ArticleBMC genomics2019
Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- The role of methylation and structural variants in shaping the recombination landscape of barley.The Plant journal : for cell and molecular biology · 2026Article
- The potential of considering photosynthesis parameters in crop yield breeding by genomic prediction.Journal of experimental botany · 2026Article
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- Genetic enhancement of root, tuber and cereal crops via pangenomics, multi-omics integration and AI-driven prediction.Frontiers in plant science · 2026Review
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- Assessment of genomic prediction capabilities of transcriptome data in a barley multi-parent RIL population.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Integrating Gene Expression Data into Single-Step Method (ssBLUP) Improves Genomic Prediction Accuracy for Complex Traits of Duroc × Erhualian FCurrent issues in molecular biology · 2024Article
- Exploring natural genetic variation in photosynthesis-related traits of barley in the field.Journal of experimental botany · 2024Article
- Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley.Journal of experimental botany · 2024Article
- Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: A case study in barley.Plant biotechnology journal · 2023Article
- Comparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.BMC biology · 2023Article
- The double round-robin population unravels the genetic architecture of grain size in barley.Journal of experimental botany · 2022Article
- Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
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- Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes.Plant biotechnology journal · 2022Article
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- Investigating the Transcriptomic and Expression Presence-Absence Variation Exist in Japanese Eel (Anguilla japonica), a Primitive Teleost.Marine biotechnology (New York, N.Y.) · 2021Article
- Merging Genomics and Transcriptomics for Predicting Fusarium Head Blight Resistance in Wheat.Genes · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBarley is the world's fourth most cultivated cereal and is an important crop model for genetic studies. One layer of genomic information that remains poorly explored in barley is presence/absence variation (PAV), which has been suggested to contribute to phenotypic variation of agronomic importance in various crops.
resultsAn mRNA sequencing approach was used to study genomic PAV and transcriptomic variation in 23 spring barley inbreds. 1502 new genes identified here were physically absent from the Morex reference sequence, and 11,523 previously unannotated genes were not expressed in Morex. The procedure applied to detect expression PAV revealed that more than 50% of all genes of our data set are not expressed in all inbreds. Interestingly, expression PAV were not in strong linkage disequilibrium with neighboring sequence variants (SV), and therefore provided an additional layer of genetic information. Optimal combinations of expression PAV, SV, and gene abundance data could enhance the prediction accuracy of predicting three different agronomic traits.
conclusionsOur results highlight the advantage of mRNA sequencing for genomic prediction over other technologies, as it allows extracting multiple layers of genomic data from a single sequencing experiment. Finally, we propose low coverage mRNA sequencing based characterization of breeding material harvested as seedlings in petri dishes as a powerful and cost efficient approach to replace current single nucleotide polymorphism (SNP) based characterizations.
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