scholarly journals Genetic diversity and population structure of the endangered basal angiospermBrasenia schreberi(Cabombaceae) in China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5296 ◽  
Author(s):  
Zhi-Zhong Li ◽  
Andrew W. Gichira ◽  
Qing-Feng Wang ◽  
Jin-Ming Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Glacial Refugia ◽  
Mantel Test ◽  
Ex Situ ◽  
Brasenia Schreberi ◽  
Genetic Diversity And Structure ◽  
Rare And Endangered

Brasenia schreberiJ.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations ofB. schreberiin China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO= 0.200,HE= 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test,r= 0.0694;P= 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution ofB. schreberiin China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.

scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

scholarly journals Genetic structure and diversity in Sorghum bicolor (L.) Moench landraces from marginal sorghum production lands in Senegal, based on SSR markers

2020 ◽  
Vol 7 (3) ◽  
pp. 134-144
Author(s):  
Amy Bodian ◽  
Bassiaka Ouattara ◽  
Awa Sarr ◽  
Boubacar Gano ◽  
Mbaye-Ndoye Sall ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Production Systems ◽  
Classification Model ◽  
Germplasm Management ◽  
Genetic Diversity And Structure ◽  
Food And Feed ◽  
Sorghum Production ◽  
In Situ Management

Data on sorghum genetic diversity in Senegal are missing despite its importance in the food and feed in the country. In order to contribute to the sustainable in situ management of sorghum germplasm, we investigated its genetic diversity and structure in its marginal production areas. Investigations were focused on Thiès, Diourbel and Kédougou regions where sorghum landraces have been less investigated and genetic information on landraces is unknown. A total of 148 sorghum accessions representative of landraces used in production systems have been sampled and analyzed with 30 microsatellite markers. A total of 138 alleles have been recorded. The number of alleles per locus varied from 3 (7 loci) to 8 (3 loci). The observed heterozygosity varied from 0 to 0.62. The low genetic distance (0.12) was recorded between Thiès and Diourbel populations and the highest distance (0.22) between Thiès and Kédougou populations. Dendrogram obtained according to Neighbour joining classification model allowed the classification of sorghum accessions into three main groups. The Genetic structure is not function to the regions indicating that landraces are not specific to a region. The results are a first step toward the sustainable in situ management of genetic resources. Data on the whole range of existing diversity of sorghum in Senegal is an important key for its germplasm management; so, the genotyping must be extended to accessions from the whole country.

scholarly journals Management Practices and Breeding History of Varieties Strongly Determine the Fine Genetic Structure of Crop Populations: A Case Study Based on European Wheat Populations

2020 ◽  
Vol 12 (2) ◽  
pp. 613
Author(s):  
Abdul Rehman Khan ◽  
Isabelle Goldringer ◽  
Mathieu Thomas
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Management Practices ◽  
Genetic Group ◽  
Ex Situ ◽  
History Of ◽  
Breeding History ◽  
On Farm ◽  
Different Levels

As the effects of climate change begin to be felt on yield stability, it is becoming essential to promote the use of genetic diversity in farmers’ fields. The presence of genetic variability in variety could fulfil this purpose. Indeed, the level of intra-varietal genetic diversity influences the spatio-temporal stability of yields and the disease susceptibility of crop species. Breeding history of varieties and their management practices are two factors that should influence intra-varietal genetic diversity. This paper describes the genetic diversity of eight wheat samples covering a gradient from modern single varieties to on-farm mixtures of landraces. This gradient discriminates between landrace, historical and modern varieties, considering the breeding history of varieties, between single-varieties and mixtures of varieties, and between ex situ and in situ de facto strategy in terms of management practices. Genetic diversity of these samples was analyzed with the help of 41 single nucleotide polymorphism markers located in neutral regions, through computing genetic indices at three different levels: Allelic, haplotypic and genetic group level. Population structure and kinship were depicted using discriminant analysis and kinship network analysis. Results revealed an increase in the complexity of the genetic structure as we move on the gradient of variety types (from modern single variety to in situ on-farm mixtures of landraces). For the landraces, the highest levels of genetic diversity have been observed for a landrace (Solina d’Abruzzo) continuously grown on-farm in the region of Abruzzo, in Italy, for many decades. This landrace showed an excess of haplotypic diversity compared to landraces or the historical variety that were stored in genebanks (ex situ conservation). Genetic analyses of the mixtures revealed that, despite a very high selfing rate in wheat, growing in evolutionary mixtures promotes recombination between different genetic components of the mixture, a second way to increase the level of haplotype diversity. When management practices such as growing in mixture and on-farm management are combined, they substantially increase the different levels of genetic diversity of the populations (allelic, haplotypic, genetic group diversity), and consequently promote their adaptability. Our results confirm the need to develop and manage evolving diversified large populations on-farm. These results invite crop diversity managers such as genebank curators, community seed bank managers and farmers’ organizations to adapt their management strategies to the type of variety they wish to manage, because we have shown that their choices have a strong influence on the genetic composition of the crop populations.

scholarly journals Genetic diversity and structure of wild Vaccinium populations - V. myrtillus, V. vitis-idaea and V. uliginosum in the Baltic States

