In Arabidopsis hybrids and Hybrid Mimics up-regulation of cell wall biogenesis is associated with increased plant size
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE131682 | GEO | 2019/11/07
REPOSITORIES: GEO
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Project description:F1 hybrids in Arabidopsis and crops species are uniform and high yielding. The F2 generation loses much of the yield advantage and the plants have heterogeneous phenotypes. We generated pure breeding Hybrid Mimic lines by recurrent selection and also selected a pure breeding Small phenotype line. The Hybrid Mimics are almost completely homozygous with chromosome segments from each parent. Four particular chromosomal segments from C24 and eight from Ler were present in all of the Hybrid Mimic lines whereas in the F6 Small phenotype line the 12 segments were each derived from the alternative parent. Loci critical for promoting hybrid vigor may be contained in each of these 12 conserved segments. We have identified genes with similar altered expression in Hybrid Mimics and F1 plants but not in the Small phenotype line. These genes may be critical for the generation of hybrid vigour. Analysis of transcriptomes indicated that increased expression of the transcription factor PHYTOCHROME-INTERACTING FACTOR (PIF4) may contribute to hybrid vigor by targeting the auxin biosynthesis gene YUCCA8 and the auxin signalling gene IAA29. A number of auxin responsive genes promoting leaf growth were upregulated in the F1 hybrids and Hybrid Mimics suggesting increased auxin biosynthesis and signaling contribute to the hybrid phenotype. The Hybrid Mimic seeds had earlier germination as did the seeds of the F1 hybrids indicating co-segregation of the genes for rosette size and the germination trait. Early germination may be an indicator of vigorous hybrids.
2017-04-05 | GSE94547 | GEO
Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased. Whole plants in Col, C24, and their F1 hybrids with two replications
2012-03-06 | E-GEOD-36273 | biostudies-arrayexpress
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: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
Project description:Heterosis, a phenomenon where hybrids exhibit superior performance in various traits such as yield, quality, and resistance compared to their parents, has long been a focus of agricultural research. Although tobacco biomass significantly affects tobacco yield and economic profitability, the underlying reasons for the dominance of tobacco biomass hybrids and their formation remain unclear. To address this, we selected 5 tobacco varieties (lines) with large differences in tobacco biomass as the parents and formulated F1 hybrids to analyze the expression of tobacco biomass heterosis. Our findings demonstrate that tobacco leaf biomass exhibits a clear heterosis advantage. In particular, the hybrid Va116×GDH94 showed strong heterosis, with 76.69% of differentially expressed genes (DEGs) displaying Overdominant expression pattern. Notably, these Overdominant DEGs were significantly enriched in biological processes such as photosynthesis and respiration. During photosynthesis, transgressive up-regulation of Lhc improved light-harvesting efficiency, while the up-regulation of Psa and Psb in the photosystem enhanced the defense of chloroplasts against strong light. Additionally, the up-regulation of rbcl promoted the increase of photosynthetic products in the hybrids. During respiration, the down-regulation of MDH, ACO, and OGDH suppressed the tricarboxylic acid cycle (TCA cycle) and weakened respiratory consumption in the hybrids. Furthermore, we observed that the net photosynthetic rate and intercellular CO2 concentration of the hybrids were significantly higher than those of the parents. Taken together, our results suggest that the overdominant expression effect of DEGs plays a crucial role in the formation of tobacco biomass hybrid advantage. The overdominant expression effect of photosynthesis and respiration-related genes enhanced the photosynthetic capacity of the hybrids, reduced respiration consumption, and promoted the increase of tobacco biomass, thus demonstrating the obvious hybrid advantage.
2024-01-01 | GSE252097 | GEO
Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of small RNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.
2011-12-22 | E-GEOD-34656 | biostudies-arrayexpress
Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of mRNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.
2011-12-22 | E-GEOD-34655 | biostudies-arrayexpress
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 âlike phenotype, we have by recurrent selection produced pure breeding F5/F6 lines âHybrid Mimicsâ, 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 - 150μmol 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 - 150μmol 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 - 150μmol 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-64742 | biostudies-arrayexpress
Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor.
2011-12-22 | GSE34656 | GEO