Limited Genetic Diversity and High Differentiation in Angelica Dahurica Resulted by Domestication: Insights to Breeding and Conservation

2021 ◽  
Author(s):  
Rong Huang ◽  
Yinrong Liu ◽  
Jianling Chen ◽  
Zuyu Lu ◽  
Jiajia Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Clustering Analysis ◽  
Large Scale ◽  
Angelica Dahurica ◽  
Significant Genetic Differentiation ◽  
Large Scale Analysis ◽  
Domestication Process ◽  
Resources Conservation

Abstract Background： Angelica dahurica, belonging to the Apiaceae family, whose dry root is a famous traditional Chinese medicine named as “Bai zhi”. There are two cultivars (A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’), which have been domesticated for thousands of years. Long term artificial selection has led to great changes in root phenotypes of the two cultivars, and also decreased their adaptability to environment. We proposed hypothesis that the cultivars may lose some genetic diversity and highly differentiate from wild A. dahurica during the domestication process. However, few studies have been carried out on how domestication affects the genetic variation of this species. Here, we accessed the levels of genetic variation and differentiation within and between wild A. dahurica and its cultivars using 12 SSR markers. Results: The results revealed that the genetic diversity of the cultivars was much lower than that of wild A. dahurica, and A. dahurica cv. ‘Qibaizhi’ had lower genetic diversity compared to A. dahurica cv. ‘Hangbaizhi’. AMOVA analysis showed significant genetic differentiation between the wild and cultivated A. dahurica, and between A. dahurica cv. ‘Hangbaizhi’ and A. dahurica cv. ‘Qibaizhi’. The results of Bayesian, UPGMA, NJ and PcoA clustering analysis indicated that all 15 populations were assigned to two genetic clusters corresponding to the wild and cultivated resources. Bayesian clustering analysis further divided the cultivated resources into two sub-clusters corresponding to the two cultivars. Conclusions：Our study suggests that domestication process is likely the major factor resulting in the loss of genetic diversity in cultivated A. dahurica and significant genetic differentiation from the wild resources due to founder effect and/or artificially directional selections. This large-scale analysis of population genetics could provide valuable information for genetic resources conservation and breeding programs of Angelica dahurica.

scholarly journals Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1185
Author(s):  
Helena Eklöf ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Picea Abies ◽  
Norway Spruce ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Complexity Reduction ◽  
Exome Capture ◽  
Genome Wide ◽  
Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

Genetic diversity and differentiation in populations of Japanese stone pine (Pinuspumila) in Japan

1996 ◽  
Vol 26 (8) ◽  
pp. 1454-1462 ◽  
Author(s):  
Naoki Tani ◽  
Nobuhiro Tomaru ◽  
Masayuki Araki ◽  
Kihachiro Ohba
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Phylogenetic Trees ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Group Method ◽  
Stone Pine ◽  
Arithmetic Means ◽  
Pair Group

Japanese stone pine (Pinuspumila Regel) is a dominant species characteristic of alpine zones of high mountains. Eighteen natural populations of P. pumila were studied in an effort to determine the extent and distribution of genetic diversity. The extent of genetic diversity within this species was high (HT = 0.271), and the genetic differentiation among populations was also high (GST = 0.170) compared with those of other conifers. In previous studies of P. pumila in Russia, the genetic variation within the species was also high, but the genetic differentiation among populations was low. We infer that this difference originates from differences in geographic distribution and ecological differences between the two countries. The genetic variation within each population tended, as a whole, to be smaller within marginal southern populations than within northern populations. Genetic relationships among populations reflect the geographic locations, as shown by unweighted pair-group method with arithmetic means and neighbor-joining phylogenetic trees.

scholarly journals Evolution during seed production for ecological restoration? A molecular analysis of 19 species finds only minor genomic changes

2021 ◽  
Author(s):  
Malte Conrady ◽  
Christian Lampei ◽  
Oliver Bossdorf ◽  
Walter Durka ◽  
Anna Bucharova
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ecological Restoration ◽  
Seed Production ◽  
Large Scale ◽  
Gene Diversity ◽  
Natural Populations ◽  
Genetic Change ◽  
Breeding Systems ◽  
Wild Plants

