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

Abstract

To elucidate the potential of single nucleotide polymorphism (SNP) markers in rye, a set of 48 barley EST (expressed sequence tag) primer pairs was employed to amplify from DNA prepared from five rye inbred lines. A total of 96 SNPs and 26 indels (insertion-deletions) were defined from the sequences of 14 of the resulting amplicons, giving an estimated frequency of 1 SNP per 58 bp and 1 indel per 214 bp in the rye transcriptome. A mean of 3.4 haplotypes per marker with a mean expected heterozygosity of 0.66 were observed. The nucleotide diversity index (p) was estimated to be in the range 0.0059-0.0530. To improve assay cost-effectiveness, 12 of the 14 SNPs were converted to a cleaved amplified polymorphic sequence (CAPS) format. The resulting 12 SNP loci mapped to chromosomes 1R, 3R, 4R, 5R, 6R, and 7R, at locations consistent with their known map positions in barley. SNP genotypic data were compared with genomic simple sequence repeat (SSR) and EST-derived SSR genotypic data collected from the same templates. This showed a broad equivalence with respect to genetic diversity between these different data types.

Developing SNP markers and DNA typing using multiplexed single nucleotide primer extension (SNuPE) in Paraserianthes falcataria

“…SNPs provided convictive evidence for human forensic analysis (Brandstatter et al 2003, Vallone et al 2004, for identification and paternity analysis in animals (Heaton et al 2002, Werner et al 2004, Rohrer et al 2007, and for various applications in plants (Jin et al 2003, Batley et al 2003, Jones et al 2007, Osman et al 2003, Varshney et al 2007, Germano and Klein, 1999, Gros-Louis et al 2005. Because of its low information content, however, approximately three times as many SNPs are needed than SSRs for linkage studies, parentage testing and individual identification (Aitken et al 2004, Brumfield et al 2003.…”

Cytological dissection and molecular characterization of chromosome 1R derived from 'Burgas 2' common wheat

“…These dissection lines would be useful in the construction of detailed cytological maps of chromosome 1R when more markers like the ESTs and EST-based markers (e.g. SNPs) used for wheat and barley chromosome mapping (Varshney et al, 2007) become available. Although we need to select critical plants in the progeny of the hemizygous dissection lines, we can easily do so by PCR analysis using some of the markers used in this study, as well as by GISH/ FISH.…”

Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping

“…The approach has been used for assaying SNPs in many crop species, e.g. chickpea (Varshney et al 2007d;Rajesh and Muehlbauer 2008), rye (Varshney et al 2007a), rice (Komuri and Nitta 2005). Development of SNP markers and their optimization into CAPS assay is underway at ICRISAT (Reddy et al unpublished).…”

“…When these markers are used in the genetic diversity studies, they assay the functional genetic variation in the germplasm collection and therefore can be used for allele mining and association genetics studies. Due to their origin from conserved proportion of the genome, gene-based markers of a species can be used in related species for a variety of applications including enhancing the density of genetic maps (Varshney et al 2007a) and understanding the genome relationships and evolution ). The utility of gene-based markers has been illustrated in selected two areas in following sections.…”