scholarly journals The Tsushima leopard cat exhibits extremely low genetic diversity compared with the Korean Amur leopard cat: Implications for conservation

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7297 ◽  
Author(s):  
Hideyuki Ito ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Management Strategies ◽  
Korean Population ◽  
Ex Situ ◽  
Genetic Management ◽  
Founding Population ◽  
Low Genetic Diversity ◽  
Regional Population ◽  
Leopard Cat

We examined genetic diversity of the wild Tsushima leopard cat—a regional population of the Amur leopard cat—using microsatellite markers. In addition, we compared genetic diversity of the Tsushima leopard cat with that of the Korean population of Amur leopard cat. Although bias should be considered when applying cross-species amplification, the Tsushima leopard cat showed a lower index of molecular genetic diversity than did the Korean population. These results were consistent with those obtained using other genetic markers, such as mitochondrial DNA and Y chromosome sequences. This low genetic diversity of the wild Tsushima leopard cat may be derived from the founding population. Furthermore, our results suggest that the captive populations held in Japanese zoos may show extremely low genetic diversity, leading to difficulties in genetic management of the Tsushima leopard cat. Moreover, the two regional populations were clearly separated using these marker sets. In the present study, we demonstrated that the genetic diversity of the Tsushima leopard cat is extremely low compared with that of the continental regional population. Importantly, the Japanese captive population for ex situ conservation was derived from a founding population with extremely low genetic diversity; hence, we assume that both the captive and wild populations showed extremely low genetic diversities. Our findings emphasize the need to develop carefully considered management strategies for genetic conservation.

scholarly journals Genetic Diversity and Genetic Structure of the Wild Tsushima Leopard Cat from Genome-Wide Analysis

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1375
Author(s):  
Hideyuki Ito ◽  
Nobuyoshi Nakajima ◽  
Manabu Onuma ◽  
Miho Murayama
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
De Novo ◽  
Draft Genome ◽  
Amplicon Sequencing ◽  
Snp Markers ◽  
Domestic Cat ◽  
Ex Situ ◽  
Genetic Management ◽  
Leopard Cat

The Tsushima leopard cat (Prionailurus bengalensis euptilurus) lives on Tsushima Island in Japan and is a regional population of the Amur leopard cat; it is threatened with extinction. Its genetic management is important because of the small population. We used genotyping by random amplicon sequencing-direct (GRAS-Di) to develop a draft genome and explore single-nucleotide polymorphism (SNP) markers. The SNPs were analyzed using three genotyping methods (mapping de novo, to the Tsushima leopard cat draft genome, and to the domestic cat genome). We examined the genetic diversity and genetic structure of the Tsushima leopard cat. The genome size was approximately 2.435 Gb. The number of SNPs identified was 133–158. The power of these markers was sufficient for individual and parentage identifications. These SNPs can provide useful information about the life of the Tsushima leopard cat and the pairings and for the introduction of founders to conserve genetic diversity with ex situ conservation. We identified that there are no subpopulations of the Tsushima leopard cat. The identifying units will allow for a concentration of efforts for conservation. SNPs can be applied to the analysis of the leopard cat in other regions, making them useful for comparisons among populations and conservation in other small populations.

scholarly journals Genetic Diversity and Population Structure of Two Endangered Neotropical Parrots Inform In Situ and Ex Situ Conservation Strategies

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 386
Author(s):  
Carlos I. Campos ◽  
Melinda A. Martinez ◽  
Daniel Acosta ◽  
Jose A. Diaz-Luque ◽  
Igor Berkunsky ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Management Strategies ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Genetic Management ◽  
Captive Populations ◽  
In Captivity ◽  
In The Wild ◽  
Genetic Signatures

A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.

