scholarly journals The Genetic Diversity and Geographic Differentiation of the Wild Soybean in Northeast China Based on Nuclear Microsatellite Variation

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Hongkun Zhao ◽  
Yumin Wang ◽  
Fu Xing ◽  
Xiaodong Liu ◽  
Cuiping Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Northeast China ◽  
Wild Soybean ◽  
Population Level ◽  
Mantel Test ◽  
Microsatellite Variation ◽  
Information Index ◽  
Ssr Loci ◽  
The Mean

In this study, the genetic diversity and population structure of 205 wild soybean core collections in Northeast China from nine latitude populations and nine longitude populations were evaluated using SSR markers. A total of 973 alleles were detected by 43 SSR loci, and the average number of alleles per locus was 22.628. The mean Shannon information index (I) and the mean expected heterozygosity were 2.528 and 0.879, respectively. At the population level, the regions of 42°N and 124°E had the highest genetic diversity among all latitudes and longitudes. The greater the difference in latitude was, the greater the genetic distance was, whereas a similar trend was not found in longitude populations. Three main clusters (1N, <41°N-42°N; 2N, 43°N-44°N; and 3N, 45°N–>49°N) were assigned to populations. AMOVA analysis showed that the genetic differentiation among latitude and longitude populations was 0.088 and 0.058, respectively, and the majority of genetic variation occurred within populations. The Mantel test revealed that genetic distance was significantly correlated with geographical distance (r=0.207, p<0.05). Furthermore, spatial autocorrelation analysis showed that there was a spatial structure (ω=119.58, p<0.01) and the correlation coefficient (r) decreased as distance increased within a radius of 250 km.

scholarly journals Is it possible to obtain zero estimates of genetic diversity? A case study of the Nigerian indigeneous goat breeds at the β-lactoglobulin gene locus

2017 ◽  
Vol 33 (4) ◽  
pp. 375-388
Author(s):  
Emeka Ezewudo ◽  
Geka Abubakar ◽  
Sunday Egena ◽  
Olushola Alabi
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Locus ◽  
Polymorphic Locus ◽  
Information Index ◽  
Expected Heterozygosity ◽  
Goat Population ◽  
The Mean ◽  
Β Lactoglobulin

The current investigation was conducted to appraise the genetic diversity and genetic distance of three goat populations namely; Red Sokoto, Sahel and West African Dwarf (WAD), in Nigeria, making use of blood samples collected from 20, 20 and 20 individual from which blood DNAs were extraction, respectively. The DNAs extracted were used to study polymorphism at the ?-lactoglobulin gene locus using RLFP-PCR process. Results revealed that the mean total number of alleles was 1 while the effective number of alleles was also 1. The percentage of polymorphic locus was 0% while Shannon?s information index, observed homozygousity, expected heterozygosity, unbiased expected heterozygosity and inbreeding coefficient (F) were all observed to be 0.000. The pairwise Fst was 0.000 between all the breeds of goats. Variation within and between the populations of goats was 0% at p>0.05. The genetic distance between the goat breeds was 0.000. The present study revealed that RLFP-PCR may not be a powerful tool for the study of the ?-lactoglobulin gene locus and hence other methodologies should be employed for a broader judgment on the genetic status of the goat population at the locus.

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

Genetic variation in 26 populations of Racospermaauriculiforme and Racospermamangium using allozymes

1994 ◽  
Vol 24 (6) ◽  
pp. 1123-1132 ◽  
Author(s):  
P.D. Khasa ◽  
W.M. Cheliak ◽  
J. Bousquet
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Unknown Origin ◽  
Population Level ◽  
Genetic Distances ◽  
Starch Gel Electrophoresis ◽  
Introduced Populations ◽  
Linear Relationships ◽  
Starch Gel ◽  
The Mean

Racospermaauriculiforme (Cunn. ex Benth.) Pedley and Racospermamangium (Willd.) Pedley are two fast-growing multipurpose leguminous species that have great potential for reforestation in the subhumid and humid tropics. The level and distribution of genetic variability were evaluated among and within 13 populations of each species at 18 loci encoding 10 enzymes, using starch gel electrophoresis. At the population level, the mean number of alleles per locus, the mean percentage of polymorphic loci, and mean expected heterozygosity were, respectively, 1.9, 52.1%, and 0.122 for R. auriculiforme, and 1.5, 24.3%, and 0.064 for R. mangium. Therefore, R. mangium appeared genetically depauperate compared with R. auriculiforme. The proportion of the total genetic diversity that resided among populations in R. auriculiforme (18%) was twice that in R. mangium (9%). No linear relationships were detected between genetic and geographic distances among populations. Cluster analysis of Nei's genetic distances and discriminant analysis did not show any significant geographic pattern of population differentiation for R. mangium. These same analyses revealed two distinct clusters of populations for R. auriculiforme, one in Queensland, Australia, and Papua New Guinea, and the other in the Northern Territory of Australia and Indonesia. For both taxa, seed of unknown origin of some introduced populations in Zaire and Congo could be identified. The genetic distance between the two species (D = 0.097) was, as expected, much larger than the average intraspecific genetic distance derived from comparisons of conspecific populations (D = 0.034 for R. auriculiforme and D = 0.007 for R. mangium). However, the amplitude of the interspecific genetic distance calculated is representative of divergence levels usually observed among subspecific taxa. Based on this, and the lower levels of genetic diversity found in R. mangium, it is suggested that R. mangium derived recently from R. auriculiforme.

