Highly variable SSR markers suitable for rice genotyping using agarose gels

Singh, Harvinder; Deshmukh, Rupesh; Singh, A. K.; Singh, Ashok Kumar; Gaikwad, Kishor; Sharma, Tilak Raj; Mohapatra, Trilochan; Singh, Nagendra

doi:10.1007/s11032-009-9328-1

Cited by 99 publications

(79 citation statements)

References 15 publications

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“…Taipei 309. Therefore, they corroborate previous investigations (Nagaraju et al, 2002;Ravi et al, 2003;Sarla et al, 2005;Brondani et al, 2006;Lapitan et al, 2007;Singh et al, 2010) in which SSR markers had been able to discriminate among cultivars.…”

Section: Discussionsupporting

confidence: 91%

Microsatellite marker-based genetic variability in Spanish rice cultivars and landraces

Wankhade

Cornejo²,

Mateu‐Andrés

1970

Span. j. agric. res.

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The genetic relationships among japonica rice cultivars and landraces were studied. Most of them are of Spanish origin, and were developed and cultivated for varying time periods over more than a century. To uncover genetic diversity within each cultivar, we analysed 30 plants per cultivar or accession using 10 fluorescently labelled primer pairs for SSR markers. Six cultivars were included in the study, with accessions from four different regions of Spain of the traditional cultivar Bomba. A total of 37 alleles were detected with a mean of 3.7 alleles per locus. Polymorphism information content (PIC) ranged from 0 to 0.78 with an average of 0.51 per locus. Genetic diversity for cvs. Albufera, Bahia, Taipei 309 and Jsendra ranged between 0.008 and 0.062. Cultivar Bomba accessions displayed higher number of alleles and genetic diversity, with Tarragona the lowest (0.08) and Valencia the highest (0.16) genetic diversity. Although infrequent, some heterozygous individuals were detected in cvs. Bomba, Bahia and Taipei 309. Cluster analysis enabled to categorize four accessions of cv. Bomba and cv. Albufera in one group and cvs. Bahia, Taipei 309, Jsendra and Senia in a second group supporting previously known relationships among varieties. These results show the utility of SSR markers for characterization of rice cultivars. In addition, the use of high number of individuals per cultivar, enabled to evaluate both inter-and intra-varietal genetic diversity. Therefore, this investigation should be useful in rice breeding programmes for genotype identification and for the evaluation of germplasm purity.Additional key words: japonica rice; molecular characterization; Oryza sativa L.; SSR markers. Resumen Variabilidad genética de los cultivares y razas locales de arroz español mediante marcadores microsatéliteSe estudian las relaciones genéticas entre cultivares y razas locales de arroz de tipo japonica. La mayoría de ellas son de origen español, desarrolladas y cultivadas durante más de un siglo. La diversidad genética se estudió en 30 individuos de cada cultivar usando 10 pares de cebadores para microsatélites (SSR). Se estudiaron seis cultivares con muestras de cuatro regiones diferentes de España para el cultivar tradicional Bomba. El número total de alelos fue de 37 con una media de 3,7 alelos por locus. El polimorfismo de dichos loci varió entre 0 y 0,78, siendo 0,51 el promedio por locus. La diversidad genética de los cultivares Albufera, Bahia, Taipei 309 y Jsendra varió entre 0,008 y 0,062, mientras que el cv. Bomba presentó valores más elevados (0,12). Aunque poco frecuentes, se encontraron individuos heterozigóticos en los cultivares Bomba, Bahia y Taipei 309. El análisis cluster situó las muestras de las cuatro procedencias de cv. Bomba y el cv. Albufera en un mismo grupo, mientras que los cultivares Bahia, Taipei 309, Jsendra y Senia se situaron en otro grupo de acuerdo con las relaciones previamente conocidas entre variedades. Estos resultados muestran la utilidad de los marcadores SSR para la caract...

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Section: Discussionsupporting

confidence: 91%

Microsatellite marker-based genetic variability in Spanish rice cultivars and landraces

Wankhade

Cornejo²,

Mateu‐Andrés

1970

Span. j. agric. res.

