research reveals distinctions among specimens resembling O. vigorsii from the Krishna and Godavari riverine systems. Notably, specimens identified as O. vigorsii from the Indian Museum exhibit two pairs of barbels, while those from the Godavari River in this study are identified as O. tikarpadaensis. Inter-species genetic divergence and maximum likelihood phylogeny provide clear delineation between O. vigorsii and O. tikarpadaensis. The study suggests that O. vigorsii may be limited to the Krishna River system in southern India, while O. tikarpadaensis could potentially extend from the Mahanadi River in central India to the Godavari River in southern India. Proposed revision to morphological features for both species, accompanied by revised taxonomic keys, aim to facilitate accurate differentiation among Osteobrama congeners. The data generated by this research provide a resource for future systematic investigations into cyprinids in India and surrounding regions. Further, the genetic diversity information obtained from various riverine systems for Osteobrama species will be instrumental in guiding aquaculture practices and formulating effective conservation action plans.

Genetic Diversity of Bamboo (Yushinia alpina) Borer Larvae in the Mau Forest Complex, Kenya

Bamboo borer larvae have caused major losses of bamboo cover in natural forests and plantations. Lack of information on the fauna of bamboo trees has been cited as the contributing factor to poor management of bamboo stands. Genetic diversity information helps understand the effects of different fauna in guiding management plans. Genetic diversity information has recently become an important tool in conservation science. This paper aimed to determine the genetic diversity of the bamboo borer larvae in the Mau Forest complex in order to generate information that could guide the management and conservation of bamboo trees (Yushinia Alpina) in the Mau Forest Complex. The mitochondrial C oxidase Subunit 1 (COI) of 12 isolates was sequenced and analyzed. A similarity search of the bamboo borer larvae was carried out using the National Center for Biotechnology Information (NCBI) BLAST search to identify the larvae species. The genetic diversity and genetic pairwise distances were determined, and Tajimas D and Nei’s FU Fs statistics were calculated to estimate the population expansion that has occurred. The results showed genetic diversity (haplotype diversity 0.956) in the bamboo borer larvae population of the Mau Forest Complex. The nucleotide diversity (0.283) was found to be low. The similarity search showed that the bamboo borer larvae of Yushinia alpina belonged to four (4) species of noctuid larvae (Lepidoptera). The identity matches to the similar species scored an average of 94%. The Tajimas D (0.374) and FUs Fs (5.547) collectively indicated no rare excess mutations in the population. The results reveal high genetic diversity, which is key in the management of forest species

Characterization of the complete chloroplast genome of Gastrochilus sinensis (Orchidaceae, Epidendroideae), a beautiful epiphytic orchid from China

Gastrochilus sinensis is a beautiful epiphytic orchid with high ornamental value. In this study, the first complete chloroplast genome sequence of G. sinensis was determined using next-generation sequencing (NGS). The de novo assembled chloroplast genome was 148,020 bp in length, including a pair of inverted repeat regions (IRs; 25,987 bp), a small single-copy region (SSC; 11,045 bp), and a large single-copy region (LSC; 85,001 bp). The chloroplast genome encodes 109 unique genes, including 75 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the chloroplast genome was 36.8%. The phylogenetic analysis showed a close relationship between G. sinensis and G. formosanus species. The complete chloroplast genome provides fundamental information for genetic diversity and phylogenetic relationships in Gastrochilus.

