Zea mays subsp. mays breed:Maize inbred line A188
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA299127 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2886960_1.fastq.gz | Fastqsanger.gz | |||
| SRR2886960_2.fastq.gz | Fastqsanger.gz | |||
| SRR2886970_1.fastq.gz | Fastqsanger.gz | |||
| SRR2886970_2.fastq.gz | Fastqsanger.gz | |||
| SRR2886951_1.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq from whole V3 maize seedlings (roots and shoots) for the B73 inbred line and A188 x B73 hybrid.
2022-01-27 | GSE175914 | GEO
Project description:Zea mays strain:A188 | cultivar:A188 Genome sequencing
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Project description:BackgroundThe maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies.ResultsHere, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus.ConclusionsThe A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.
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Project description:We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 13 parental inbred lines (4 Dent, 9 Flint) of European maize (Zea mays L.). The selection of oligonucleotides was based on 47k-array expression data from a 14x7 factorial with 98 hybrids (GSE17754). The main fraction of oligonucleotides (1639) represents genes that showed differential expression between the parental genotypes in the 14x7 factorial and consistent association with HP for GY in cross validation runs to estimate prediction accuracies for this trait. In addition the array contains partial overlapping fractions of genes that correlated with HP/GY (378), HP/GDMC (200), or MPH/GY (345) and 205 representatives of the 6 most overrepresented biological processes among genes correlated with HP/GY in the 14x7 factorial.
2016-08-18 | GSE85283 | GEO
Project description:In the current study a microarray (46k, University of Arizona, USA) analysis of 21 European maize (Zea mays L.) parental inbred lines (14 dent and 7 flint) was applied. The aim was the identification of parental genes which expression levels are correlated to heterosis and/or hybrid performance for grain yield (GY) and grain dry matter content (GDMC) in the hybrid progeny (F1). Therefore gene expression profiles of differentially expressed genes of the parental inbred lines at the seedling stage were correlated with GY- and GDMC-field data of 98 flint x dent factorial crosses gained at six different locations in Germany. The identification of heterosis-correlated genes is an approach for the characterization and also for the prediction of this phenomenon. For the analyses total RNA of seven days old seedlings was extracted and aminoallyl-labeled RNA probes were synthesized. RNA labeling (Cy3, Cy5) and hybridizations were performed according to the protocol of the maize oligonucleotide array project (http://www.maizearray.org). The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). An experimental interwoven loop design was developed aiming to yield in a preferably low average variance among the hybridizations, especially between intergroup (dent lines vs. flint lines) hybridizations. As a result 12288 (28.3%) of the genes showed differential expression between any combination of inbred lines. These differentially expressed genes were used for subsequent field data correlation analyses.
2010-08-21 | GSE17754 | GEO
Project description:High temperature is increasingly becoming one of the prominent environmental factors affecting the growth and development of maize (Zea mays L.). Therefore, it is critical to identify key genes and pathways related to heat stress (HS) tolerance in maize. Here, we identified a heat-resistant (Z58D) and heat-sensitive (AF171) maize inbred lines at seedling stage. Transcriptomic analysis identified 3,006 differentially expressed genes (DEGs) in AF171 and 4,273 DEGs in Z58D under HS treatments, respectively. Subsequently, GO enrichment analysis showed that shared upregulated genes in AF171 and Z58D involved in response to HS, protein folding, abiotic and temperature stimulus pathway. Moreover, the comparison between the two inbred lines under HS showed that response to heat and response to temperature stimulus significantly overrepresented for the 1,234 upregulated genes. Furthermore, commonly upregulated genes in Z58D and AF171 had higher expression level in Z58D than AF171. In addition, maize inbred CIMBL55 had been verified to be more tolerant than B73 and commonly upregulated genes had higher expression level in CIMBL55 than B73 under HS. The consistent results indicated that heat-resistant inbred lines may coordinate the remarkable expression of genes in order to recover from HS. Additionally, 35 DEGs were conserved among 5 inbred lines by a comparative transcriptomic analysis. Most of them were more pronounced in Z58D than AF171 at expression level. Those candidate genes may confer thermotolerance in maize.
2024-03-01 | GSE254852 | GEO
Project description:Zea mays cultivar:A188 Raw sequence reads
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Project description:Zea mays cultivar:A188 Genome sequencing and assembly
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Project description:Zea mays strain:A188 Transcriptome or Gene expression
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