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Small RNAs as important regulators for the hybrid vigour of super-hybrid rice

ABSTRACT: Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis.

ORGANISM(S): Oryza sativa

PROVIDER: GSE51468 | GEO | 2014/08/17

SECONDARY ACCESSION(S): PRJNA223270

REPOSITORIES: GEO

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Small RNAs as important regulators for the hybrid vigour of super-hybrid rice

Project description:Heterosis is an important biological phenomenon; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents using high-throughput sequencing technology, and identified 355 distinct mature microRNAs and trans-acting small interfering RNAs, 69 of which were differentially expressed sRNAs (DES) between the hybrid and the mid-parental value. Among these, 34 DES were predicted to target 176 transcripts, of which 112 encoded 94 transcription factors. Further analysis showed that 67.6% of DES expression levels were negatively correlated with their target mRNAs either in flag leaves or panicles. The target genes of DES were significantly enriched in some important biological processes, including the auxin signalling pathway, in which existed a regulatory network mediated by DES and their targets, closely associated with plant growth and development. Overall, 20.8% of DES and their target genes were significantly enriched in quantitative trait loci of small intervals related to important rice agronomic traits including growth vigour, grain yield, and plant architecture, suggesting that the interaction between sRNAs and their targets contributes to the heterotic phenotypes of hybrid rice. Our findings revealed that sRNAs might play important roles in hybrid vigour of super-hybrid rice by regulating their target genes, especially in controlling the auxin signalling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis. We constructed six sRNA sequencing libraries and six mRNA sequencing libraries of flag leaves and panicles of the super-hybrid rice Liangyou-pei9 (LYP9) combination at the grain-filling stage. The above hybrid rice combination includes F1 hybrid LYP9 and its parental lines including the male-sterile line Peiai64s (PA64s) and the restorer line 93-11.

2014-08-17 | E-GEOD-51468 | biostudies-arrayexpress

Gene Expression of a Hybrid Rice Strain(LYP9) and Its Parental Cultivars

Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE We constructed nine SAGE libraries parallelly, including root at the first tillering stage, leaf at the milky stage of rice grain maturation, and panicle at the pollen-maturing stage of hybrid rice (LYP9) and its paternal lines (9311, PA64s).

2007-06-07 | E-GEOD-8048 | biostudies-arrayexpress

Gene Expression of a Hybrid Rice Strain(LYP9) and Its Parental Cultivars

2007-06-08 | GSE8048 | GEO

Rice Hybrid Weakness is Caused mainly by the Enhanced Stress-Response

Project description:Hybrid weakness is a type of reproductive barrier found in many plant species and is important to plant evolution. Compared with heterosis, hybrid weakness has received less attention in evolutionary genetics studies. In rice, the hybrid weakness of the F1 progenies between the Jamaica- and temperate Japonica-types has been intensively genetically surveyed, and it has been found to be controlled by two complementary genes, Hwc1 and Hwc2. The defective development of the hybrid F1 seedlings was found to be mainly due to abnormal root growth, resulting in non-continuous growth and the eventual lethality of the plants. Detailed genome-wide analyses using the hybrid F1 plant and parents showed that, in contrast to heterosis, in which photosynthesis- and starch metabolism-related genes are preferentially expressed, the abscisic acid (ABA)-response and abiotic-/biotic- and defense-related genes were significantly up-regulated in the roots of the hybrid F1, resulting in suppressed growth of the whole plant. This indicates that the mechanisms of heterosis and hybrid weakness differ and provides informative clues to facilitate the understanding of the mechanisms controlling the reproductive isolation and hybrid weakness.

2015-02-03 | GSE24977 | GEO

Project description:Heterosis has long been exploited for crop breeding; however, the genetic mechanisms, particularly the initial establishment of heterosis during the early vegetative growth phase, remain elusive. The biggest challenge for that is to exclude noise genes from the identified heterosis-related candidates. Herein, we use nutrient-deficient hybrid with no measurable growth heterosis as control to filter potential background noise differentially expressed genes In this dataset, we compared the differentially expressed genes in both heterotic and non-heterotic hybrid. After filtering these irrelevant genes, only 336 differentially expressed genes (DEGs), which is significantly lower than those of previous reports, were identified as heterosis-related genes in a super hybrid rice of Liang-You-Pei-Jiu (LYP9) at early-tillering stage

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Positive feedback between TOR singling, energy metabolism and lysine acetylation drives heterosis in elite hybrid rice

