ArticleBMC plant biology2007
Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne.
Article in BMC plant biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 67 citations in OpenAlex.
- A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species.Molecular ecology resources · 2022Article
- Insights into the Response of Perennial Ryegrass to Abiotic Stress: Underlying Survival Strategies and Adaptation Mechanisms.Life (Basel, Switzerland) · 2022Review
- Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass.Genes · 2021Article
- Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Low pyrrolizidine alkaloid levels in perennial ryegrass is associated with the absence of a homospermidine synthase gene.BMC plant biology · 2018Article
- An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping.Frontiers in plant science · 2018Article
- An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly.Annals of botany · 2016Article
- Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility.PloS one · 2016Article
- Using a Candidate Gene-Based Genetic Linkage Map to Identify QTL for Winter Survival in Perennial Ryegrass.PloS one · 2016Article
- A horizontally transferred nuclear gene is associated with microhabitat variation in a natural plant population.Proceedings. Biological sciences · 2015Article
- Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice.Scientific reports · 2015Article
- Population Structure, Genetic Variation, and Linkage Disequilibrium in Perennial Ryegrass Populations Divergently Selected for Freezing Tolerance.Frontiers in plant science · 2015Article
- Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.PloS one · 2015Article
- The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution.Nature genetics · 2013Article
- Association of candidate genes with drought tolerance traits in diverse perennial ryegrass accessions.Journal of experimental botany · 2013Article
- Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots.PloS one · 2013Article
- Association study between the gibberellic acid insensitive gene and leaf length in a Lolium perenne L. synthetic variety.BMC plant biology · 2011Article
- Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice.Molecular genetics and genomics : MGG · 2011Article
- High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response.BMC plant biology · 2011Article
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5 authors at 1 institution in 1 country.
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Abstract
backgroundAssociation analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses.
results11 expressed disease resistance candidate (R) genes including 6 nucleotide binding site and leucine rich repeat (NBS-LRR) like genes and 5 non-NBS-LRR genes were analyzed for nucleotide diversity. For each of the genes about 1 kb genomic fragments were isolated from 20 heterozygous genotypes in ryegrass. The number of haplotypes per gene ranged from 9 to 27. On average, one single nucleotide polymorphism (SNP) was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed a high degree of nucleotide diversity, with one SNP every 22 bp between two randomly sampled sequences. NBS-LRR like gene fragments showed very high non-synonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with on average one SNP every 10 bp between two sequences. In contrast, non-NBS LRR resistance candidate genes showed a lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency (<5%) within the collection of 20 genotypes. Low intragenic LD was detected for most R genes, and rapid LD decay within 500 bp was detected.
conclusionSubstantial LD decay was found within a distance of 500 bp for most resistance candidate genes in this study. Hence, LD based association analysis is feasible and promising for QTL fine mapping of resistance traits in ryegrass.
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