ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 20 citations in OpenAlex.
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- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses.Molecular biology and evolution · 2023Article
- A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species.Molecular ecology resources · 2022Article
- High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.Nature communications · 2022Article
- Identification of the genes atFrontiers in plant science · 2022Article
- Seasonal Differences in Structural and Genetic Control of Digestibility in Perennial Ryegrass.Frontiers in plant science · 2021Article
- High-Throughput Genome-Wide Genotyping To Optimize the Use of Natural Genetic Resources in the Grassland Species Perennial Ryegrass (G3 (Bethesda, Md.) · 2020Article
- HapAsmbl: A reference-aided pipeline for assembling haplotypes in Nanopore amplicon sequence data of polymorphic populations.Applications in plant sciencesArticle
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions. To overcome challenges of variant calling in heterogeneous outbreeding species, we used two complementary strategies to explore sequence diversity. First, four variant calling pipelines were integrated with the VariantMetaCaller to reach maximal sensitivity. Additional multiplex amplicon sequencing was used to empirically estimate an appropriate precision threshold. Second, a de novo assembly strategy was used to reconstruct divergent alleles for each gene. The advantage of this approach was illustrated by discovery of 28 novel alleles of LpSDUF247, a polymorphic gene co-segregating with the S-locus of the grass self-incompatibility system. Our approach is applicable to other genetically diverse outbreeding species. The resulting collection of functionally annotated variants can be mined for variants causing phenotypic variation, either through genetic association studies, or by selecting carriers of rare defective alleles for physiological analyses.
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