Distinct small RNA populations act antagonistically in formation of heterosis
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE51662 | GEO | 2016/10/24
SECONDARY ACCESSION(S): PRJNA224580
REPOSITORIES: GEO
Similar Datasets
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
Project description:We have used genome-wide proteomic profiling to examine leaves of hybrids for molecular phenotypes. Profiles of the proteome of maize leaves revealed hybrid-specific differences in the chloroplast and mitochondria; levels of their energy transduction complexes and ribosomes were selectively elevated 10-20% above mid-parent levels. Each of these protein machines is comprised of nuclear-encoded and organelle-encoded subunits and we refer to them as digenomic protein complexes. Expression heterosis of the organelle ribosome proteins was quantitatively predictive of growth heterosis in a set of hybrids. Ethylene biosynthetic enzyme levels were reduced in hybrids and an ethylene biosynthesis mutant in an inbred background partially phenocopied the molecular differences seen in hybrids indicating that reduced ethylene levels may play a role in maize heterosis.
2020-08-05 | MSV000085916 | MassIVE
Project description:To investigate whether small RNAs (sRNAs) participate in the regulation of heterosis, we profiled the sRNA expression patterns in the germ seeds of five inbred lines and theirs three F1 hybrids using high-throughput sequencing technology.
2017-07-01 | GSE59101 | GEO
Project description:Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include WUSCHEL, ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative Arabidopsis hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in Arabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.
2017-08-03 | GSE85759 | GEO
Project description:Heterosis is most frequently manifested by the substantially increased vigorous growth of hybrids compared with their parents. Investigating genomic variations in natural populations is essential to understand the initial molecular mechanisms underlying heterosis in plants. Here, we characterized the genomic architecture associated with biomass heterosis in 200 Arabidopsis hybrids. The genome-wide heterozygosity of hybrids makes a limited contribution to biomass heterosis, and no locus shows an obvious overdominance effect in hybrids. However, the accumulation of significant genetic loci identified in genome wide association studies (GWAS) in hybrids strongly correlates with better-parent heterosis (BPH). Candidate genes for biomass BPH fall into diverse biological functions, including cellular, metabolic, and developmental processes and stimulus-responsive pathways. Important heterosis candidates include WUSCHEL, ARGOS, and some genes that encode key factors involved in cell cycle regulation. Interestingly, transcriptomic analyses in representative Arabidopsis hybrid combinations reveal that heterosis candidate genes are functionally enriched in stimulus-responsive pathways, including responses to biotic and abiotic stimuli and immune responses. In addition, stimulus-responsive genes are repressed to low-parent levels in hybrids with high BPH, whereas middle-parent expression patterns are exhibited in hybrids with no BPH. Our study reveals a genomic architecture for understanding the molecular mechanisms of biomass heterosis in Arabidopsis, in which the accumulation of the superior alleles of genes involved in metabolic and cellular processes improve the development and growth of hybrids, whereas the overall repressed expression of stimulus responsive genes prioritizes growth over responding to environmental stimuli in hybrids under normal conditions.
2017-08-03 | GSE100595 | GEO
Project description:Compared to understanding of biological shape and form, knowledge is sparse regarding what regulates growth and body size of a species. For example, the genetic and physiological causes of heterosis (hybrid vigor) have remained elusive for nearly a century. Here we investigate gene-expression patterns underlying growth heterosis in the Pacific oyster (Crassostrea gigas) in two partially inbred (f=0.375) and two hybrid larval populations produced by a reciprocal cross between the two inbred families. We cloned cDNA and generated 8.6 million sequence tags with massively parallel signature sequencing (MPSSâ). The sequences contain 23,277 distinct signatures that are expressed at statistically non-zero levels and show a highly positively skewed distribution with median and modal counts of 9.25 and 3 transcripts per million, respectively. Approximately 9100 nuclear transcripts are found in all four larval populations, in agreement with the number of genes expressed in sea urchin embryo. For half of the 23,277 signatures, expression level depends on genotype and is predominantly non-additive (hybrids deviate from the inbred average). Statistical contrasts suggest ~350 candidate heterosis genes that exhibit concordant non-additive expression in reciprocal hybrids. Patterns of gene expression, which include dominance for low expression and even underdominance of expression, are more complex than predicted from classical dominant or overdominant explanations of heterosis. Preliminary identification of ribosomal proteins among candidate genes supports the suggestion from previous studies that efficiency of protein metabolism plays a role in heterosis. Keywords: MPSS heterosis larvae expression profiling
2006-11-10 | GSE3596 | GEO
Project description:Loop-design (triangle design with the comparison of each triplet: hybrid + parent 1 and parent 2) and pairwise design (hybrid + parent 1, hybrid + parent 2) were used in the experiment.<br> Four inbred lines and their four inter-pool hybrids were hybridized respectively in two-colour chips experiments. <br> The objective of our study was to:(i) identify differentially expressed genes in relation to heterosis for plant height, (ii) relate gene expression patterns to the dominance and overdominance hypothesis, (iii) determine the consistency of expression patterns between inbred parent - hybrid triplets also in view of differing degrees of relatedness of triplets, and to (iv) validate consistently differentially expressed genes between hybrids and their parental inbreds by real-time (qRT) PCR.
2006-08-17 | E-MEXP-764 | biostudies-arrayexpress
Project description:We demonstrated the manifestation of heterosis in hybrid maize embryo and endosperm tissue six days after fertilization in crosses of several inbred lines. Here we analyzed heterosis-associated gene expression pattern in these tissues of reciprocal crosses of two european maize inbred line combinations. Differences in gene expression were analyzed with custom microarrays by a combined approach of suppression subtractive hybridization and microarray hybridizations
2009-08-28 | GSE17821 | GEO
Project description:The improvement of breeding efficiencies for heterotic and climate-resilient crops can mitigate the food shortage crisis from overpopulation and climate change. Thus far, diverse molecular markers have been utilized for guiding field phenotypic selections, while the accurate predictions of complex heterotic traits are rarely reported. Here we present a practical metabolome-based prediction strategy for yield heterosis in rice. The dissection of population structures based on untargeted metabolite profiles, rather than the screening of predictive variables, was proved to be the initial critical step in multivariate modeling. Then the assessment of each predictive variable's contribution to predictive models was more precise according to all latent factors compared to the conventional first one. Metabolites belonging to specific pathways were tightly connected to yield heterosis, and the up-regulation of galactose metabolism represent robust yield heterosis for hybrids across different growth conditions. Our study demonstrates that metabolome-based predictive models with correctly dissected population structures and screened predictive variables can realize accurate prediction of yield heterosis and manifest great potential for establishing molecular marker-based precision breeding programs.
2019-12-10 | MTBLS742 | MetaboLights