Elsevier

Plant Science

Volume 168, Issue 1, January 2005, Pages 195-202
Plant Science

Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice

https://doi.org/10.1016/j.plantsci.2004.08.001Get rights and content

Abstract

Recent increase in the availability of expressed sequence tag (EST) data has facilitated the development of microsatellite or simple sequence repeat (SSR) markers in a number of plant species groups, including cereals. As these SSRs are derived from ESTs/genes (EST-SSRs), they exhibit a higher potential for transfer through cross-amplification in related species than SSR markers generated from genomic DNA libraries. In this study, a sub-set of 165 EST-SSR markers from a total of 185 assigned to the genetic map of barley was examined for transferability to wheat, rye and rice. A higher proportion, i.e., 78.2% of barley markers showed amplification in wheat followed by 75.2% in rye and 42.4% in rice. Furthermore, in silico comparison of SSR-ESTs (ESTs containing SSRs) corresponding to 185 mapped barley EST-SSR loci against 1,369,182 publicly available cereal ESTs showed significant homology with ESTs of wheat (93.5%), rye (37.3%), rice (57.3%), sorghum (51.9%) and maize (51.9%). Sequence similarity of the barley ESTs with 379,944 ESTs of the two model dicot species, Arabidopsis and Medicago suggested theoretical transferability of barley markers into dicot species although at low frequency (9.7% in Arabidopsis and 8.6% in Medicago). In silico comparative mapping (sequence comparison) of mapped barley SSR-ESTs against the mapping data of rye, wheat and rice indicated the presence of orthologues of the barley SSR-ESTs in the respective species. Furthermore, nine barley EST-SSRs were experimentally mapped to a rye genetic linkage map and all could be located in the expected orthologous region compared to their position in barley.

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

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