Genetic diversity and phylogeography of the rare riparian moss Dichelyma capillaceum (With.) Myr. inferred from trnL-F plastid DNA sequences

The genetic relationships of Dichelyma capillaceum (With.) Myr. are studied from chloroplast sequences of the trnL-F region. On the basis of the molecular data obtained, the German population can be considered to be derived from Scandinavian(Swedish) rather than North American populations. To judge from the genetic distances between the Swedish and German populations, the separation must have occurred along time ago.

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Genetic diversity in table grapes based on RAPD and microsatellite markers

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2011000900010 ◽

2011 ◽

Vol 46 (9) ◽

pp. 1035-1044 ◽

Cited By ~ 9

Author(s):

Patrícia Coelho de Souza Leão ◽

Sérgio Yoshimitsu Motoike

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Relationships ◽

Similarity Index ◽

Genetic Distances ◽

Table Grape ◽

Group Method ◽

Molecular Characteristics ◽

Table Grapes ◽

Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

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Genetic Diversity Based on ISSR Markers of Apple Genotypes in Ardahan/Turkey

Notulae Scientia Biologicae ◽

10.15835/nsb10410347 ◽

2018 ◽

Vol 10 (4) ◽

pp. 554-558

Author(s):

Emre SEVİNDİK ◽

Hüseyin UYSAL ◽

Zehra Tuğba MURATHAN

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Genetic Distance ◽

Uv Light ◽

Genetic Relationships ◽

Issr Markers ◽

Genetic Distances ◽

The Matrix ◽

Commercial Kits ◽

Issr Primers

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program. According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

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Microsatellite analysis of genetic variability in Waler horses from Australia

Australian Journal of Zoology ◽

10.1071/zo13062 ◽

2013 ◽

Vol 61 (5) ◽

pp. 357 ◽

Cited By ~ 5

Author(s):

Anas M. Khanshour ◽

Rytis Juras ◽

E. Gus Cothran

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Bayesian Method ◽

Genetic Relationships ◽

Similarity Measures ◽

Genetic Distances ◽

Microsatellite Analysis ◽

Population Subdivision ◽

Factorial Correspondence Analysis ◽

Horse Breed

The Waler horse breed is an integral part of Australian history. The purposes of this study were to analyse the genetic variability in Waler horses from Australia and to investigate genetic relationships with other horse breeds. We examined the genetic diversity of 70 Waler horses sampled from seven breeding stations in Australia. Also we analysed the relationships of these horses with 11 other horse breeds. Analysis of the genetic structure was carried out using 15 microsatellite loci, genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method. We found that the genetic diversity in the Waler was greater than the domestic horse mean and exceeded that of all endangered horse breeds. Our findings also revealed moderate population subdivision rather than inbreeding. All genetic similarity measures indicated that the Thoroughbred might be a key ancestor to the Waler. This study indicates that there is no immediate concern for loss of variation in Waler horses. Also, there clearly has been a strong input from the Thoroughbred into the Waler horse breed. However, the genetic evidence suggests that this input was not just direct but also came through other types of horses with a Thoroughbred cross background.

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Reindeer Population as an Indicator of Sustainable Development of the Arctic Territory

International Journal of Agricultural Extension ◽

10.33687/ijae.009.00.3718 ◽

2021 ◽

Vol 9 (4) ◽

pp. 21-28

Author(s):

Natalia V. Karmanovskaya

Keyword(s):

Genetic Diversity ◽

Dna Markers ◽

Genetic Relationships ◽

Animal Husbandry ◽

Komi Republic ◽

Genetic Distances ◽

The Arctic ◽

Murmansk Oblast ◽

The Matrix ◽

Breeding Programmes

The objectives of this study are to carry out genetic monitoring of domestic reindeer of Nenets breed raised on the territory of Taimyr; establishment of the genetic bank of domestic reindeer of Nenets breed; as well as a comparative analysis with populations of the Nenets breed from other breeding regions (Nenets and Yamalo-Nenets Autonomous Okrug, Murmansk Oblast and the Komi Republic) using DNA markers. The microsatellites were used in the studies as DNA markers of genetic diversity. Genotyping was carried out by the methods of the Laboratory of molecular selection basis of L.K. Ernst Federal Research Center for Animal Husbandry. Statistical data processing was performed using the GenAlEx 6.5, SplitsTree 4.14.5 software, as well as the software packages “diveRsity”, “pophelper”, and “adegenet” for the R computing environment. As a result of the study, it was found that the population of reindeer of Taimyr breed in the village of Tukhard is characterised by the minimum level of polymorphism and genetic diversity, as indicated by the minimum values of all population genetic indicators. The authors assume that the patterns that have been identified are primarily the result of breeding programmes on the samples presented in this study (such studies have not been conducted before). The results of the PCA analysis and the phylogenetic dendrogram of genetic relationships, built on the basis of the matrix of Jost's D pairwise genetic distances using the NeighborNet, revealed a similar genetic structure of Taimyr populations, which, most likely, could be due to the close geographical localisation of the studied individuals. The authors come to the conclusion that a low level of both allelic and genetic diversity in the future may negatively affect the adaptation of animals to environmental conditions.

