scholarly journals Development of Daphnia Magna SSR Markers and Genetic Diversity Analysis Based on RAD-Seq Technology

2021 ◽  
Author(s):  
Shengman Zhang ◽  
Yiran Xiong ◽  
Meng Tan ◽  
Siwei Chen ◽  
Zheng Han ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Daphnia Magna ◽  
Ssr Markers ◽  
Wild Population ◽  
Genetic Identity ◽  
Hunan Province ◽  
Shanxi Province ◽  
Information Index ◽  
Genetics Research

Abstract Daphnia magna belongs to the Cladocera order and plays an important role in the water ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. In our research, 26 novel microsatellite (SSR) markers were developed in an artificially domesticated of D. magna and 12 wild population of D. magna using restriction site-associated DNA sequencing (RAD-seq). The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.083 to 0.999 and 0.085 to 0.862, respectively. The PIC ranged from 0.368 to 0.805. These results indicate that the developed SSR marker is highly polymorphic. Nei’s genetic identity (H) ranged from 0.0926 to 0.3462, with a mean of 0.2233. Shannon’s Information index (I) ranged from 0.1333 to 0.4799, with an average of 0.3073; Shanxi province had the highest value and Hunan province had the lowest. Genetic distance and Nei’s genetic identity analysis, NJ tree diagram analysis, and PCoA analysis were conducted on populations of D. magna from different regions. The results show that the D. magna genetic relationship between Liaoning and Shanxi, Hunan and Anhui, and Beijing and Hainan is relatively close, while the genetic structure of D. magna in Guangdong, Jiangsu, and Sichuan is quite different from other sampling sites. An analysis of population genetic structure divided the test D. magna samples into two major groups. These results indicate that the genetic diversity of D. magna is rich, and the genetic structure of D. magna differs considerably in different regions. These research results and the newly developed polymorphic SSR markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated population and conservation genetics research.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

scholarly journals Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2504 ◽  
Author(s):  
Katarzyna Bilska ◽  
Monika Szczecińska
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Conservation Genetics ◽  
Ssr Markers ◽  
Full Range ◽  
Mantel Test ◽  
Evolutionary Potential ◽  
Functional Variation ◽  
Genetics Research ◽  
Outlier Loci

BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation inPulsatilla patenspopulations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations ofP. patensand threeP. patenspopulations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific toP. patensand three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He= 0.609,He= 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parametersFSTand ΦPTfor SSR (20%) and ΦPTfor ISJ (21%) markers was similar. Analysis conducted in theStructureprogram divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations ofP. patensfor ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

Genetic diversity of oil-tea camellia germplasms revealed by ISSR analysis

2015 ◽  
Vol 08 (05) ◽  
pp. 1550070 ◽  
Author(s):  
Lan-Ying Zhou ◽  
Xiang-Nan Wang ◽  
Li-Ping Wang ◽  
Yong-Zhong Chen ◽  
Xiao-Cheng Jiang
Keyword(s):  
Genetic Diversity ◽  
Reaction System ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Hunan Province ◽  
Information Index ◽  
Group I ◽  
Issr Pcr ◽  
Simple Sequence

Genetic diversity of 51 oil-tea camellia germplasms was analyzed using the optimized inter-simple sequence repeat (ISSR)–PCR reaction system with 22 primers screened from a set of 100 ISSR primers. The results showed that 493 discernible loci with distinct electrophoretic bands were obtained, of which, 478 loci (96.78%) were polymorphic. This indicated that oil-tea germplasms possess abundant genetic diversities. By clustering analysis performed using softwares of NTSYS 2.10 and Winboot, 51 oil-tea germplasms were divided into two groups: Group I had 48 lines of Camellia oleifera Abel, while Group II had three C. oleifera Abel related species and their similarity coefficient was 0.62. Group I was further divided into Group I-1 and Group I-2, and their similarity coefficient (Gs) was 0.634. All members of Group I-1 originated from Hunan Province, while Group I-2 included the rest of Hunan lines and those originated from other regions of China. Analyzed by software POPGENE 1.32, the Shannon's information index (I*) of genetic polymorphism was 0.3852, the genetic diversity among different region populations (Ht) was 0.2537, the genetic diversity within populations (Hs) was 0.15545, the differentiation coefficient of genetic diversity among populations (Gst) was 0.3967, and the gene flow among populations (Nm*) was 0.8262. The Nei's genetic distances between the Hunan population and the populations originated from other regions of China implied that geographic isolation strongly influenced genetic differentiation among populations. Meanwhile, seedling rootstock grafting and high grafting for tree crown produced genetic variations among clonal offsprings.

scholarly journals Development of Microsatellite Markers Derived from Expressed Sequence Tags of Polyporales for Genetic Diversity Analysis of EndangeredPolyporus umbellatus

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Yuejin Zhang ◽  
Yuanyuan Chen ◽  
Ruihong Wang ◽  
Ailin Zeng ◽  
Michael K. Deyholos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Large Scale ◽  
Gene Diversity ◽  
High Genetic Diversity ◽  
Information Index ◽  
Polyporus Umbellatus ◽  
Ssr Primers ◽  
Expressed Sequence

