Mitochondrial DNA D-loop Research Articles

Phylogenetic and population genetic analysis of Arunachali Yak (Bos grunniens) using mitochondrial DNA D-loop region.

The Arunachali yak (Bos grunniens) is an important breed native to the northeastern Himalayas of India. Understanding its genetic diversity and evolutionary relationships with other bovine species is crucial for effective conservation and breeding strategies. This study investigates the mitochondrial DNA (mtDNA) D-loop region of Arunachali yak and compares it with other bovines to elucidate these relationships. We collected blood samples from 18 Arunachali yak individuals and isolated genomic DNA. The partial mtDNA D-loop region was amplified using PCR and sequenced. Sequences were compared with those from Bos frontalis, Bos gaurus, Bos indicus, Bubalus bubalis, and Capra hircus available in GenBank. Phylogenetic relationships were assessed through Neighbor-Joining trees and median-joining networks. Genetic diversity indices and neutrality tests were applied to evaluate population genetic characteristics. Phylogenetic analysis identified three distinct clades, with Arunachali yak clustering closely with Bos indicus, and forming a separate branch from other bovine species. Median-joining networks revealed six haplogroups, with Arunachali yak uniquely representing Hap_3. Genetic diversity analysis showed no polymorphism within Arunachali yak, indicating very low genetic variation in the selected animal samples. AMOVA demonstrated significant genetic differentiation among populations (Fst = 0.30053, P < 0.001), with a substantial portion of variation occurring within populations. The Arunachali yak exhibits a close genetic relationship with Bos indicus, reflecting recent divergence. The study underscores the distinct genetic profile of Arunachali yak and highlights its limited genetic variability. These findings enhance our understanding of bovine evolutionary relationships and emphasize the need for targeted conservation measures to preserve the genetic integrity of Arunachali yak.

Association of PPARGC1A gene polymorphism and mtDNA methylation with coal-burning fluorosis: a case–control study

BackgroundCoal-burning fluorosis is a chronic poisoning resulting from the prolonged use of locally available high-fluoride coal for heating and cooking. Prolonged fluoride exposure has been demonstrated to decrease PPARGC1A levels. Therefore, this case-control aims to evaluate the genetic association of PPARGC1A gene polymorphisms and methylation of the mitochondrial D-loop region with coal-burning fluorosis.ResultThe results showed that the TT genotype at rs13131226 and the AA genotype at rs1873532 increased the risk of coal-burning fluorosis (OR = 1.84, P = 0.004; OR = 1.97, P = 0.007), the CT and CC genotypes at rs7665116 decreased the risk of coal-burning fluorosis (OR = 0.54, P = 0.003). The TT genotype at the rs2970847 site and the AA genotype at the rs2970870 site increase the risk of developing skeletal fluorosis (OR = 4.12, P = 0.003; OR = 2.22, P = 0.011). Haplotype AG constructed by rs3736265-rs1873532 increased the risk of the prevalence of coal-burning fluorosis (OR = 1.465, P = 0.005); CG decreased the risk of the prevalence of coal-burning fluorosis (OR = 0.726, P = 0.020). Haplotype CGGT constructed by rs6821591-rs768695-rs3736265-rs2970847 increased the risk of the prevalence of skeletal fluorosis (OR = 1.558, P = 0.027). A 1% increase in CpG_4 methylation levels in the mtDNA D-loop region is associated with a 2.3% increase in the risk of coal-burning fluorosis. Additionally. There was a significant interaction between rs13131226 and rs1873532; CpG_4 and CpG_8.9; rs13131224,rs6821591 and rs7665116 were observed in the occurrence of fluorosis in the Guizhou population (χ2 = 16.917, P < 0.001; χ2 = 21.198, P < 0.001; χ2 = 36.078, P < 0.001).ConclusionPPARGC1A polymorphisms rs13131226 and rs1873532 and the mitochondrial DNA D-loop methylation site CpG_4 have been associated with an increased risk of fluorosis, conversely polymorphism rs7665116 was associated with a decreased risk of fluorosis. Polymorphisms rs2970870 were associated with increased risk of skeletal fluorosis, and polymorphism rs2970847 was associated with decreased risk of skeletal fluorosis. These SNPs and CpG can be used as potential targets to assess fluorosis risk.

