scholarly journals Genetic variability of Akhal-Teke horses bred in Italy

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4889
Author(s):  
Maria C. Cozzi ◽  
Maria G. Strillacci ◽  
Paolo Valiati ◽  
Elisa Rogliano ◽  
Alessandro Bagnato ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Haplotype Diversity ◽  
Principal Component ◽  
Italian Population ◽  
Horse Population ◽  
Loop Region ◽  
Marker Loci ◽  
D Loop ◽  
Inbreeding Level ◽  
Almost All

Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.

scholarly journals The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region)

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
JOKO GUNTORO ◽  
WIRDATETI ◽  
AWAL RIYANTO
Keyword(s):  
Genetic Variability ◽  
Cytochrome Oxidase ◽  
Control Region ◽  
Haplotype Diversity ◽  
Cytochrome Oxidase I ◽  
Conservation Strategy ◽  
Wild Populations ◽  
Loop Control ◽  
Loop Region ◽  
D Loop

Abstract. Guntoro J, Wirdateti, Riyanto A. 2020. The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region). Biodiversitas 21: 2514-2520. Populations of Batagur borneoensis have been rapidly decreasing due to the harvesting of adults and eggs for food and the construction of beachfront property causing the loss of nesting areas. By the new Indonesian regulation, since 2018 this turtle listed in the protected animal. Meanwhile, IUCN placed as critically endangered which indicating a high risk of extinction in the wild in the near future (www.iucnredlist.org). We used cytochrome oxidase I (COI) and control region D-loop region to investigate intraspecific variations on Aceh Tamiang’s population of painted terrapin, Batagur borneoensis. DNA material was gathered from saliva collected from 90 juveniles in the reaching facility of Sukacita Lestari Indonesia Foundation which hatched from eggs collected from December 2015 to April 2016 from 30 nests on beach area at Aceh Tamiang. The population showed very low genetic variability (haplotype diversity, Hd = 0.457 based on COI and 0.405 based on D-loop; nucleotide diversity, π = 0.00089 based on COI and 0.00076 based on D-loop). So, we suggested that further study such as more exploration to find new wild populations and genetic study across wild populations should be done to reveal genetic variability and genetic structure which important to decide the conservation strategy. At the time for Aceh Tamiang's population, the ranching conservation program should be maintained at least to keep the successful hatchling from hunters and natural predators both during eggs laying and hatching.

scholarly journals Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences

2019 ◽  
Vol 20 (9) ◽  
Author(s):  
KAYAL VIZI KARUPPANNAN ◽  
NOR AIFAT RAHMAN ◽  
KHAIRUL AMIRIN MOHAMED ◽  
NURUL FARAH DIYANA AHMAD TAHIR ◽  
FATIN MARDHIAH NORDIN ◽  
...  
Keyword(s):  
National Parks ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Genetic Variations ◽  
Peninsular Malaysia ◽  
Asian Elephant ◽  
Loop Region ◽  
D Loop

Abstract. Karuppannan KV, Aifat NR, Mohamed KA,  Ahmad-Tahir NFD,  Nordin FM, Yaakop S, Maldonado JE, Md-Zain BM. 2019. Genetic variations among selected wild Asian elephant populations in Peninsular Malaysia based on mitochondrial D-loop region DNA sequences. Biodiversitas 20: 2494-2502. Asian elephant (Elephas maximus) is an important large mammal in Peninsular Malaysia and is completely protected by the Wildlife Conservation Act 2010 (Act 716). The conservation of this species requires strong information-based research, such as genetic evaluations. The aim of this study was to compare mitochondrial control region variation among selected elephants from the Taman Negara National Parks (TNNP) population with other selected populations in Peninsular Malaysia. DNA materials were extracted from fecal samples and amplified using partial mitochondrial D-loop region. Total 13 haplotypes with haplotype diversity (Hd) of 0.7524 were observed. A total of 34 base pair (bp) segregation sites were formed in 547 bp sequences. Both phylogenetic trees showed that a few individual elephants from the TNNP formed a clade together with individuals from other populations. The remaining individual elephants from TNNP formed a monophyletic clade supported by a high bootstrap value. Low genetic distance was detected among the tested populations, which proved that both individuals from the TNNP and other selected populations have similar genetic patterns. High gene flow among tested populations would impact on fitness and long-term resilience of the populations. This highly significant outcome provides strong baseline data for Department of Wildlife and National Parks (DWNP) in monitoring elephant populations in order to reduce number of human-elephant conflicts which indirectly minimize translocating conflict elephants to TNNP.

scholarly journals Genetic Variability of mtDNA D-loop Region in Korean Native Chickens

2009 ◽  
Vol 36 (4) ◽  
pp. 323-328 ◽  
Author(s):  
Md. Rashedul Hoque ◽  
Kie-Chul Jung ◽  
Byung-Kwon Park ◽  
Kang-Duk Choi ◽  
Jun-Heon Lee
Keyword(s):  
Genetic Variability ◽  
Loop Region ◽  
D Loop ◽  
Native Chickens

mtDNA D-loop sequence analysis of Kalang, Krayan, and Thale Noi buffaloes (Bubalus bubalis) in Indonesia and Thailand reveal genetic diversity

