scholarly journals Genetic diversity and population structure of Euscaphis japonica, a monotypic species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12024
Author(s):  
Wei-Hong Sun ◽  
De-Qiang Chen ◽  
Rebeca Carballar-Lejarazu ◽  
Yi Yang ◽  
Shuang Xiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Natural Populations ◽  
Low Frequency ◽  
Sister Group ◽  
Inter Simple Sequence Repeat ◽  
Seed Collection

Background Understanding plant genetic diversity is important for effective conservation and utilization of genetic resources. Euscaphis japonica (Thunb.) Dippel, is a monotypic species with high phenotypic diversity, narrow distribution, and small population size. In this study, we estimated the genetic diversity and population structure of E. japonica using nine natural populations and inter-simple sequence repeat (ISSR) markers. Our results could provide a theoretical reference for future conservation and utilization of E. japonica. Results We obtained a total of 122 DNA bands, of which 121 (99.18%) were polymorphic. The average number of effective alleles (Ne = 1.4975), Nei’s gene diversity index (H = 0.3016), and Shannon’s information index (I = 0.4630) revealed that E. japonica possessed a high level of genetic diversity. We observed that E. japonica consisted of both deciduous and evergreen populations. UPGMA tree showed that the evergreen and deciduous E. japonica form a sister group. There is little genetic differentiation among geographic populations based on STRUCTURE analysis. The Dice’s similarity coefficient between the deciduous and evergreen populations was low, and the Fst value was high, indicating that these two types of groups have high degree of differentiation. Conclusion Rich genetic diversity has been found in E. japonica, deciduous E. japonica and evergreen E. japonica populations, and genetic variation mainly exists within the population. The low-frequency gene exchange between deciduous and evergreen populations may be the result of the differentiation of deciduous and evergreen populations. We suggest that in-situ protection, seed collection, and vegetative propagation could be the methods for maintenance and conservation of E. japonica populations.

Genetic diversity and population structure of Vigna exilis and Vigna grandiflora (Phaseoleae, Fabaceae) from Thailand based on microsatellite variation

Botany ◽  
2013 ◽  
Vol 91 (10) ◽  
pp. 653-661 ◽  
Author(s):  
Anochar Kaewwongwal ◽  
Arunee Jetsadu ◽  
Prakit Somta ◽  
Sompong Chankaew ◽  
Peerasak Srinives
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Allelic Richness ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Natural Populations ◽  
Microsatellite Variation ◽  
Genetic Clusters ◽  
Simple Sequence

The objective of this research was to determine the genetic diversity and population structure of natural populations of two rare wild species of Asian Vigna (Phaseoleae, Fabaceae), Vigna exilis Tateishi & Maxted and Vigna grandiflora (Prain) Tateishi & Maxted, from Thailand. Employing 21 simple sequence repeat markers, 107 and 85 individuals from seven and five natural populations of V. exilis and V. grandiflora, respectively, were analyzed. In total, the markers detected 196 alleles for V. exilis and 219 alleles for V. grandiflora. Vigna exilis populations showed lower average values in number of alleles, allelic richness, observed heterozygosity, gene diversity, and outcrossing rate than V. grandiflora populations, namely 58.00% versus 114.60%, 51.96% versus 74.80%, 0.02% versus 0.18%, 0.40% versus 0.66%, and 3.24% versus 17.41%, respectively. Pairwise FST among populations demonstrated that V. exilis was much more differentiated than V. grandiflora. Analysis of molecular variance revealed that 41.83% and 15.06% of total variation resided among the populations of V. exilis and V. grandiflora, respectively. Seven and two genetic clusters were detected for V. grandiflora and V. exilis by STRUCTURE analysis. Our findings suggest that different strategies are required for in situ conservation of the two species. All V. exilis populations, or as many as possible, should be conserved to protect genetic resources of this species, while a few V. grandiflora populations can capture the majority of its genetic variation.

