scholarly journals Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3714 ◽  
Author(s):  
Jakub Cieslak ◽  
Lukasz Wodas ◽  
Alicja Borowska ◽  
Ernest G. Cothran ◽  
Anas M. Khanshour ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sequence Variation ◽  
Breeding Strategy ◽  
Conservation Program ◽  
Loop Sequence ◽  
Geographical Regions ◽  
Mtdna Sequence ◽  
Show Evidence ◽  
D Loop ◽  
Mtdna Haplotype

The Polish Primitive Horse (PPH, Konik) is a Polish native horse breed managed through a conservation program mainly due to its characteristic phenotype of a primitive horse. One of the most important goals of PPH breeding strategy is the preservation and equal development of all existing maternal lines. However, until now there was no investigation into the real genetic diversity of 16 recognized PPH dam lines using mtDNA sequence variation. Herein, we describe the phylogenetic relationships between the PPH maternal lines based upon partial mtDNA D-loop sequencing of 173 individuals. Altogether, 19 mtDNA haplotypes were detected in the PPH population. Five haplotypes were putatively novel while the remaining 14 showed the 100% homology with sequences deposited in the GenBank database, represented by both modern and primitive horse breeds. Generally, comparisons found the haplotypes conformed to 10 different recognized mtDNA haplogroups (A, B, E, G, J, M, N, P, Q and R). A multi-breed analysis has indicated the phylogenetic similarity of PPH and other indigenous horse breeds derived from various geographical regions (e.g., Iberian Peninsula, Eastern Europe and Siberia) which may support the hypothesis that within the PPH breed numerous ancestral haplotypes (found all over the world) are still present. Only in the case of five maternal lines (Bona, Dzina I, Geneza, Popielica and Zaza) was the segregation of one specific mtDNA haplotype observed. The 11 remaining lines showed a higher degree of mtDNA haplotype variability (2–5 haplotypes segregating in each line). This study has revealed relatively high maternal genetic diversity in the small, indigenous PPH breed (19 haplotypes, overall HapD = 0.92). However, only some traditionally distinguished maternal lines can be treated as genetically pure. The rest show evidence of numerous mistakes recorded in the official PPH pedigrees. This study has proved the importance of maternal genetic diversity monitoring based upon the application of molecular mtDNA markers and can be useful for proper management of the PPH conservation program in the future.

Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation

2006 ◽  
Vol 38 (1) ◽  
pp. 146-154 ◽  
Author(s):  
Song-Jia Lai ◽  
Yi-Ping Liu ◽  
Yan-Xing Liu ◽  
Xue-Wei Li ◽  
Yong-Gang Yao
Keyword(s):  
Genetic Diversity ◽  
Sequence Variation ◽  
Chinese Cattle ◽  
Loop Sequence ◽  
D Loop

scholarly journals Genetic diversity of Myanmar cattle breeds using complete mitochondrial D-loop sequence

2018 ◽  
Vol 46 (2) ◽  
pp. 57-67 ◽  
Author(s):  
Moe LWIN ◽  
Su Lai Yee MON ◽  
Yukio NAGANO ◽  
Kotaro KAWABE ◽  
Hideyuki MANNEN ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cattle Breeds ◽  
Loop Sequence ◽  
D Loop

The Lusitano horse maternal lineage based on mitochondrial D-loop sequence variation

2005 ◽  
Vol 36 (3) ◽  
pp. 196-202 ◽  
Author(s):  
M. S. Lopes ◽  
D. Mendonça ◽  
T. Cymbron ◽  
M. Valera ◽  
J. da Costa-Ferreira ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Maternal Lineage ◽  
Loop Sequence ◽  
D Loop

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 Mitochondrial D-loop sequence variation among Central Javanese Duck in Indonesia

2017 ◽  
Vol 39 (4) ◽  
pp. 449 ◽  
Author(s):  
R Susanti ◽  
Retno Sri Iswari ◽  
Fidia Fibriana ◽  
Retno Ika Sari
Keyword(s):  
Sequence Variation ◽  
Loop Sequence ◽  
D Loop

Abundant genetic diversity and maternal origins of modern horses

2019 ◽  
Vol 99 (4) ◽  
pp. 929-934
Author(s):  
Hongzhao Lu ◽  
Hao Bai ◽  
Ling Wang ◽  
Tao Zhang
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Gene Flow ◽  
Domestic Horse ◽  
European Regions ◽  
Geographical Regions ◽  
D Loop ◽  
Ancient Times

To clarify the origin and genetic diversity of modern horses, mitochondrial DNA (mtDNA) D-loop sequences were generated for 3965 horses from 12 geographical regions. From these sequences, we observed 439 haplotypes defined by 138 polymorphic nucleotide sites. All horses were genetically diverse (HD = 0.973 ± 0.001, π = 0.0243 ± 0.0005), which showed that maternal lineages of the domestic horse are worldwide highly diverse. In general, all 18 haplogroups were presented in the Asian horse. The majority of modern horse sequences belong to haplogroups L, Q, and A. At the same time, 194 archaeological samples from four geographical regions were obtained. Indeed, haplogroup distributions are overlapping in modern and ancient samples, indicating that most haplogroups were already present in ancient times at least in Europe and Asia. The network showed that breeds of Asian and Europe regions overlapped, suggesting that extensive gene flow had occurred between different horse breeds in Asian and European regions.

scholarly journals Genetic Diversity of Sheep Breeds from Albania, Greece, and Italy Assessed by Mitochondrial DNA and Nuclear Polymorphisms (SNPs)

2011 ◽  
Vol 11 ◽  
pp. 1641-1659 ◽  
Author(s):  
Lorraine Pariset ◽  
Marco Mariotti ◽  
Maria Gargani ◽  
Stephane Joost ◽  
Riccardo Negrini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Geographical Isolation ◽  
Good Correspondence ◽  
Sheep Breeds ◽  
Snp Data ◽  
Loop Sequence ◽  
D Loop ◽  
Historical Times ◽  
Geographical Locations

We employed mtDNA and nuclear SNPs to investigate the genetic diversity of sheep breeds of three countries of the Mediterranean basin: Albania, Greece, and Italy. In total, 154 unique mtDNA haplotypes were detected by means of D-loop sequence analysis. The major nucleotide diversity was observed in Albania. We identified haplogroups, A, B, and C in Albanian and Greek samples, while Italian individuals clustered in groups A and B. In general, the data show a pattern reflecting old migrations that occurred in postneolithic and historical times. PCA analysis on SNP data differentiated breeds with good correspondence to geographical locations. This could reflect geographical isolation, selection operated by local sheep farmers, and different flock management and breed admixture that occurred in the last centuries.

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