Short Communication: Mitochondrial DNA D-loop sequence diversity and origin of Chinese pony breeds (Equus caballus)

2013 ◽  
Vol 93 (3) ◽  
pp. 313-319 ◽  
Author(s):  
Sheng-lin Yang ◽  
Ai-Ping Li ◽  
Long-xing Xu ◽  
Haibing Yang
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Short Communication ◽  
Phylogenetic Analyses ◽  
Haplotype Diversity ◽  
Equus Caballus ◽  
Sequence Diversity ◽  
Maternal Origin ◽  
Loop Sequence ◽  
D Loop

Yang, S.-l., Li, A.-P., Xu, L.-x. and Yang, H. 2013. Short Communication: Mitochondrial DNA D-loop sequence diversity and origin of Chinese pony breeds ( Equus caballus ). Can. J. Anim. Sci. 93: 313–319. Previous studies based on mitochondrial DNA (mtDNA) data have shown that Chinese horses have high genetic diversity. However, little is known about the genetic diversity of mtDNA D-loop sequences and maternal origin of five Chinese pony breeds. In the present study, genetic diversity of 343-bp D-loop sequences for136 individuals representing five Chinese pony breeds was analyzed. To address the question of the single and multiple maternal origin of Chinese pony populations, 13 partial mtDNA D-loop reference sequences from GenBank representing eight ancient and modern horse breeds (Connemara, Garrano, Sorraia, Pottok, Losino, Cheju, Tuva and a Swedish horse) were added to conduct the phylogenetic analyses. A total of 59 haplotypes and 50 polymorphic loci were detected, the haplotype diversity (h) ranged from 0.894 to 0.947 and nucleotide diversity (π) ranged from 0.0184 to 0.0229, suggesting relatively abundant genetic diversity in the Debao, Yunnan and the Guizhou breeds. The phylogenetic tree and median-joining network show multiple maternal origins of the five Chinese pony breeds.

scholarly journals Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

2021 ◽  
Author(s):  
Athumani Nguluma
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Capra Hircus ◽  
Maternal Origin ◽  
High Genetic Diversity ◽  
Ecological Zones ◽  
Goat Population ◽  
D Loop ◽  
Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

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.

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism

2018 ◽  
Vol 30 (3) ◽  
pp. 242-251 ◽  
Author(s):  
Kristina Gvozdanović ◽  
Vladimir Margeta ◽  
Polona Margeta ◽  
Ivona Djurkin Kušec ◽  
Dalida Galović ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Microsatellite Markers ◽  
Sequence Polymorphism ◽  
Pig Breeds ◽  
Loop Sequence ◽  
D Loop

scholarly journals Maternal Origins and Haplotype Diversity of Seven Russian Goat Populations Based on the D-loop Sequence Variability

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1603
Author(s):  
Tatiana Deniskova ◽  
Nekruz Bakoev ◽  
Arsen Dotsev ◽  
Marina Selionova ◽  
Natalia Zinovieva
Keyword(s):  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Maternal Origin ◽  
Migration Routes ◽  
Altai Mountain ◽  
Loop Sequence ◽  
Genetic Pattern ◽  
D Loop ◽  
Diverse Groups ◽  
Official Recognition

The territory of modern Russia lies on the crossroads of East and West and covers various geographical environments where diverse groups of local goats originated. In this work, we present the first study on the maternal origin of Russian local goats, including Altai Mountain (n = 9), Dagestan Downy (n = 18), Dagestan Local (n = 12), Dagestan Milk (n = 15), Karachaev (n = 21), Orenburg (n = 10), and Soviet Mohair (n = 7) breeds, based on 715 bp D-loop mitochondrial DNA (mtDNA) sequences. Saanen goats (n = 5) were used for comparison. Our findings reveal a high haplotype (HD = 0.843–1.000) and nucleotide diversity (π = 0.0112–0.0261). A total of 59 haplotypes were determined in the Russian goat breeds, in which all differed from the haplotypes of the Saanen goats. The haplotypes identified in Altai Mountain, Orenburg, Soviet Mohair, and Saanen goats were breed specific. Most haplotypes (56 of 59) were clustered together with samples belonging to haplogroup A, which was in accordance with the global genetic pattern of maternal origin seen in most goats worldwide. The haplotypes that were grouped together with rare haplogroups D and G were found in the Altai Mountain breed and haplogroup C was detected in the Soviet Mohair breed. Thus, our findings revealed that local goats might have been brought to Russia via various migration routes. In addition, haplotype sharing was found in aboriginal goat populations from overlapping regions, which might be useful information for their official recognition status.