Genetic Diversity and Distribution of Haplotypes of Freshwater Eel in Baltic Lakeland Based on Mitochondrial DNA D-Loop and Cytochrome b Sequence Variation

The European eel (Anguilla anguilla (L.)) is a unique catadromous euryhaline fish and the only anguillid eel species classified as ‘critically endangered’. The Baltic Lakeland area contains naturally recruited and introduced eels. There is great uncertainty regarding a baseline for the location and number of naturally dispersed eels in the region. Little is known about the genetic structure of the European eel populations in Baltic countries. The estimation of population genetic structure is important for the efficient management of naturally recruited and introduced eels. Two mitochondrial regions were used to investigate the genetic structure within and between eel samples from 11 waterbodies. In this study, new, unique, and widely distributed haplotypes were revealed. The studied eel population in the Baltic Lakeland shows high genetic diversity, which is possibly a result of intensive restocking programs. Sequences characterized for Anguilla rostrata were revealed in both mitochondrial regions. Understanding the genetic structure of eel populations worldwide is crucial for conservation efforts. Eel restocking in waterbodies where natural migration is restricted contributes to diversity loss for the world gene pool of eels.

Atlantic connectivity of a major green sea turtle Chelonia mydas foraging aggregation at the Banc d’Arguin, Mauritania

Understanding population connectivity is paramount for effective conservation. While genetic tools have elucidated sea turtle migration patterns, notable data gaps limit our understanding of ocean-wide connectivity, especially regarding east Atlantic green turtles. We characterized the genetic composition of a globally important green turtle foraging aggregation at the Banc d’Arguin, Mauritania, incorporating data from 323 individuals captured between 2018 and 2021. Using extended mitochondrial DNA D-loop (738 base pairs [bp]) and mitochondrial short tandem repeat (mtSTR; ~200 bp) markers, we assessed the genetic structure of Atlantic green turtle foraging aggregations and estimated the most likely origin of immature green turtles from the Banc d’Arguin using mixed stock analyses (MSAs). We identified 6 D-loop haplotypes, with a clear dominance of CM-A8.1 (91.8%) followed by CM-A5.1 (6.3%) and 4 rare haplotypes: CM-A1.4, CMA6.1, CM24.1 and CM36.1. We found 13 mtSTR haplotypes, with ‘7-12-4-4’ being dominant (89.0%). The genetic composition at the Banc d’Arguin differed significantly from the only foraging aggregation studied in West Africa to date—in the archipelago of Cabo Verde (located ca. 750 km from the Banc d’Arguin)—dominated by haplotype CM-A5. The MSA combining both genetic markers indicated that 87.6% of immature green turtles at the Banc d’Arguin originate from the major East Atlantic rookery at Poilão (Guinea-Bissau), but 11.6% come from more distant rookeries in South America (8.1%) and potentially Ascension Island (3.4%). We suggest that green turtle transatlantic movements may be more common than previously thought and highlight the importance of the Banc d’Arguin as a regional foraging hub for this species.

Mitochondrial DNA D-loop SNPs unveil molecular signatures of milk production variation in Murrah buffalo.

The Murrah buffalo, pivotal in Asian agriculture, faces challenges in maximizing milk production despite significant breeding efforts. Recognizing its economic importance, this studyinvestigates mtDNA D-loop variations in Murrah buffalo as potential indicators of milk production variability, addressing challenges in maximizing yield despite significant breeding efforts. Analyzing mtDNA D-loop sequences from 50 buffaloes, we categorized them into Low (Group 1), Medium (Group 2), and High ECM (Group 3) groups based on milk yields, fat and protein percentage of a 30-day period data. Somatic cell mtDNA D-loop analysis revealed distinct genetic variations, with significant differences among ECM groups. Group 2 showed higher SNP prevalence, group 3 had more insertions/deletions, and Group 1 exhibited the highest transition frequency. Notably, a consistent "C" deletion at the 714th position occurred in Groups 1 and 3, prevalent in 68% of Group 2. A G-A variation at the 93rd position was specific to the medium ECM group. Negative Tajima D values indicated unique variations in each group, with Group 1 having the highest number, and a specific SNP linked to Group 2 was identified. These SNPs in the D-loop region could impact mtDNA replication, influencing mitochondrial content among animals. Our results provide valuable insights into the role of mtDNA D-loop polymorphisms in milk production traits in Murrah buffalo. Our research highlights the potential for valuable markers of cellular energy efficiency in Murrah buffalo. Exploring diverse cytoplasmic backgrounds opens avenues for mtDNA-based selection strategies, enhancing milk production and optimizing genetic traits for the dairy industry.

