Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations

Crustaceana ◽  
2019 ◽  
Vol 92 (7) ◽  
pp. 841-851
Author(s):  
Xuekai Han ◽  
Ruyi Xu ◽  
Yuyu Zheng ◽  
Meirong Gao ◽  
Liying Sui
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Food Items ◽  
Geographical Populations ◽  
Geographic Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.

scholarly journals Development of Highly Polymorphic Expressed Sequence Tags-Simple Sequence Repeat Markers and Their Application in Analysis of Genetic Diversity of Chinese Bayberry (Morella rubra)

HortScience ◽  
2016 ◽  
Vol 51 (3) ◽  
pp. 227-231 ◽  
Author(s):  
Wenting Wang ◽  
Chao Feng ◽  
Zehuang Zhang ◽  
Liju Yan ◽  
Maomao Ding ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Mean Value ◽  
Sequence Repeat ◽  
Chinese Bayberry ◽  
Cultivated Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Chinese bayberry (Morella rubra) is an economically important subtropical evergreen fruit crop native to China and other Asian countries. For facilitating cultivar discrimination and genetic diversity analysis, a total of 38 high-quality and highly polymorphic expressed sequence tags-simple sequence repeat (EST-SSR) markers, with little or no polymerase chain reaction (PCR) stutter bands, including 21 screened from those obtained previously and 17 newly developed markers, were developed. The average number of alleles (Na) per locus was 5.6, and polymorphism information content varied from 0.34 to 0.86, with a mean value of 0.57. With these markers, all 42 Chinese bayberry accessions analyzed were successfully discriminated and the phylogenetic relationship between accessions was revealed. The accessions can be separated into two groups with six subgroups. The grouping of four main cultivars in three subgroups and 12 white-fruited accessions, each with little or no anthocyanin accumulation in ripe fruit, into five subgroups suggested the preservation of broad diversity among cultivated populations. These EST-SSR markers and the findings obtained in this study can assist the discrimination of cultivars and lines and contribute to genetic and breeding studies in Chinese bayberry.

Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugensStål)

2011 ◽  
Vol 102 (1) ◽  
pp. 113-122 ◽  
Author(s):  
S. Jing ◽  
B. Liu ◽  
L. Peng ◽  
X. Peng ◽  
L. Zhu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Large Scale ◽  
Brown Planthopper ◽  
Nilaparvata Lugens ◽  
Rice Varieties ◽  
Genetics And Genomics ◽  
Expressed Sequence ◽  
Simple Sequence

AbstractTo assess genetic diversity in populations of the brown planthopper (Nilaparvata lugensStål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopperN. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 277-290 ◽  
Author(s):  
Eline van Zijll de Jong ◽  
Kathryn M Guthridge ◽  
German C Spangenberg ◽  
John W Forster
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
Sequence Repeat ◽  
Pasture Grass ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

scholarly journals Development of Expressed Sequence Tag-Drived Simple Sequence Repeat Markers and Diversity Analysis of Phytophthora capsici in China

2013 ◽  
Vol 2 (3) ◽  
pp. 137-146
Author(s):  
Liu Pei-Qing ◽  
Wu Min-Liang ◽  
Li Ben-Jin ◽  
Lan Cheng-Zhong ◽  
Weng Qi-Yong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Phytophthora Capsici ◽  
Management Strategies ◽  
Diversity Analysis ◽  
Evolutionary Potential ◽  
Genetic Clusters ◽  
Expressed Sequence ◽  
Simple Sequence

Phytophthora capsici is a highly dynamic and destructive pathogen of vegetable and great interests on the genetic structure of P. capsici have grown in the world. However, there is little genetic information about P. capsici based on the EST-SSR markers. In this study, 193 SSR markers were developed and 33 selected markers were successfully detected and they were polymorphic with the number of alleles per locus ranging from 2 to 7. 4 SSR markers were further selected for genetic diversity analysis and Nei’s genetic diversity values of 15 populations ranged from 0.38 to 0.66, with an average of 0.53. The higher polymorphism and greater transport ability of these markers among P. capsici species were proved by the expected heterozygosity (He =0.64) and Shannon’s index of diversity (I =1.14), indicating that they maintained a substantial level of genetic diversity. Additionally, the genetic differentiation among the 4 markers (Fst =0.15) was moderate and the gene flow among groups was consequent (Nm =1.69). Clustering analyses revealed that 15 populations are made of two differentiated genetic clusters and are similar regarding genetic diversity composition. Our results suggest that there are considerable evolutionary potential of P. capsici in China and useful management strategies should be adapt to it.

scholarly journals Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China

Forests ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 644 ◽  
Author(s):  
Li Dong ◽  
Yuhan Sun ◽  
Keqi Zhao ◽  
Jing Zhang ◽  
Yuwei Zhang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Diversity Analysis ◽  
Simple Method ◽  
Genetic Diversity Analysis ◽  
Ssr Loci ◽  
Robinia Pseudoacacia L ◽  
Expressed Sequence ◽  
Simple Sequence

Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4–15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427–0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

scholarly journals Genetic Diversity Analysis between Different Varieties of Chickpea (Cicer arietinum L.) Using SSR Markers

2019 ◽  
Vol 7 (2) ◽  
pp. 236-242
Author(s):  
Summy Yadav ◽  
Vaidehi Shah ◽  
Bhavya Mod
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genomic Dna ◽  
Physiological Data ◽  
Diversity Analysis ◽  
Hierarchical Tree ◽  
Cicer Arietinum L ◽  
Equal Distance ◽  
Genomic Regions ◽  
Simple Sequence

The paper aims at evaluating genetic diversity among genomes of chickpea comprising of 5 different varieties with the help of simple sequence repeats (SSR) molecular markers. Genomic DNA isolated from all varieties was checked with 15 different SSR markers specific for ENDPOINT PCR using PCR based techniques. Amplification bands with different markers enabled identification of the genomic regions responsible for Drought Tolerance in chickpea. All 15 SSR markers chosen gave monomorphic bands.  A hierarchical tree was also constructed using UPGMA Dendogram for figuring out the exact genetic distance of cultivars using band amplification data. It depicted GUJ-1 and GUJ-2 are closest of all cultivars. GUJ-5 is at the center having GUJ-3 and UJJAVAL at an almost equal distance but GUJ-5 and GUJ-3 are more related. Physiological data also supported this genetic evidence. Int. J. Appl. Sci. Biotechnol. Vol 7(2): 236-242

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.

Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)

2004 ◽  
Vol 109 (4) ◽  
pp. 800-805 ◽  
Author(s):  
N. Nicot ◽  
V. Chiquet ◽  
B. Gandon ◽  
L. Amilhat ◽  
F. Legeai ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence
Sign in / Sign up

Export Citation Format

Share Document