POLYMORPHISM Inter Simple Sequence Repeats (ISSR) PRIMERS FOR GENETIC DIVERSITY FOR POOTI PLANTS (Hopea gregaria)

Pooti (Hopea gregaria) is a medium size tree that can grow up to 35 m from the Dipterocarpaceae family. Since 1998, the International Union for Conservation of Nature (IUCN) has reported the pooti tree as endangered, and the species has a narrow distribution, found only in Southeast Sulawesi. One of the efforts to overcome the rarity of the Pooti plant is through a tree breeding program. However, this tree breeding program will only be successful with the support of genetic diversity information. The study of genetic diversity can be done using a molecular-based approach using Inter Simple Sequence Repeats (ISSR) markers. Samples of Pooti leaves used in the study were taken from Botanical Forest Park Nipa-Nipa (Tahura) and Protected Forest Nanga-Nanga, Kendari City, Southeast Sulawesi Province. A total of 50 samples were extracted using the CTAB (Cetyl Trimethyl Ammonium Bromide) method. Ten types of primers that have been carried out obtained seven primers that can produce bright polymorphic bands and can be continued for study genetic diversity, namely UBC 810, UBC 813, UBC 814, UBC 822, UBC 823, UBC 827, and UBC 830.

Genetic Diversity of Bamboo (Yushinia alpina) Borer Larvae in the Mau Forest Complex, Kenya

Bamboo borer larvae have caused major losses of bamboo cover in natural forests and plantations. Lack of information on the fauna of bamboo trees has been cited as the contributing factor to poor management of bamboo stands. Genetic diversity information helps understand the effects of different fauna in guiding management plans. Genetic diversity information has recently become an important tool in conservation science. This paper aimed to determine the genetic diversity of the bamboo borer larvae in the Mau Forest complex in order to generate information that could guide the management and conservation of bamboo trees (Yushinia Alpina) in the Mau Forest Complex. The mitochondrial C oxidase Subunit 1 (COI) of 12 isolates was sequenced and analyzed. A similarity search of the bamboo borer larvae was carried out using the National Center for Biotechnology Information (NCBI) BLAST search to identify the larvae species. The genetic diversity and genetic pairwise distances were determined, and Tajimas D and Nei’s FU Fs statistics were calculated to estimate the population expansion that has occurred. The results showed genetic diversity (haplotype diversity 0.956) in the bamboo borer larvae population of the Mau Forest Complex. The nucleotide diversity (0.283) was found to be low. The similarity search showed that the bamboo borer larvae of Yushinia alpina belonged to four (4) species of noctuid larvae (Lepidoptera). The identity matches to the similar species scored an average of 94%. The Tajimas D (0.374) and FUs Fs (5.547) collectively indicated no rare excess mutations in the population. The results reveal high genetic diversity, which is key in the management of forest species

Evaluating potential of leaf reflectance spectra to monitor plant genetic variation

Remote sensing of vegetation by spectroscopy is increasingly used to characterize trait distributions in plant communities. How leaves interact with electromagnetic radiation is determined by their structure and contents of pigments, water, and abundant dry matter constituents like lignins, phenolics, and proteins. High-resolution (“hyperspectral”) spectroscopy can characterize trait variation at finer scales, and may help to reveal underlying genetic variation—information important for assessing the potential of populations to adapt to global change. Here, we use a set of 360 inbred genotypes of the wild coyote tobacco Nicotiana attenuata: wild accessions, recombinant inbred lines (RILs), and transgenic lines (TLs) with targeted changes to gene expression, to dissect genetic versus non-genetic influences on variation in leaf spectra across three experiments. We calculated leaf reflectance from hand-held field spectroradiometer measurements covering visible to short-wave infrared wavelengths of electromagnetic radiation (400–2500 nm) using a standard radiation source and backgrounds, resulting in a small and quantifiable measurement uncertainty. Plants were grown in more controlled (glasshouse) or more natural (field) environments, and leaves were measured both on- and off-plant with the measurement set-up thus also in more to less controlled environmental conditions. Entire spectra varied across genotypes and environments. We found that the greatest variance in leaf reflectance was explained by between-experiment and non-genetic between-sample differences, with subtler and more specific variation distinguishing groups of genotypes. The visible spectral region was most variable, distinguishing experimental settings as well as groups of genotypes within experiments, whereas parts of the short-wave infrared may vary more specifically with genotype. Overall, more genetically variable plant populations also showed more varied leaf spectra. We highlight key considerations for the application of field spectroscopy to assess genetic variation in plant populations.

