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.

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

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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 among Canadienne, Brown Swiss, Holstein and Jersey cattle based on mitochondrial D-loop sequence variation

2003 ◽  
Vol 83 (1) ◽  
pp. 39-44 ◽  
Author(s):  
C. Hansen ◽  
J. N. B. Shrestha ◽  
R. J. Parker ◽  
G. H. Crow ◽  
P. J. McAlpine ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Bos Taurus ◽  
Sequence Divergence ◽  
Single Nucleotide ◽  
Brown Swiss ◽  
Jersey Cattle ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Polymorphisms creating 36 unique haplotypes were observed with in breeds at 55 sites in the displacement loop (D-loop) region of the mitochondrial DNA (mtDNA) consisting of 814 bp. The majority (56%) of the differences observed were the result of nucleotide substitution events with 19 transitions, 12 transversions, 11 deletions, 12 insertions and 1 inversion. In all cases, the insertions and deletions were of a single nucleotide. Canadienne cattle were found to have 60% unique haplotypes within the population compared to 89% in Brown Swiss, 90% in Holstein and 100% in Jersey cattle, possibly reflecting the narrow genetic base in the Canadienne breed. The degree of sequence divergence in the D-loop region of mtDNA was based on samples from 20 Canadienne, 9 Brown Swiss, 10 Holstein and 10 Jersey cattle and a phylogenetic analysis showed that these cattle (Bos taurus) were not evolutionarily distinct. All four breeds grouped together when a strict consensus tree was generated. Intra-breed variability proved to be high for the Canadienne, Holstein and Jersey breeds (57–73%) but not the Brown Swiss breed (29%). The Canadienne and Brown Swiss (45%), and Brown Swiss and Holstein (43%) showed the lowest degree of inter-breed variability. The greatest variability among the four breeds was between Canadienne and Jersey (80%) cattle. These findings question the validity of phenotypic assessment of genetic diversity, such as Canadienne cattle being described as “Black Jersey”. Key words: Genetic distance, phylogenetic analysis, D-loop sequence, cattle

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 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.

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 Biodiversity of Russian Local Sheep Breeds Based on Pattern of Runs of Homozygosity

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 360
Author(s):  
Tatiana Deniskova ◽  
Arsen Dotsev ◽  
Marina Selionova ◽  
Gottfried Brem ◽  
Natalia Zinovieva
Keyword(s):  
Genetic Diversity ◽  
Biodiversity Loss ◽  
Inbreeding Coefficient ◽  
Loss Estimation ◽  
Runs Of Homozygosity ◽  
Sheep Breeds ◽  
Snp Data ◽  
Population Sizes ◽  
The Mean ◽  
Genomic Inbreeding

Russian sheep breeds traditionally raised in specific environments are valuable parts of sociocultural heritage and economic component of the regions. However, the import of commercial breeds negatively influences the population sizes of local sheep populations and might lead to biodiversity loss. Estimation of the runs of homozygosity (ROH) in local sheep genomes is an informative tool to address their current genetic state. In this work, we aimed to address the ROH distribution and to estimate genome inbreeding based on SNP data to evaluate genetic diversity in Russian local sheep breeds. Materials for this study included SNP-genotypes from twenty-seven Russian local sheep breeds which were generated using the Illumina OvineSNP50 BeadChip (n = 391) or the Illumina Ovine Infinium HD BeadChip (n = 315). A consecutive runs method was used to calculate ROH which were estimated for each animal and then categorized in the ROH length classes. The ROH were found in all breeds. The mean ROH length varied from 86 to 280 Mb, while the ROH number ranged from 37 to 123. The genomic inbreeding coefficient varied from 0.033 to 0.106. Our findings provide evidence of low to moderate genomic inbreeding in major local sheep populations.

scholarly journals Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1970
Author(s):  
Emel Özkan Ünal ◽  
Fulya Özdil ◽  
Selçuk Kaplan ◽  
Eser Kemal Gürcan ◽  
Serdar Genç ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Regions ◽  
D Loop ◽  
Significant Comparison ◽  
Loop Regions ◽  
Frequent Haplotype

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

scholarly journals Genetic divergence analysis in eggplant (Solanum melongena L.)

1970 ◽  
Vol 34 (4) ◽  
pp. 705-712
Author(s):  
AKM Quamruzzaman ◽  
MA Rashid ◽  
S Ahmad ◽  
M Moniruzzaman
Keyword(s):  
Genetic Diversity ◽  
Genetic Divergence ◽  
Leaf Blade ◽  
Solanum Melongena ◽  
Fruit Weight ◽  
Geographical Isolation ◽  
Pedicel Length ◽  
Cluster Distance ◽  
Geographical Locations ◽  
Number Of Branches

Genetic divergence among 19 eggplant genotypes was estimated using Mahalanobis's D2 statistic. Altogether five clusters were formed. Cluster I contained the highest number of genotypes (7) and cluster IV and V contained the lowest (2). The pattern of distribution of genotypes from different geographical locations into five clusters was random, demonstrating that geographical isolation may not be the only factor causing genetic diversity. The highest intra-cluster distance was observed for cluster V (1.067) and the lowest for cluster III (0.916). The highest inter-cluster distance was observed between cluster IV and V (10.748). Cluster V recorded the highest mean for plant height at last harvest (cm), leaf blade length (cm), leaf blade diameter (cm), leaf pedicel length (cm), fruit pedicel length (cm), prickle on calyx. Whereas, number of branches per plant, fruit diametre (cm), individual fruit weight (g), fruit yield (t/ha) and prickle on fruit pedicel were in cluster II with the highest means. Therefore, more emphasis should be given on cluster V for selecting genotypes as parents for crossing with the genotypes of cluster II which may produce new recombinants with desired traits. Key Words: Genetic diversit; eggplant (Solanum melongena L.); cluster analysis. DOI: 10.3329/bjar.v34i4.5845Bangladesh J. Agril. Res. 34(4) : 705-712, December 2009

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