scholarly journals Assessing the Genetic Diversity and Population Structure of a Tunisian Melon (Cucumis melo L.) Collection Using Phenotypic Traits and SSR Molecular Markers

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1121
Author(s):  
Hela Chikh-Rouhou ◽  
Najla Mezghani ◽  
Sameh Mnasri ◽  
Neila Mezghani ◽  
Ana Garcés-Claver
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Crop Improvement ◽  
Molecular Data ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Genetic Diversity And Structure

The assessment of genetic diversity and structure of a gene pool is a prerequisite for efficient organization, conservation, and utilization for crop improvement. This study evaluated the genetic diversity and population structure of 24 Tunisian melon accessions, by using 24 phenotypic traits and eight microsatellite (SSR) markers. A considerable phenotypic diversity among accessions was observed for many characters including those related to agronomical performance. All the microsatellites were polymorphic and detected 30 distinct alleles with a moderate (0.43) polymorphic information content. Shannon’s diversity index (0.82) showed a high degree of polymorphism between melon genotypes. The observed heterozygosity (0.10) was less than the expected heterozygosity (0.12), displaying a deficit in heterozygosity because of selection pressure. Molecular clustering and structure analyses based on SSRs separated melon accessions into fivegroups and showed an intermixed genetic structure between landraces and breeding lines belonging to the different botanical groups. Phenotypic clustering separated the accessions into two main clusters belonging to sweet and non-sweet melon; however, a more precise clustering among inodorus, cantalupensis, and reticulatus subgroups was obtained using combined phenotypic–molecular data. The discordance between phenotypic and molecular data was confirmed by a negative correlation (r = −0.16, p = 0.06) as revealed by the Mantel test. Despite these differences, both markers provided important information about the diversity of the melon germplasm, allowing the correct use of these accessions in future breeding programs. Together they provide a powerful tool for future agricultural and conservation tasks.

scholarly journals Genetic polymorphism among natural populations of Anacardium humile A. ST-HIL

2020 ◽  
Vol 42 (1) ◽  
Author(s):  
Silvia Correa Santos ◽  
Raquel dos Santos Carvalho ◽  
Livia Maria Chamma Davide
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphism ◽  
Genetic Variability ◽  
Genetic Divergence ◽  
Genomic Dna ◽  
Reproductive Strategies ◽  
Rapd Markers ◽  
Phenotypic Diversity ◽  
Diversity Index ◽  
Natural Populations

Abstract The genus Anacardium presents nine species, of these, three have sub-bush size, common in the Cerrado of the Center-West of Brazil. The objective of this work was to evaluate the genetic variability of the species, collected in eleven provenances, using RAPD markers. Genomic DNA from 122 accessions was extracted and amplified with 25 decamer primers. The results indicated polymorphism, ranging from 77.71% to 96.18%. The distribution of genetic diversity among and within populations shows that 27.14% of the variability is found between populations and 37.44% within the populations, suggesting the existence of genetic variability that may be related to the reproductive strategies adopted by the species throughout its evolution. The index of variation within the provenances (93.36%) was higher than the index found among populations (6.64%). Molecular analysis indicated that there is genetic divergence between and within the studied populations of Anacardium humile A. St. - Hill. The origin of Itajá-GO presented the highest genetic diversity, presenting the highest values of genetic diversity index, phenotypic diversity and higher percentage of polymorphic loci.

scholarly journals Genetic Diversity, Population Structure, and Formation of a Core Collection of 1197 Citrullus Accessions

HortScience ◽  
2016 ◽  
Vol 51 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Haiying Zhang ◽  
Jianguang Fan ◽  
Shaogui Guo ◽  
Yi Ren ◽  
Guoyi Gong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Diversity Index ◽  
Gene Diversity ◽  
Association Studies ◽  
Economic Benefits ◽  
Genetic Distances ◽  
Genetic Variations ◽  
Average Value ◽  
Core Set