Silva Fennica ◽  
2020 ◽  
Vol 54 (5) ◽  
Author(s):  
Agnese Gailīte ◽  
Anita Gaile ◽  
Dainis Ruņģis
Keyword(s):  
Genetic Diversity ◽  
Wild Species ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Managed Forests ◽  
Baltic Countries ◽  
Genetic Diversity And Structure ◽  
The Baltic ◽  
Selection Of

L., L. and L. belong to the genus . These wild species are widely distributed and ecologically important within the Baltic countries but they have not been extensively studied using molecular markers. EST-SSR and cpSSR markers were used to investigate the population structure and genetic diversity of these species to obtain information useful for the development of conservation strategies. Wild species populations are moderately genetically differentiated, with some populations more highly differentiated, but without higher order clustering of groups of populations, indicating that there are no dispersal barriers for these species within the Baltic countries. Genetic diversity of populations growing in protected areas, managed forests and intensively utilised public recreational areas is similar. The results from this study can be utilised for the selection of populations for the conservation of the studied species. In addition, complementary conservation strategies can be used for the preservation of rare varieties (e.g. var. ).VacciniummyrtillusV. vitis-idaeaV. uliginosumVacciniumin situVacciniumin situVacciniumex situV. myrtillusleucocarpum

scholarly journals Genetic diversity and structure of the critically endangered Artocarpus annulatus, a crop wild relative of jackfruit (A. heterophyllus)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9897
Author(s):  
Leta Dickinson ◽  
Hilary Noble ◽  
Elliot Gardner ◽  
Aida Shafreena Ahmad Puad ◽  
Wan Nuur Fatiha Wan Zakaria ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic Data ◽  
Allelic Diversity ◽  
Crop Wild Relatives ◽  
Ex Situ ◽  
Wild Relative ◽  
Mature Trees ◽  
Crop Genetic Diversity ◽  
Genetic Diversity And Structure

Limestone karsts of Southeast Asia can harbor high levels of endemism, but are highly fragmented, increasingly threatened, and their biodiversity is often poorly studied. This is true of the Padawan Limestone Area of Sarawak, Malaysia, home to the endemic Artocarpus annulatus, the closest known wild relative of two important and underutilized fruit tree crops, jackfruit (A. heterophyllus) and cempedak (A. integer). Identifying and conserving crop wild relatives is critical for the conservation of crop genetic diversity and breeding. In 2016 and 2017, five A. annulatus populations were located, and leaf material, locality information, and demographic data were collected. Microsatellite markers were used to assess genetic diversity and structure among populations, and to compare levels of genetic diversity to closely related congeneric species. Results indicate no evidence of inbreeding in A. annulatus, and there is no genetic structure among the five populations. However, diversity measures trended lower in seedlings compared to mature trees, suggesting allelic diversity may be under threat in the youngest generation of plants. Also, genetic diversity is lower in A. annulatus compared to closely related congeners. The present study provides a baseline estimate of A. annulatus genetic diversity that can be used for comparison in future studies and to other species in the unique limestone karst ecosystems. Considerations for in situ and ex situ conservation approaches are discussed.

Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides

2014 ◽  
Vol 21 (5) ◽  
pp. 601-609
Author(s):  
Wang Deyun ◽  
Peng Jie ◽  
Chen Yajing ◽  
Lü Guosheng ◽  
Zhang Xiaoping ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Endangered Species ◽  
Rare And Endangered Species ◽  
Rare And Endangered

scholarly journals The Patterns and Puzzles of Genetic Diversity of Endangered Freshwater Mussel Unio crassus Philipsson, 1788 Populations from Vistula and Neman Drainages (Eastern Central Europe)

Life ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 119
Author(s):  
Adrianna Kilikowska ◽  
Monika Mioduchowska ◽  
Anna Wysocka ◽  
Agnieszka Kaczmarczyk-Ziemba ◽  
Joanna Rychlińska ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Scales ◽  
Freshwater Mussel ◽  
Its Region ◽  
Strong Relationship ◽  
Mantel Test ◽  
Freshwater Ecosystems ◽  
Hierarchical Organization ◽  
Anthropogenic Factors

Mussels of the family Unionidae are important components of freshwater ecosystems. Alarmingly, the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species identifies almost 200 unionid species as extinct, endangered, or threatened. Their decline is the result of human impact on freshwater habitats, and the decrease of host fish populations. The Thick Shelled River Mussel Unio crassus Philipsson, 1788 is one of the examples that has been reported to show a dramatic decline of populations. Hierarchical organization of riverine systems is supposed to reflect the genetic structure of populations inhabiting them. The main goal of this study was an assessment of the U. crassus genetic diversity in river ecosystems using hierarchical analysis. Different molecular markers, the nuclear ribosomal internal transcribed spacer ITS region, and mitochondrial DNA genes (cox1 and ndh1), were used to examine the distribution of U. crassus among-population genetic variation at multiple spatial scales (within rivers, among rivers within drainages, and between drainages of the Neman and Vistula rivers). We found high genetic structure between both drainages suggesting that in the case of the analyzed U. crassus populations we were dealing with at least two different genetic units. Only about 4% of the mtDNA variation was due to differences among populations within drainages. However, comparison of population differentiation within drainages for mtDNA also showed some genetic structure among populations within the Vistula drainage. Only one haplotype was shared among all Polish populations whereas the remainder were unique for each population despite the hydrological connection. Interestingly, some haplotypes were present in both drainages. In the case of U. crassus populations under study, the Mantel test revealed a relatively strong relationship between genetic and geographical distances. However, in detail, the pattern of genetic diversity seems to be much more complicated. Therefore, we suggest that the observed pattern of U. crassus genetic diversity distribution is shaped by both historical and current factors i.e. different routes of post glacial colonization and history of drainage systems, historical gene flow, and more recent habitat fragmentation due to anthropogenic factors.