Shared alleles and genetic structures in different Thai domestic cat breeds: the possible influence of common racial origins

Over hundreds of years, cats have been domesticated and selectively bred, resulting in numerous pedigreed breeds expedited by recent cat shows and breeding associations. Concerns have been raised about the limited breeding options and the genetic implications of inbreeding, indicating challenges in maintaining genetic diversity and accurate identification in purebred cats. In this study, genetic variability and structure were examined in 5 Thai domestic cat breeds using 15 microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequencing. In total, 184 samples representing the Wichien Maat (WCM), Suphalak (SL), Khao-Manee (KM), Korat (KR), and Konja (KJ) breeds were analyzed. High genetic diversity (Ho and He > 0.5) was observed in all breeds, and mtDNA analysis revealed two primary haplogroups (A and B) that were shared among all domestic cat breeds in Thailand and globally. However, minor differences were observed between Thai domestic cat breeds based on clustering analyses, in which a distinct genetic structure was observed in the WCM breed. This suggests that allele fixation for distinctive morphological traits has occurred in Thai domestic cat breeds that emerged in isolated regions with shared racial origins. Analysis of relationships among individuals within the breed revealed high identification efficiency in Thai domestic cat breeds (P(ID)sibs < 10−4). Additionally, diverse and effective individual identification can be ensured by optimizing marker efficiency by using only nine loci. This comprehensive genetic characterization provides valuable insights into conservation strategies and breeding practices for Thai domestic cat breeds.

Characterizing the Phan Rang Sheep: A First Look at the Y Chromosome, Mitochondrial DNA, and Morphometrics.

The Phan Rang sheep, considered the sole indigenous breed of Vietnam, are primarily concentrated in the two central provinces of Ninh Thuan and Binh Thuan, with Ninh Thuan accounting for more than 90% of the country's sheep population. These provinces are known for their high temperatures and frequent droughts. The long-standing presence of the Phan Rang sheep in these regions suggests their potential resilience to heat stress-a trait of increasing interest in the face of global climate change. Despite the breed's significance, a critical knowledge gap hinders conservation and breeding programs. To address this, our study employed a two-pronged approach. First, we collected body conformational data to aid in breed identification. Second, we analyzed mitochondrial DNA (D-loop) and Y chromosome markers (SRY and SRYM18) to elucidate the maternal and paternal lineages. Among the 68 Phan Rang sheep analyzed for their D-loop, 19 belonged to mitochondrial haplogroup A, while 49 belonged to haplogroup B. The haplogroups can be subdivided into 16 unique haplotypes. All 19 rams surveyed for their paternal lineages belonged to haplotypes H5 and H6. These findings strongly support the hypothesis of dual origins for the Phan Rang sheep. This study presents the first genetic data for the Phan Rang breed, providing crucial insights for future research and conservation efforts.

Insight into the genetic diversity of Selle Français horse populations based on whole D-loop sequencing of mitochondrial DNA

The Selle Français (SF) breed originated from native France horses crossed with Thoroughbreds, Arabs, Anglo-Arabs and French Trotters, which allowed for individuals to be obtained with excellent predispositions and a versatile usage for equestrian sports. The performance of the SF horse is widely accepted in the fields of show jumping and eventing; however, they have successfully started to compete in other areas such as dressage, vaulting, carriage driving and TREC competitions. To date, information about the genetic structure of the SF breed has been very limited. In the present report, Sanger sequencing was applied to analyse the whole D-loop of mitochondrial DNA of 98 samples representing Selle Français horses originating from two populations: Algerian (n=47) and French (n=51). The result obtained showed the presence of 19 SNPs, which allowed us to divide the samples into 41 haplotypes (OR909723‐OR909773). A higher number of haplotypes was detected in the Algerian population (n=24) compared to the French population (n=14), but both populations did not represent unique clusters and showed a high degree of genetic similarities. The result showed that the identified haplotypes of the SF belonged to four clades: L, A, B and G. The present report gives strong evidence that the Selle Français breed has been established based on a great influence of the Thoroughbred, whose close connection is more visible in the French population. The haplogroup assignment to L clades proved that the SF breed has European origin as ancestral haplogroup L was assigned to West and South Europe while A to West Asia and G and B to Middle East. Our results show SF as an example of a contemporary breed of sport horses with European roots further influenced by local breeds.