Marked differences in genetic diversity and differentiation between the centre and edge of the geographical range of Megaleranthis saniculifolia (Ranunculaceae), a Korean endemic species

2012 ◽  
Vol 60 (7) ◽  
pp. 582
Author(s):  
Ji Hee Jeong ◽  
Zin-Suh Kim
Keyword(s):  
Genetic Diversity ◽  
Peripheral Region ◽  
Issr Markers ◽  
Ex Situ ◽  
Allele Frequency Distribution ◽  
Low Genetic Diversity ◽  
Long Time ◽  
Megaleranthis Saniculifolia ◽  
Degree Of Differentiation ◽  
Substantial Degree

The amount and distribution of genetic diversity within and between Megaleranthis saniculifolia Ohwi populations were compared between the central and peripheral regions of the species distribution. Allozyme and ISSR markers were used for genetic analysis of six populations from the central region (DY) and five populations from the peripheral region (MJ). Genetic diversity was substantially higher in the DY region than in the MJ region. Relatively uniform homozygote excess at many loci in most populations indicated that M. saniculifolia was influenced by a substantial degree of inbreeding in both regions. The degree of differentiation between populations was remarkably higher in the MJ region than in the DY region. Cluster analysis showed a trend towards separation between regions, although populations in the MJ region exhibited a slightly different trend according to the markers. We conclude that genetic drift has been affecting the populations in the MJ region for a long time, on the basis of their low genetic diversity, high differentiation, U-shaped allele-frequency distribution, and fixation of alleles towards opposing frequencies (1 or 0) among populations. In contrast, the DY region maintained relatively stable populations, although evidence of a recent bottleneck was found in one population. Along with some practical measures for genetic conservation, we present an optimal sample size for ex situ conservation to secure as many common alleles as possible.

scholarly journals MONITORING OF Aegilops L. LOCAL SPECIES GENETIC DIVERSITY OF KAZAKHSTAN’S FLORA

2018 ◽  
Vol 22 (4) ◽  
pp. 484-490 ◽  
Author(s):  
R. Urazaliev ◽  
M. Yessimbekova ◽  
K. Mukin ◽  
A. Chirkin ◽  
G. Ismagulova
Keyword(s):  
Genetic Diversity ◽  
Global Climate ◽  
Molecular Genetic ◽  
Crop Wild Relatives ◽  
Molecular Genetic Analysis ◽  
Ex Situ ◽  
Marker Allele ◽  
New Genes ◽  
Local Species ◽  
Allelic Variations

Cereal Crop Wild Relatives (CWR) are a very  important gene pool for cereal/wheat improvement. New genes for resistance to diseases and pests are urgently needed to avoid using pesticides and to raise adaptivity to the environmental stresses caused by global climate change. In this regard, the study is aimed at ex situ conservation of Aegilops L. genus local ecotypes’ genetic diversity, which is very relevant and promising for breeding. In order to establish breeding utility and form an ex situ collection reflecting the intra- and inter-specific diversity, the phenotypic screening of Kazakhstan’s local populations of Aegilops L. genus (Ae. cylindrica, Ae. tauschii, Ae. triuncialis and Ae. crassa) was conducted on the basis of multiple indicators. For the first time molecular-genetic analysis of 50 representatives of Aegilops L. genus from Kazakhstan’s flora was performed. The microsatellite analysis with the use of 11 EST-SSR markers revealed eight of them to be most effective. For each marker, allele frequency and average heterozygosity was calculated. For the most informative markers the presence of 5 and 6 respective allelic variations was found. A bank of genomic DNA was created and kept in ex situ storage (–70 °С, long-term) in the IMBB of the MES of RK.

scholarly journals Molecular genetic diversity and mating system in sacha inchi progenies1

2017 ◽  
Vol 47 (4) ◽  
pp. 480-487 ◽  
Author(s):  
Mágno Sávio Ferreira Valente ◽  
Maria Teresa Gomes Lopes ◽  
Francisco Célio Maia Chaves ◽  
Mozanil Correia Pantoja ◽  
Francy Mary Galúcio Sousa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Urban Communities ◽  
Molecular Genetic ◽  
Aflp Markers ◽  
Ex Situ ◽  
Breeding Programs ◽  
Molecular Genetic Diversity ◽  
Sacha Inchi ◽  
Allogamous Species

