Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags

Abstract

The genetic map of rye contains predominantly restriction fragment length polymorphism (RFLP) markers but also a limited number of microsatellite markers, which are known to be more reliable and easier to apply. We report here the saturation of the genomic map of rye with additional microsatellite-derived markers that we obtained from the rye expressed sequence tag (EST) databases and the Gatersleben collection of wheat microsatellite markers (WMS). A total of 99 loci (39 EST and 60 WMS) were mapped into the RFLP frameworks of four rye mapping populations consisting of 139, 64, 58 and 60 RFLPs, respectively. For another ten WMS loci, which amplified PCR products not polymorphic in any of the mapping populations, chromosome and chromosome arm locations were determined using wheat-rye addition lines. Chromosomes 1R, 2R, 3R, 4R, 5R, 6R and 7R were enriched with 9, 19, 9, 13, 27, 16 and 16 microsatellite loci, respectively. The microsatellite loci mapped were evenly distributed along the chromosomes, which is important for the further application of these markers for gene mapping or diversity studies in rye. Forty-four of the WMS loci mapped in rye were found to be homologous to those mapped in bread wheat ( Triticum aestivum L.).

Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies

“…However, in recent years, as with other crops, SSRs have come to represent the markers of choice for breeding applications (Gupta and Varshney 2000). In an attempt to increase the limited number of functional SSR assays in rye, Khlestkina et al (2004Khlestkina et al ( , 2005 developed SSR markers from rye ESTs (expressed sequence tags) and also transferred the wheat-originating SSRs (Rö der et al 1998(Rö der et al , 2004 to the rye genetic maps. They were able to map a number of both EST-derived (eSSR) and genomic (gSSRs) loci in four rye mapping populations.…”

A consensus map of chromosome 6R in rye (Secale cereale L.)

“…In the last decade, the sequence-specific PCR markers (SSR, STS, SCAR) for the rye genome became more available for map construction. Microsatellites seem to especially be useful for this purpose [11,12]. In our study, sequence-specific markers were applied to establish maps for all four analyzed mapping populations, but above all they allowed for the integration of the segregation data into one consensus map of chromosome 6R.…”

“…The methods used for the RAPD, ISSR, SCAR and STS analyses were described previously [13,24,26,27]. Polymorphisms in the microsatellite markers (SSR-s) developed by Hackauf and Wehling [11] were analyzed using a modified version of the method given by Khlestkina et al [12]. The PCR mixture (10 μl) contained a reaction buffer (70 mM Tris-HCl, pH 8.3, 16.6 mM ammonium sulphate, 2.5 mM MgCl 2 ), 0.5 pmol of the forward primer (with an M13 17-bp tail), 2.5 pmol of the reverse primer, 1.5 pmol BigDye modified M13 primer, 0.5 U hot-start Taq-polymerase (Viva Taq-polymerase from Novazym, Poznań, Poland), 140 μM of each deoxynucleotide, and 15-20 ng of template DNA.…”

“…Over the past 15 years, a large number of molecular markers for rye have been elucidated by constructing molecular maps [2][3][4][5][6][7][8][9][10][11][12][13]. Maps based on molecular markers are also suitable tools for mapping the genes and QTLs underlying agronomic traits [14][15][16][17][18][19].…”

Bioinformatics tools for development of fast and cost effective simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs)

“…The tool is written in Perl and is therefore platform independent, but it requires as installation of Primer3 for primer search (Thiel et al, 2003). MISA has been applied for SSR identification in coffee (Aggarwal et al, 2007), barley (Thiel et al, 2003;Kota et al, 2001), wheat (Yu et al, 2004), rye (Khlestkina et al, 2004) and peanut (Liang et al, 2009). Another SSR search tool called as 'Repeat Finder' (Volfovsky et al, 2001) (http://www.cbcb.umd.edu/software/RepeatFinder/) finds SSRs in four steps.…”