High genetic diversity within and low differentiation among Juniperus excelsa M. Bieb. populations: Molecular markers reveal their genetic structure patterns

AFLP, RAPD and SSR molecular markers were used to study the genetic diversity and genetic structure of the Híbrido de Timor germplasm. The principal coordinate analysis, UPGMA cluster analysis based on genetic dissimilarity of Jaccard, Bayesian model-based cluster analysis, percentage of polymorphic loci, Shannon's information index and Nei gene diversity were employed to assess the genetic diversity. The analyses demonstrated a high genetic diversity among Híbrido de Timor accessions. UPGMA and Bayesian cluster analyses grouped the accessions into three clusters. The genetic structure of Híbrido de Timor is reported. The management of Híbrido de Timor germplasm variability and its potential use in breeding programs are discussed.

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Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210828 ◽

2020 ◽

Vol 21 (8) ◽

Author(s):

M. DANIE AL MALIK ◽

NI PUTU DIAN PERTIWI ◽

ANDRIANUS SEMBIRING ◽

NI LUH ASTRIA YUSMALINDA ◽

ENEX YUNIARTI NINGSIH ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Short Communication ◽

Management Plan ◽

P Value ◽

High Genetic Diversity ◽

Population Structure Analysis ◽

Fisheries Sustainability ◽

Java Sea ◽

Longtail Tuna

Abstract. Al Malik MD, Pertiwi NPD, Sembiring A, Yusmalinda NLA, Ningsing EY, Astarini IA. 2020. Short Communication: Genetic structure of Longtail Tuna Thunnus tonggol (Bleeker, 1851) in Java Sea, Indonesia. Biodiversitas 21: 3637-3643. Thunnus tonggol (Longtail Tuna) is an economically important fish found in Indonesia waters, however, the information regarding this fish is lacking. Known to be a neritic fish and found in shallow water, Java Sea is one of the ideal habitats for T. tonggol species. Due to high fishing rates activities in Java Sea, a better management plan to ensure the conservation and fisheries sustainability around this area is needed, especially to protect T. tonggol population. In order to complete the Indonesian tuna data, we aim to study the diversity and genetic structure of T. tonggol in Java Sea at three different locations; i.e. Semarang, Banjarmasin, and Jakarta. In this study, population genetic methods with the marker of mitochondrial DNA (mtDNA) control region were used in population structure analysis. A total of 115 specimens were collected from the fish market around the area of study locations and amplified using polymerase chain reaction (PCR) and sequenced using Sanger methods. The result showed genetic diversity (Hd) value of 0.99366, and nucleotide diversity (π) value of 0.01906. Both of these values indicated high genetic diversity. Population analyses using Analysis of Molecular Variance (AMOVA) showed nonsignificant differences between the three populations of study (mixing population), with the ΦST value of 0,00375 (p-value > 0.05). Based on this result, the fisheries management for T. tonggol in Java Sea needs to be managed as one single population management.

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Phenotypic and genotypic signature of saponin chemical composition in Chinese wild soybean (Glycine soja): revealing genetic diversity, geographical variation and dispersal history of the species

Crop and Pasture Science ◽

10.1071/cp18214 ◽

2018 ◽

Vol 69 (11) ◽

pp. 1126

Author(s):

Yuya Takahashi ◽

Xiang-Hua Li ◽

Chigen Tsukamoto ◽

Ke-Jing Wang

Keyword(s):

Genetic Diversity ◽

Chemical Composition ◽

Genetic Structure ◽

Southern China ◽

Glycine Soja ◽

Wild Soybean ◽

Ice Age ◽

High Genetic Diversity ◽

The North ◽

Or Genes

Saponin chemical composition was phenotyped and genotyped, and saponin composition-based geographical genetic diversity and differentiation were evaluated in Chinese wild soybean (Glycine soja Sieb. & Zucc.). Thirty-two phenotypes and 34 genotypes were confirmed from 3805 wild soybean accessions. Eleven phenotypes (AaαK, AaαIK, AaαIJK, AaBcEαJ, AaBcαK, AbEαIJ, AbαK, AbαIK, AbαIJK, AbβHAb and Aβ0) were newly detected. Four genes had frequencies: Sg-1a 78.8% and Sg-1b 21.0% at the Sg-1 locus; Sg-4 30.7% and Sg-6e 13.7% at their respective loci. The north-eastern and southern populations showed high genetic diversity; the Northeast region contained more novel variants (AuAe, A0, A0Bc, αH, αI αJ, αK, and AbβHAb), and the southern populations contained high frequencies of the Sg-4 gene. Gene differentiation (Fst) analysis suggested that Sg-4 and four group-α saponin alleles or genes (Sg-6e, Sg-6h, Sg-6i, Sg-6j) were important factors influencing the genetic structure and differentiation in Chinese wild soybeans. Geographical differentiation was characterised mainly by latitudinal differences, with two primary groups (north and south) based on saponin genes. Chinese wild soybean accessions differed from Japanese and South Korean ones in genetic structure based on saponin composition, the latter two being likely to have spread from southern China in the glacial stages during the last Ice Age.