A growing number of restoration projects require large amounts of seeds. As harvesting natural populations cannot cover the demand, wild plants are often propagated in large-scale monocultures. There are concerns that this cultivation process may cause genetic drift and unintended selection, which would alter the genetic properties of the cultivated populations and reduce their genetic diversity. Such changes could reduce the pre-existing adaptation of restored populations, and limit their adaptability to environmental change. We used single nucleotide polymorphism (SNP) markers and a pool-sequencing approach to test for genetic differentiation and changes in gene diversity during cultivation in 19 wild grassland species, comparing the source populations and up to four consecutive cultivation generations grown from these sources. We then linked the magnitudes of genetic changes to the species breeding systems and seed dormancy, to understand the roles of these traits in genetic change. The propagation of native seeds for ecosystem restoration changed the genetic composition of the cultivated generations only moderately. The genetic differentiation we observed as a consequence of cultivation was much lower than the natural genetic differentiation between different source regions, and the propagated generations harbored even higher gene diversity than wild-collected seeds. Genetic change was stronger in self-compatible species, probably as a result of increased outcrossing in the monocultures. Synthesis and applications: Our study indicates that large-scale seed production maintains the genetic integrity of natural populations. Increased genetic diversity may even increase the adaptive potential of propagated seeds, which makes them especially suitable for ecological restoration. However, we have been working with seeds from Germany and Austria, where the seed production is regulated and certified. Whether other seed production systems perform equally well remains to be tested.

Genetic variation within and relationships among five subpopulations of Slovak Thoroughbred

2004 ◽  
Vol 52 (3) ◽  
pp. 259-265
Author(s):  
Daniela Šátková-Jakabová ◽  
J. Trandžík ◽  
Ľudmila Hudecová-Kvasňáková ◽  
Erika Hegedüšová-Zetochová ◽  
A. Bugarský ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
International Society ◽  
Microsatellite Loci ◽  
Genetic Relationships ◽  
Allele Frequencies ◽  
Weinberg Equilibrium ◽  
Hardy Weinberg Equilibrium

Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the observed and expected heterozygosities were calculated. POPGENE v. 1.31 (Yeh et al., 1997) was used to test for deviations from the Hardy-Weinberg (H-W) equilibrium and to assign FIS estimates (Weir, 1990). The utility of microsatellites for evaluating genetic diversity of horses is discussed.

scholarly journals Genetic diversity among forty coffee varieties assessed by RAPD markers associated with restriction digestion

2005 ◽  
Vol 48 (4) ◽  
pp. 511-521 ◽  
Author(s):  
Leandro Eugênio Cardamoni Diniz ◽  
Claudete de Fátima Ruas ◽  
Valdemar de Paula Carvalho ◽  
Fabrício Medeiros Torres ◽  
Eduardo Augusto Ruas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Clustering Analysis ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Restriction Digestion ◽  
Agronomic Features

The genetic variability of 40 accessions of_C. arabica was evaluated using a combination of the random amplified polymorphic DNA (RAPD) technique and restriction digestion of genomic DNA. The genetic variability and the relatedness among all accessions were initially evaluated using 195 RAPD primers which revealed a very low level of genetic variation. To improve the efficiency in the detection of polymorphism, the genomic DNA of all accessions were submitted to digestion with restriction endonucleases prior to PCR amplification. A total of 24 primers combined with restriction digestion of DNA rendered 318 bands, of which 266 (83.65%) were polymorphic. The associations among genotypes were estimated using UPGMA-clustering analysis. The accessions were properly clustered according to pedigree and agronomic features. The ability to distinguish among coffee accessions was greater for RAPD plus restriction digestion than for RAPD alone, providing evidences that the combination of the techniques was very efficient for the estimation of genetic relationship among_C. arabica genotypes.

scholarly journals Is the Murciano-Granadina a single goat breed? A molecular genetics approach

2010 ◽  
Vol 62 (5) ◽  
pp. 1191-1198 ◽  
Author(s):  
A.M. Martínez ◽  
J.L. Vega-Pla ◽  
J.M. León ◽  
M.E. Camacho ◽  
J.V. Delgado ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Success Rate ◽  
Molecular Genetics ◽  
Clustering Analysis ◽  
Genetic Evaluation ◽  
Goat Breed ◽  
Genetic Groups

The population structure of the Murciano-Granadina breed was determined using 25 microsatellites from 266 goats of seven populations. The results of the genetic differentiation analysis showed that it is possible to differentiate the Murciana and Granadina populations even though a low F ST value (0.0432) had been obtained. Individuals could be assigned to their populations with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed that Murciana and Granadina populations were grouped in different clusters since K=3. The results demonstrate that Murciana and Granadina are still two different genetic groups included into Murciano-Granadina denomination. There is the opportunity to the genetically manage these populations, under a single herd-book but adding the necessary modifications to respect the conservation of the genetic diversity based on the use of multibreed models of genetic evaluation.