Testing the applicability of environmental DNA metabarcoding to landscape genetics.

Landscape genetics is a field dealing with local genetic differences and contributes to strategic conservation planning. Recently, environmental DNA (eDNA) metabarcoding has proven useful not only for detecting species but also for assessing genetic diversity and genetic structure on a large scale such as in phylogeography. However, it remains unclear whether eDNA analysis also has sufficient power to perform the landscape genetics, which focuses on a local scale. To reveal the applicability of eDNA to landscape genetics, we conducted an eDNA metabarcoding analysis of the mitochondrial DNA D-loop region of the fluvial sculpin Cottus nozawae in the upper Sorachi River in Japan and compared the results with inferences based on traditional tissue-based approaches by the same D-loop region and genome-wide SNP data. As a result, the spatial distribution of haplotypes was generally consistent between the eDNA- and tissue-based approaches. In addition, the genetic differentiation statistics calculated using eDNA and tissue samples were highly correlated when comparing both in the D-loop region. The removal of low-frequency reads or the conversion to semi-quantitative rankings of eDNA data did not alter the correlation of genetic diversity and differentiation statistics with tissue-based approaches much. Finally, we confirmed that analyses using eDNA data can reveal patterns such as isolation-by-distance shown in previous studies on this species, indicating the applicability of eDNA to basic landscape genetics. Even though some limitations remain, eDNA may have great potential for conducting basic landscape genetics.

High genetic diversity in anguillid glass eels across three Southeast Asian countries revealed through mitochondrial DNA D-loop sequences, with notes on population structure

Understanding the genetic diversity and population structure of anguillid eels is crucial for effective management. In this study, we used the mitochondrial DNA (mtDNA) D-loop marker to identify anguillid glass eels and assessed their genetic diversity across six sampling sites spanning three Southeast Asian countries. We also examined the population structures of Anguilla marmorata and A. celebesensis. We validated nine distinct species and subspecies of anguillid eels from 465 specimens collected in Indonesia (n = 246), the Philippines (n = 119), and Vietnam (n = 100). High gene diversities were observed across the species, ranging from 0.979 (A. celebesensis) to 1.000 (A. bicolor bicolor, A. marmorata, and A. interioris). Correspondingly, nucleotide diversity values were relatively low, varying from 0.036 (A. marmorata) to 0.057 (A. interioris). A. marmorata (n = 162) displayed a broad distribution, being observed across all six sites, with a significant yet low average fixation index of 0.05755. Pairwise comparisons of FST values between Cimandiri and other locations (except for Cagayan) were relatively high and statistically significant (p < 0.01), indicating significant genetic differentiation of Cimandiri samples compared to most locations in this study. On the other hand, A. celebesensis (n = 110), exhibited a non-significant and low fixation index (0.007), indicating no genetic differentiation in samples from Poso and Poigar Rivers, Indonesia. Our findings highlight the essential need for coordinated management strategies among regions that share common stocks. Additionally, this study underscores the efficacy of the mtDNA D-loop in precisely identifying glass eel species/subspecies and elucidating the genetic diversity and population structure of tropical anguillid eels.

Small but Mighty: Genetic Diversity of the Thai Ridgeback Dog Population.

Originating in Thailand, the Thai Ridgeback dog is known for its unique fur ridge that grows in the opposite direction along its back. Selective breeding and a limited populations in Thailand have led to significant close inbreeding among related individuals. The current Thai Ridgeback population is assumed to have experienced a loss of genetic diversity and bottleneck events. Furthermore, studies on the genetic diversity and structure of Thai Ridgeback dogs are limited. Therefore, the aim of this study was to assess the genetic diversity in Thai Ridgeback dogs. Microsatellite genotyping and mitochondrial DNA D-loop sequences were used to assess genetic diversity in 105 Thai Ridgeback dogs from various farms throughout Thailand. Significant genetic diversity and minimal inbreeding were observed in the current Thai Ridgeback population. Signs of bottlenecks were not observed because the exchange of genetic material among Thai Ridgeback owners effectively preserved the genetic diversity. Moreover, the genetic parameters in this study supported owner-to-owner exchanges animals for mating programs. To sustain the genetic diversity of Thai Ridgeback dogs, the use of genetic parameters to manage genetic closeness while preserving breed characteristics is essential. These data are crucial for ensuring demographic stability, which is pivotal for long-term conservation and effective population management.

