ArticleBMC plant biology2011
High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response.
Article in BMC plant biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Genome-wide analysis of genetic diversity in Anopheles darlingi from Rondônia State, Brazil.Communications biology · 2025Article
- The Evolution of Wisteria Vein Mosaic Virus: A Case Study Approach to Track the Emergence of New Potyvirus Threats.Pathogens (Basel, Switzerland) · 2024Article
- Unveiling the distinctive traits of functional rye centromeres: minisatellites, retrotransposons, and R-loop formation.Science China. Life sciences · 2024Article
- Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding.Plants (Basel, Switzerland) · 2022Review
- Association mapping of autumn-seeded rye (Secale cereale L.) reveals genetic linkages between genes controlling winter hardiness and plant development.Scientific reports · 2022Article
- Identification of New QTLs for Dietary Fiber Content inInternational journal of molecular sciences · 2022Article
- Genomic prediction of preliminary yield trials in chickpea: Effect of functional annotation of SNPs and environment.The plant genome · 2022Article
- Quantitative trait loci and candidate genes associated with freezing tolerance of winter triticale (× Triticosecale Wittmack).Journal of applied genetics · 2022Article
- Discovery of a novel powdery mildew (Blumeria graminis) resistance locus in rye (Secale cereale L.).Scientific reports · 2021Article
- Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel.Food and energy security · 2021Article
- Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Frontiers in plant science · 2021Article
- Deep sampling and pooled amplicon sequencing reveals hidden genic variation in heterogeneous rye accessions.BMC genomics · 2020Article
- Article
- Volatile composition and classification ofHorticulture research · 2019Article
- Article
- Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data.Frontiers in plant science · 2018Article
- Exploring new alleles for frost tolerance in winter rye.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- Geographical distribution of genetic diversity in Secale landrace and wild accessions.BMC plant biology · 2016Article
- A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population.Proceedings. Biological sciences · 2015Article
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7 authors.
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Abstract
backgroundRye (Secale cereale L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic diversity and the extent of linkage disequilibrium (LD) we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations.
resultsA total of 147 single nucleotide polymorphisms (SNPs) and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype diversity of candidate genes were high with average values π = 5.6 × 10(-3) and Hd = 0.59, respectively. According to an analysis of molecular variance (AMOVA), most of the genetic variation was found between individuals within populations. Haplotype frequencies varied markedly between the candidate genes. ScCbf14, ScVrn1, and ScDhn1 were dominated by a single haplotype, while the other 8 genes (ScCbf2, ScCbf6, ScCbf9b, ScCbf11, ScCbf12, ScCbf15, ScIce2, and ScDhn3) had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low.
conclusionsThe Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide diversity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.
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