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 Genetic Diversity of a Natural Population of Akebia trifoliata (Thunb.) Koidz and Extraction of a Core Collection Using Simple Sequence Repeat Markers

2021 ◽  
Vol 12 ◽  
Author(s):  
Yicheng Zhong ◽  
Yue Wang ◽  
Zhimin Sun ◽  
Juan Niu ◽  
Yaliang Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Simple Sequence Repeat ◽  
Core Collection ◽  
Polymorphic Information Content ◽  
Germplasm Conservation ◽  
Sequence Repeat ◽  
Information Index ◽  
Molecular Identity ◽  
Simple Sequence

Understand genetic diversity and genetic structure of germplasm is premise of germplasm conservation and utilization. And core collection can reduce the cost and difficulty of germplasm conservation. Akebia trifoliata (Thunb.) Koidz is an important medicinal, fruit and oil crop, particularly in China. In this study, 28 simple sequence repeat (SSR) markers were used to assess the genetic diversity and genetic structure of 955 A. trifoliata germplasms, determine their molecular identity and extract a core collection. The genetic diversity of the 955 germplasms was moderately polymorphic. The average number of alleles (Na), observed heterozygosity (HO), expected heterozygosity (HE), Shannon’s information index (I∗), and polymorphic information content (PIC) were 3.71, 0.24, 0.46, 0.81, and 0.41, respectively. Four subpopulations were identified, indicating a weak genetic structure. A 955 germplasms could be completely distinguished by the characters of s28, s25, s74, s89, s68, s30, s13, s100, s72, s77, and s3. And each germplasm’s molecular identity was made up of eleven characters. The core collection was composed of 164 germplasms (17.2% of 955 total germplasms in the population) and diversity parameters differed significantly from those of a random core collection. These results have implications for germplasm conservation. At the same time, based on the results, the 955 germplasm could be better used and managed.

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 Genetic Diversity and Population Structure of Endangered Catfish Rita rita (Hamilton, 1822) Revealed by Heterologous DNA Microsatellite Markers

2021 ◽  
Vol 34 (2) ◽  
Author(s):  
MUHAMMAD FORHAD ALI ◽  
◽  
MD. RAFIQUL ISLAM SARDER ◽  
MOHAMMAD MATIUR RAHMAN ◽  
MD. FAZLUL AWAL MOLLAH ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Genetic Difference ◽  
Information Index ◽  
Hardy Weinberg Equilibrium ◽  
High Gene ◽  
High Level ◽  
Dna Microsatellite

Genetic information is essential for conservation and future aquaculture development of the endangered catfish Rita rita (Hamilton, 1822). Two hundred catfish, R. rita, 50 from four rivers, the Old Brahmaputra, Jamuna, Meghna and Kangsa were collected and analysed to evaluate the genetic diversity and population structure using five microsatellite primers (Cba06-KUL, Cba08-KUL, Cba09-KUL, Phy03-KUL and Phy07-KUL). Four of the five amplified loci were found polymorphic (P95) in all the populations and 46 alleles were recorded with 9 to 14 alleles per locus. Differences were observed in the total number of alleles ranging from 41 to 44, effective number of alleles from 29.96 to 37.46, observed heterozygosity from 0.57 to 0.76, Shannon’s information index from 2.09 to 2.30 and polymorphic information content from 0.84 to 0.88 among the four populations. Results exposed the highest levels of genetic diversity in the Meghna population while the lowest in the Kangsa population of R. rita. All the populations were significantly deviated (P < 0.001) from the Hardy-Weinberg equilibrium for all the loci. Nei’s genetic distance between populations ranged 0.007 to 0.017 with low overall genetic difference FST = 0.011 and high gene flow Nm = 24.333, indicating that R. rita populations were not subdivided. This study revealed a high level of gene diversity with deficiency in genetic heterogeneity in all the populations of R. rita, emphasising natural management, conservation and rehabilitation measures of this species.

