Genetic analysis for the Grain shape and Grain weight heterosis of a super-hybrid rice WFYT025 combination
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ABSTRACT:
PROVIDER: PRJNA781194 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16964300_1.fastq.gz | Fastqsanger.gz | |||
| SRR16964300_2.fastq.gz | Fastqsanger.gz | |||
| SRR16964301_1.fastq.gz | Fastqsanger.gz | |||
| SRR16964301_2.fastq.gz | Fastqsanger.gz | |||
| SRR16964302_1.fastq.gz | Fastqsanger.gz |
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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.
2022-11-17 | GSE189012 | GEO
Project description:Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Our genetic and molecular evidences pinpointed the QTL-OsglHAT1’s allelic variations to a 1.2-kilobase region upstream of the gene body, which is consistent with its function as a positive regulator of the traits. Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. OsglHAT1 localizes to the nucleus, where it likely functions through the regulation of transcription. Despite its positive agronomical effects on grain weight, yield and plant biomass, the rare allele elevating OsglHAT1 expression has so far escaped human selection. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding.
2015-02-10 | GSE62554 | GEO
Project description:Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Our genetic and molecular evidences pinpointed the QTL-OsglHAT1’s allelic variations to a 1.2-kilobase region upstream of the gene body, which is consistent with its function as a positive regulator of the traits. Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. OsglHAT1 localizes to the nucleus, where it likely functions through the regulation of transcription. Despite its positive agronomical effects on grain weight, yield and plant biomass, the rare allele elevating OsglHAT1 expression has so far escaped human selection. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding. Two replicates of Nipponbare as control, three replicates of GW6a-4.6 substitution lines and three replicates of OsglHAT1-OE transgenic lines.
2015-02-10 | E-GEOD-62554 | biostudies-arrayexpress
Project description:To investigate the role of OsGSE9 in grain shape, we generate its overexpressing lines, and knockout lines by CRISPR/Cas9 system. We then performed gene expression profiling analysis using data obtained from RNA-seq of the panicles of the WT and OsGSE9 transgenic lines
2023-08-20 | GSE218565 | GEO
Project description:BACKGROUND:Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. RESULTS:Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DGHP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DGHP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DGHP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DGHP enriched in the KEGG pathway with QTLs associated with grain number, several DGHP were located on the same chromosomal segment with some of these grain number QTLs. CONCLUSION:Through young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DGHP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs.
| S-EPMC6003258 | biostudies-literature
Project description:Grain length is a prominent determinant for the grain weight and appearance quality of rice. To elucidate the genetic basis of the control of grain length, we conducted quantitative trait locus (QTL) mapping to determine a genomic interval responsible for the a long-grain phenotype observed in a japonica cultivar HD385 by using an F2:3 population and recombinant inbred line (RIL) population, which is are derived from a cross between the long-grain japonica cultivar HD385 and short-grain japonica cultivar Nipponbare (NIP). This led to the identification of a novel QTL, which is located on chromosome 3, for grain length, named qIGL1 (for Increased Grain Length 1); the HD385-derived allele showed enhancement effects on grain length, and such an allele as well as NIP-derived allele are were thus designated qigl1 HD385 and qIGL1NIP, respectively. Genetic analysis revealed that qigl1HD385 displayed semi-dominant effects on grain length. To further narrow down the qIGL1 region, we developed a few advanced backcross populations to determine the precise location of qIGL1. Eventually, qIGL1 was delimited to a 70.8-kb region containing 9 open reading frames (ORFs). A comprehensive analysis indicated that ORF6 and ORF9, separately corresponding to LOC_Os03g30530 and LOC_Os03g30550, are were found to carry base substitutions and/or deletions, which resulted in changes or losses of amino acid residues. However, these alterations in coding sequences does did not significantly change the expression levels of both ORFs. To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP, and discovered that introduction of qigl1HD385 into the NIP background significantly lead resulted into the elevations of grain length and 1000-grain weight. Closer inspection of outer epidermal cells of grain surfaces of both lines revealed that the cell length and width in the longitudinal direction are were significantly longer in NIL-qigl1HD385 compared with in NIL-qIGL1NIP, which may might stem partly from the downregulation of several cell cycle-related genes. Hence, our study studies identify identified a new semi-dominant natural allele contributing to the increase of grain length, and further shed light on the regulatory mechanisms of grain length.
2023-08-22 | GSE241093 | 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
2016-11-07 | GSE85765 | GEO
Project description:Regulation of grain size is a crucial strategy for improving crop yield and is also a fundamental aspect of developmental biology. However, the underlying molecular mechanisms governing grain development in wheat remain largely unknown. In this study, we identified a wheat atypical basic helix-loop-helix (bHLH) transcription factor, TabHLH489, which is tightly associated with grain length through genome-wide association study and map-based cloning. Knockout of TabHLH489 and its homologous genes resulted in increased grain length and weight, whereas overexpression led to decreased grain length and weight. TaSnRK1α1, the α-catalytic subunit of plant energy sensor SnRK1, interacted with and phosphorylated TabHLH489 to induce its degradation, thereby promoting wheat grain development. Sugar treatment induced TaSnRK1α1 protein accumulation while reducing TabHLH489 protein levels. Moreover, brassinosteroid (BR) promotes grain development by decreasing TabHLH489 expression through the transcription factor BRASSINAZOLE RESISTANT1 (BZR1). Importantly, natural variations in the promoter region of TabHLH489 affect the TaBZR1 binding ability, thereby influencing TabHLH489 expression. Taken together, our findings reveal that the TaSnRK1α1-TabHLH489 regulatory module integrates BR and sugar signaling to regulate grain length, presenting potential targets for enhancing grain size in wheat.
2024-02-04 | GSE253343 | GEO
Project description:qTGW3 encodes a GLYCOGEN SYNTHASE KINASE 3 (GSK3)/SHAGGY-like family protein kinase GSK5. We demonstrate that GSK5 interacts with and phosphorylates the AUXIN RESPONSE FACTOR (ARF) transcription factor ARF4. Both GSK5 and ARF4 are mainly expressed in reproductive tissues, and loss-of-function mutation of ARF4 also increases rice grain length and weight. ARF4 functions as a transcriptional repressor in plants and RNA-Seq analysis reveals that, compared to the wild-type plants, totally 887 and 1179 genes were up-regulated in the GSK5 and ARF4 mutants, respectively. Among them, 373 genes were commonly up-regulated in both mutants. In contrast, there were 681 and 669 genes were down-regulated in the GSK5 and ARF4 mutants, respectively. Among them, 288 genes were commonly up-regulated in both mutants. These results showed that GSK5 and ARF4 have overlapping roles and regulate a common set of genes during rice grain development.
2017-05-15 | GSE98924 | 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