Novel blood and tissue-based mitochondrial D-loop mutations detected in an Iranian NAFLD patient cohort

Non-alcoholic fatty liver disease (NAFLD) is an increasingly prevalent chronic liver disease characterized by an elusive etiology. In its advanced stages, this condition can pose life-threatening implications. Mitochondrial dysfunction due to its impact on hepatic lipid homeostasis, cytokine release, ROS production, and cell death, contributes to the pathogenesis of NAFLD. Previous research reveals a direct link between NAFLD genetic predictors and mitochondrial dysfunction. The emphasis on the D-loop stems from its association with impaired mtDNA replication, underscoring its crucial role in NAFLD progression. We included 38 Iranian NAFLD patients (comprising 16 patients with non-alcoholic fatty liver [NAFL] and 22 patients with non-alcoholic steatohepatitis [NASH]), with matched blood and liver tissue samples collected from each to compare variations in the mitochondrial D-loop sequence within samples. The mitochondrial DNA (mtDNA) D-loop region was amplified using PCR, and variations were identified through sequencing. The resultant sequences were compared with the reference sequence of human mtDNA available in the MITOMAP Database for comparative analysis. In this study, 97 somatic mutations in the mtDNA D-loop region were identified in NAFLD patients. Our study revealed significant difference between the NAFLD patients and control group in 13 detected mutations (P ≤ 0.05). Novel mutations were discovered in hepatic tissues, while mutation 16220-16221ins C was found in both tissues and blood. A significant difference was found in the distribution of D310 and mt514-mt523 (CA)n repeat variations between NAFLD patients and the control group (P < 0.001). C to T and T to C transitions were the prevalent substitution among patients. Identification of the 16220-16221ins C mutation in both blood and tissue samples from NAFLD patients holds substantial promise as a potential diagnostic marker. However, further research is imperative to corroborate these findings.

Genetic diversity of common carp Cyprinus carpio in the base population of a selective breeding programme in India

A selective breeding program for developing a suitable strain of Cyprinus carpio (Linnaeus, 1758) for inland saline aquaculture in India is in progress. At ICAR-CIFE, various geographical populations of common carp of India, viz. Madhya Pradesh (MP), Haryana (HR), Tripura (TR), Andhra Pradesh (AP), Manipur (MN), and Maharashtra (MH) formed the base population for selective breeding. The present study assesses the genetic diversity of these stocks using truss morphometry and mitochondrial DNA D loop marker analysis. The images of 600 fish were captured and digitized. The landmarks were identified, and an image network was constructed for truss analysis using tpsDig2 and PAST software. The data was subjected to scale transformation and factor analysis using SAS for Academics. The top 3 factors could explain 85.40% of the total variation. The results indicate stock-wise and sex-wise groupings. The mitochondrial DNA (D-loop) sequence analysis was conducted on 169 samples using MEGA6 software. The overall average haplotype and nucleotide diversity of the population were 0.08129 and 0.01134, respectively. Among stocks, the MP stock had a maximum of four haplotypes. The AMOVA results reveal that the stock AP is unique, and the other stocks form a single grouping. The information generated from the present study delineates genetic diversity among stocks and will aid in designing breeding plans.

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.

Identification of CRISPR/Cas12a (Cpf1) guideRNA Sequence Targeting the Mitochondrial DNA D-loop Region in Wild Pig (Sus scrofa) Through Homology Difference and Mismatch Analysis

Identification of CRISPR/Cas12a (Cpf1) guideRNA Sequence Targeting the Mitochondrial DNA D-loop Region in Wild Pig (Sus scrofa) Through Homology Difference and Mismatch Analysis

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.

DNA variants and population structure of Magelang ducks across generation

Magelang ducks (MD) are Indonesian local ducks and are known as dual-purpose type ducks which have high egg production, duck day production (DDP), and body weight size. Nowadays, the MD is selected to establish the pure line to advance the egg production trait in the Breeding and Rearing Center of Non-Ruminant Animals Banyubiru, Central Java. The mitochondrial DNA (mtDNA) Dloop region, is highly polymorphic and could be used to analyze the population genetics. The present research aims to examine the impacts of continuous selection on population structure and genetic mutations on MD across two generations using the mtDNA D-loop region. Thirty-six blood samples from the second (G2) and third (G3) generations were examined using the sequencing method. The MEGA X and DnaSP software were applied to calculate the genetic diversity, genetic distance, and to generate a phylogenetic tree. The number of haplotypes (H), haplotype diversity (Hd), and Tajima's D are 26, 0.9746, and -1.46, respectively. The Fst value of MD is 0.156. The genetic distance among populations ranges from 0.0000 – 2.097. The UPGMA analysis constructs one clade in a phylogenetic tree between MD, Indonesian local Ducks, Indian Ducks, Vietnamese Ducks, and Chinese Ducks. The study found that the genetic variation and population structure did not significantly change between the second and third generations.