scholarly journals Assessment of Genetic Diversity and Population Structure of Tunisian Barley Accessions (Hordeum vulgare L.) Using SSR Markers

2020 ◽  
Vol 73 (4) ◽  
Author(s):  
Salem Marzougui ◽  
Mohamed Kharrat ◽  
Mongi Ben Younes
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Polymorphic Information Content ◽  
Hordeum Vulgare L ◽  
Software Analysis ◽  
Average Value ◽  
Allele Number ◽  
Cultivar Development ◽  
Principal Coordinates ◽  
Ssr Loci

In barley breeding programs, information about genetic dissimilarity and population structure is very important for genetic diversity conservation and new cultivar development. This study aimed to evaluate the genetic variation in Tunisian barley accessions (<em>Hordeum</em><em> </em><em>vulgare </em>L.) based on simple sequence repeat (SSR). A total of 89 alleles were detected at 26 SSR loci. The allele number per locus ranged from two to five, with an average of 3.4 alleles per locus detected from 32 barley accessions, and the average value of polymorphic information content was 0.45. A cluster analysis based on genetic similarity was performed, and the 32 barley resources were classified into five groups. Principal coordinates (PCoA) explained 12.5% and 9.3% of the total variation, and the PCoA was largely consistent with the results of cluster separation of STRUCTURE software analysis. The analysis of genetic diversity in barley collection will facilitate cultivar development and effective use of genetic resources.

scholarly journals Comparing the efficiency of sampling strategies to establish a representative in the phenotypic-based genetic diversity core collection of orchardgrass (Dactylis glomerata L.)

2013 ◽  
Vol 49 (No. 1) ◽  
pp. 36-47 ◽  
Author(s):  
M. Studnicki ◽  
W. Mądry ◽  
J. Schmidt
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Dactylis Glomerata ◽  
Sampling Strategy ◽  
Sampling Strategies ◽  
Core Collections ◽  
The Core ◽  
Entire Collection ◽  
The Mean ◽  
Dactylis Glomerata L

Establishing a core collection that represents the genetic diversity of the entire collection with a minimum loss of its original diversity and minimal redundancies is an important problem for gene bank curators and crop breeders. In this paper, we assess the representativeness of the original genetic diversity in core collections consisting of one-tenth of the entire collection obtained according to 23 sampling strategies. The study was performed using the Polish orchardgrass Dactylis glomerata L. germplasm collection as a model. The representativeness of the core collections was validated by the difference of means (MD%) and difference of mean squared Euclidean distance (d‒D%) for the studied traits in the core subsets and the entire collection. In this way, we compared the efficiency of a simple random and 22 (20 cluster-based and 2 direct cluster-based) stratified sampling strategies. Each cluster-based stratified sampling strategy is a combination of 2 clusterings, 5 allocations and 2 methods of sampling in a group. We used the accession genotypic predicted values for 8 quantitative traits tested in field trials. A sampling strategy is considered more effective for establishing core collections if the means of the traits in a core are maintained at the same level as the means in the entire collection (i.e., the mean of MD% in the simulated samples is close to zero) and, simultaneously, when the overall variation in a core collection is greater than in the entire collection (i.e., the mean of d‒D% in the simulated samples is greater than that obtained for the simple random sampling strategy). Both cluster analyses (unweighted pair group method with arithmetic mean UPGMA and Ward) were similarly useful in constructing those sampling strategies capable of establishing representative core collections. Among the allocation methods that are relatively most useful for constructing efficient samplings were proportional and D2 (including variation). Within the Ward clusters, the random sampling was better than the cluster-based sampling, but not within the UPGMA clusters.