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“…One possible reason behind such an observation could be biased selection of class I microsatellites carrying sequences from the complete data set for development of markers. Class I microsatellites have been found more polymorphic as compared to class II microsatellites in earlier studies also (Singh et al 2010). Analysis of selected sequences for their 'Var' score further improved the proportion of polymorphic markers.…”

Section: Microsatelites In Coding Regionsmentioning

confidence: 65%

Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

Jain

Chaudhary

Sharma

2013

Physiol Mol Biol Plants

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Gene based microsatellite markers are becoming more popular as compared to traditional random genomic microsatellite markers due to rapid and inexpensive method of isolation and their cross species portability. The present study documents occurrence of microsatellites in the transcriptome of seabuckthorn, a plant with immense medicinal, nutritional and ecological value. De novo assembly of over 80 million high quality short reads generated by high throughput next generation sequencing yielded 88297 putative unigenes. Of these, 7.69 % unigenes harbored microsatellite repeats with an average of one microsatellite per 6.704 Kb transcriptome. Dinucleotide repeats were most abundant followed by trinucleotide repeats. Microsatellites were densely populated in coding regions followed by 3′ and 5′ untranslated regions. AG and AAG type repeats were most frequently represented. Of the microsatellite positive unigenes, 48.81 % could be assigned gene ontology (GO) terms in order to assess associations between microsatellite containing unigenes and biological role of known genes. Utility of unigene specific microsatellites was assessed on the basis of polymorphism(s) detected in 18 seabuckthorn collections from Leh (India) using a set of randomly selected 25 unigene specific microsatellites. The findings presented here are likely to find immense use in future breeding and molecular biology research projects in seabuckthorn aiming at its overall development as a crop.

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“…According to the length variation analysis of microsatellites in rice, all primers with a repeat length ≥15 bp were selected, a large proportion of which are the type I SSR markers (repeat length ≥20 bp), deemed to have a high chance of showing polymorphism (Singh et al, 2010). A subset of 343 primers without more than four continuous single base repeats in the primer pairs was synthesized and tested for amplification.…”

Section: Primer Design and Polymorphism Testing Of Ssr Locimentioning

confidence: 99%

Development of genic SSR markers from transcriptome sequencing of pear buds

Yue

Liu

Zong

et al. 2014

J. Zhejiang Univ. Sci. B

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A total of 8375 genic simple sequence repeat (SSR) loci were discovered from a unigene set assembled from 116 282 transcriptomic unigenes in this study. Dinucleotide repeat motifs were the most common with a frequency of 65.11%, followed by trinucleotide (32.81%). A total of 4100 primer pairs were designed from the SSR loci. Of these, 343 primer pairs (repeat length ≥15 bp) were synthesized with an M13 tail and tested for stable amplification and polymorphism in four Pyrus accessions. After the preliminary test, 104 polymorphic genic SSR markers were developed; dinucleotide and trinucleotide repeats represented 97.11% (101) of these. Twenty-eight polymorphic genic SSR markers were selected randomly to further validate genetic diversity among 28 Pyrus accessions. These markers displayed a high level of polymorphism. The number of alleles at these SSR loci ranged from 2 to 17, with a mean of 9.43 alleles per locus, and the polymorphism information content (PIC) values ranged from 0.26 to 0.91. The UPGMA (unweighted pair-group method with arithmetic average) cluster analysis grouped the 28 Pyrus accessions into two groups: Oriental pears and Occidental pears, which are congruent to the traditional taxonomy, demonstrating their effectiveness in analyzing Pyrus phylogenetic relationships, enriching rare Pyrus EST-SSR resources, and confirming the potential value of a pear transcriptome database for the development of new SSR markers.

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Highly variable SSR markers suitable for rice genotyping using agarose gels

Cited by 99 publications

References 15 publications

Microsatellite marker-based genetic variability in Spanish rice cultivars and landraces

Microsatellite marker-based genetic variability in Spanish rice cultivars and landraces

Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome

Development of genic SSR markers from transcriptome sequencing of pear buds

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