Mitochondrial DNA D-Loop Polymorphisms among the Galla Goats Reveals Multiple Maternal Origins with Implication on the Functional Diversity of the HSP70 Gene.

Despite much attention given to the history of goat evolution in Kenya, information on the origin, demographic history, dispersal route, and genetic diversity of Galla goats remains unclear. Here, we examined the genetic background, diversity, demographic history, and population genetic variation of Galla goats using mtDNA D-loop and HSP70 single-nucleotide polymorphism markers. The results revealed 90 segregating sites and 68 haplotypes in a 600-bp mtDNA D-loop sequence. The overall mean mitochondrial haplotype diversity was 0.993. The haplotype diversities ranged between 0.8939 ± 0.0777 and 1.0000 ± 0.0221 in all populations supporting high genetic diversity. Mitochondrial phylogenetic analysis revealed three Galla goat haplogroups (A, G, and D), supporting multiple maternal ancestries, of which haplogroup A was the most predominant. Analysis of molecular variance (AMOVA) showed considerable variation within populations at 94.39%, evidence of high genetic diversity. Bimodal mismatch distribution patterns were observed while most populations recorded negative results for Tajima and Fu's Fs neutrality tests supporting population expansion. Genetic variation among populations was also confirmed using HSP70 gene fragment sequences, where six polymorphic sites which defined 21 haplotypes were discovered. Analysis of molecular variance revealed a significant FST index value of 0.134 and a high FIS index value of 0.746, an indication of inbreeding. This information will pave the way for conservation strategies and informed breeding to improve Galla or other goat breeds for climate-smart agriculture.

Mitochondrial DNA D-loop variants correlate with a primary open-angle glaucoma subgroup.

Primary open-angle glaucoma (POAG) is a characteristic optic neuropathy, caused by degeneration of the optic nerve-forming neurons, the retinal ganglion cells (RGCs). High intraocular pressure (IOP) and aging have been identified as major risk factors; yet the POAG pathophysiology is not fully understood. Since RGCs have high energy requirements, mitochondrial dysfunction may put the survivability of RGCs at risk. We explored in buffy coat DNA whether mtDNA variants and their distribution throughout the mtDNA could be risk factors for POAG. The mtDNA was sequenced from age- and sex-matched study groups, being high tension glaucoma (HTG, n=71), normal tension glaucoma patients (NTG, n=33), ocular hypertensive subjects (OH, n=7), and cataract controls (without glaucoma; n=30), all without remarkable comorbidities. No association was found between the number of mtDNA variants in genes encoding proteins, tRNAs, rRNAs, and in non-coding regions in the different study groups. Next, variants that controls shared with the other groups were discarded. A significantly higher number of exclusive variants was observed in the D-loop region for the HTG group (~1.23 variants/subject), in contrast to controls (~0.35 variants/subject). In the D-loop, specifically in the 7S DNA sub-region within the Hypervariable region 1 (HV1), we found that 42% of the HTG and 27% of the NTG subjects presented variants, while this was only 14% for the controls and OH subjects. As we have previously reported a reduction in mtDNA copy number in HTG, we analysed if specific D-loop variants could explain this. While the majority of glaucoma patients with the exclusive D-loop variants m.72T>C, m.16163 A>G, m.16186C>T, m.16298T>C, and m.16390G>A presented a mtDNA copy number below controls median, no significant association between these variants and low copy number was found and their possible negative role in mtDNA replication remains uncertain. Approximately 38% of the HTG patients with reduced copy number did not carry any exclusive D-loop or other mtDNA variants, which indicates that variants in nuclear-encoded mitochondrial genes, environmental factors, or aging might be involved in those cases. In conclusion, we found that variants in the D-loop region may be a risk factor in a subgroup of POAG, possibly by affecting mtDNA replication.

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.