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Intraspecific variation of recombination rate in maize

Eva Bauer1*, Matthieu Falque2, Hildrun Walter1, Cyril Bauland2, Christian Camisan3, Laura Campo4, Nina Meyer5, Nicolas Ranc6, Renaud Rincent2357, Wolfgang Schipprack8, Thomas Altmann9, Pascal Flament3, Albrecht E Melchinger8, Monica Menz6, Jesús Moreno-González4, Milena Ouzunova5, Pedro Revilla10, Alain Charcosset2, Olivier C Martin2 and Chris-Carolin Schön1

  • * Corresponding author: Eva Bauer

  • † Equal contributors

Author affiliations

1 Plant Breeding, Technische Universität München, 85354 Freising, Germany

2 INRA, UMR de Génétique Végétale/Université Paris-Sud - CNRS, 91190 Gif-sur-Yvette, France

3 Limagrain Europe, 63720 Chappes, France

4 Centro Investigacións Agrarias Mabegondo (CIAM), 15080 La Coruña, Spain

5 KWS SAAT AG, 37574 Einbeck, Germany

6 Syngenta SAS, 31790 Saint-Sauveur, France

7 BIOGEMMA, Genetics and Genomics in Cereals, 63720 Chappes, France

8 Plant Breeding, Universität Hohenheim, 70599 Stuttgart, Germany

9 Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany

10 Misión Biológica de Galicia (CSIC), 36080 Pontevedra, Spain

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Citation and License

Genome Biology 2013, 14:R103  doi:10.1186/gb-2013-14-9-r103

Published: 19 September 2013



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.


Here, we report on the variation of recombination rates between 22 European maize inbred lines that belong to the Dent and Flint gene pools. We genotype 23 doubled-haploid populations derived from crosses between these lines with a 50 k-SNP array and construct high-density genetic maps, showing good correspondence with the maize B73 genome sequence assembly. By aligning each genetic map to the B73 sequence, we obtain the recombination rates along chromosomes specific to each population. We identify 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 reveals 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.