scholarly journals Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0245965
Author(s):  
Catherine Kiwuka ◽  
Eva Goudsmit ◽  
Rémi Tournebize ◽  
Sinara Oliveira de Aquino ◽  
Jacob C. Douma ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Allelic Variation ◽  
Coffea Canephora ◽  
Ex Situ ◽  
Negative Effects ◽  
Robusta Coffee ◽  
Genetic Diversity And Structure ◽  
Adaptive Diversity ◽  
Southern Central

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

scholarly journals AUTOCHTHONOUS BREEDS OF DOMESTIC ANIMALS AND CONSERVATION MEASURES

AGROFOR ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Zoran MALETIC
Keyword(s):  
Genetic Diversity ◽  
Biological Diversity ◽  
Domestic Animals ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Animal Genetic Resources ◽  
Diversity Preservation ◽  
The Republic ◽  
International Conventions

Recently, highly productive breeds of various species of domestic animals have been used in livestock production, which has resulted in the destruction of indigenous breeds of domestic animals around the world, even in our area. This is the first reason why indigenous races and strains have been endangered. Another reason is that domestic, indigenous breeds were crossed with specialized breeds, which were imported, and in that way their genetic diversity was negatively affected. Resistance is lost, adaptation to the conditions in which they were created, the ability to survive in nature. Indigenous breeds of different species of domestic animals, which are recognized in the Republic of Srpska (BiH) are gatačko cattle and buša (cattle), Vlašić pramenka, Podveleška pramenka, Kupres pramenka (sheep), domestic Balkan horned goat (goats), Bosnian mountain horse (horses), mangulica (pigs) and pogrmuša hen or živičarka hen (poultry). By acceding to international conventions, BiH /Republic of Srpska has committed itself to establishing a system of measures that will enable the conservation of biological diversity and the protection of indigenous and endangered breeds of domestic animals. The choice of a strategy for the conservation of diversity, the establishment of an adequate conservation scheme, and the implementation of a conservation strategy are some of the key elements of any process for the conservation of genetic diversity. Preservation of autochthonous and protected breeds of domestic animals is possible through preservation in the original environment (in situ) and preservation outside the original environment (ex situ). There is a possibility of combining these models of conservation of animal genetic resources.

Estimation of Genetic Diversity Among Teressa Goat Population of A and N Islands by using Microsatellite Markers

2020 ◽  
Author(s):  
Jai Sunder ◽  
S. Jeyakumar ◽  
S. P. Yadav ◽  
A. K. De ◽  
A. Kundu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ex Situ ◽  
Mode Shift ◽  
Information Index ◽  
Goat Population ◽  
Indigenous Goat ◽  
Nicobar Islands ◽  
Sparse Population

Background: Teressa goat is an indigenous goat breed of Andaman and Nicobar Islands. These goats are mainly distributed in the Nicobar group of islands, however, sparse population is also available in the Andaman Islands. In order to understand the genetic diversity and variation among the population of Teressa goat, the studies on the molecular characterization was done by using microsatellite molecular markers. Methods: Randomly a total of 48 blood samples were collected different areas of the Nicobar Islands representing the breeding tract of the Teressa goat. Based on the guidelines of ISAG and FAO, a total of 15 recommended microsatellite markers were selected for the microsatellite analysis study. The data were analysed to study the diversity analysis at each locus by using GENETIX software package. Bottleneck hypothesis was also studied by using BOTTLENECK 1.2.01 and FIS, FIT and FIT values were calculated and heterozygosity deficiency at each locus using FSTAT software. Result: A total of 50 genotypes were observed across the 15 loci. The number of genotype varied between (MAF70; SRCRSP3) 1 and 6 (SRCRSP15). The effective number of alleles (Ne) varied from 2 to 6.98 in Teressa goat. Shannon’s Information Index (I) value was found to be high (1.1856±0.4369), it indicated that the level of diversity among the population of the Teressa goat is high. All the values of FIS obtained were negative which is suggestive of no inbreeding within the populations and the animals were outbred. The mode-shift test indicated the genetic bottleneck in Teressa and needs greater attention towards in situ/ex situ conservation. The present study provides the valuable information about the genetic makeup of the Teressa goat, however, detail study is required to carry out to study the important traits linked with production for further utilization of this breed.

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