High-density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia

IntroductionCommon bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies.MaterialsTwo hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers.ResultsThe overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classification. Model-based structure analysis delineated the 289 common bean genotypes into six hypothetical ancestoral populations.ConclusionsThe genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing effective collection and conservation for efficient utilization for the improvement of the crop.

Genetic polymorphism and variability in the Guangdong Hakka, Teochew, and Cantonese groups: A comprehensive analysis of 19 X-STRs.

X chromosomeshort tandem repeat (X-STR) loci are playing an increasingly important role inforensic work, identifying female traces in male contamination and explainingcomplex kinship analyses. In this study, we analyzed thegenetic polymorphism of 19 X-STR loci in the Guangdong Hakka, Teochew and Cantonese groups, respectively, aswell as in the Guangdong Hakka, Teochew andCantonese pooled Han. The genetic diversity and forensic characteristics of the19 X-STRs and 7 linkage groups were investigated, respectively. The experiments showed that the genetic diversity (GD) and polymorphism information content (PIC) in the pooledGuangdong Han ranged from 0.5320 to 0.9234 and 0.4369 to 0.9171, respectively, and the cumulative power of discrimination for males (PDM), power of discrimination for females (PDF) and mean paternity exclusion chance (MEC) were higher than 0.9999999, indicating that the 19 X-STRs had high geneticpolymorphism and discriminatory power. Genetic differences among Chinese Hansubgroups and among different Chinese populations were investigated byphylogenetic reconstruction and principal component analysis (PCA), respectively. Genetic analyses based on neighbor-joining (NJ) tree and principal component analysis plot showed that Cantonese, Teochew and Hakka were closely genetically related, and different populations with closer linguistic components had more genetic affinity. This study adds to the forensic X-STR database and demonstrates the forensic efficiency of 19 X-STRs for the Hakka, Teochewand Cantonese populations in Guangdong, and the pooled Han of Hakka, Teochewand Cantonese people in Guangdong.

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

Baseline genetic distinctiveness supports structured populations of thornback ray in the Mediterranean Sea

Abstract The thornback ray (Raja clavata) is the most important chondrichthyan in terms of landings in the Mediterranean Sea. Intense harvesting may induce negative genetic effects reducing the resilience of overfished species. For this reason, genetic diversity information should be considered in fisheries management and conservation policies. Microsatellite markers were used to unravel the genetic features (variability, connectivity, sex‐biased dispersal) of R. clavata populations, both at the small (around the coast of Sardinia, western Mediterranean Sea) and larger spatial scales (at the pan‐Mediterranean level, and between the Atlantic Ocean and the Mediterranean Sea). Individual clustering, multivariate and variance analyses rejected the hypothesis of genetic homogeneity, with significant genetic differences between Mediterranean and Atlantic rays, as well as within the Mediterranean Sea between its western and eastern basins. The data indicated that both the Strait of Gibraltar and the Sicilian Channel seem to be effective in limiting the dispersal of thornback ray individuals, but a further structuring was identified, with the significant genetic differentiation of the populations located in the Algero‐Provençal and Tyrrhenian basins. Such a fine‐scale arrangement suggests the occurrence of additional barriers to species dispersal. A lack of significant genetic differentiation, stable over the years, was measured at a local scale among R. clavata Sardinian samples. Several possible mechanisms, both biological and abiotic (e.g. migratory behaviour, waterfronts and oceanographic discontinuities), are discussed. Overall, the genetic data presented, both at the local and regional level, could represent the baseline information for the temporal monitoring of populations and assessing the effects of present or future fisheries‐related management actions. The data obtained are information of paramount importance for minimizing the gaps in our current knowledge of the genetic diversity of thornback rays and maximizing the information needed for the correct protection of R. clavata populations.

