Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 795-804 ◽  
Author(s):  
Luciana Rossini Pinto ◽  
Karine Miranda Oliveira ◽  
Eugênio César Ulian ◽  
Antonio Augusto Franco Garcia ◽  
Anete Pereira de Souza
Keyword(s):  
Simple Sequence Repeats ◽  
Expressed Sequence Tags ◽  
Expressed Sequence Tag ◽  
Leaf Roll ◽  
Cdna Libraries ◽  
Genomic Libraries ◽  
Est Sequencing ◽  
Tetranucleotide Repeats ◽  
Expressed Sequence ◽  
Simple Sequence

Sugarcane microsatellites or simple sequence repeats (SSR) were developed in an economical and practical way by mining EST databases. A survey in the SUCEST (sugarcane EST) database revealed a total of 2005 clusters out of 43 141 containing SSRs. Of these, 8.2% were dinucleotide, 30.5% were trinucleotide, and 61.3% were tetranucleotide repeats. Except for dinucleotides, the CG-rich motif types were the most common. Differences in abundance of trinucleotide motif types were observed between EST-SSRs and those isolated from sugarcane genomic libraries. Among the different cDNA libraries used for EST sequencing, SSRs were more frequent in the ones derived from leaf roll (LR). Twenty-three out of 30 tested SSRs produced scorable polymorphisms in 18 sugarcane commercial clones. These EST-SSRs showed a moderate level of polymorphism with some SSRs producing unique fingerprints. The number of alleles observed among the 18 clones evaluated varied from 2 to 15, with an average of 6.04 alleles/locus. The polymorphism information content (PIC) values ranged from 0.28 to 0.90 with a mean of 0.66. The EST-SSRs screened over both parents (SP 80-180; SP 80-4966) and 6 F1 individuals produced 52 segregating markers that could potentially be used for sugarcane mapping. The EST-SSRs were found in clusters that had significant homology to proteins involved in important metabolic pathways such as sugar biosynthesis, proving that EST-SSRs are a valuable tool for the construction of a functional sugarcane map.Key words: sugarcane, polyploid, expressed sequence tags (ESTs), microsatellites (SSRs), genetic mapping.

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 and characterization of microsatellite markers from tropical forage Stylosanthes species and analysis of genetic variability and cross-species transferability

Genome ◽  
2011 ◽  
Vol 54 (12) ◽  
pp. 1016-1028 ◽  
Author(s):  
Amaresh Chandra ◽  
K.K. Tiwari ◽  
D. Nagaich ◽  
N. Dubey ◽  
S. Kumar ◽  
...  
Keyword(s):  
Genetic Improvement ◽  
Expressed Sequence Tag ◽  
Intraspecific Diversity ◽  
Genomic Libraries ◽  
Tropical Forage ◽  
Genomic Ssr ◽  
Functional Molecular Markers ◽  
Expressed Sequence ◽  
Simple Sequence

A limited number of functional molecular markers has slowed the desired genetic improvement of Stylosanthes species. Hence, in an attempt to develop simple sequence repeat (SSR) markers, genomic libraries from Stylosanthes seabrana B.L. Maass & ’t Mannetje (2n = 2x = 20) using 5′ anchored degenerate microsatellite primers were constructed. Of the 76 new microsatellites, 21 functional primer pairs were designed. Because of the small number of primer pairs designed, 428 expressed sequence tag (EST) sequences from seven Stylosanthes species were also examined for SSR detection. Approximately 10% of sequences delivered functional primer pairs, and after redundancy elimination, 57 microsatellite repeats were selected. Tetranucleotides followed by trinucleotides were the major repeated sequences in Stylosanthes ESTs. In total, a robust set of 21 genomic–SSR (gSSR) and 20 EST–SSR (eSSR) markers were developed. These markers were analyzed for intraspecific diversity within 20 S. seabrana accessions and for their cross-species transferability. Mean expected (He) and observed (Ho) heterozygosity values with gSSR markers were 0.64 and 0.372, respectively, whereas with eSSR markers these were 0.297 and 0.214, respectively. Dendrograms having moderate bootstrap value (23%–94%) were able to distinguish all accessions of S. seabrana with gSSR markers, whereas eSSR markers showed 100% similarities between few accessions. The set of 21 gSSRs, from S. seabrana, and 20 eSSRs, from selected Stylosanthes species, with their high cross-species transferability (45% with gSSRs, 86% with eSSRs) will facilitate genetic improvement of Stylosanthes species globally.

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