scholarly journals Short note: Development of Six EST-SSR Markers in Larch

2011 ◽  
Vol 60 (1-6) ◽  
pp. 161-163 ◽  
Author(s):  
X. Yang ◽  
X. Sun ◽  
S. Zhang
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Short Note ◽  
Biological Applications ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Six simple sequence repeats (SSR) markers were developed from expressed sequence tags (ESTs) in the genus Larix. Based on evaluation with 49 L. kaempferi genotypes, the number of alleles per locus ranged from two to four, and the expected (He) and observed (Ho) heterozygosity values were 0.225−0.694 and 0.201−0.656, respectively. The inbreeding coffcient (FIS) for all loci were less than zero except that LAReSSR85 was 0.4383. All the six EST-SSR markers were transferable to L. gmelini, L. olgensis var Koreana, L. principisrupprechtii and L. olgensis. BlastX analysis showed that five of the EST-SSRs were homologous to known genes. The six EST-SSR markers developed here can be valuable for biological applications in Larix.

Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 985-998 ◽  
Author(s):  
Siva P Kumpatla ◽  
Snehasis Mukhopadhyay
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Rapid Development ◽  
Dinucleotide Repeats ◽  
High Throughput Analysis ◽  
Species Markers ◽  
Nucleotide Repeats ◽  
Expressed Sequence ◽  
Simple Sequence

Simple sequence repeat (SSR) markers are widely used in many plant and animal genomes due to their abundance, hypervariability, and suitability for high-throughput analysis. Development of SSR markers using molecular methods is time consuming, laborious, and expensive. Use of computational approaches to mine ever-increasing sequences such as expressed sequence tags (ESTs) in public databases permits rapid and economical discovery of SSRs. Most of such efforts to date focused on mining SSRs from monocotyledonous ESTs. In this study, we have computationally mined and examined the abundance of SSRs in more than 1.54 million ESTs belonging to 55 dico tyledonous species. The frequency of ESTs containing SSRs among species ranged from 2.65% to 16.82%. Dinucleotide repeats were found to be the most abundant followed by tri- or mono-nucleotide repeats. The motifs A/T, AG/GA/CT/TC, and AAG/AGA/GAA/CTT/TTC/TCT were the predominant mono-, di-, and tri-nucleotide SSRs, respectively. Most of the mononucleotide SSRs contained 15–25 repeats, whereas the majority of the di- and tri-nucleotide SSRs contained 5–10 repeats. The comprehensive SSR survey data presented here demonstrates the potential of in silico mining of ESTs for rapid development of SSR markers for genetic analysis and applications in dicotyledonous crops.Key words: simple sequence repeats, expressed sequence tags, SSRs, ESTs, bioinformatics, mining, survey, dicotyledonous species, markers.

scholarly journals Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library inPerilla frutescens(L.)

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Eun Soo Seong ◽  
Ji Hye Yoo ◽  
Jae Hoo Choi ◽  
Chang Heum Kim ◽  
Mi Ran Jeon ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Medicinal Plant ◽  
Cdna Library ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Full Length ◽  
Full Length Cdna ◽  
Expressed Sequence ◽  
Simple Sequence

Perilla frutescensis valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses ofP. frutescensare limited due to a lack of gene annotations and characterization. A full-length cDNA library fromP. frutescensleaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as primer pairs. This study is the first to report comparative genomics and EST-SSR markers fromP. frutescenswill help gene discovery and provide an important source for functional genomics and molecular genetic research in this interesting medicinal plant.

scholarly journals Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

2013 ◽  
Vol 138 (4) ◽  
pp. 290-296 ◽  
Author(s):  
Raúl De la Rosa ◽  
Angjelina Belaj ◽  
Antonio Muñoz-Mérida ◽  
Oswaldo Trelles ◽  
Inmaculada Ortíz-Martín ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tag ◽  
Paternity Testing ◽  
High Level ◽  
Repeated Motifs ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Olive Breeding ◽  
Genomic Project

In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (Olea europaea L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.

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.

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

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.

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.

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