Hybrid performance in maize predicted with combinations of omics data
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE106098 | GEO | 2017/10/31
SECONDARY ACCESSION(S): PRJNA416346
REPOSITORIES: GEO
Similar Datasets
Project description:Hybrid performance in maize predicted with combinations of omics data
| PRJNA416346 | ENA
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
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.
2014-08-17 | GSE51468 | GEO
Project description:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement.
2007-10-01 | GSE2771 | GEO
Project description:Hybrid breeding is of economic importance in agriculture for increasing yield, yet the basis of the heterosis is not well understood. In Arabidopsis, crosses between different accessions produce hybrids with varied levels of heterosis relative to parental phenotypes in biomass. In all hybrids the advantages of the F1 hybrid is lost in the F2 for both phenotypic uniformity and yield gain. Success in generating F5/F6 Hybrid Mimic from the cross between C24 and Landsberg erecta (Ler) demonstrated that the large plant phenotype of the F1 hybrids can be stabilized. Hybrid Mimics selection was applied to Wassilewskija (Ws)/Ler and Col/Ler hybrids. The two hybrids showing different levels of heterosis. At 30 DAS, the Col/Ler hybrid generated Hybrid Mimics with rosette diameter and fresh weight equivalent to the F1 hybrid; Ws/Ler Hybrid Mimics outperformed the F1 hybrids in both the rosette size and biomass. Transcriptome analysis revealed up-regulation of cell wall biosynthesis and expansion genes could be a common pathway in increased size in Arabidopsis hybrids and Hybrid Mimics. Intercross of two independent Hybrid Mimic lines can further increase the biomass gain. Our results encourage the use of Hybrid Mimics for breeding and for investigating the molecular basis of heterosis.
2019-11-07 | GSE131682 | GEO
Project description:Recent advances in single cell RNA sequencing allow users to pool multiple samples into one run and demultiplex in downstream analysis, greatly increasing the experimental efficiency and cost-effectiveness. However, the expensive reagents for cell labeling, limited pooling capacity, non-ideal cell recovery rate and calling accuracy remain great challenges for this approach. To date, there are two major demultiplexing methods, antibody-based cell hashing and Single Nucleotide Polymorphism (SNP)-based genomic signature profiling, and each method has advantages and limitations. Here, we propose a hybrid demultiplexing strategy that increases calling accuracy and cell recovery at the same time. We first develop a computational algorithm that significantly increases calling accuracy of cell hashing. Next, we cluster all single cells based on their SNP profiles. Finally, we integrate results from both methods to make corrections and retrieve cells that are only identifiable in one method but not the other. By testing on several real-world datasets, we demonstrate that this hybrid strategy combines advantages of both methods, resulting in increased cell recovery and calling accuracy at lower cost.
2024-05-29 | GSE230810 | GEO
Project description:F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1 –like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines “Hybrid Mimics”, in which the characteristics of the F1 Hybrid are stabilized. These Hybrid Mimic lines, like the F1 Hybrid, have larger leaves than the parent plant, the leaves having increased photosynthetic cell numbers, and in some lines increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 Hybrid with those of eight Hybrid Mimic lines has identified metabolic pathways altered in both; these pathways include down regulation of defense response pathways and altered abiotic response pathways. F6 Hybrid Mimic lines are mostly homozygous at each locus in the genome yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of trans-regulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding Hybrid Mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.
2015-08-17 | GSE64742 | GEO
Project description:F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1 –like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines “Hybrid Mimics”, in which the characteristics of the F1 Hybrid are stabilized. These Hybrid Mimic lines, like the F1 Hybrid, have larger leaves than the parent plant, the leaves having increased photosynthetic cell numbers, and in some lines increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 Hybrid with those of eight Hybrid Mimic lines has identified metabolic pathways altered in both; these pathways include down regulation of defense response pathways and altered abiotic response pathways. F6 Hybrid Mimic lines are mostly homozygous at each locus in the genome yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of trans-regulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding Hybrid Mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture.
2015-08-17 | GSE64740 | GEO
Project description:The aim of this project is to promote the breath volatile marker concept for colorectal cancer (CRC) screening by advancing developing the application of a novel hybrid analyzer for the purpose.