ABSTRACT Sacha inchi (Plukenetia volubilis L.) is a species with nutraceutical benefits traditionally consumed by Amazonic indigenous and urban communities. Studies on the genetic diversity and mating system are required to preserve and make the best use of the genetic resources for this species. This study aimed to estimate the genetic diversity and mating system parameters of sacha inchi progenies using Amplified Fragment Length Polymorphism (AFLP) markers. A total of 360 progenies from 30 accessions of sacha inchi were analyzed using three AFLP primers combinations. The percentage variation between and within families and the crossing rate, among other parameters, were estimated. The AFLP markers were efficient in genetically differentiating progenies, revealing 251 (98.82 %) polymorphic fragments. The analysis of molecular variance showed that the strongest variation occurs between progenies (57.16 %). However, the genetic differentiation within progenies was considerable (42.84 %), and could be exploited in breeding programs. The estimated population outcrossing rate was high (0.957), indicating it is a predominantly allogamous species. On the other hand, 33.7 % of the crosses occurred between related individuals. The estimate for biparental crosses revealed that the progenies consisted mainly of half-siblings (66.9 %) and full-siblings (28.8 %). For purposes of breeding and ex situ genetic conservation, sacha inchi seeds should be collected from a large number of parent plants.

Managing gene flow among isolated population fragments

2019 ◽  
pp. 115-134
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Information ◽  
Management Strategies ◽  
Genetic Data ◽  
Isolated Population ◽  
Detailed Data ◽  
Genetic Management ◽  
Flow Management ◽  
The Status

Even without detailed genetic data, sound genetic management strategies for augmenting gene flow can be instituted by considering population genetics theory, and/or computer simulations. When detailed data are lacking, moving (translocating) some individuals into isolated inbred population fragments is better than moving none, as long as the risk of outbreeding depression is low. With more detailed genetic information, more precise genetic management of fragmented populations can be achieved. Using mean kinship within and between populations (estimated from modeling, pedigrees, genetic markers or genomes), and moving individuals among fragments with the lowest between fragment mean kinships provides the best approach to gene flow management. Populations should then be monitored to confirm that movement of individuals has resulted in the desired levels of gene flow, genetic diversity has been enhanced, and that the status of the population is improving.

scholarly journals Genetic diversity in clustered colonies of an Antarctic marine mesopredator: a role for habitat quality?

2021 ◽  
pp. 1-10
Author(s):  
Emiliano Mori ◽  
Claudia Brunetti ◽  
Antonio Carapelli ◽  
Lucia Burrini ◽  
Niccolò Fattorini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Quality ◽  
Ross Sea ◽  
Molecular Genetic ◽  
Assignment Test ◽  
Pygoscelis Adeliae ◽  
Seabird Species ◽  
Low Genetic Diversity ◽  
Key Species

Abstract Genetic structure may be highly variable across seabird species, and particularly among those that are distributed over large geographical areas. The Adélie penguin (Pygoscelis adeliae) is a numerically dominant Antarctic seabird that is considered to be a key species in coastal ecosystems. Since the Last Glacial Maximum, penguin colonization of the Antarctic coastline occurred at varying geographical and temporal scales, contributing to an incomplete understanding of how modern colonies relate to each other at local or regional scales. We assessed the population genetic structure of Adélie penguins (n = 86 individuals) from three adjacent colonies along the Victoria Land coast using molecular genetic markers (i.e. seven microsatellite loci isolated through next-generation sequencing). Our results indicate meta-population dynamics and possibly relationships with habitat quality. A generally low genetic diversity (Nei's index: 0.322–0.667) was observed within each colony, in contrast to significant genetic heterogeneity among colonies (pairwise FST = 0.071–0.148), indicating that populations were genetically structured. Accordingly, an assignment test correctly placed individuals within the respective colonies from which they were sampled. The presence of inter-colony genetic differentiation contrasts with previous studies on this species that showed a lack of genetic structure, possibly due to higher juvenile or adult dispersal. Our sampled colonies were not panmictic and suggest a lower migration rate, which may reflect relatively stable environmental conditions in the Ross Sea compared to other regions of Antarctica, where the ocean climate is warming.

