P4000 Specific polymorphisms in mitochondrial region D-loop of the Tunisian domestic goat

Traditionally, the morphological attributes and the range of Trichechus species have been clearly established. However, we herein show that morphological traits, like belly and pectoral flipper coloration in South American manatees may be polymorphic. Karyotypic analysis of T. manatus allowed the precise identification of this species and confirmed the variability of the observed morphological findings. Molecular analysis based on cytochrome b DNA and the D-loop mitochondrial region showed shared haplotypes between T. inunguis and T. manatus, suggesting the presence of an ancestral polymorphism. These findings showed the need of improving the identification of these species before implementing conservation strategies. Finally, we present a complete report on the extant distribution of these species in South America.

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Strong phylogeographic relationships among three goat breeds from the Canary Islands

Journal of Dairy Research ◽

10.1017/s0022029904000342 ◽

2004 ◽

Vol 71 (3) ◽

pp. 257-262 ◽

Cited By ~ 40

Author(s):

Marcel Amills ◽

Juan Capote ◽

Anna Tomàs ◽

Lucía Kelly ◽

Gabriela Obexer-Ruff ◽

...

Keyword(s):

Canary Islands ◽

Dairy Products ◽

Phylogeographic Structure ◽

Mitochondrial Haplotype ◽

Domestic Goat ◽

Loop Region ◽

D Loop ◽

Identity Test ◽

Migratory Movements ◽

Single Cluster

We partially sequenced the mitochondrial D-loop region in 47 individuals from eleven Spanish and foreign goat breeds. Phylogenetic analysis of these sequences allowed us to identify a particular D-loop haplotype shared by individuals from the Palmera, Majorera and Tinerfeña Canarian breeds. Genotyping of 281 goats from 17 different breeds by PCR-HpaII RFLP evidenced that the geographical distribution of this haplotype is restricted to the Canary Islands. This ancestral mitochondrial haplotype might originate in the domestic goat herds brought by the native Canarian inhabitants approximately 3000 years ago. Although we observed other miscellaneous D-loop haplotypes in the Palmera, Majorera and Tinerfeña breeds, any of them allowed us to group individuals from these three populations in a single cluster, a feature that suggests that these haplotypes might have diverse origins. The remarkable degree of phylogeographic structure of the Canary goat breeds with regard to other Spanish and foreign populations might be attributed to the isolation of these breeds in the Canary Islands for approximately 2500 years, without exposure to the migratory movements and commercial trading events that probably affected the genesis of most domestic goat breeds worldwide. The Canarian D-loop haplotype can be efficiently genotyped by using DNA isolated from milk and cheese samples, which paves the way for the future establishment of a Canary breed identity test for these dairy products.

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Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

Frontiers in Genetics ◽

10.3389/fgene.2021.723964 ◽

2021 ◽

Vol 12 ◽

Author(s):

Randa Alaqeely ◽

Bader H. Alhajeri ◽

Faisal Almathen ◽

Hasan Alhaddad

Keyword(s):

Sequence Variation ◽

Haplotype Diversity ◽

Dromedary Camel ◽

Nuclear Markers ◽

Mitochondrial Region ◽

Hair Samples ◽

D Loop ◽

Almost All ◽

Future Work ◽

Tail Hair

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

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Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction

Neotropical Ichthyology ◽

10.1590/1982-0224-20180071 ◽

2019 ◽

Vol 17 (1) ◽

Author(s):

Bruno A. Galindo ◽

Dhiego G. Ferreira ◽

Caroline Apolinário-Silva ◽

Mariana C. Terra ◽

Nícollas G. O. Aprígio ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Paraná River ◽

Neotropical Fish ◽

Conservation Area ◽

Restricted Area ◽

Parana River ◽

Mitochondrial Region ◽

D Loop

ABSTRACT Brycon nattereri is an endangered Neotropical fish reported along conserved stretches of the upper Paraná, Tocantins and São Francisco rivers. Populations of this species have been very rare in some Paraná River sub basins. This study analyzes the genetic diversity and population structure of B. nattereri in a restricted area of occurrence recently identified in upper Paraná River basin. Seven microsatellite loci and 497 bp of D-Loop mitochondrial region were examined in 92 individuals from four points along the area of occurrence. Both molecular markers indicated a single population distributed along a stretch of the river approximately 80 km long. Although some of the data suggest an ancient bottleneck, current levels of genetic diversity (H E = 0.574 and h = 0.616) were similar to those of other species of the genus Brycon. The results suggest that the population of B. nattereri has been able to maintain satisfactory levels of genetic diversity, in spite of the small area of occurrence. These data have highlighted an important conservation area and action may prove essential to improve the quality of the environment, and especially the water and riparian plant life, if the area is to be managed and conserved efficiently.