scholarly journals Constructing a Core Collection of the Medicinal Plant Angelica biserrata Using Genetic and Metabolic Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Man Liu ◽  
Xin Hu ◽  
Xu Wang ◽  
Jingjing Zhang ◽  
Xubing Peng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Medicinal Plant ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Sampling Strategy ◽  
Market Demand ◽  
Conservation Assessment ◽  
Information Index ◽  
Ssr Loci ◽  
Metabolic Data

Angelica biserrata is an important medicinal plant in Chinese traditional medicine. Its roots, which are known as Duhuo in Chinese, are broadly applied to treat inflammation, arthritis, and headache. With increasing market demand, the wild resources of A. biserrata have been overexploited, and conservation, assessment of genetic resources and breeding for this species is needed. Here, we sequenced the transcriptome of A. biserrata and developed simple sequence repeat (SSR) markers from it to construct a core collection based on 208 samples collected from Changyang-related regions. A total of 132 alleles were obtained for 17 SSR loci used with the polymorphic information content (PIC) ranging from 0.44 to 0.83. Abundant genetic diversity was inferred by Shannon’s information index (1.51), observed (0.57) and expected heterozygosity (0.72). The clustering analysis resulted into two sample groups and analysis of molecular variance (AMOVA) showed only 6% genetic variation existed among populations. A further metabolic analysis of these samples revealed the main coumarin contents, such as osthole and columbianadin. According to the genetic and metabolic data, we adopted the least distance stepwise sampling strategy to construct seven preliminary core collections, of which the 20CC collection, which possessed 42 A. biserrata individuals accounting for 90.20% of the genetic diversity of the original germplasm, represented the best core collection. This study will contribute to the conservation and management of A. biserrata wild germplasm resources and provide a material basis for future selection and breeding of this medicinal plant.

scholarly journals Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

2012 ◽  
Vol 4 (3) ◽  
pp. 757-767 ◽  
Author(s):  
M. M. Hassan ◽  
A. K. M. Shamsuddin ◽  
M. M. Islam ◽  
K. Khatun ◽  
J. Halder
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Allele Number ◽  
Rice Landraces ◽  
Efficient Management ◽  
Ssr Loci ◽  
Pattern Of Variation ◽  
Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

scholarly journals Genetic diversity and population structure of Meretrix petechialis in China revealed by sequence-related amplified polymorphism markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8723 ◽  
Author(s):  
Qiaoyue Xu ◽  
Junhong Zheng ◽  
Hongtao Nie ◽  
Qingzhi Wang ◽  
Xiwu Yan
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Scientific Basis ◽  
Germplasm Resources ◽  
Polymorphic Loci ◽  
Information Index ◽  
Geographical Populations ◽  
Meretrix Petechialis

Genetic variation in nine stocks of Meretrix petechialis collected from China was analyzed using sequence-related amplified polymorphism (SRAP) markers. Eight primer pairs produced 132 polymorphic loci with an average of 16.5 loci per primer pair. A population from Jiangsu had the highest percentage of polymorphic loci at 27.27%, suggesting that these resources had a rich genetic diversity. The Nei’s gene diversity of the nine populations ranged from 0.0647 to 0.0793; a population from Shandong was the lowest and a population from North Korea the highest. The Shannon’s information index was between 0.1023 and 0.1202, with the lowest in the Shandong population and the highest in the Jiangsu population. The Nei’s unbiased genetic distance between the nine populations was 0.0243–0.0570 and the genetic similarity was 0.9446–0.9760; the genetic distance between Guangxi and Shandong populations was the furthest (0.0570) and the genetic distance between Shandong and Jiangsu populations was the closest (0.0243). Nei’s gene diversity analysis indicated that the genetic variance was mainly found within individual geographical populations, and the analysis of molecular variance revealed low but significant genetic differentiation among local and regional populations. The limited gene flow (Nm = 0.555) was inferred as a major reason for the extent of genetic differentiation in M. petechialis. The results obtained here indicated that M. petechialis have high degree of genetic diversity and the potential of further breeding with excellent germplasm resources. This study provides a scientific basis for the protection of germplasm resources and the breeding of M. petechialis.

