ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2018
Transcriptome-referenced association study of clove shape traits in garlic.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 39 citations in OpenAlex.
- A single-cell transcriptomic atlas reveals the cell differentiation trajectory and the response to virus invasion in swelling clove of garlic.Horticulture research · 2025Article
- Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel.Journal of advanced research · 2024Article
- Molecular Mechanism Underlying thePlants (Basel, Switzerland) · 2023Article
- Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Horticulture research · 2023Article
- Large-scale population structure and genetic architecture of agronomic traits of garlic.Horticulture research · 2023Article
- Turning Garlic into a Modern Crop: State of the Art and Perspectives.Plants (Basel, Switzerland) · 2023Review
- A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges.Current research in food science · 2023Review
- Full-length fruit transcriptomes of southern highbush (Vaccinium sp.) and rabbiteye (V. virgatum Ait.) blueberry.BMC genomics · 2022Article
- Combination analysis of single-molecule long-read and Illumina sequencing provides insights into the anthocyanin accumulation mechanism in an ornamental grass, Pennisetum setaceum cv. Rubrum.Plant molecular biology · 2022Article
- A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population.PLoS genetics · 2022Article
- Molecular Cloning and Functional Characterization of Heat Stress-Responsive Superoxide Dismutases in Garlic (Antioxidants (Basel, Switzerland) · 2021Article
- Parallel analysis of global garlic gene expression and alliin content following leaf wounding.BMC plant biology · 2021Article
- Transcriptome analysis and genetic diversity ofMitochondrial DNA. Part B, Resources · 2021Article
- A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield.BMC plant biology · 2020Article
- PacBio single-molecule long-read sequencing shed new light on the transcripts and splice isoforms of the perennial ryegrass.Molecular genetics and genomics : MGG · 2020Article
- De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweedPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Article
- Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum).BMC genomics · 2019Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.
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Registered trials
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.