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

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Relation http://oar.icrisat.org/3026/
http://dx.doi.org/10.1007/s00122-007-0504-6
 
Title Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies
 
Creator Varshney, R K
Beier, U
Khlestkina, K E
Kota, R
Korzun, V
Graner, A
Borner, A
 
Subject Genetics and Genomics
 
Description 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.
 
Publisher Springer Verlag
 
Date 2007
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
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Identifier http://oar.icrisat.org/3026/1/Single_nucleotide_polymorphisms_in_rye_%28Secale_cereale_L.discovery%2C_frequency%2C_and_applications_for_genome_mapping_and_diversity_studies.pdf
Varshney, R K and Beier, U and Khlestkina, K E and Kota, R and Korzun, V and Graner, A and Borner, A (2007) Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies. TAG Theoretical and Applied Genetics, 114. pp. 1105-1116.