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Molecular characterization based on chloroplast (trnl-f) DNA sequence of the apple genotypes in Ardahan/Turkey

Bangladesh Journal of Botany ◽

10.3329/bjb.v48i4.49058 ◽

2019 ◽

Vol 48 (4) ◽

pp. 1099-1106

Author(s):

Emre Sevindik ◽

Zehra Tuğba Murathan ◽

Sümeyye Filiz ◽

Kübra Yalçin

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Dna Sequence ◽

Dna Sequences ◽

Genomic Dna ◽

Nucleotide Composition ◽

Neighbor Joining ◽

Sequencing Data ◽

F Region ◽

Phylogenetic Studies

Genetic diversity among Turkish apple genotypes in Ardahan province was conducted based on cpDNA trnL-F sequences. Apple genotypes were plotted on a phylogenetic tree where Pyrus x bretschneideri was used as the outgroup. The plant samples were collected from different locations and genomic DNA was isolated from healthy and green leaves. For sequence in trnL-F region trnLe and trnFf primers were used. Later obtained DNA sequences were edited using the BioEdit and FinchTV. Sequencing data were analyzed using MEGA 6.0 software. Neighbor joining and bootstrap trees were constructed in order to verify the relationships among the apple genotypes. Phylogenetic tree consisted of two clades. The divergence values of trnL-F sequences differed between 0.000 and 0.005. Average nucleotide composition was 38.3 T, 14.9 C, 31.9 A and 14.9% G. The phylogenetic tree constructed based on trnL-F region sequences was nearly parallel to prior phylogenetic studies on apple genotypes.

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Molecular data indicate a cryptic species in Neotoma albigula (Cricetidae: Neotominae) from northwestern México

Journal of Mammalogy ◽

10.1093/jmammal/gyv169 ◽

2015 ◽

Vol 97 (1) ◽

pp. 187-199

Author(s):

Robert D. Bradley ◽

Matthew R. Mauldin

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Nuclear Gene ◽

Molecular Data ◽

Genetic Distances ◽

Dehydrogenase Gene ◽

Mitochondrial Cytochrome B ◽

Northwestern Mexico ◽

Morphological Differences ◽

Intron 2

Abstract DNA sequences from the mitochondrial cytochrome- b gene were obtained from 41 specimens of Neotoma albigula from the southwestern United States and northwestern México. Phylogenetic analyses depicted that samples of N. a. melanura from southern Sonora and northern Sinaloa formed a clade separate from representatives of the other sampled subspecies of N. albigula ( albigula , laplataensis , mearnsi , seri , sheldoni , and venusta ). Genetic distances detected between these clades (7.41%) approached divergence levels reported for other sister species of woodrats and indicated that N. a. melanura is presumably a cryptic and genetically differentiated species relative to N . albigula . Analyses of DNA sequences from a nuclear gene (intron 2 of the alcohol dehydrogenase gene, Adh 1-I2) indicated that samples of N. a. melanura formed a separate, monophyletic clade relative to the remainder of N. albigula . Further, habitat, geographic distinctions, and morphological differences were apparent between members of the 2 clades. Together, those data support the elevation of N. a. melanura to species status. Secuencias de ADN del gen mitocondrial citocromo- b se obtuvieron de 41 especímenes de Neotoma albigula provenientes del suroeste de los Estados Unidos y del noroeste de México. Análisis filogenéticos revelaron que las muestras de N. a. melanura del sureste de Sonora y del norte de Sinaloa formaron un clado separado de especímenes que representan a las otras subspecies de N. albigula (albigula, laplataensis, mearnsi, seri, sheldoni , y venusta ). Las distancias genéticas detectadas entre estos clados (7.41%) se aproximan a los valores de divergencia reportados para otras especies de ratas magueyeras, indicando que N. a. melanura es presumiblemente una especie críptica y relativamente diferenciada genéticamente de N. albigula . Los análisis de secuencias de ADN de un gen nuclear (intron 2 del gen alcohol deshidrogenasa, Adh -I2) indicaron que las muestras de N. a. melanura formaron un clado separado relativamente a especímenes de N. albigula . Adicionalmente, hábitat, distinciones geográficas, y diferencias morfológicas fueron aparentes entre miembros de los dos clados. Todos estos datos soportan la elevación de N. a. melanura al estatus de especie.

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Phylogenetic relationships in Polygalaceae based on plastid DNA sequences from the trnL‐F region

Taxon ◽

10.2307/1223706 ◽

2001 ◽

Vol 50 (3) ◽

pp. 763-779 ◽

Cited By ~ 44

Author(s):

Claes Persson

Keyword(s):

Dna Sequences ◽

Phylogenetic Relationships ◽

Plastid Dna ◽

F Region

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Genetic relationships among North American bison populations

Canadian Journal of Zoology ◽

10.1139/z96-084 ◽

1996 ◽

Vol 74 (4) ◽

pp. 738-749 ◽

Cited By ~ 11

Author(s):

Renee O. Polziehn ◽

Curtis Strobeck ◽

Robin Beech ◽

Jane Sheraton

Keyword(s):

Mitochondrial Dna ◽

North American ◽

Sequence Data ◽

Genetic Relationships ◽

Genetic Distances ◽

Bison Bison ◽

Mitochondrial Haplotypes ◽

Length Polymorphisms ◽

Wood Bison ◽

Paraphyletic Group

North American bison are presently divided into two subspecies: wood bison (Bison bison athabascae) and plains bison (B. b. bison). A survey was undertaken to determine the distribution of mitochondrial DNA haplotypes among subspecies and populations. Twelve haplotypes were identified with sequence data from the control region of mitochondrial DNA from 32 bison. Mitochondrial haplotypes for 269 bison from nine populations were then determined using the polymerase chain reaction and analyzed for restriction fragment length polymorphisms. Haplotype frequencies suggest genetic distances among bison populations from 0.0715 to 0.362. The extent of differentiation varies considerably. Based on the composition and phylogeny of haplotypes in the bison herds, plains bison form a paraphyletic group and wood bison form a polyphyletic group. Because neither subspecies of bison is derived from one lineage, neither is a well-defined taxon.

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