Watermelon belongs to the genus Citrullus. There have been continuing interests in breeding of watermelon for economic benefits, but information on the scope and utilization of genetic variations in Citrullus is still limited. The present study was conducted in 2012–13, to evaluate the genetic diversity and population structure of the 1197 line watermelon collection maintained by the Beijing Vegetable Research Center (BVRC), which belongs to seven Citrullus species including Citrullus naudinianus, Citrullus colocynthis, Citrullus rehmii, Citrullus ecirrhosus, Citrullus amarus, Citrullus mucosospermus, and Cirullus lanatus subsp. vulgaris. Twenty-three highly informative microsatellite markers evenly distributed in the watermelon genome were used to assess genetic diversity in this collection. The markers detected on an average of 6.05 alleles per locus with the average value of polymorphism information content (PIC) at 0.49. A high level of gene diversity [Nei’s gene diversity index (Nei) = 0.56] and a low observed heterozygosity (Ho = 0.10) were revealed within the collection. Structure analysis grouped the 1197 accessions into two main populations (Pop I and Pop II) and an admixture group. Pop I contained 450 accessions from C. lanatus subsp. vulgaris (446) and C. mucosospermus (4). Pop II comprised 465 accessions, 379 of which belonged to C. lanatus subsp. vulgaris and 86 to C. naudinianus (3), C. ecirrhosus (2), C. rehmii (2), C. colocynthis (11), C. amarus (58), and C. mucosospermus (10). The remaining 282 accessions were classified as an admixture group. The two main populations were further subdivided into four subgroups. The groupings were consistent with the estimation of F statistics (Fst) and Nei’s genetic distances in collections. We confirmed the distinct genetic backgrounds between American and East Asian ecotypes. Subsequently, we defined a core set consisting of 130 accessions including 47 from Pop I, 68 from Pop II, and 15 from the Admixture group. This core set was able to capture all 133 alleles detected by 23 simple sequence repeats (SSRs) in 1197 accessions. These results will facilitate efficient use of genetic variations in Citrullus in watermelon breeding and help optimization of accessions in genomewide association studies.

scholarly journals Genetic and phenotypic diversity of selected Kenyan mung bean (Vigna radiata L. Wilckzek) genotypes

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Jedidah Wangari Mwangi ◽  
Oduor Richard Okoth ◽  
Muchemi Peterson Kariuki ◽  
Ngugi Mathew Piero
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Mung Bean ◽  
Phenotypic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Breeding Programs ◽  
Population Structure Analysis

Abstract Background Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. Results Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). Conclusion These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.

scholarly journals Assessment of Genetic Diversity of an Endangered Species Fraxinus hupehensis Based on ISSR Markers

2019 ◽  
Vol 47 (4) ◽  
pp. 1308-1315
Author(s):  
Peng-Li ZHENG ◽  
Jian-Ru CHENG ◽  
Long-Qing CHEN ◽  
Ming-Qin ZHOU
Keyword(s):  
Genetic Diversity ◽  
Endangered Species ◽  
Diversity Index ◽  
Gene Diversity ◽  
Natural Populations ◽  
Population Level ◽  
Issr Markers ◽  
Group Method ◽  
Digital Object Identifier ◽  
Protection Measures

Investigation on the level and pattern of genetic diversity of 10 natural populations of the endangered species Fraxinus hupehensis using inter-simple sequence repeat (ISSR) markers was crucial for understanding the structure of the population and assessing the best genetic protection strategies. A total of 180 polymorphic bands with the polymorphic rate of 100.00% were amplified by 14 primers. The genetic diversity at population level (Percentage of polymorphic loci, PPL=64.06; Nei’s gene diversity index, h=0.1519; Shannon’s information index, I=0.2434) was lower than that at species level (PPL= 100.00%, h=0.1833, I=0.3041). Analysis of molecular variance (AMOVA) demonstrated the low level of the genetic variation occurred between the populations (16.05%). This also can be corroborated by the gene flow (Nm 2.424) and the coefficient of gene differentiation (Gst=0.1710) among populations. Cluster analysis based on the unweighted pair group method with arithmetic averages (UPGMA) revealed four groups for 10 populations according to Nei’s genetic identity and seven categories for the 196 individuals according to SM values. Furthermore, the endangered mechanism and genetic structure of F. hupehensis were discussed, and appropriate targeted protection measures were proposed based on these findings.   ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 4, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********