2021 ◽  
Vol 46 (2) ◽  
pp. 93-105
Author(s):  
S. Suhardi ◽  
P. Summpunn ◽  
S. Wuthisuthimethavee
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
Relationship Patterns ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Kalang (KBuf), Krayan (KrBuf), and Thale Noi buffaloes (TBuf) are swamp buffalo genetic resources in Indonesia and Thailand. The maternally inherited mitochondrial DNA (mtDNA), particularly D-loop region is an important material for phylogenetic inference and analyzing genetic diversity. Therefore, the objectives of the present study were to evaluate genetic diversity and to reconstruct the phylogenetic tree within buffalo breeds in Kalimantan, Indonesia, and Phatthalung, Thailand using mtDNA D-loop sequences. A total of one hundred forty buffaloes (70 males and 70 females) were observed including 40 buffaloes from North (NK), 40 from East (EK), and 40 from South Kalimantan (SK) provinces Indonesia and 20 from Phatthalung (PT) province, Thailand. DNA samples were isolated from buffalo tail hairs. DNA sequences were manually assembled using BioEdit program with consideration of gaps and ambiguous sequences. The phylogenetic tree of buffalo was generated by PHYLIP software. The observed variables included haplotype diversity, genetic distance, and genetic tree. The 956 bp of amplified mtDNA D-loop fragment presented a total of 24 haplotypes with several mutations that included transitions (293), transversions (60), deletions (15), and insertions (20). The neighbor-joining tree using the Kimura 2 parameter model demonstrated two local buffalo clusters among buffalo from Kalimantan and Thailand with four buffalo relationship patterns observed from buffaloes in Kalimantan Island (KBuf and KrBuf), Indonesia. The Results of the present study demonstrated that the buffaloes sequence analysis revealed relatively high diversity and is a good basis to perform selection and modern buffalo breeding development.

scholarly journals Preliminary qualitative analysis on mtDNA in Astyanax fasciatus populations Cuvier, 1819 (Teleostei; Characidae) indicate population distinctiveness

2010 ◽  
Vol 53 (3) ◽  
pp. 663-667 ◽  
Author(s):  
Daniele Aparecida Matoso ◽  
Cesar Martins ◽  
Roberto Ferreira Artoni ◽  
Pedro Manoel Galetti Jr
Keyword(s):  
Genetic Variability ◽  
Qualitative Analysis ◽  
Enzymatic Digestion ◽  
Loop Region ◽  
Astyanax Fasciatus ◽  
D Loop

A preliminary qualitative analysis of genetic variability status in Astyanax fasciatus (Cuvier, 1819) from upper Tibagi River headwaters and Vila Velha State Park (VVSP) was carried out by enzymatic digestion (RFLP) of D-Loop region from mtDNA. The results showed that Tibagi and VVSP populations were genetically different.

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

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.

scholarly journals Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin

2018 ◽  
Author(s):  
Miroslav Marinov ◽  
Denitsa Teofanova ◽  
Georgi Radoslavov ◽  
Peter I Hristov
Keyword(s):  
Hypervariable Region ◽  
Balkan Peninsula ◽  
Human Society ◽  
Loop Region ◽  
Hunting Dog ◽  
D Loop ◽  
South Eastern Europe ◽  
Phylogenetic Origin ◽  
Ancient Times ◽  
Almost All

The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study has been to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed according to HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound dog: Barak, n=34; Bulgarian Scenthound dog: Gonche, n=45) as well as from a Bulgarian Shepherd dog (n=51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades – A, B, C and D – in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of the C clade, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial diversity of native dog breeds in Bulgaria. The results show a clear difference of haplogroups dissemination in native hunting and shepherd dogs that suggests a dual independent phylogenetic origin without hybridization events between them.

scholarly journals Mitochondrial D-loop sequence variation among Hucul horse

2013 ◽  
Vol 58 (No. 10) ◽  
pp. 437-442 ◽  
Author(s):  
V. Czerneková ◽  
T. Kott ◽  
I. Majzlík
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Information ◽  
Sequence Variation ◽  
Dna Typing ◽  
Conservation Strategies ◽  
Base Pairs ◽  
Horse Population ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Genetic variation in the Czech Hucul horse population was analyzed using a sequence analysis of the D-loop region of mitochondrial DNA. One hundred and sixty-five Hucul horses were tested. Sequencing of the 700-base pairs fragment of the mitochondrial DNA D-loop region revealed 38 mutation sites representing 14 haplotypes, which were clustered into six haplogroups. The genetic information obtained from the mitochondrial DNA typing is of utmost importance for the future breed-conservation strategies.  

scholarly journals Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5060 ◽  
Author(s):  
Miroslav Marinov ◽  
Denitsa Teofanova ◽  
Dimitar Gadjev ◽  
Georgi Radoslavov ◽  
Peter Hristov
Keyword(s):  
Hypervariable Region ◽  
Balkan Peninsula ◽  
Human Society ◽  
Loop Region ◽  
Hunting Dog ◽  
Clade C ◽  
D Loop ◽  
South Eastern Europe ◽  
Phylogenetic Origin ◽  
Almost All

The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak,n = 34; Bulgarian Scenthound Dog: Gonche,n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs.

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