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Series GSE50558 Query DataSets for GSE50558
Status Public on Sep 05, 2013
Title Intraspecific variation of recombination rate in maize
Organism Zea mays
Experiment type SNP genotyping by SNP array
Summary 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.
Overall design We genotyped 2233 maize DH lines from 24 biparental populations, and the 23 parents of these populations using the Illumina MaizeSNP50 BeadChip. We created two large half-sib panels, one each for the Dent and the Flint germplasm. The Dent populations have the prefix CFD, the Flint populations have the prefix CFF. In each panel, a common central parent was crossed to diverse founder lines, and doubled haploids were generated from the respective F1 plants. For a detailed description of the material, see Bauer et al. (2013) Genome Biology (submitted).
We submit here three datasets: 1) Dataset Parents comprises all 23 parental lines. 2) Dataset CFD comprises all 1005 DH lines from Dent crosses, 3) Dataset CFF comprises all 1262 DH lines from Flint crosses.
Contributor(s) Bauer E
Citation(s) 24050704, 25236445
Submission date Sep 03, 2013
Last update date Oct 07, 2014
Contact name Eva Bauer
Phone ++49 8161 715243
Organization name Technical University of Munich
Department Plant Breeding
Street address Liesel-Beckmann-Str. 2
City Freising
ZIP/Postal code 85354
Country Germany
Platforms (1)
GPL17677 Illumina MaizeSNP50 BeadChip
Samples (2290)
GSM1221233 Parental line, B73
GSM1221234 Parental line, D06
GSM1221235 Parental line, D09
BioProject PRJNA218068

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE50558_CFD_intensities_GEO.txt.gz 716.8 Mb (ftp)(http) TXT
GSE50558_CFD_matrix_GEO.txt.gz 505.9 Mb (ftp)(http) TXT
GSE50558_CFF_intensities_GEO.txt.gz 898.5 Mb (ftp)(http) TXT
GSE50558_CFF_matrix_GEO.txt.gz 626.7 Mb (ftp)(http) TXT
GSE50558_Parental_intensities_GEO.txt.gz 17.1 Mb (ftp)(http) TXT
GSE50558_Parental_matrix_GEO.txt.gz 13.1 Mb (ftp)(http) TXT
Raw data is available on Series record
Processed data included within Sample table
Processed data is available on Series record

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