scholarly journals Molecular Dissection for Boll Shedding in Upland Cotton Using Microsatellites

2021 ◽  
pp. 34-41
Author(s):  
Kanwal Zia ◽  
Syed Bilal Hussain
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Association Studies ◽  
Molecular Genetic ◽  
Phenotypic Traits ◽  
Marker Assisted Breeding ◽  
Molecular Genetic Diversity ◽  
Low Genetic Diversity ◽  
Cotton Genotypes ◽  
Single Cluster

DNA markers application in marker-assisted breeding of cotton is handicapped due to low genetic diversity in cotton germplasm. The present study was designed to identify DNA markers, predominately simple sequence repeats (SSRs), associated with tolerance/resistance to heat stress as a consequence of boll shedding. To find out the genetic diversity a total of 24 cotton genotypes and 50 SSR primers were used. Total 288 alleles were produced with an average of 5.7 alleles per primer. Bootstrap cluster analysis used to generate a dendrogram that cluster the 24 accessions into two main clusters. Eleven out of 24 genotypes fall in a single cluster. Phenotypically H-4074 gives more diversity, while genotypically H-4074 sheared the same genetic background as H-4070, H-4091 and H-4090. Low genetic diversity was observed among both genotypic and phenotypic as maximum varieties fall in single group. This study helps for selecting diverse accessions with multiple phenotypic traits, which were drought to boll shedding. It suggests further elaborating the molecular genetic diversity by using new SSR marker to improve the yield of cotton cultivars. These preliminary results set the stage for initiating in depth marker-trait association studies, which will be instrumental for initiating marker-assisted breeding in cotton.

scholarly journals Genetic diversity and core subset selection in ex situ seed collections of the banana crop wild relative Musa balbisiana

2019 ◽  
Vol 17 (6) ◽  
pp. 536-544 ◽  
Author(s):  
Yves Bawin ◽  
Bart Panis ◽  
Samuel Vanden Abeele ◽  
Zhiying Li ◽  
Julie Sardos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Crop Wild Relatives ◽  
Ex Situ ◽  
Musa Balbisiana ◽  
Centre Of Origin ◽  
Low Genetic Diversity ◽  
Feral Populations ◽  
Unique Variation ◽  
Seed Collections

AbstractCrop wild relatives (CWRs) play a key role in crop breeding by providing beneficial trait characteristics for improvement of related crops. CWRs are more efficiently used in breeding if the plant material is genetically characterized, but the diversity in CWR genetic resources has often poorly been assessed. Seven seed collections of Musa balbisiana, an important CWR of dessert and cooking bananas, originating from three natural populations, two feral populations and two ex situ field collections were retrieved and their genetic diversity was quantified using 18 microsatellite markers to select core subsets that conserve the maximum genetic diversity. The highest genetic diversity was observed in the seed collections from natural populations of Yunnan, a region that is part of M. balbisiana's centre of origin. The seeds from the ex situ field collections were less genetically diverse, but contained unique variation with regards to the diversity in all seed collections. Seeds from feral populations displayed low genetic diversity. Core subsets that maximized genetic distance incorporated almost no seeds from the ex situ field collections. In contrast, core subsets that maximized allelic richness contained seeds from the ex situ field collections. We recommend the conservation and additional collection of seeds from natural populations, preferentially originating from the species' region of origin, and from multiple individuals in one population. We also suggest that the number of seeds used for ex situ seed bank regeneration must be much higher for the seed collections from natural populations.

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