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Characteristics and a comparison of three classes of microsatellite-based markers and their application in plants

100%

Rakoczy-Trojanowska M., Bolibok H.

Cellular and Molecular Biology Letters

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2004

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tom 09

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nr 2

Microsatellites (SSR - simple sequence repeats, STR - short tandem repeats, SSLP - simple sequence length polymorphism, VNTR - variable number of tandem repeats) are the class of repetitive DNA sequences present in all living organisms. Particular characterstics of microsatellites, such as their presence in the genomes of all living organisms, high level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for a number of approaches like genotyping, mapping and positional clonig of genes. The three most popular types of markers containing microsatellite sequences that are presently used are: (1) SSR (simple sequence repeats), generated by amplifying in a PCR reaction with the use of primers complementary to flanking regions; (2) ISSR (inter-simple sequence repeats), based on the amplification of regions between inversely oriented closely spaced microsatellites; and (3) SAMPL (selective amplification of microsatellite polymorphic loci), which utilises AFLP (amplified fragment-length polymorphism) methodology, with one exception - for the second amplification, one of the starters is complementary to the microsatellite sequence. The usefulness of the three above-mentioned markers for numerous purposes has been well documented for plants.

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The identification of QTLs associated with the in vitro response of rye [Secale cereale L.]

81%

Bolibok H., Gruszczynska A., Hromada-Judycka A., Rakoczy-Trojanowska M.

Cellular and Molecular Biology Letters

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2007

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tom 12

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nr 4

523-535

This study was conducted in order to identify quantitative trait loci (QTLs) for the in vitro culture response of winter rye (Secale cereale L.) immature embryos and immature inflorescences. A genetic linkage map comprising 67 SSRs, 9 ISSRs, 13 SAMPLs, 7 RAPDs, 2 SCARs and one EST marker was created based on the analyses of 102 recombinant inbred lines from the cross between lines L318 (which has a good response in tissue cultures) and L9 (which is unable to regenerate plants from somatic tissues and anthers). The map spans 979.2 cM, and the average distance between markers is 9.9 cM. Two characteristics were evaluated: callus induction (CI) and somatic embryogenesis ability (SE). They were expressed as the percentage of immature embryos/inflorescences producing callus (designated ECI/ICI) and the percentage of explants producing somatic embryos (ESE/ISE). All the analysed traits showed continuous variation in the mapping population but a non-normal frequency distribution. We identified nine putative QTLs controlling the tissue culture response of rye, explaining up to 41.6% of the total phenotypic variation: two QTLs for ECI — eci-1, eci-2; 4 for ESE — ece-1, ese-2, ese-3, ese-4; 2 for ICI — ici-1, ici2; and 1 for ISE — ise-1. They were detected on chromosomes 1R, 4R, 5R, 6R and 7R.

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Identification of microsatellite markers in the rye genome

71%

Bolibok H., Rakoczy-Trojanowska M., Wyrzykowska M., Radecka M., Orczyk W.

Cellular and Molecular Biology Letters

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2006

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tom 11

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nr 2

The rye genomic library, which consists of DNA fragments in the range of 0.5–1.1 kb, was screened for the presence of tri-and tetranucleotide and compound microsatellites. Of the 1,600,000 clones analysed, 102 clones were positive and 41 were suitable for SSR primer pair design. Twenty-six primer pairs amplified specific products, and six of them were capable of detecting polymorphism among 30 rye accessions of different genetic backgrounds. Using a set of Chinese Spring-Imperial wheat-rye addition lines, it was possible to locate 3 newly identified microsatellites on chromosomes 3R, 4R and 7R.

Ograniczanie wyników

3 Cellular and Molecular Biology Letters

3 Bolibok H.

3 Rakoczy-Trojanowska M.

1 Gruszczynska A.

1 Hromada-Judycka A.

1 Orczyk W.

1 Radecka M.

1 Wyrzykowska M.

1 2007

1 2006

1 2004

Characteristics and a comparison of three classes of microsatellite-based markers and their application in plants

The identification of QTLs associated with the in vitro response of rye [Secale cereale L.]

Identification of microsatellite markers in the rye genome