Molecular characterization of some landraces and varieties of Date palm (Phoenix dactylifera L.) from Afar region of Ethiopia using ISSR markers

2019 ◽  
Author(s):  
Meera Indracanti ◽  
Dawud Takele Mekonnen ◽  
Mesfin Tsegaw
Keyword(s):  
Genetic Diversity ◽  
Date Palm ◽  
Polymorphic Information Content ◽  
Phoenix Dactylifera ◽  
Issr Markers ◽  
Snp Markers ◽  
Discrimination Power ◽  
Information Index ◽  
Phoenix Dactylifera L ◽  
Afar Region

Abstract Back ground Date palm (Phoenix dactylifera L.) is one of the oldest fruit trees in hot arid region of the world including North Africa. In some areas of Afar region of Ethiopia, date palm grow as landraces, are in danger due to introduction of improved cultivars. Present study was carried out to fill knowledge gap about molecular diversity of this crop in Afar region. Molecular studies of 5 landraces and 3 introduced cultivars of date palm from Afar region of Ethiopia were tested using 21 randomly selected ISSR primers for amplification and polymorphism detection using genomic DNA. ISSR markers across 8 date palm varieties were scored for their presence (1) or absence (0). Shannon's Information index (I) and polymorphic information content (PIC) were analyzed by popGENE 32 and online PIC calculator respectively. Results 17 out of 21 ISSR markers used for this study produced a total of 557 scorable DNA fragments with average of 33.52 per marker and 61.68, 43.93 and 68.22% polymorphism were obtained within local landraces, introduced varieties and among all samples respectively. The genetic distance among all samples ranged from 0.1402 to 0.5953; and the dendrogram separated date palm varieties into seven clusters. ISSR markers used for this study have high discrimination power and the average values of Shannon's information index and PIC were 0.318 and 0.76 respectively. Conclusion Genetic diversity was observed among all date palms studied in this investigation. To have better understanding on genetic diversity of date palm in the Afar region, further research should be done using SNP markers and landraces should be registered.

Genetic diversity of selected accessions for seed protein among pigeonpea minicore collection

2016 ◽  
Author(s):  
L. G. Jaggal ◽  
B. R. Patil ◽  
P. M. Naik ◽  
K. Priya
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Core Collection ◽  
Seed Protein ◽  
Polymorphic Information Content ◽  
Efficient System ◽  
Major Allele Frequency ◽  
Entire Collection ◽  
Major Allele ◽  
Simple Sequence

Protein is an important part of our diet and legumes viz., pigeonpea, chickpea, groundnut, cowpea, blackgram, greengram, etc are very rich source of protein. Among them, pigeonpea consists of about 20 to 22% of seed protein. Minicore collection set is consisted of approximately 10 % of core collection and 1% of entire collection with lot of diversity present in it. Nitrogen content of pigeonpea minicore collection set was estimated using Micro-Kjeldhal method and was ranged from 9.82 to 21.45 %. Based on per cent seed protein, twelve accessions of high and twelve accessions of low seed protein were selected for molecular characterization using 23 simple sequence repeat (SSR) markers. The PowerMarker result depicted that, among twenty three amplified markers, twenty markers generated polymorphism with mean polymorphic information content (PIC), major allele frequency (MAF) and genetic diversity of 0.479, 0.589 and 0.525 respectively. Based on molecular characterization, the dendrogram was constructed using DARwin 5.0 software distinguished the selected accessions of both high and low seed protein separately into different clusters showing diversity The results illustrate the potential of marker systems to distinguish the content of seed protein in pulses crop at genus level. Use of these markers also offers an efficient system for the assessment of genetic diversity within minicore set of pigeonpea.

Genetic diversity studies of alfalfa germplasm (Medicago sativa L. subsp. sativa) of United States origin using microsatellite analysis

2017 ◽  
Author(s):  
Shuying Yin ◽  
Yanrong Wang ◽  
Zhibiao Nan
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Polymorphic Information Content ◽  
The United States ◽  
Microsatellite Analysis ◽  
Information Index ◽  
Diversity Studies ◽  
Two Populations

This study aimed to understand the genetic diversity and population structure of alfalfa germplasm from the United States. In this study, the population structure and genetic diversity of six alfalfa cultivars of United States origin were investigated by microsatellite analysis with 40 individuals per cultivar. A total of 312 discernible alleles were amplified from the whole genome with an average of 31.2 alleles per locus. The average values of polymorphic information content and Shannon’s information index were 0.928 and 0.133, respectively, showing high levels of genetic diversity. Two populations were identified by STRUCTURE software with principal coordinate analysis and neighbour-joining clustering. Analysis of molecular variance analysis (AMOVA) revealed that the majority of genetic variation was within cultivars (96.42%) rather than between cultivars (3.58%). In conclusion, analyses of genetic diversity and population structure may be useful for the genetic analysis and utilization of genetic variation in alfalfa breeding.