scholarly journals Assessment of Genetic Diversity and Population Structure of the Endangered Astragalus exscapus subsp. transsilvanicus through DNA-Based Molecular Markers

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2732
Author(s):  
Katalin Szabo ◽  
Doru Pamfil ◽  
Alexandru Sabin Bădărău ◽  
Monica Hârţa
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Diversity Index ◽  
Gene Diversity ◽  
Population Level ◽  
Conservation Strategy ◽  
Limited Information ◽  
Subspecies Level ◽  
Total Genetic Diversity ◽  
Fragmentation Processes

Astragalus exscapus L. subsp. transsilvanicus (Schur) Nyár. (Fabaceae) is a rare plant endemic to the Transylvanian Plateau, represented by 24 identified populations. Limited information on the genetic variation and population structure is available, which obstructs efficient measures for conservation strategy. The present study aimed to analyze the genetic diversity and population structure of eight populations of A. exscapus subsp. transsilvanicus revealed by sequence-related amplified polymorphism (SRAP) markers. A total of 164 bands were amplified, 96.7% of which (159) were polymorphic. Nei’s gene diversity index (He) was estimated to be 0.228 at the population level and 0.272 at the subspecies level. The genetic differentiation among populations (Gst) was 0.165, which indicated a low proportion of total genetic diversity. The analysis of molecular variance (AMOVA) indicated that 17% of the total variation of A. exscapus subsp. transsilvanicus is found among the populations, while 83% was found within the populations. A UPGMA dendrogram, principal coordinate analysis, and the STRUCTURE software grouped the populations into two clusters uncorrelated with the provenience of the 125 individuals, which might be attributed to fragmentation processes, insect pollination, population size, and specific environmental conditions of the habitats.

Population structure and core collection construction of apricot (Prunus armeniaca L.) in North Africa based on microsatellite markers

2015 ◽  
Vol 15 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Hedia Bourguiba ◽  
Mohamed-Amine Batnini ◽  
Lamia Krichen ◽  
Neila Trifi-Farah ◽  
Jean-Marc Audergon
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Markers ◽  
North Africa ◽  
Core Collection ◽  
Diversity Index ◽  
Gene Diversity ◽  
Association Studies ◽  
Conservation Strategies ◽  
Phenotypic Data

North Africa enclosed original apricot genetic resources with the cohabitation of grafting and seed-propagated accessions. In this study, we assessed the genetic diversity and population structure of 183 apricot accessions using 24 microsatellite markers distributed evenly in the Prunus genome. A total of 192 alleles and a high level of gene diversity (0.593) were detected among the whole panel. Genetic structure analysis revealed the presence of four genetic clusters. We also found that both geographical origin and mode of propagation are important factors structuring genetic diversity in apricot species. Results confirmed the presence of gene exchange between the northern and southern countries of the Mediterranean Basin. Subsequently, a core collection of 98 accessions based on M (maximization) strategy showing 99.47% of allele retention ratio was constructed. No significant differences for Shannon's information index and Nei's diversity index were observed between the core and entire collections. Our results provide an effective aid for future germplasm preservation and conservation strategies as well as genetic association studies development in relation to phenotypic data.

Inter-Simple Sequence Repeat (ISSR) Markers Revealed Genetic Diversity and Population Structure Among 9 Wild Species of Clematis L.