Genetic Diversity of Crossbred Cattle using Cytochrome Oxidase Subunit I (COI) Gene in South Sulawesi, Indonesia

Background: The genetic diversity information of local cattle and crossbred in South Sulawesi, Indonesia is essential for the establishment of conservation and breeding strategies. This research targeted to evaluate the phylogenetic relationship and genetic diversity of local and crossbred (CB) cattle. Methods: The present research organized at the Animal Laboratory, Professor Nidom Foundation, Surabaya, Indonesia from February to October 2021. The genome was isolated from 20 whole blood samples from seven purebreed belongs to Singosari National Artificial Insemination Center Malang, Indonesia, four crossbred in Gowa and nine crossbred in Sidrap, South Sulawesi, Indonesia. Partial sequences of mtDNA cytochrome oxidase subunit I (COI) gene were amplified employing the polymerase chain reaction technique. Result: This study revealed that a lot of single nucleotide polymorphism (SNP) found in local cattle (Bali and Peranakan Ongole) and CB cattle in Gowa and Sidrap indicated various genetic diversity can be used as a marker candidate and potential to be developed into future research knowing the correlation of the SNP with the growth rate of CB. Thus, this information will be helpful for further strategy in breeding development program.

Genetic Diversity and Population Structure of Selected Ethiopian Indigenous Cattle Breeds Using Microsatellite Markers.

In Ethiopia, livestock contributes 45% of agricultural GDP. Despite the economic role played by the sector, there have been little efforts to genetically improve the indigenous cattle. Morphological characterization of selected Ethiopian indigenous cattle has been made for (Bonga, Jimma, and Kerayu) cattle types. But, the selected indigenous cattle were not characterized at molecular level (genetic diversity information). Hence, this work was initiated to detect and determine the genetic diversity and population structure of selected Ethiopian indigenous cattle ecotypes using microsatellite markers. Different alleles were identified (131) and thirty-three of these alleles were unique to specific ecotypes. All loci used were informative with PIC values ranging from 0.5 (TGLA126) to 0.84 (ETH10) with a mean of 0.70 per locus. The Shannon information index ranged from (I = 1.02) ILST006 to (I = 1.63) ETH10 with an average of 1.28 revealing there is genetic diversity. Moreover, analysis of molecular variance (AMOVA) revealed 84% genetic variation within a population and 13% variation among populations. The value of F-statistics (Fst) (0.129 = 13%) indicated that there was moderate genetic differentiation among ecotypes. The (UPGMA) revealed, Bonga and Jimma clustered together while Kerayu cattle were relatively distinct, Principal coordinates analysis (PCOA) and structure analysis grouped the individual into different clusters confirming the presence of ecotype admixture due to geographical origins and uncontrolled mating. In general, this study has successfully characterized the genetic diversity and population structure of Bonga, Jimma, and Kerayu cattle ecotypes using high polymorphic/informative microsatellite markers. According to this study, Kerayu cattle have high AR and PA when compared to Bonga and Jimma cattle populations. So, the Kerayu population is more diverse than others and it is the hotspot for genetic diversity study. The generated information is very relevant for breeder and genetic conservation.

Assessment of the Genetic Structure and Diversity of Orobanche cumana populations from Turkey Using Simple Sequence Repeat Markers