Simple Sequence Repeat (SSR) Polymorphisms and Population Genetics in Sichuan Wild Rhesus Macaques

2011 ◽  
Vol 343-344 ◽  
pp. 690-697
Author(s):  
Di Yan Li ◽  
Yong Fang Yao ◽  
Xiao Feng Huang ◽  
An Chun Cheng ◽  
Huai Liang Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Rhesus Macaques ◽  
Genetic Management ◽  
Future Studies ◽  
Ssr Loci ◽  
Different Populations ◽  
Polymerase Chain ◽  
High Level ◽  
Simple Sequence

Cross-species amplification of twenty-five SSR loci from the DNA of five rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Seven of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these five samples, were also used to amplify SSR loci for 111 Sichuan wild rhesus macaques of five different populations. The analysed microsatellite markers produced 109 alleles, varied from 4 to 16 alleles each locus. The number of alleles per population ranged from 6.79 to 11.38. Polymorphic information content showed that all seven loci were highly informative (mean = 0.9017±0.0166, >0.5). The average observed heterozygosity was less than the expected (mean = 0.6795 and mean = 0.8559, respectively). Genetic differentiation among the populations was considerably low with the overall and pairwise FST values (mean = 0.0375), and showed fairly low level of inbreeding (indicated by a mean FIS value of 0. 0.1991). Maintaining genetic diversity is a major issue in conservation biology. In comparison to other captive Macaca mulatta studies, these wild rhesus macaque populations showed a relatively high level of genetic diversity, and there was low gene flow among these populations. Careful genetic management is important for maintaining genetic variability levels. None of the seven informative loci are linked which screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.

scholarly journals Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasus L.) genetic resources collections

2011 ◽  
Vol 65 (1-2) ◽  
pp. 21-28
Author(s):  
Gunārs Lācis ◽  
Isaak Rashal ◽  
Viktor Trajkovski
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Resources ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Polymorphic Information Content ◽  
Sour Cherry ◽  
Prunus Cerasus ◽  
Discrimination Power ◽  
Ssr Loci

Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasusL.) genetic resources collectionsForty-one sour cherry (Prunus cerasusL.) accessions were evaluated using three SSR markers to characterise genetic diversity in the sour cherry genetic resource collections at the Latvia State Institute of Fruit-Growing (LIFG), Dobele, Latvia and the Division of Horticultural Genetics and Plant Breeding at Balsgård, Department of Crop Sciences, Swedish University of Agricultural Sciences (SLU-Balsgård), Sweden, and to test the usability and reliability of a small set of SSR markers for preliminary characterisation of sour cherry germplasm collections. The SSR loci were highly polymorphic with 7-14 alleles per locus. Heterozygosity and Polymorphic Information Content values ranged from 0.750 to 1.000 and 0.748-0.899, respectively, while discrimination power per locus varied from 0.716 to 0.965. Five to thirty genotypes were found in the sour cherry collections for the three tested SSR loci. The combined discrimination power of all loci was effectively 0.994 and 0.999 for the LIFG and SLU-Balsgård collections, respectively. The SSRs used were able to uniquely identify all accessions in the analysed genetic resources collections. The genotype data allowed estimation of genetic diversity and genetic characterisation of accessions in the collections. Genetic similarity analysis showed higher genetic similarity among the Baltic and Scandinavian sour cherry varieties, than between Baltic and Eastern European varieties.

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