Dataset Information

Investigation of maize inbreds genetic variants

ABSTRACT: An investigation into genetic variantion of maize inbreds in China

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea Mays

SUBMITTER: Beijing Lantron Seed

PROVIDER: PRJEB64281 | EVA | 2023-09-05

REPOSITORIES: EVA

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Dataset's files

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			Action	DRS
	140_maf0.05mis0.2het0.2.accessioned.vcf.gz	Vcf
	140_maf0.05mis0.2het0.2.accessioned.vcf.gz.csi	Vcf
	140_maf0.05mis0.2het0.2.vcf.csi	Other
	140_maf0.05mis0.2het0.2.vcf.gz	Vcf
	203_maf0.05mis0.2.accessioned.vcf.gz	Vcf

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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.

Dataset Information

Investigation of maize inbreds genetic variants

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