A large scale of EST sequences of Polyporales was screened in this investigation in order to identify EST-SSR markers for various applications. The distribution of EST sequences and SSRs in five families of Polyporales was analyzed, respectively. Mononucleotide was the most abundant type, followed by trinucleotide. Among five families, Ganodermataceae occupied the most SSR markers, followed by Coriolaceae. Functional prediction of SSR marker-containing EST sequences inGanoderma lucidumobtained three main groups, namely, cellular component, biological process, and molecular function. Thirty EST-SSR primers were designed to evaluate the genetic diversity of 13 naturalPolyporus umbellatusaccessions. Twenty one EST-SSRs were polymorphic with average PIC value of 0.33 and transferability rate of 71%. These 13P.umbellatusaccessions showed relatively high genetic diversity. The expected heterozygosity, Nei’s gene diversity, and Shannon information index were 0.41, 0.39, and 0.57, respectively. Both UPGMA dendrogram and principal coordinate analysis (PCA) showed the same cluster result that divided the 13 accessions into three or four groups.

scholarly journals Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0137528 ◽  
Author(s):  
Jian-Wei Zong ◽  
Tian-Tian Zhao ◽  
Qing-Hua Ma ◽  
Li-Song Liang ◽  
Gui-Xi Wang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Ssr Markers ◽  
Population Genetic Structure ◽  
Population Genetic

scholarly journals Genetic diversity and fingerprinting of 33 standard flue-cured tobacco varieties for use in distinctness, uniformity, and stability testing

2020 ◽  
Author(s):  
Binbin He ◽  
Ruimei Geng ◽  
Lirui Cheng ◽  
Xianbin Yang ◽  
Hongmei Ge ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationships ◽  
Morphological Identification ◽  
Information Index ◽  
Nicotiana Tabacum L ◽  
Dus Testing ◽  
Identification Technique ◽  
Technical Basis ◽  
Simple Sequence

Abstract Background: At present, the distinctness, uniformity, and stability (DUS) testing of flue-cured tobacco ( Nicotiana tabacum L.) depends on field morphological identification, which is problematic in that it is intensive, time-consuming, and susceptible to environmental impacts. In order to improve the efficiency and accuracy of tobacco DUS testing, the development of a molecular marker-based method for genetic diversity identification is urgently needed. Results: In total, 91 simple sequence repeats (SSR) markers with clear and polymorphic amplification bands were obtained with polymorphism information content, Nei index, and Shannon information index values of 0.3603, 0.4040, and 0.7228, respectively. Clustering analysis showed that the 33 study varieties, which are standard varieties for flue-cured tobacco DUS testing, could all be distinguished from one another. Further analysis showed that a minimum of 25 markers were required to identify the genetic diversity of these varieties. Following the principle of two markers per linkage group, 48 pairs of SSR markers were selected. Correlation analysis showed that the genetic relationships revealed by the 48 SSR markers were consistent with those found using the 91 SSR markers. Conclusions: The genetic fingerprints of the 33 standard varieties of flue-cured tobacco were constructed using 48 SSR markers, and an SSR marker-based identification technique for new tobacco varieties was developed. This study provides a reliable technological approach for determining the novelty of new tobacco varieties and offers a solid technical basis for the accreditation and protection of new tobacco varieties.

scholarly journals Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Santalum Album ◽  
High Genetic Diversity ◽  
Information Index ◽  
Genomic Ssr ◽  
Santalum Album L

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127 expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

scholarly journals ECUADORIAN POTATO LANDRACES: TRADITIONAL NAMES AND GENETIC IDENTITY

2017 ◽  
Vol 40 (4) ◽  
pp. 481-489 ◽  
Author(s):  
Alvaro Monteros-Altamirano ◽  
Johanna Buitrón-Bustamante ◽  
Katherine Orbe-Vergara ◽  
Xavier Cuesta-Subía
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Resource ◽  
Solanum Tuberosum L ◽  
Genetic Identity ◽  
Tuber Morphology ◽  
Molecular Profiles ◽  
The Relationship ◽  
Simple Sequence ◽  
High Diversity

Ecuadorian potato landraces (Solanum tuberosum L.) are an important genetic resource, but they have been poorly described. Simple Sequence Repeats (SSR) markers were applied to 152 landraces to assess the genetic diversity of potatoes collected in three areas of high diversity: the Carchi, Chimborazo and Loja provinces. These SSR markers were previously used in the genotyping of more than 800 European potato varieties. The number of alleles and Polymorphism Information Content (PIC) of the markers found in this study were similar to those in European cultivars; however, the overlap in alleles was small. Based on SSR data, the relationship between local names of landraces and genetic identity showed several landraces with different names but identical molecular profiles. It also showed that landraces with identical names but obvious differences in tuber morphology were almost always genetically different. There was no clear grouping of material collected according to the regions under study that suggests extensive movement of seed potatoes all over Ecuador.

Sign in / Sign up

Export Citation Format

Share Document