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Genetic diversity in portuguese native Vitis vinifera L. ssp. vinifera and ssp. sylvestris

Czech Journal of Genetics and Plant Breeding ◽

10.17221/2447-cjgpb ◽

2010 ◽

Vol 46 (Special Issue) ◽

pp. S54-S56 ◽

Cited By ~ 3

Author(s):

J. Cunha ◽

M. Teixeira Santos ◽

J. Brazăo ◽

L.C. Carneiro ◽

M. Veloso ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Genetic Structure ◽

Vitis Vinifera ◽

Gene Pool ◽

Western Europe ◽

Eastern European ◽

Starting Point ◽

Probable Origin ◽

Different Origins

To assess the different origins of Portuguese grapevine varieties, we used six nuclear and four chloroplastidal microsatellites as molecular markers, in order to compare the genetic structure of native wild-vines with native grapevine varieties. Both native subspecies have a great diversity, and a high interrelationship across the six nuclear microsatellites. Although identical numbers of alleles were found in each population, their distribution was different in the <I>vinifera </I>and <I>sylvestris </I>subspecies. Portuguese wild-vines have only chlorotypes A and B; A being the most frequent. The fifty-seven analysed Portuguese varieties have chlorotypes A, B, C, and D. The most frequent was the chlorotype A (75%), followed by D (21%). The results obtained reinforced the idea of Western Europe as having been one of the domestication centres for the grapevine, with contributions from the Eastern European gene pool. The observed genetic structure is a starting point from which to clarify the high number of native cultivars found in Portugal, and reinforces their probable origin in the Iberian Peninsula.

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Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae), from Mekong Basin

International Journal of Zoology ◽

10.1155/2017/5976421 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Surapon Yodsiri ◽

Komgrit Wongpakam ◽

Adisak Ardharn ◽

Chadaporn Senakun ◽

Sutthira Khumkratok

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Demographic History ◽

Hydropower Plant ◽

Mekong River ◽

Demographic Expansion ◽

High Genetic Diversity ◽

History Analysis ◽

History Of ◽

Important Food Source

The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

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Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

Animal Genetics ◽

10.1111/age.12429 ◽

2016 ◽

Vol 47 (4) ◽

pp. 463-470 ◽

Cited By ~ 8

Author(s):

S. M. F. Vahidi ◽

M. O. Faruque ◽

M. Falahati Anbaran ◽

F. Afraz ◽

S. M. Mousavi ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Genetic Structure ◽

Population Genetic ◽

High Genetic Diversity ◽

Indigenous Sheep

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Genetic Variation and Population Differentiation in the Bovine Lymphocyte Antigen DRB3.2 Locus of South African Nguni Crossbred Cattle

Animals ◽

10.3390/ani11061651 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1651

Author(s):

Lwamkelekile Sitshilelo Mkize ◽

Oliver Tendayi Zishiri

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

South African ◽

Population Genetic Structure ◽

Population Genetic ◽

Heterozygote Advantage ◽

Crossbred Cattle ◽

High Genetic Diversity ◽

Lymphocyte Antigen ◽

Bovine Lymphocyte

The bovine lymphocyte antigen (BoLA-DRB3) gene is an important region that codes for glycoproteins responsible for the initiation of an immune response. BoLA-DRB3 alleles have been demonstrated to be associated with disease resistance/tolerance. Therefore, great genetic diversity is correlated with better adaptation, fitness, and robustness. The current study was conducted to assess the population genetic structure of the BoLA-DRB3 gene in Nguni crossbred cattle using polymerase chain reaction-sequence based typing (PCR-SBT). High genetic diversity was detected, with 30 alleles, 11 of which are novel to the study. Alleles DRB3*0201, DRB3*0701, DRB*0901, and DRB*1601 were present in all populations and accounted for nearly around 50% of all observed alleles. A mean genetic diversity (HE) of 0.93 was detected. The high overall genetic diversity is possibly associated with pathogen-assisted selection and heterozygote advantage. Such high diversity might explain the hardiness of the Nguni crossbred cattle to the Southern African region. Low population genetic structure was identified (FST = 0.01), suggesting possible gene flow between populations and retention of similar alleles. The study was undertaken to bridge the dearth of such studies in South African breeds and it is imperative for effective sustainability of indigenous breeds and the implementation of effective breeding strategies.

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Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

Royal Society Open Science ◽

10.1098/rsos.140255 ◽

2015 ◽

Vol 2 (8) ◽

pp. 140255 ◽

Cited By ~ 7

Author(s):

Claire C. Keely ◽

Joshua M. Hale ◽

Geoffrey W. Heard ◽

Kirsten M. Parris ◽

Joanna Sumner ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Dna Sequences ◽

Nuclear Dna ◽

Urban Expansion ◽

Nuclear Gene ◽

Management Approach ◽

Natural Habitats ◽

High Genetic Diversity ◽

Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

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Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

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First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽

10.12688/f1000research.3567.1 ◽

2014 ◽

Vol 3 ◽

pp. 66 ◽

Cited By ~ 3

Author(s):

Javier Monzón

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Genetic Structure ◽

Dna Sequences ◽

Canis Latrans ◽

Regional Analysis ◽

Model Organism ◽

Nucleotide Polymorphisms ◽

Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

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