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 Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

2020 ◽  
Author(s):  
Lei Zhu ◽  
Hua yu Zhu ◽  
Yan man Li ◽  
Xiang bin Wu ◽  
Jin tao Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomics ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Diversity Analysis ◽  
Motif Length ◽  
Genetic Diversity Analysis ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Abstract Background The Cucurbita genus contains important economic crops in the world, while limited molecular markers have been developed in the past years. Simple sequence repeats (SSR) markers are powerful tools for the study of genetic mapping construction, genetic diversity analysis and genome wide association. The availability of pumpkin genome information has made it possible to analyze SSRs in genome wide across three Cucurbita species. Results In this paper, based on the whole genome sequences, 34,375 SSR loci were found in C. moschata, 30,577 SSR loci were found in C. maxima and 38,104 SSR loci were found in C. pepo. C. pepo has the maximum density of SSRs with an average of 145 SSR/Mb. In general, the frequency in total SSR loci decreased with the increase of the motif length, dinucleotide motifs were the most common motifs in the three species, and for the same repeat types, the SSR frequency decreased sharply with the increase of the repeat number. Most of those SSR loci were suitable for marker development (84.75% in C. moscata, 94.53% in C. maxima and 95.09% in C. pepo). Based on those markers, we compared and analyzed the cross-species SSR markers between C. pepo and other Cucurbitaceae species by silico-PCR. Using these cross-species primers, the high collinear relationships between C. pepo and the other two species were detected, respectively. Furthermore, the application of SSR markers in genetic diversity analysis was tested in C. pepo, the results showed that they were good tools to be used in genetic diversity analysis. Conclusion In this study, the genome wide SSR markers were detected from three Cucurbita species, and some of their applications were proved by comparative genomics and genetic diversity analysis. The large number of genome-wide SSR markers and crossspecies markers would promote the basic and applied studies of Cucurbita species, such as gene mapping, QTLs mapping, comparative genomics and marker-assisted breeding.

scholarly journals Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats

2018 ◽  
Vol 19 (9) ◽  
pp. 2492 ◽  
Author(s):  
Qi Guo ◽  
Xiuyu Li ◽  
Shuhong Yang ◽  
Zhiheng Yang ◽  
Yuhan Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tag ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Ex Situ ◽  
Ssr Primers ◽  
Robinia Pseudoacacia L ◽  
Expressed Sequence ◽  
Simple Sequence

Understanding the genetic diversity and differentiation of the genetic resources of a species is important for the effective use and protection of forest tree resources. Ex situ development is a common method for the protection of genetic diversity and an essential resource for users who require ready access to a species’ germplasm. In this study, we collected seeds of black locust (Robinia pseudoacacia L.) from 19 provenances, covering most of its natural distribution; we randomly selected 367 tender leaves with well-grown and different maternal strains from this group for further analysis. Forty-eight simple sequence repeat (SSR) primers were successfully selected from 91 pairs of SSR primers using native-deformation polyacrylamide gel electrophoresis. In addition, we identified identical genotypes among all individuals and evaluated the quality of the markers. From this, 35 loci were confirmed for analyses of genetic diversity and differentiation of the black locust provenances, which contained 28 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and 7 genomic DNA-derived simple sequence repeats (G-SSRs). We observed high genetic diversity among the native black locust provenances, from which Wright’s fixation index and molecular variance suggested that a majority of the genetic differentiation variation could be attributed to within-provenance differences. The genetic distance and identity results indicated that geographic distance was not a dominating factor influencing the distribution of black locust. This is the first study to evaluate provenance genetic variation in native black locust samples using two types of SSR markers, which provides a comprehensive theoretical basis for ex situ conservation and utilization of genetic resources, with an emphasis on breeding applications.

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 Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance

2007 ◽  
Vol 42 (3) ◽  
pp. 377-384 ◽  
Author(s):  
Fernanda de Oliveira Pinto ◽  
Mirian Perez Maluf ◽  
Oliveiro Guerreiro-Filho
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Defense Mechanisms ◽  
Leaf Miner ◽  
Gene Transcript ◽  
Est Database ◽  
Hybrid Frequency ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

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 Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee

2011 ◽  
Vol 46 (12) ◽  
pp. 1650-1656 ◽  
Author(s):  
Gabriella Santos Pereira ◽  
Lilian Padilha ◽  
Edila Vilela Resende Von Pinho ◽  
Rita de Kássia Siqueira Teixeira ◽  
Carlos Henrique Siqueira de Carvalho ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Ssr Markers ◽  
Expressed Sequence Tag ◽  
Leaf Miner ◽  
Est Database ◽  
Ssr Loci ◽  
Leucoptera Coffeella ◽  
Coffee Leaf Miner ◽  
Expressed Sequence ◽  
Simple Sequence

The objective of this work was to analyze coffee (Coffea arabica) genotypes resistant to the coffee leaf miner (Leucoptera coffeella) using microsatellite markers. Sixty-six loci were evaluated, of which 63 were obtained from the Brazilian Coffee Expressed Sequence Tag (EST) database. These loci were amplified in bulks of individuals from F5 progenies of 'Siriema' (C. arabica x C. racemosa) resistant and susceptible to the insect, in eight samples of C. racemosa, and in a F6 population of 'Siriema' with 91 individuals segregating for resistance to the leaf miner. Polymorphisms were verified for two simple sequence repeat (SSR) loci in bulks of the susceptible progenies. The two polymorphic alleles were present in around 70% of the susceptible genotypes in F5 and in approximately 90% of the susceptible individuals in F6. However, the polymorphic EST-SSR markers among populations contrasting for resistance to leaf miner were not correlated to the evaluated characteristics. SSR markers show inter- and intraspecific polymorphism in C. arabica and C. racemosa.

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