European maize diversity
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB14212 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1462650_1.fastq.gz | Fastqsanger.gz | |||
| ERR1462650_2.fastq.gz | Fastqsanger.gz | |||
| ERR1462660_1.fastq.gz | Fastqsanger.gz | |||
| ERR1462660_2.fastq.gz | Fastqsanger.gz | |||
| ERR1462670_1.fastq.gz | Fastqsanger.gz |
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Project description:BACKGROUND: Climate change will lead in the future to an occurrence of heat waves with a higher frequency and duration than observed today, which has the potential to cause severe damage to seedlings of temperate maize genotypes. In this study, we aimed to (I) assess phenotypic variation for heat tolerance of temperate European Flint and Dent maize inbred lines, (II) investigate the transcriptomic response of temperate maize to linearly increasing heat levels and, (III) identify genes associated with heat tolerance in a set of genotypes with contrasting heat tolerance behaviour. RESULTS: Strong phenotypic differences with respect to heat tolerance were observed between the examined maize inbred lines on a multi-trait level. We identified 607 heat responsive genes as well as 39 heat tolerance genes. CONCLUSION: Our findings indicate that individual inbred lines developed different genetic mechanisms in response to heat stress. We applied a novel statistical approach enabling the integration of multiple genotypes and stress levels in the analysis of abiotic stress expression studies.
2016-10-20 | GSE88917 | GEO
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:We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 13 parental inbred lines (9 Dent, 4 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 | GSE85286 | GEO
Project description:We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 29 parental inbred lines (16 Dent,13 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 | GSE85285 | GEO
Project description:We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 13 parental inbred lines (9 Dent, 4 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 | GSE85288 | GEO
Project description:We applied a custom 2k micro-array with 2232 oligonucleotide sequences (50-70 nt) to a factorial with 20 parental inbred lines (14 Dent, 6 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 | GSE85287 | GEO
Project description:Genetic diversity in Staphylococcus aureus (European collection)
| PRJEB2478 | ENA
Project description:affy_cellwall_maize - affy_cellwall_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription.-Comparison of internodes from 5 maize lines grown in field conditions
2010-12-07 | GSE24624 | GEO
Project description:affy_en-tj_maize - affy_en_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of 2 maize lines : Cm484: good digestibility F98902: bad digestibility) , at the following developmental stade 2: male flowering Keywords: genotype comparaison
2011-06-01 | GSE18857 | GEO
Project description:affy_en-tj_maize - affy_tj_maize - Maize, Zea mays, is one of the most widely grown crops in the world as it provides cereal grain for human purposes and feedstock for cattle. Maize is increasingly used as a biomass fuel, such as ethanol. Studies have shown that maize stem is made up of different lignified cell types: epidermis, sclerenchyma (a few layers under the epidermis and surrounding vascular bundles in the rind), parenchyma (mostly lignified near the epidermis). One of the aims of this work is to find out if it is the proportion of these different cell types or their number (especially for vascular bundles) which influences the degree of digestibility of maize lines. For that the objective of our work is to develop a genomic strategic approach allowing an improvement of traits involved in cell wall degradability. The work will include the mapping of genes considered as strategic in the cell wall biosynthesis, the search of new genes of interest through bio-analysis, the functional analysis of genes suspected to be of importance in cell wall pathway, the search of candidate underlying QTL, and transcriptomic approaches in order to find genes co-regulation, transcription, and eQTL.-Comparison of 2 maize lines : Cm484: good digestibility F98902: bad digestibility at the following development stage : 21 days after sowing -7 leaves- Keywords: genotype comparaison
2011-06-01 | GSE18846 | GEO