The hybrid analyzer concept is expected to benefit of combining metal-oxide (MOX) and infrared spectrum (IR) sensor acquired data. The current study will be the first globally to address this concept in CRC detection. In addition, traditional methods, in particular, gas chromatography coupled to mass spectrometry (GC-MS) will be used to address the biological relevance of the VOCs emission from cancer tissue and will assist in further advances of the hybrid-sensing approach.
| 2399547 | ecrin-mdr-crc
Project description:F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor which form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants which have a F1like phenotype, we have by recurrent selection produced pure breeding F5/F6 linesHybrid Mimics, in which the characteristics of the F1 Hybrid are stabilized. These Hybrid Mimic lines, like the F1 Hybrid, have larger leaves than the parent plant, the leaves having increased photosynthetic cell numbers, and in some lines increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 Hybrid with those of eight Hybrid Mimic lines has identified metabolic pathways altered in both; these pathways include down regulation of defense response pathways and altered abiotic response pathways. F6 Hybrid Mimic lines are mostly homozygous at each locus in the genome yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of trans-regulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding Hybrid Mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture. Plant Materials: Seeds were sterilized and sown onto plates containing MSN medium (MS salts supplemented with 1% (w/v) sucrose, pH7 with KOH, 0.6% wt/vol Noble agar). After 2 days at 4°C, the plates were transferred to a growth room with conditions of 22°C/18°C (day/night) and 16h light/8h dark cycle under Philips Cool Daylight TLD 58W/840 fluorescent tubes providing a photosynthetic photon flux density of 130 - 150 umol photons m-2·s-1 as measured using a quantum meter (Model MQ-200 calibrated for electric light source, Apogee). At 18 days after sowing (DAS), the plants were transferred to soil and grown to the reproductive stage in a growth room with controlled light conditions (OSRAM L 36W/865 LumLux Daylight, 130 - 150 umol photons m-2·s-1). To minimize the edge effects, the positioning of both plates and trays on the shelves was rotated every two days. All the plants were grown under the condition described above unless specified. Plant sample preparation and RNA extraction: For the transcriptomes of 15 DAS plants, the aerial tissues of 15 day seedlings were sampled. For the transcriptomes of plants at 28 DAS, the four largest leaves of 28 day plants from the parental lines (C24, Ler), the reciprocal Hybrids and eight F4 Hybrid Mimic lines were harvested. Each sample comprised a pool of five plants. Two biological replicates of each sample were sequenced. Total RNA was isolated using QIAGEN RNeasy MiniKitTM following the product instructions. To eliminate variation in experimental conditions in different positions in the growth room, nine F4 plant lines were divided into two batches to ensure plants were grown on the same shelves in each experiment. Parental lines C24 and Ler and the F1 Hybrid from which the F4 lines derived from were grown under the same conditions in each experiment as controls. The first batch including samples C24 (RepA and RepB), Ler (RepA and RepB), C24 x Ler F1, F4-L1-1, F4-L1-2, F4-L2-1, F4-L2-2 and F4-S-1 were grown under the condition describe above, we also sampled the five smallest C24 seedlings and five smallest Ler seedlings among the population (n = 50); the mRNA sequencing was performed by the Australian Genome Research Facility (AGRF). The second batch including C24 (RepC and RepD), Ler (RepC and RepD), Ler x C24 F1 Hybrid, F4-L3-1, F4-L3-2, F4-L4-1 and F4-L4-2 were grown in the same light intensity as above but under different light tubes (SYLVANIA PREMIUM extra FL36W/865 Super Daylight deluxe light tube). For the transcriptome of the two F6 Hybrid Mimic lines at 15 DAS, C24, Ler, Ler x C24 F1 Hybrids and three siblings from each F6 line (L3-1-1-2 and L4-2-1-2) were grown on MS medium (MS salts supplemented with 1% (w/v) sucrose, pH 5.7 with KOH, add 0.6% wt/vol agar) with controlled light conditions (SYLVANIA PREMIUM extra FL36W/865 Super Daylight deluxe, 130 - 150 umol photons m-2·s-1). The mRNA sequencing service was provided by AGRF on the Illumina platform, 100bp paired ends.
2015-08-17 | E-GEOD-64740 | biostudies-arrayexpress