Development of simple sequence repeat markers in rye (Secale cereale L.).

Area of Science:

• Plant genetics
• Molecular markers
• Genomics

Background:

• Simple sequence repeats (SSRs), also known as microsatellites, are PCR-based DNA markers utilized in plant and mammalian genomes.
• SSRs exhibit higher polymorphism levels than other DNA markers, particularly in self-pollinating crops.
• Their technical advantages over RFLP markers suggest utility in outcrossing crops like rye.

Purpose of the Study:

• To evaluate the effectiveness of SSR markers in rye (Secale cereale) genetics and breeding.
• To identify and characterize SSR motifs within the rye genome.
• To compare the polymorphic information content of SSRs with RFLP markers in rye.

Main Methods:

• Screening of rye genomic libraries for (CT/GA)n and (GT/CA)n dinucleotide repeats.
• Sequencing of positive clones to identify perfect SSR motifs.
• Design and testing of primer pairs for SSR amplification.
• Genetic mapping of SSR markers and comparison with RFLP markers in two open-pollinated rye cultivars.

Main Results:

• The frequency of (CT/GA)n and (GT/CA)n dinucleotide repeats in the rye genome was estimated at one per 268-519 kb.
• Of 74 sequenced clones, 56.8% contained perfect repeats, with (GT/CA)n being predominant (61.9%).
• 27 out of 57 designed primer pairs yielded specific SSR markers, with 20 successfully mapped to chromosomes or chromosome arms.
• SSR markers demonstrated higher expected heterozygosity (0.62 vs. 0.43) and allele numbers (5.9 vs. 3.4) compared to RFLP markers.

Conclusions:

• SSR markers are highly informative and valuable tools for rye genetics and breeding.
• SSRs provide a significant advantage over RFLP markers in terms of polymorphism and allele diversity in rye.
• The developed SSR markers are suitable for genetic mapping and can enhance marker-assisted selection in rye improvement programs.