scholarly journals PSIII-14 Genetic Diversity and Haplogroup Distribution of Asian Chicken Populations using Mitochondrial DNA sequence

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 236-236
Author(s):  
Hee-Jong Roh ◽  
Chang-Yeon Cho ◽  
Seung-Chang Kim ◽  
Dong-Kyo Kim ◽  
Jinwook Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Rhode Island ◽  
Reference Data ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Loop Region ◽  
Red Jungle Fowl ◽  
D Loop ◽  
Mtdna Diversity

Abstract Estimating the genetic diversity and origins is critical for the identification and conservation of valuable animal genetic resources. Mitochondrial DNA (mtDNA) polymorphisms have played a significant role in tracing the origin of specific breeds and the genetic diversity of domestic chicken and other livestock species due to their maternal inheritance, greater rate of substitution relative to unclear genes, and much lower rate of recombination. In this study, we analyzed the mtDNA D-loop region of 457 genomic DNA samples from 28 Asian chicken populations (Korea: 6, Laos: 4, Bangladesh: 3, Cambodia: 3, Indonesia: 3, Vietnam: 2, Kyrgyzstan: 1, Mongolia: 1, Nepal: 1, Sri Lanka: 1 and White Leghorn, Cornish, Rhode Island Red) from ten Asian countries to clarify their genetic diversity and phylogenetic relationships. In addition, 49 reference data (43: Oka et al data, 6: red jungle fowl) were used. We found 82 haplotypes defined by 81 variable sites. Overall haplotype and nucleotide diversity were 0.978±0.01 and 0.0018, respectively. Phylogenetic analyses revealed seven haplogroups (Type A-G). The most of Asian chickens were included in haplogroup A(44.9%), B(22.8%), C(19.3%). Haplogroup F did not belong to any Asian chicken populations (include only 2 reference data). Mongolia chickens were only clustered in haplogroup A and Indonesian chickens did only haplogroup C. About half of Kyrgyzstani chicken populations (43.4%) were clustered in haplogroup E. Vietnamese chicken populations belong to all haplogroup except F. In case of red jungle fowl, G.g.gallus and G.g.bankiva were clustered in haplogroup C. G.g.spadiceus was clusterd in haplogroup E or A. As a result, it was possible to identify the mtDNA diversity and origin of Asian chicken populations. In future studies, it is necessary to understand the origin of each haplogroup by adding more reference data and red jungle fowl sequence data.

scholarly journals PSVII-23 Phylogenetic analysis of mitochondrial DNA D-loop region for excavated horse bones at the Asian archaeological sites

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 311-312
Author(s):  
Jihye Cha ◽  
Haesu Ko ◽  
Bong-Hwan Choi ◽  
Gulwon Jang ◽  
Dajeong Lim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Reference Sequence ◽  
Archaeological Sites ◽  
Migration Route ◽  
Human Society ◽  
Loop Region ◽  
Domestic Horses ◽  
D Loop

Abstract Horses have played a significant role in the development of human society. As an important domestic animal, horses have been used for transport, labor, food and recreation. It is widely accepted that the horse was probably first domesticated on the Eurasian steppes from Ukraine to Turkestan between the fifth and fourth millennium BC, and the earliest domesticated horses subsequently spread out from their original range. However, we currently have little genetic evidence to demonstrate whether Korean domestic horse breeds originated in Korea or if it came into the area via an ancient migration route. In the present study, to obtain more knowledge of the origin and genetic diversity of Korean domestic horses, we analyzed seventeen 247-bp mitochondrial DNA (mtDNA) D-loop sequences of ancient horse bones excavated from seven archaeological sites located in the southern Korean Peninsula and Mongolia, aged between the fifth century B.C and nineteenth century A.D. The seventeen ancient horses revealed 9 variable positions when compared with the reference sequence (GenBank X79547). All the substitutions were transitions, and defined a total of 11 unique haplotypes with the haplotype diversity value of 0.9118±0.056. Among the 11 haplotypes, 3 haplotypes were detected more than once and were thus shared by individuals from the same or close archaeological sites. The largest haplotype consisted of 5 individuals, with another two haplotypes containing 2 individuals respectively, and eight haplotypes were singletons. The data indicate an abundant genetic diversity of the Korean ancient horses, and also suggest that the origin of Korean domestic horses is complex, and several maternal lines were introduced into the gene pool of Korean horses after their initial domestication.

