Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice
Introduction
The advent of DNA marker technology has facilitated the rapid generation of many high-density genetic and physical maps and has permitted genetic map comparisons through the use of common markers between both closely and, less commonly, distantly related species. Despite the fact that the genome size of cereals varies up to 40-fold, comparative genetic mapping among several species of Poaceae has revealed extensive genome colinearity [1], [2]. In this context, it has proved possible to demonstrate that 30 linkage blocks from the rice genetic map are sufficient to reconstitute the seven Triticeae (e.g., wheat (Triticum aestivum L.), rye (Secale cereale L.) and barley (Hordeum vulgare L.)), 12 rice and the 10 maize chromosomes [1]. Among the different kinds of molecular markers that are available, restriction fragment length polymorphisms (RFLPs) provided the major means for resolution of genomic conserved synteny and colinearity. Because of their hybridization-based ability to identify orthologous DNA fragments, even if sequence conservation is as low as 70%, comparative mapping could be performed in a number of plant species including cereals (e.g., [3], [4], [5]). Due to their simple and cost-effective deployment, microsatellite or simple sequence repeat (SSR) markers have replaced RFLPs for most applications related to plant breeding [6]. SSR markers have been generated in large numbers for most major crop species despite the labour, time and cost-intensive nature of their development from genomic DNA libraries [7]. An important feature of genomic SSRs is their locus-specificity, which is an invaluable advantage when working with allopolyploid species such as wheat, in which only one of three homoeologous loci should ideally be tagged [8]. On the other hand their locus specificity has prevented them from being useful for comparative mapping studies [9], [10].
Due to the availability of large EST datasets, it has become possible to systematically search for SSRs in EST sequences with the help of bioinformatics tools [11], [12], [13], [14]. Since these SSRs are derived from ESTs, corresponding to the transcribed component of a gene unit, they have been shown to possess a high potential for inter-specific transferability [14], [15], [16]. In the present study we have performed a quantitative assessment of the potential of barley EST-derived SSRs (EST-SSRs) to be transferred to related species and to be used for comparative mapping in wheat, rye and rice by employing both computational and experimental approaches.
Section snippets
Plant materials
To examine the transferability of barley EST-SSR markers, two rye accessions (‘P87’ and ‘P105’), up to three accessions of wheat (‘Chinese Spring’, ‘Opata85’, ‘W7984’) and one accession of rice (‘Nipponbare’) were used. In addition, the barley cultivar ‘Barke’ was used as a control because the majority of EST-SSRs used in this study originated from ESTs derived from this cultivar ([17], http://pgrc.ipk-gatersleben.de/cr-est/). A set of nine markers displaying polymorphism between rye genotypes
Experimental analysis in cereal species
In order to determine the potential for cross species amplification, primer pairs of 165 mapped barley EST-SSR markers were tested in wheat, rye and rice under the same PCR-conditions as originally applied for amplification in barley. As a criterion for successful transferability the presence of distinct amplicons after agarose gel electrophoresis was applied. Of the used barley primer pairs, 78.2% yielded amplicons in wheat, 75.2% in rye and 42.4% in rice (Table 1). As expected, not all
Transferability of barley EST-SSR markers
In recent years, it has been shown for several species that EST-derived SSRs show a considerable degree of transferability to related species [14], [15], [16], by contrast with genomic SSRs that show less efficient cross amplification [9], [10], [25]. Even in an amphiploid species like bread wheat with three related genomes, only 20–30% of the genomic SSRs detected homoeoloci [8], [22]. Higher levels of transferability of EST-derived SSRs as compared to genomic DNA-derived SSRs reflect the
Note
Primer sequences for transferable barley markers in wheat, rye and rice are available upon request for academic research purposes. In addition, data on polymorphism between two rye genotypes (‘P87’ and ‘P105’) as well as between ITMI parental genotypes of wheat (‘Opata85’ and ‘W7984’) are also available.
Acknowledgements
We thank Ju-Kyung Yu (Cornell University, Ithaca, USA), Sukhwinder Singh (Kansas State University Manhattan, USA), and Thomas Thiel (IPK-Gatersleben, Germany) for developing some of the wheat and barley SSR markers mentioned in the present study. We acknowledge the support by Heiko Keller in some wet lab experiments and Hangning Zhang in computational analysis of barley ESTs with rice genome. We are grateful to Bernd Hackauf and Peter Wehling (Federal Centre for Breeding Research on Cultivated
References (34)
- et al.
Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum
Plant Sci.
(2001) - et al.
MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations
Genomics
(1987) - et al.
Grasses, line up and form a circle
Curr. Biol.
(1995) - et al.
Genome relationships: the grass model in current research
Plant Cell
(2000) - et al.
RJ, Comparative genomics of plant chromosomes
Plant Cell
(2000) - et al.
RFLP-based genetic map of the homoeologous group 3 chromosomes of wheat and rye
Theor. Appl. Genet.
(1992) - et al.
Comparative RFLP maps of the homoeologous group-2 chromosomes of wheat, rye and barley
Theor. Appl. Genet.
(1993) - et al.
Anchor probes for comparative mapping of grass genera
Theor. Appl. Genet.
(1998) - R.K. Varshney, V. Korzun, A. Börner, Molecular maps in cereals: methodology and progress, in: P.K. Gupta, R.K. Varshney...
- et al.
The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat
Euphytica
(2000)
Characterization of microsatellites and development of chromosome specific STMS markers in bread wheat
Plant Mol. Biol. Rep.
Abundance, variability and chromosomal location of microsatellites in wheat
Mol. Gen. Genet.
Transferability of wheat microsatellites to diploid Triticeae species carrying the A, B and D genomes
Theor. Appl. Genet.
Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat
Plant Mol. Biol.
In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species
Cell Mol. Biol. Lett.
Analysis of microsatellites in major crops assessed by computational and experimental approaches
Mol. Breed.
Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.)
Theor. Appl. Genet.
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