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Detection of pork in meatballs using probe TaqMan Real-time Polymerase Chain Reaction

Food Research ◽

10.26656/fr.2017.4(5).227 ◽

2020 ◽

Vol 4 (5) ◽

pp. 1563-1568

Author(s):

S. Orbayinah ◽

A. Hermawan ◽

Sismindari ◽

A. Rohman

Keyword(s):

Polymerase Chain Reaction ◽

Wild Boar ◽

Real Time ◽

Chain Reaction ◽

Specific Primers ◽

Taqman Probes ◽

Mitochondrial Region ◽

D Loop ◽

Polymerase Chain ◽

Species Specific

This study aimed to develop a TaqMan Real-Time Polymerase Chain Reaction method, using a novel primer for detection of pork adulteration in meatballs. The study is important as it described a TaqMan method for product adulteration analysis. TaqMan is known to have a more specific result compared to SYBR green analytical method. Assay in the study combined species-specific primers and TaqMan probes to targeting 153 bp fragment of D-loop mitochondrial region of pork. A specificity test was conducted on fresh tissues of pork, beef, chicken, wild boar, dog, and mouse. Meatballs as samples were prepared from a mixture of pork-beef and wild boar-beef with concentrations as follows: 5%, 10%, 25%, 75%, 90%, and 100%. The linearity and sensitivity of the method were performed by measuring the amplification curve from the dilution series, namely 1000, 200, 100, 10, 5, 1, and 0.5 pg/μL of DNA, extracted from 100% pork meatballs. A repeatability test was conducted as many as six repetitions on 100% pork and 100% wild boar meatballs. This study showed that mitochondrial D-loop species-specific primers and TaqMan probes could identify the DNA of pork and wild boar on the fresh tissues. Additionally, it also resulted in a threshold cycle (Ct) of 17.02 and 17.95 for pork, 22.22 for wild boar, while the negative result for others. The detection limit has shown 5 pg in the meatball formulation. The Relative Standard Deviation (RSD) of repeatability was 1.936% for pork, while 2.140% for wild boar. The developed method was also applied to analyzing commercial meatballs. A TaqMan real-time PCR analytical method using specific primer targeting on 153 bp fragment of the D-loop mitochondrial region could be applied as a standard method for identifying pork and wild boar in food samples intended for halal authentication studies

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Polymorphisms and distribution of South American manatees (Trichechus spp.)

10.7287/peerj.preprints.27787 ◽

2019 ◽

Author(s):

Cibele Rodrigues Bonvicino ◽

Maria Carolina Viana ◽

Edivaldo HC de Oliveira ◽

Renata Emin-Lima ◽

José de Sousa e Silva Júnior ◽

...

Keyword(s):

Morphological Traits ◽

Conservation Strategies ◽

South American ◽

Ancestral Polymorphism ◽

Karyotypic Analysis ◽

Morphological Attributes ◽

Morphological Findings ◽

Mitochondrial Region ◽

D Loop ◽

Complete Report

Traditionally, the morphological attributes and the range of Trichechus species have been clearly established. However, we herein show that morphological traits, like belly and pectoral flipper coloration in South American manatees may be polymorphic. Karyotypic analysis of T. manatus allowed the precise identification of this species and confirmed the variability of the observed morphological findings. Molecular analysis based on cytochrome b DNA and the D-loop mitochondrial region showed shared haplotypes between T. inunguis and T. manatus, suggesting the presence of an ancestral polymorphism. These findings showed the need of improving the identification of these species before implementing conservation strategies. Finally, we present a complete report on the extant distribution of these species in South America.

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