ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2007
Single nucleotide polymorphisms in rye (Secale cereale L.): discovery, frequency, and applications for genome mapping and diversity studies.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Article
- Article
- Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions.BMC genomics · 2020Article
- Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye.PloS one · 2019Article
- Phylogeny and genetic structure in the genus Secale.PloS one · 2018Article
- Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane.Plant cell reports · 2016Article
- Molecular Diversity of Seed-borne Fusarium Species Associated with Maize in India.Current genomics · 2016Article
- Geographical distribution of genetic diversity in Secale landrace and wild accessions.BMC plant biology · 2016Article
- Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.PloS one · 2015Article
- Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea.PloS one · 2014Article
- High Variation in Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (Indels) in the Highly Invasive Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Middle East-Asia Minor 1 (MEAM1).Neotropical entomology · 2013Article
- Functional markers in wheat: current status and future prospects.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Review
- Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci.BMC plant biology · 2012Article
- Article
- Article
- Anthocyanin biosynthesis genes location and expression in wheat-rye hybrids.Molecular genetics and genomics : MGG · 2009Article
- Physical analysis of the complex rye (Secale cereale L.) Alt4 aluminium (aluminum) tolerance locus using a whole-genome BAC library of rye cv. Blanco.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- A set of EST-SNPs for map saturation and cultivar identification in melon.BMC plant biology · 2009Article
- Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- A SNP transferability survey within the genus Vitis.BMC plant biology · 2008Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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 (pi) 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.