Orobanche cumana Wallr. known as sunflower broomrape is a holoparasitic plant that causes huge yield losses in sunflower (Helianthus annuus L.) fields. Genetic characterization, genetic diversity, and race determination studies in O. cumana are very significant for preventing threats in sunflower fields. In this study, the broomrape populations sampled from Edirne, Kırklareli, Tekirdağ, and Adana provinces were used for genetic characterization. The sensitive Özdemirbey sunflower variety was used for growing O. cumana individuals. Eight simple sequence repeat (SSR) loci (Ocum52, Ocum70, Ocum81, Ocum87, Ocum108, Ocum141, Ocum160, and Ocum196) were used for the evaluation of genetic characterization and diversity of broomrape populations. All studied SSR loci were found to be polymorphic and yielded a total of 22 alleles in 143 samples analyzed. Na = 2.089 (mean number of alleles per locus), Ne = 1.390 (mean effective alleles), I = 0.392 (mean Shannon’s information index), Ho = 0.156 (mean observed heterozygosity), He = 0.239 (mean expected heterozygosity), and PIC = 0.228 (mean polymorphic information content) were calculated to assess genetic diversity of O. cumana populations.. As a result of molecular variance analysis, it was concluded that found that the genetic diversity of the populations was 38% among the population. The remaining 23% and 39% were due to among individuals and within individuals, respectively. The UPGMA method and STRUCTURE analysis divided the studied populations into 2 groups. Cluster I included LK2013, HT2016, T2018, and LE2013 populations, while group 2 included AE2003, AD2018, and MT2013 populations. The results we obtained have enabled us to reach important genetic diversity information about O. cumana, and the information obtained will provide important contributions for planned studies in the future.

Genetic Diversity, Population Structure and Subset Development in a Sesbania sesban Collection

Sesbania sesban (L.) Merr. is a multipurpose legume tree grown primarily for fodder and forage in the tropical and subtropical world. In this study, the Sesbania sesban collection maintained in the International Livestock Research Institute (ILRI) forage Genebank was studied using genome-wide markers generated on the DArTseq platform. Genotyping produced 84,673 and 60,626 SNP and SilicoDArT markers with a mean polymorphic information content of 0.153 and 0.123, respectively. From the generated markers, 7587 and 15,031 highly informative SNP and SilicoDArT markers, respectively, were filtered and used for genetic diversity analysis and subset development. Analysis of molecular variance (AMOVA) revealed higher variability 'within' (52.73% for SNP markers and 67.36% for SilicoDArT markers) than 'between' accessions. Hierarchical cluster analysis showed the presence of four main clusters in the collection. Mantel correlation analysis showed a lack of relationship between genetic variation of the germplasm and their geographical origin. A representative subset of 34 accessions containing germplasm from diverse origins and agro-ecologies was developed using SNP markers. The genetic diversity information generated in this study could be used for marker-assisted screening for stress tolerance, gap analysis and identification and acquisition of new distinct genotype(s) to broaden the genetic basis of the collection for future improvement programs to develop high-yielding, stress-tolerant varieties for enhancing food and environmental security in crop-livestock-based production systems.

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.

GENETIC DIVERSITY OF ALPINIA MALACCENSIS (BURM.F.) ROSCOE (ZINGIBERACEAE) IN JAVA ISLAND, INDONESIA

Alpinia malaccensis (Burm.f.) Roscoe is a rare plant in Java, Indonesia, that produces essential oils. Its sustained decline causes great concern for future uses. Therefore, the study of its diversity in its natural habitat to predict future survival needs serious focus. The present study aims to determine the genetic diversity of A. malaccensis in Java based on ISSR markers. The sampling of a total of 11 populations yielded 33 accessions, which underwent amplifying using 12 ISSR primers. Using the molecular data analyzed their relationships, population structure, and genetic diversity. The UPGMA cluster, structure, and principal component analysis (PCA) demonstrated that the accessions divide in three groups, a result that correlates with their geography in Java. Group I consisted of var. malaccensis populations, while groups II and III comprised the var. nobilis populations, which proved truer among populations of var. nobilis. The genetic diversity category of A. malaccensis showed moderate based on Nei's genetic diversity (h = 0.2892) and Shannon's information index (I = 0.4438). The coefficient of genetic differentiation (GST) and molecular variance among the populations displayed higher within the individual population, which revealed a significant genetic variance among the 11 populations of A. malaccensis. The latest results confirm that ISSR markers can help distinguish the genotypes of A. malaccensis.

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.