ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2018
A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 39 citations in OpenAlex.
- Identification of SNPs and Candidate Genes Associated with Major Drought Tolerance QTL on Wheat Chromosome 4A.Plants (Basel, Switzerland) · 2026Article
- Elucidation of theFrontiers in plant science · 2026Article
- Crown rot in wheat: pathogen biology, host responses, and management strategies.Stress biology · 2025Review
- Plasticity of Root System Architecture and Whole Transcriptome Responses Underlying Nitrogen Deficiency Tolerance Conferred by a Wild Emmer Wheat QTL.Plant, cell & environment · 2025Article
- Transcriptomic insights into shared responses to Fusarium crown rot infection and drought stresses in bread wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley by exploiting near isogenic lines, transcriptome profiling, and a large near isogenic line-derived population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Transcriptome profiling at the transition to the reproductive stage uncovers stage and tissue-specific genes in wheat.BMC plant biology · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Fine mapping of theFrontiers in plant science · 2022Article
- Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat.Frontiers in plant science · 2022Article
- Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance.BMC plant biology · 2021Article
- Identification of a novel genomic region associated with resistance to Fusarium crown rot in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Loci associated with variation in gene expression and growth in juvenile salmon are influenced by the presence of a growth hormone transgene.BMC genomics · 2020Article
- Validation and delineation of a locus conferring Fusarium crown rot resistance on 1HL in barley by analysing transcriptomes from multiple pairs of near isogenic lines.BMC genomics · 2019Article
- Development of tightly linked markers and identification of candidate genes for Fusarium crown rot resistance in barley by exploiting a near-isogenic line-derived population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Multiple Near-Isogenic Lines Targeting a QTL Hotspot of Drought Tolerance Showed Contrasting Performance Under Post-anthesis Water Stress.Frontiers in plant science · 2019Article
- Transcriptome analysis reveals potential mechanisms for different grain size between natural and resynthesized allohexaploid wheats with near-identical AABB genomes.BMC plant biology · 2018Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
key messageThis study demonstrates how identification of genes underpinning disease-resistance QTL based on differential expression and SNPs can be improved by performing transcriptomic analysis on multiple near isogenic lines. Transcriptomic analysis has been widely used to understand the genetic basis of a trait of interest by comparing genotypes with contrasting phenotypes. However, these approaches identify such large sets of differentially expressed genes that it proves difficult to isolate which genes underpin the phenotype of interest. This study tests whether using multiple near isogenic lines (NILs) can improve the resolution of RNA-seq-based approaches to identify genes underpinning disease-resistance QTL. A set of NILs for a major effect Fusarium crown rot-resistance QTL in barley on the 4HL chromosome arm were analysed under Fusarium crown rot using RNA-seq. Differential gene expression and single nucleotide polymorphism detection analyses reduced the number of putative candidates from thousands within individual NIL pairs to only one hundred and two genes, which were differentially expressed or contained SNPs in common across NIL pairs and occurred on 4HL. Our findings support the value of performing RNA-seq analysis using multiple NILs to remove genetic background effects. The enrichment analyses indicated conserved differences in the response to infection between resistant and sensitive isolines suggesting that sensitive isolines are impaired in systemic defence response to Fusarium pseudograminearum.
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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.