Project description:Heterosis refers to the superior performance of the hybrid compared with its parental lines. Despite several genetic models and different molecular pathways proposed to explain heterosis, it remains unclear how hybrid cells integrate complementary gene expression, metabolic accumulation and/or hormone signaling to drive heterotic growth. In this work, using integrative omics combined with biochemical analyses, we uncovered an enhanced TORC1 signaling in the elite hybrid rice Shanyou 63 (SY63) relative to the parental lines, which was associated with accumulation of growth-promoting (translation, cell division) and energy metabolic (glycolysis and TCA) proteins, enhanced energy metabolic activities, increased histone H3 and cellular protein lysine acetylation, and superior growth of the panicle meristem. Metabolism of nuclear-cytosolic acetyl-Coenzyme A was also enhanced in the hybrid, which paralleled with increases of histone H3 acetylation to selectively target growth-promoting and metabolic genes expression. Lysine acetylation of cellular proteins including TORC1, ribosomal proteins, and energy metabolic enzymes was also augmented and/or remodeled, potentially modulating their activities. The data indicate that the positive feedback loop between TOR-signaling, energy-producing metabolic activity, lysine acetylation, and growth-promoting gene expression is a mechanism underling the superior growth rate of the hybrid. The results imply that any enhanced activity within the loop would drive and sustain the TOR signaling to promote superior growth of hybrids, which may represent a general mechanistic model for heterosis.

2023-10-24 | PXD035495 | Pride

Positive feedback between TOR singling,energy metabolism and lysine acetylation drives heterosis in elite hybrid rice

Project description:Heterosis refers to the superior performance of the hybrid compared with its parental lines. Despite several genetic models and different molecular pathways proposed to explain heterosis, it remains unclear how cells integrate complementary gene expression, metabolic accumulation and/or hormone signaling to drive heterotic growth. In this work, using multiple omics combined with biochemical analyses, we showed an enhanced TORC1 signaling of the elite hybrid rice Shanyou 63 (SY63) relative to the parental lines, which was associated with accumulation of growth-promoting (translation, cell division) and energy metabolic (glycolysis and TCA) proteins energy metabolic activities, and superior growth of panicle meristem. Metabolism of nuclear-cytosolic acetyl-Coenzyme A was also enhanced in the hybrid, which paralleled with increases of histone H3 acetylation to selectively target growth-promoting and metabolic genes expression. Lysine acetylation of cellular proteins including TORC1, ribosomal proteins, and energy metabolic enzymes was also augmented and/or remodeled, potentially modulating their activities. The data revealed that the positive feedback loop between TOR-signaling, energy-producing metabolic activity, lysine acetylation, and growth-promoting gene expression is a mechanism underling the superior growth rate of the hybrid. The results implied that an enhanced activity in hybrids would drive and sustain the TOR signaling feedback loop to promote superior growth, which may represent a general mechanistic model for heterosis.

2023-10-24 | PXD035543 | Pride

Distinct small RNA populations act antagonistically in formation of heterosis

Project description:This research reports the analysis of sRNAs in 14 and 7 inbred lines from a breeding population. We analyzed the contribution of sRNAs to the formation of heterosis via integrative association analysis with field data of 98 hybrids generated from the set of inbred lines. Our results indicate a contribution of sRNAs to heterosis. We were able to identify different sets of sRNAs associated with heterosis with distinct length and genome distribution patterns. Analysis of sRNA contribution to the formation of heterosis in maize by an association study in a breeding population.

2016-10-24 | E-GEOD-51662 | biostudies-arrayexpress

Role of the Snf2-Related Protein required to maintain repression1 (RMR1) in Heterosis

Project description:Combining dissimilar parents often leads to increased vigor in the hybrid offspring. “Heterosis” describes both this behavior and its underlying Mendelian and non-Mendelian interactions [1], although its molecular basis remains largely unknown. Recent comparisons of small RNA (sRNA) profiles from parents and their heterotic progeny identified correlations between interparental 24-nucleotide (24-nt) RNA variation and non-additive 24-nt RNA changes in the resulting hybrid [2,3]. 24-nt RNAs guide de novo cytosine methylation, and several proteins are required for their biogenesis, including a Snf2-like ATPase: required to maintain repression1 (RMR1) [4]. We found height variation between heterotic hybrids +/- RMR1 activity, implicating a role for RMR1 in heterosis. Based on the published correlations mentioned above [2,3], we hypothesized that RMR1-loss reduces parental sRNAs, altering their relative ratios and changing the sRNA profiles in the resulting hybrid from those of a standard hybrid (from +RMR1 parents). To probe this hypothesis, we profiled sRNAs from parents and hybrids +/- RMR1 function, limiting the parental diversity to only portions of chromosomes 6 and 9. Our analysis will address how RMR1 loss changes hybrid sRNAs in the presence and absence of underlying genetic variation and help to determine how this loss results in different phenotypic outcomes from heterotic crosses. 1. Shull (1948) Genetics 2. Groszmann et al (2011) PNAS 3. Barber et al (2012) PNAS 4. Hale et al (2007) PLoS Biology

2014-06-04 | GSE52103 | GEO

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Project description:Purpose:The purpose of this study is to explore the transcriptome analysis of the heterosis of the grain type and grain weight of the super rice WFYT025 hybrid combination at the grain filling stage.

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