2021 ◽  
Vol 15 (5) ◽  
pp. 580-588
Author(s):  
Yonghui Li ◽  
Shipeng Li ◽  
Jingjing Li ◽  
Xiangli Yu ◽  
Fawei Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Diversity Index ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Mantel Test ◽  
Information Index ◽  
Ctab Method ◽  
Different Populations

To analyze the genetic diversity of 9 species of Clematis from 31 different populations, we extracted DNA by the improved CTAB method, used ISSR-PCR for amplification, and then selected 9 primers with clear amplified bands from amongst 220 primers. A total of 127 clear bands were amplified, of which 126 were polymorphic bands, yielding a ratio of 99.2%. The polymorphism information index (PIC) of the primers ranged from 0.9326 to 0.9649. The Nei’s genetic diversity index (H) was 0.2750, the total gene diversity (Ht) was 0.2845, and the genetic differentiation coefficient (Gst) was 0.6696, indicating high genetic differentiation among populations of Clematis. After cluster analysis, the 31 Clematis populations were divided into 3 categories. Principal coordination analysis (PCoA) of 9 Clematis species then showed that the genetic relationship between samples of the same Clematis germplasms was closer than that of samples from the same region. The mantel test revealed a significant positive correlation between genetic distance and geographical distance among the populations. The population clustering results are broadly consistent with the clustering graphs of UPGMA and PCoA. We can conclude the polymorphism of the 9 primers is good, and that the genetic diversity of 31 Clematis populations is rich. Individual Clematis germplasms are closely related and will gather together preferentially.

scholarly journals Research Genetic diversity of Ottelia acuminata (Hydrocharitaceae) from the Eastern Himalayas, revealed by ISSR markers

1970 ◽  
Vol 7 ◽  
pp. 56-63 ◽  
Author(s):  
Chunlin Long ◽  
Zhutan Jiang ◽  
Zhiling Dao
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Natural Populations ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Ex Situ ◽  
Eastern Himalayas ◽  
Average Value ◽  
Geographical Distances ◽  
High Level

Ottelia acuminata (Gagnep.) Dandy (Hydrocharitaceae), an endangered aquatic species, was investigated in the Eastern Himalayas, especially in Yunnan Province of Southwest China. The genetic diversity among seven populations was examined using inter-simple sequence repeat (ISSR) amplification markers. The field survey showed that 43.5% natural populations of O. acuminata have become extinct during the last 30 years. Among 13 remaining wild populations, eight (61.5%) are on the edge of extinction and only five (38.5%) were unaffected. For the study on seven populations based on ten primers, 147 clear and reproducible DNA fragments were generated, of which 144 (97.96%) were polymorphic. Within populations, however, the polymorphic bands (PPB) generated by ISSRs was 53 and occupied 36.05% in population B, and similarly within population J (51 and 34.69%, respectively). The results showed that genetic variation is much higher among populations of O. acuminata than within populations. Analyses of Nei’s gene diversity, genetic distance and Shannon’s index also agreed with these results. The average value of Nei’s gene diversity (h) equaled 0.3710. The coefficient of genetic differentiation (Gst) equaled 0.5487, which means that 54.87% of the total molecular variance existed among populations. Such a high level of divergence present among populations may be caused by the complex topography and separated habitats which effectively restrict gene flow. Moreover, there is a lack of significant association between genetic and geographical distances (r = 0.28889, P > 0.05) in the populations of O. acuminata. Therefore, we proposed an appropriate strategy for conserving the genetic resources of O. acuminata in the Eastern Himalayas; namely, rescuing and conserving the core populations in situ, while selecting and preserving more populations with fewer individuals from each population ex situ. Key-words: Ottelia acuminata, genetic diversity, conservation, Eastern Himalayas, Yunnan Plateau, China DOI: 10.3126/botor.v7i0.4374Botanica Orientalis – Journal of Plant Science (2010) 7: 56-63

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