Allozyme variation and population structure of Carex humilis var. nana (Cyperaceae) in Korea

2001 ◽  
Vol 79 (4) ◽  
pp. 457-463 ◽  
Author(s):  
Man Kyu Huh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
North American ◽  
Population Level ◽  
Allozyme Variation ◽  
Population Divergence ◽  
Geographic Ranges ◽  
The Mean ◽  
Allozyme Loci

Genetic diversity and population structure of 22 Carex humilis var. nana Ohwi (Cyperaceae) populations in Korea were determined using genetic variation at 23 allozyme loci. This is a long-lived herbaceous species with a widespread distribution in eastern Asia. The 12 enzymes revealed 23 putative loci, of which 11 were polymorphic (47.8%). Genetic diversity at the varietal level and at the population level was 0.131 and 0.118, respectively. Total genetic diversity (HT = 0.274) and within population genetic diversity (HS = 0.256) were high, whereas the extent of the population divergence was relatively low (GST = 0.068). An indirect estimate of the number of migrants per generation (Nm = 3.42) indicated that gene flow was high among Korean populations. Wide geographic ranges, perennial herbaceous nature, and the persistence of multiple generations are associated with the high level of genetic variation. A distinct difference between Asian and North American Carex is shown in the proportion of genetic variation (GST) (p < 0.001). The mean GST of Asian Carex was estimated as 0.056; thus, only 5.6% of genetic variability was distributed among populations, whereas the mean GST of North American Carex was estimated as 19.5% (3.5 times higher). It is probable that the geographical distance between population pairs and presence or absence of glacial history may play roles in the substantial difference between both groups.Key words: Carex humilis var. nana, genetic diversity, population structure.

scholarly journals Genetic Diversity of Tef [Eragrostis tef (Zucc.)Trotter] as Revealed by Microsatellite Markers

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Mahilet Tadesse ◽  
Mulugeta Kebede ◽  
Dejene Girma
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Eragrostis Tef ◽  
Human Consumption ◽  
Gene Pools ◽  
Information Index ◽  
Geographical Regions ◽  
The Mean ◽  
High Level

Genetic variability is the fundamental prerequisite of any crop-breeding program to develop superior cultivars. There are about 350 Eragrostis1 species, of which, tef is the only species cultivated for human consumption. Currently, the Ethiopian Biodiversity Institute (EBI) collected over five thousand tef accessions from different geographical regions, diverse in terms of climate and elevation, which are uncharacterized yet. The objective of this study was to evaluate the genetic diversity among 64 tef accessions using 10 selected polymorphic simple sequence repeats (SSRs) markers. A total of 314 alleles were detected with an average of 14.5 alleles per locus and amplicon size ranged from 90 bp–320 bp. The mean value of polymorphic information content (PIC) was 0.87, appearing polymorphic for all loci. The lowest Fst value (0.05) was recorded among the studied tef populations. The mean value of major allele frequency and the number of effective alleles were 0.33 and 3.32, respectively. The mean value of gene flow (Nm) and Shannon’s information index (I) was 4.74 and 1.65, respectively. The observed (Ho) and expected (He) heterozygosities varied from 0.34 to 0.56 and from 0.58 to 0.76, respectively. The cluster analysis has grouped the 64 tef accessions into three distinct clusters based on their similarity. The PCoA analysis showed that clustering is basing on the geographical origin of accessions. Analysis of molecular variance revealed 56%, 39% and 5% of the total variation due to variation within populations, among individuals and among populations, respectively. Structure bar-plot also inferred three gene pools, but with high level of admixtures. Thus, the present study shows that the identified tef accessions could be of great interest for the initiation of a planned breeding and conservation programs.

scholarly journals Microsatellite Markers Developed from `Bluecrop' Reveal Polymorphisms in the Genus Vaccinium and Are Suitable for Cultivar Fingerprinting

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1122B-1122 ◽  
Author(s):  
Peter Boches ◽  
Lisa J. Rowland ◽  
Kim Hummer ◽  
Nahla V. Bassil
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Distance Measures ◽  
Hybrid Origin ◽  
Pedigree Information ◽  
Species Relationships ◽  
Ssr Loci

Microsatellite markers for blueberry (Vaccinium L.) were created from a preexisting blueberry expressed sequence tag (EST) library of 1305 sequences and a microsatellite-enriched genomic library of 136 clones. Microsatellite primers for 65 EST-containing simple sequence repeats (SSRs) and 29 genomic SSR were initially tested for amplification and polymorphism on agarose gels. Potential usefulness of these SSRs for estimating species relationships in the genus was assessed through cross-species transference of 45 SSR loci and cluster analysis using genetic distance values from five highly polymorphic EST-SSR loci. Cross-species amplification for 45 SSR loci ranged from 17% to 100%, and was 83% on average in nine sections. Cluster analysis of 59 Vaccinium species based on genetic distance measures obtained from 5 EST-SSR loci supported the concept of V. elliotii Chapm. as a genetically distinct diploid highbush species and indicated that V. ashei Reade is of hybrid origin. Twenty EST-SSR and 10 genomic microsatellite loci were used to determine genetic diversity in 72 tetraploid V. corymbosum L. accessions consisting mostly of common cultivars. Unique fingerprints were obtained for all accessions analyzed. Genetic relationships, based on microsatellites, corresponded well with known pedigree information. Most modern cultivars clustered closely together, but southern highbush and northern highbush cultivars were sufficiently differentiated to form distinct clusters. Future use of microsatellites in Vaccinium will help resolve species relationships in the genus, estimate genetic diversity in the National Clonal Germplasm Repository (NCGR) collection, and confirm the identity of clonal germplasm accessions.

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