Identification of microsatellite markers in the rye genome

Bolibok, Hanna; Rakoczy-Trojanowska, Monika; Wyrzykowska, M.; Radecka, Magdalena; Orczyk, Wacław

doi:10.2478/s11658-006-0023-5

Cited by 10 publications

(6 citation statements)

References 16 publications

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“…Of the many available methods of SSR marker development, to date, genomic libraries (Saal and Wricke, 1999; Bolibok et al, 2006), BAC-end-sequences (Kopecký et al, 2009), and EST sequences (Hackauf and Wehling, 2002; Haseneyer et al, 2011) had been used for this purpose in rye. To our knowledge a development of SSR markers based on DArT marker sequences has not been attempted before in any species.…”

Section: Discussionmentioning

confidence: 99%

DArT Markers Effectively Target Gene Space in the Rye Genome

et al. 2016

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Large genome size and complexity hamper considerably the genomics research in relevant species. Rye (Secale cereale L.) has one of the largest genomes among cereal crops and repetitive sequences account for over 90% of its length. Diversity Arrays Technology is a high-throughput genotyping method, in which a preferential sampling of gene-rich regions is achieved through the use of methylation sensitive restriction enzymes. We obtained sequences of 6,177 rye DArT markers and following a redundancy analysis assembled them into 3,737 non-redundant sequences, which were then used in homology searches against five Pooideae sequence sets. In total 515 DArT sequences could be incorporated into publicly available rye genome zippers providing a starting point for the integration of DArT- and transcript-based genomics resources in rye. Using Blast2Go pipeline we attributed putative gene functions to 1101 (29.4%) of the non-redundant DArT marker sequences, including 132 sequences with putative disease resistance-related functions, which were found to be preferentially located in the 4RL and 6RL chromosomes. Comparative analysis based on the DArT sequences revealed obvious inconsistencies between two recently published high density consensus maps of rye. Furthermore we demonstrated that DArT marker sequences can be a source of SSR polymorphisms. Obtained data demonstrate that DArT markers effectively target gene space in the large, complex, and repetitive rye genome. Through the annotation of putative gene functions and the alignment of DArT sequences relative to reference genomes we obtained information, that will complement the results of the studies, where DArT genotyping was deployed, by simplifying the gene ontology and microcolinearity based identification of candidate genes.

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Section: Discussionmentioning

confidence: 99%

DArT Markers Effectively Target Gene Space in the Rye Genome

et al. 2016

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“…The chromosomal localization of the isolated ScCbf s were performed using nine Chinese Spring wheat × Imperial rye [CS/IMP-1R, -2R, -3R, -4R, -5R, -5RL (long arm only), -5RS (short arm only), -6R, -7R] disomic addition lines, kindly provided by Dr. J.P. Gustafson (USDA, ARS, University of Missouri). Rye chromosome-specific microsatellite markers (RMS markers, Chebotar et al 2003 ; WRM, Bolibok et al 2006 ; REMS and GWM, Khlestkina et al 2004 ; and SCM, Saal and Wricke 1999 ) were used to confirm the presence of each single rye chromosome in each wheat/rye addition line -1R (RMS10, SCM9), -2R (SCM75), -3R (RMS28), -4R (WRM216), -5R (SCM138, SCM268), -5RL (RMS115, REMS1205, REMS1218, REMS1237, REMS1264; GWM1059, SCM109, SCM120), -6R (GWM1103, SCM180) and -7R (SCM86) as previously described (Silkova et al . 2006 ).…”

Section: Methodsmentioning

confidence: 99%

Comparative expression of Cbf genes in the Triticeae under different acclimation induction temperatures

et al. 2009

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In plants, the C-repeat binding factors (Cbfs) are believed to regulate low-temperature (LT) tolerance. However, most functional studies of Cbfs have focused on characterizing expression after an LT shock and have not quantiWed diVerences associated with variable temperature induction or the rate of response to LT treatment. In the Triticeae, rye (Secale cereale L.) is one of the most LT-tolerant species, and is an excellent model to study and compare Cbf LT induction and expression proWles. Here, we report the isolation of rye Cbf genes (ScCbfs) and compare their expression levels in springand winter-habit rye cultivars and their orthologs in two winter-habit wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) cultivars. Eleven ScCbfs were isolated spanning all four major phylogenetic groups. Nine of the ScCbfs mapped to 5RL and one to chromosome 2R. Cbf expression levels were variable, with stronger expression in winter-versus spring-habit rye cultivars but no clear relationship with cultivar diVerences in LT, down-stream cold-regulated gene expression and Cbf expression were detected. Some Cbfs were expressed only at warmer acclimation temperatures in all three species and their expression was repressed at the end of an 8-h dark period at warmer temperatures, which may reXect a temperature-dependent, light-regulated diurnal response. Our work indicates that Cbf expression is regulated by complex genotype by time by inductiontemperature interactions, emphasizing that sample timing, induction-temperature and light-related factors must receive greater consideration in future studies involving functional characterization of LT-induced genes in cereals.

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“…The three groups of SSR primer pairs listed below were used to screen for polymorphism between the parental lines. Group I consisted of 85 primer pairs (pp), developed from rye genomic libraries: 41 pp (WRM) by Bolibok et al [17]; 27 pp (SCM) by Saal and Wricke [18]; and 17 pp (RMS) by Lochow Petkus GmbH, Bergen, Germany, supplied as aliquots by Dr. V. Korzun. Group II consisted of 159 pp developed from EST sequences deposited in public data bases: 99 pp (SCM0) designed by Hackauf and Wehling [19]; and 60 pp (REMS) developed by Khlestkina et al [20] and provided by Dr. V. Korzun.…”

Section: Molecular Marker Analysesmentioning

confidence: 99%

The identification of QTLs associated with the in vitro response of rye (Secale cereale L.)

Bolibok

Gruszczynska

Hromada-Judycka

et al. 2007

Cellular and Molecular Biology Letters

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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

Cited by 10 publications

References 16 publications

DArT Markers Effectively Target Gene Space in the Rye Genome

DArT Markers Effectively Target Gene Space in the Rye Genome

Comparative expression of Cbf genes in the Triticeae under different acclimation induction temperatures

The identification of QTLs associated with the in vitro response of rye (Secale cereale L.)

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