The transcriptomes for primary panicle in four near-isogenic lines combined of different allele of two major grain length loci GS3 and qGL3 in rice
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE59619 | GEO | 2014/07/22
SECONDARY ACCESSION(S): PRJNA255773
REPOSITORIES: GEO
Similar Datasets
Project description:To investigate the genetic relationship between two major grain length loci GS3 and qGL3, we developed the near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) in the background of 93-11 (gs3/qGL3) by crossing and MAS approach. Four samples was analyzed: three near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3), NIL-qgl3 (gs3/qgl3), NIL-GS3/qgl3 (GS3/qgl3) and their background of 93-11. Every sample had three independed duplications. And the primary panicle with 3-6 cm length from the three NILs and 93-11 were used for RNA preparation and hybrid with Rice Genome OneArray Microarray (Phalanx Biotech Group).
2014-07-22 | E-GEOD-59619 | biostudies-arrayexpress
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:Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6). Heatmap analysis, along with GO analysis suggested that the diversity of clusters for NILs were likely due to variation of the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play pivotal role in determination of the cluster pattern, and that WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions.
2014-04-16 | GSE48524 | GEO
Project description:Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6). Heatmap analysis, along with GO analysis suggested that the diversity of clusters for NILs were likely due to variation of the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play pivotal role in determination of the cluster pattern, and that WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions. 22 samples were sequenced, 11 inoculated with P. sojae, the other 11 were mock-inoculated
2014-04-16 | E-GEOD-48524 | biostudies-arrayexpress
Project description:Effect of high grain protein locus on barley grain protein accumulation. Gene expression levels were analysed in Karl, a low grain protein variety with its near-isogenic line 10_11(has high grain protein locus, chromosome 6)using Barley1 22k affymetrix chip. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Aravind Jukanti. The equivalent experiment is BB53 at PLEXdb.] developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications); developmental stage: 14 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications); developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications); developmental stage: 14 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications); developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Leaves(3-replications); developmental stage: 21 days past anthesis - genotype: Karl - tissue type: Kernels(3-replications); developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Leaves(3-replications); developmental stage: 21 days past anthesis - genotype: 10-11 (NIL with high grain protein locus) - tissue type: Kernels(3-replications)
2011-11-22 | E-GEOD-33413 | biostudies-arrayexpress
Project description:DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-controlled DMRs provided an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at the cis-controlled DMRs during NIL population development. DNA methylation level was associated with local genotypes in all of the >30,000 examined cases except one. Additionally, the majority of the DMRs were not associated with small RNA. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits cis-controlled inheritance patterns, is highly stable and does not require active programming by small RNAs for maintenance. Methylation profiles in seedling tissue of maize near-isogenic lines (NILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array.
2014-04-01 | E-GEOD-51567 | biostudies-arrayexpress
Project description:Whole genome transcriptome profiling of bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage The aim of this study was to identify candidate genes responsible for grain number per panicle by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 20 differentially expressed genes, respectively. The differentially expressed genes were shorted to 4 on the basis of their occurance in the QTL region (responcible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1. RNA from the stage '0' panicle primordia of 10 RILs with high grain number and 10 with low grain number were bulked and analysed in two different biological replications (A and B) making total four samples
2009-12-31 | E-GEOD-17169 | biostudies-arrayexpress
Project description:Fusarium graminearum causes Fusarium head blight (FHB), which represents one of the major wheat diseases worldwide, determining reduction in grain quality, yield and the accumulation of mycotoxins. To mine the molecular response associated to the wheat 2DL FHB resistance quantitative trait locus (QTL), derived from the cultivar Wuhan-1, and to identify candidate genes implicated in such resistance, a comprehensive transcriptomic analysis of the early response to F. graminearum infection at 3 days post inoculation of spikelet and rachis was performed with the RNA-Seq and miRNA-Seq techniques. The analyses were conducted on two Near Isogenic Lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null).
2018-02-28 | E-MTAB-6383 | biostudies-arrayexpress
Project description:Whole genome transcriptome profiling of bulked RILs with high and low grain number per panicle derived from 2 cultivars at panicle primordia stage The aim of this study was to identify candidate genes responsible for grain number per panicle by combining QTLs analysis with expression analysis. Microarray analysis of RNA extracted from the panicle primordia showed 20 differentially expressed genes, respectively. The differentially expressed genes were shorted to 4 on the basis of their occurance in the QTL region (responcible for grain number regulation) detected in RIL population derived from Pusa 1266 and Pusa Basmati 1.
2010-01-01 | GSE17169 | GEO
Project description:NILs containing five parental lines, three wild barley genotypes ssp. spontaneum: HID 4 (A), Iraq; HID 64 (B), Turkey; and HID 369 (C), Israel, one ssp. agriocrithon: HID 382(D)) and cv. Morex (ssp. vulgare, USA). Purpose: Variant calling to identifie markers associated with a awn length QTL on the distal part of chromosome 7HL
2017-03-08 | GSE85338 | GEO