ArticleRice (New York, N.Y.)2016
Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs.
Article in Rice (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 18 citations in OpenAlex.
- Impact of Allele-Specific Expression on Ripening and Quality Characteristics of ABB Banana Fruit.International journal of molecular sciences · 2025Article
- STW-MD: a novel spatio-temporal weighting and multi-step decision tree method for considering spatial heterogeneity in brain gene expression data.Briefings in bioinformatics · 2024Article
- Article
- Allele expression biases in mixed-ploid sugarcane accessions.Scientific reports · 2022Article
- Unraveling regulatory divergence, heterotic malleability, and allelic imbalance switching in rice due to drought stress.Scientific reports · 2021Article
- Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera).Plant molecular biology · 2021Article
- The disadvantages of being a hybrid during drought: A combined analysis of plant morphology, physiology and leaf proteome in maize.PloS one · 2017Article
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14 authors at 5 institutions in 4 countries.
Funding
Abstract
backgroundInformation on the effect of stress on the allele-specific expression (ASE) profile of rice hybrids is limited. More so, the association of allelically imbalanced genes to important traits is yet to be understood. Here we assessed allelic imbalance (AI) in the heterozygote state of rice under non- and water-stress treatments and determined association of asymmetrically expressed genes with grain yield (GY) under drought stress by in-silico co-localization analysis and selective genotyping. The genotypes IR64, Apo and their F1 hybrid (IR64 × Apo) were grown under normal and water-limiting conditions. We sequenced the total RNA transcripts for all genotypes then reconstructed the two chromosomes in the heterozygote.
resultsWe are able to estimate the transcript abundance of and the differential expression (DE) between the two parent-specific alleles in the rice hybrids. The magnitude and direction of AI are classified into two categories: (1) symmetrical or biallelic and (2) asymmetrical. The latter can be further classified as either IR64- or Apo-favoring gene. Analysis showed that in the hybrids grown under non-stress conditions, 179 and 183 favor Apo- and IR64-specific alleles, respectively. Hence, the number of IR64- and Apo-favoring genes is relatively equal. Under water-stress conditions, 179 and 255 favor Apo- and IR64-specific alleles, respectively, indicating that the number of allelically imbalanced genes is skewed towards IR64. This is nearly 40-60 % preference for Apo and IR64 alleles, respectively, to the hybrid transcriptome. We also observed genes which exhibit allele preference switching when exposed to water-stress conditions. Results of in-silico co-localization procedure and selective genotyping of Apo/IR64 F3:5 progenies revealed significant association of several asymmetrically expressed genes with GY under drought stress conditions.
conclusionOur data suggest that water stress skews AI on a genome-wide scale towards the IR64 allele, the cross-specific maternal allele. Several asymmetrically expressed genes are strongly associated with GY under drought stress which may shed hints that genes associated with important traits are allelically imbalanced. Our approach of integrating hybrid expression analysis and QTL mapping analysis may be an efficient strategy for shortlisting candidate genes for gene discovery.
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