scholarly journals High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1680
Author(s):  
Nattakan Ariyaraphong ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
Thitipong Panthum ◽  
Syed Farhan Ahmad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Dairy Cattle ◽  
Large Scale ◽  
Genetic Relationships ◽  
Extensive Study ◽  
Distribution Analysis ◽  
Cattle Breeds ◽  
D Loop

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

Conservation genetics of Hill’s thistle (Cirsium hillii)

Botany ◽  
2010 ◽  
Vol 88 (12) ◽  
pp. 1073-1080 ◽  
Author(s):  
Joanna R. Freeland ◽  
Joy Gillespie ◽  
Claudia Ciotir ◽  
Marcel E. Dorken
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Habitat Loss ◽  
Perennial Herb ◽  
Great Lakes Region ◽  
Species At Risk ◽  
Foreseeable Future ◽  
Species Combination ◽  
Private Alleles

Populations at the edges of their geographical ranges are often characterized by reduced genetic diversity and increased genetic differentiation. These patterns may be exacerbated by specialized associations between plants and uncommon habitats. Together, reduced diversity and increased subdivision may increase the risk of population extirpation, an issue that is particularly important for plants classified as rare or threatened. Hill’s thistle (Cirsium hillii (Canby) Fernald), is a perennial herb endemic to the Great Lakes region and is considered threatened in Canada where its northernmost distribution occurs. We used microsatellite markers to genotype plants from 11 populations of Hill’s thistle that span the range of the species distribution within Canada. These data were used to investigate levels of genetic diversity within populations and genetic differentiation between populations, and to evaluate associations between patterns of genetic variation and those expected under ongoing habitat loss. Genetic differentiation among populations was low, although significant pairwise FST values, along with the presence of private alleles in most populations, was consistent with moderate to low gene flow. Nevertheless, in comparison with a congeneric rare species (Cirsium pitcheri) that occurs in the same geographical region in Canada, genetic diversity within most populations was high, and we suggest that this is at least partially attributable to this species’ combination of sexual and clonal reproduction. Despite high levels of genetic diversity, Hill’s thistle should probably remain a designated species at risk because of ongoing habitat loss; however, our data suggest that Hill’s thistle is unlikely to suffer from reduced genetic diversity in the foreseeable future.

scholarly journals High Genetic Diversity and Insignificant Interspecific Differentiation inOpisthopappusShih, an Endangered Cliff Genus Endemic to the Taihang Mountains of China

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Rongmin Guo ◽  
Lihua Zhou ◽  
Hongbo Zhao ◽  
Fadi Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Species Level ◽  
Endangered Plants ◽  
High Genetic Diversity ◽  
Fragmented Distribution ◽  
Polymorphic Bands ◽  
Genetic Structures ◽  
Different Levels

OpisthopappusShih is endemic to the Taihang Mountains, China. It grows in the crevice of cliffs and is in fragmented distribution. This genus consists of two species, namely,O. taihangensis(Ling) Shih andO. longilobusShih, which are both endangered plants in China. This study adopted intersimple sequence repeat markers (ISSR) to analyze the genetic diversity and genetic structure from different levels (genus, species, and population) in this genus. A total of 253 loci were obtained from 27 primers, 230 of which were polymorphic loci with a proportion of polymorphic bands (PPB) of up to 90.91% at genus level. At species level, bothO. taihangensis(PPB=90.12%,H=0.1842, andI=0.289) andO. longilobus(PPB=95.21%,H=0.2226, andI=0.3542) have high genetic diversity. Their respective genetic variation mostly existed within the population. And genetic variation inO. longilobus(84.95%) was higher than that inO. taihangensis(80.45%). A certain genetic differentiation among populations inO. taihangensiswas found (Gst=0.2740,Φst=0.196) and genetic differentiation inO. longilobuswas very small (Gst=0.1034,Φst=0.151). Gene flow in different degrees (Nm=1.325and 4.336, resp.) and mating system can form the existing genetic structures of these two species. Furthermore, genetic differentiation coefficient (Gst=0.0453) between species and the clustering result based on the genetic distance showed that interspecific differentiation betweenO. taihangensisandO. longilobuswas not significant and could occur lately.

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