Study of interspecific SSR polymorphism among 14 species from Triticum-Aegilops group
S. Sharma, H.S. Balyan, P.L. Kulwal, N. Kumar, R.K. Varshney1, M. Prasad1 and P.K. Gupta*
Molecular Biology Laboratory, Department of Agricultural
Botany, Ch. Charan Singh University, Meerut-250 004 (U.P.), India
1Present address: Institute for Plant Genetics and Crop Plant Research,
Corrensst. 3, D06466, Gatersleben, Germany
Summary
In the present study, using in-gel hybridization and PCR based approaches, interspecific SSR polymorphism was studied among 14 species of Triticum-Aegilops group. The material represented seven different genomes and three ploidy levels (2x, 4x, 6x). In-gel hybridization involved 13 probe-enzyme combinations (four SSR oligonucleotide probes in combination with 2-4 enzymes) and resolved 5 to 20 bands (0.40kb to >23kb) in each of the 14 individual species. This suggested ubiquitous distribution and interspecific polymorphism of SSRs among different species of Triticum-Aegilops group. The available polymorphism also proved helpful in discriminating not only the species with different ploidy levels and possessing different genomes, but also those possessing similar or very closely related genomes. The amplification of SSR loci using 15 primer pairs derived from hexaploid wheat was also carried out in all the 14 species. The primer pairs, each amplified SSR loci not only in species containing A, B and D genomes, but also in 2 to 10 of the remaining species that contained other genomes. This suggested that wheat SSRs might have been derived from the corresponding SSRs in an ancestral genome and are conserved across a number of species in the Triticum-Aegilops group. Also, two pairs of SSRs (one consisting of WMC243 and WMC415 and the other consisting of WMC35 and WMC404) each discriminated all the 14 species examined during the present study. Therefore, one can infer from the present study that SSR primers can be used in studies on DNA polymorphism, genetic diversity, gene mapping and synteny conservation across different species of Triticum-Aegilops group.
Key words: in-gel hybridization, microsatellite, polymorphism, Triticum, Aegilops
Introduction
Molecular markers have been extensively utilized for the study of genetic diversity and genomic constitutions in a number of species of the tribe Triticeae. Genome-specific molecular markers have also been identified in several crops including wheat (Roder et al. 1998; Pestsova et al. 2000; Gupta et al. 2002). Among the different types of molecular markers, microsatellites or simple sequence repeats (SSRs)/simple tandem repeats (STRs) have become the markers of choice due to their abundance and ubiquitous distribution in both the nuclear and organellar genomes. It has also been shown that SSRs are frequent in both repetitive and unique sequences of the nuclear genome (for a review, see Gupta and Varshney 2000; Morgante et al. 2002).
SSR markers can also be used for distinguishing related genomes, since often homoeoloci in related genomes that are characteristic of RFLPs are infrequent among SSR loci. Wheat SSRs, therefore, facilitated a variety of studies that involved mapping and gene tagging (for review see Gupta et al. 1999; Varshney et al. 2000b; Varshney et al. 2001; Gupta et al. 2002), genetic diversity (Plaschke et al. 1995; Roder et al. 1995; Prasad et al. 2000), in-gel hybridization (Varshney et al. 1998) and in-situ hybridization (Cuadrado and Schwararchzer 1998). They have also been used for studying the role of natural selection in differentiation (Li et al. 1999, 2000). A proportion of SSRs derived from wheat and Ae. tauschii have also been used in related species containing A, B and D genomes (Sourdille et al. 2001; Guyomarc'h et al. 2002). In the present study, we examined the distribution and organization of SSRs in 14 different diploid and polyploid species of Triticum-Aegilops group through in-gel hybridization and PCR based amplification of SSR loci. This facilitated an assessment of the potential of SSR oligonucleotide probes and SSR primers for a study of molecular marker- based studies in the tribe Triticeae.