scholarly journals Characterization of genetic diversity of an invasive Lessepsian Migrant, Nemipterus randalli Russell, 1986 from its native and non-native regions using mitochondrial DNA marker

2020 ◽  
Author(s):  
MURUGESAN SRIHARI ◽  
SUSANTHI SILPA ◽  
ANNAM PAVAN-KUMAR ◽  
YARON TIKOCHINSKI ◽  
DANIEL GOLANI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Mediterranean Sea ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Population ◽  
D Loop ◽  
The Mediterranean ◽  
Network Tree

This study assessed and compared the genetic diversity of Nemipterus randalli across its native and non-native regions analysing the mitochondrial DNA D-loop region. Including all the geographical population samples, 68 haplotypes were observed with an average haplotype diversity value of 0.92±0.04. Relatively, a smaller number of haplotypes was observed in the invasive range of the Mediterranean Sea. All other native geographical samples showed high haplotype and nucleotide diversity values. A significant high genetic differentiation value was observed between the native population samples of India and the invasive samples of the Mediterranean Sea. In the median-joining network tree, N. randalli from the Mediterranean Sea and the Red Sea formed a single haplogroup while other samples from India are clustered into two haplogroups.

scholarly journals The genetic profiles and maternal origin of local sheep breeds on Java Island (Indonesia) based on complete mitochondrial DNA D-loop sequences

2020 ◽  
Vol 13 (12) ◽  
pp. 2625-2634
Author(s):  
Alek Ibrahim ◽  
I Gede Suparta Budisatria ◽  
Rini Widayanti ◽  
Wayan Tunas Artama
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Relationships ◽  
Haplotype Diversity ◽  
Maternal Origin ◽  
Loop Analysis ◽  
High Genetic Diversity ◽  
Sheep Breeds ◽  
Loop Region ◽  
D Loop ◽  
Genetic Profiles

Background and Aim: Java Island is one of the islands in Indonesia which has local sheep breeds with specific characteristics and native development geography in certain regions. This study aimed to determine the genetic profiles and maternal origin of six local sheep breeds on Java Island. Materials and Methods: This study was conducted by identifying the profiles of complete mitochondrial DNA (mtDNA) displacement loop (D-loop) region sequences on a total of 22 individual in six local sheep breeds on Java Island, including Javanese thin-tailed (JTT), Javanese Fat-Tailed (JFT), Batur (BTR), Wonosobo (WSB), Garut (GRT), and Priangan (PRG) sheep. The D-loop region was amplified using specific primers, and the polymerase chain reaction (PCR) was performed. The PCR products were purified and sequenced. Results: The mtDNA D-loop analysis identified 21 haplotypes in the analyzed 22 animals with 123 polymorphic sites (V) consisting of 60 singleton variable sites (S) and 63 parsimony informative sites (P). Within all breeds tested, the haplotype diversity, the average number of pairwise differences (K), and nucleotide diversity (Pi) were 0.99567, 25.36364, and 0.02153, respectively. The genetic distance (D) within groups and between groups was 0.001-0.006 and 0.004-0.036, respectively. The phylogeny resulted in the presence of two haplogroups (Hap), which are 5 Hap A and 16 Hap B. All JTT, JFT, BTR, and WSB breeds were in the same cluster in Hap B, whereas GRT and PRG breeds were in clusters in both Hap A and Hap B. Conclusion: The high genetic diversity in six local sheep breeds on Java Island suggests that they originated from different genetic sources. JTT sheep have closer genetic relationships to JFT, BTR, and WSB sheep, and they are close to European sheep, whereas GRT sheep have closer genetic relationships to PRG sheep. Both are closer to Asian sheep than to European sheep.

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