Maize
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA335627 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptomic and Epigenetic Adaptation of the Maize Chromosome in Oat–Maize Addition Lines
| PRJNA438867 | ENA
Project description:MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.
2020-03-22 | GSE132167 | GEO
Project description:maize rhizosphere metagenome Raw sequence reads
| PRJNA555161 | ENA
Project description:maize rhizosphere soil Raw sequence reads
| PRJNA732943 | ENA
Project description:Maize Soil Metagenome Raw sequence reads
| PRJNA622831 | ENA
Project description:The data set submitted here contains the raw SNP genotyping data obtained from the analysis of 24 biparental segregating maize (Zea mays L.) populations and their respective parents. The processed and filtered data were used to construct genetic linkage maps which we used in our study of variation of recombination rate in maize. In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation. In our study, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotyped 23 doubled-haploid populations derived from crosses between these lines with a 50k-SNP array and constructed high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtained the recombination rates along chromosomes specific to each population. We identified significant differences in recombination rates at the genome-wide, chromosome, and intrachromosomal levels between populations, as well as significant variation for genome-wide recombination rates among maize lines. Crossover interference analysis using a two-pathway modeling framework revealed a negative association between recombination rate and interference strength. To our knowledge, the present work provides the most comprehensive study on intraspecific variation of recombination rates and crossover interference strength in eukaryotes. Differences found in recombination rates will allow for selection of high or low recombining lines in crossing programs. Our methodology should pave the way for precise identification of genes controlling recombination rates in maize and other organisms.
2013-09-05 | GSE50558 | GEO
Project description:Many existing centromeres may have originated as neocentromeres that activated de novo from non-centromeric regions. However, the evolutionary path from a neocentromere to a mature centromere has been elusive. Here we analyzed the centromeres of six chromosomes that were transferred from maize into oat as the result of an inter-species cross. Centromere size and location were assayed by chromatin immunoprecipitation for the histone variant CENH3, which is a defining feature of functional centromeres. Maize and oat are highly divergent and differ in genome size by four fold. Two isolates of maize chromosome proved to contain neocentromeres in the sense that they had moved from the original site, whereas the remaining seven centromeres (1, 2, 5, 6, 8, 9 and 10) were retained in the same area in both species. In all cases the CENH3-binding domains were dramatically expanded to encompass a larger area in the oat background (~4 Mb) than the average centromere size in maize (~2 Mb). The expansion of maize centromeres appeared to be restricted by the transcription of genes located in regions flanking the original centromeres. The results from the current study provide evidence that (1) centromere size is regulated; (2) centromere sizes tend to be uniform within a species regardless of chromosome size or origin of the centromere; and (3) neocentromeres emerge and expand preferentially in gene poor regions. Our results, together with data from several animal species, suggest that centromere size expansion may be a key factor in the survival of neocentric chromosomes in natural populations.
2013-09-01 | GSE47342 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX