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Fijnaart, Netherlands

Flood P.J.,Max Planck Institute for Plant Breeding Research | van Heerwaarden J.,Wageningen University | Becker F.,Wageningen University | de Snoo C.B.,Rijk Zwaan R and D Fijnaart | And 2 more authors.
Current Biology | Year: 2016

Strong selection on a beneficial mutation can cause a selective sweep, which fixes the mutation in the population and reduces the genetic variation in the region flanking the mutation [1-3]. These flanking regions have increased in frequency due to their physical association with the selected loci, a phenomenon called "genetic hitchhiking" [4]. Theoretically, selection could extend the hitchhiking to unlinked parts of the genome, to the point that selection on organelles affects nuclear genome diversity. Such indirect selective sweeps have never been observed in nature. Here we show that strong selection on a chloroplast gene in the wild plant species Arabidopsis thaliana has caused widespread and lasting hitchhiking of the whole nuclear genome. The selected allele spread more than 400 km along the British railway network, reshaping the genetic composition of local populations. This demonstrates that selection on organelle genomes can significantly reduce nuclear genetic diversity in natural populations. We expect that organelle-mediated genetic draft is a more common occurrence than previously realized and needs to be considered when studying genome evolution. Flood et al. discover that strong selection on a chloroplast gene has extended to the nuclear genome, which has hitched a ride along with the selected chloroplast. This is the first description of organelle-mediated genetic draft and shows that selection on organelles can directly impact nuclear genetic diversity. © 2016 Elsevier Ltd. Source


Wijnker E.,Wageningen University | Wijnker E.,University of Strasbourg | James G.V.,Max Planck Institute for Plant Breeding Research | Ding J.,Max Planck Institute for Plant Breeding Research | And 15 more authors.
eLife | Year: 2013

Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an ~80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of ~25-50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs. Source


Wijnker E.,Wageningen University | Wijnker E.,University of Strasbourg | Deurhof L.,Wageningen University | Van De Belt J.,Wageningen University | And 11 more authors.
Nature Protocols | Year: 2014

Hybrid crop varieties are traditionally produced by selecting and crossing parental lines to evaluate hybrid performance. Reverse breeding allows doing the opposite: selecting uncharacterized heterozygotes and generating parental lines from them. With these, the selected heterozygotes can be recreated as F 1 hybrids, greatly increasing the number of hybrids that can be screened in breeding programs. Key to reverse breeding is the suppression of meiotic crossovers in a hybrid plant to ensure the transmission of nonrecombinant chromosomes to haploid gametes. These gametes are subsequently regenerated as doubled-haploid (DH) offspring. Each DH carries combinations of its parental chromosomes, and complementing pairs can be crossed to reconstitute the initial hybrid. Achiasmatic meiosis and haploid generation result in uncommon phenotypes among offspring owing to chromosome number variation. We describe how these features can be dealt with during a reverse-breeding experiment, which can be completed in six generations (∼1 year). © 2014 Nature America, Inc. All rights reserved. Source


Wijnker E.,Wageningen University | Van Dun K.,Rijk Zwaan R and D Fijnaart | De Snoo C.B.,Rijk Zwaan R and D Fijnaart | Lelivelt C.L.C.,Rijk Zwaan R and D Fijnaart | And 7 more authors.
Nature Genetics | Year: 2012

Traditionally, hybrid seeds are produced by crossing selected inbred lines. Here we provide a proof of concept for reverse breeding, a new approach that simplifies meiosis such that homozygous parental lines can be generated from a vigorous hybrid individual. We silenced DMC1, which encodes the meiotic recombination protein DISRUPTED MEIOTIC cDNA1, in hybrids of A. thaliana, so that non-recombined parental chromosomes segregate during meiosis. We then converted the resulting gametes into adult haploid plants, and subsequently into homozygous diploids, so that each contained half the genome of the original hybrid. From 36 homozygous lines, we selected 3 (out of 6) complementing parental pairs that allowed us to recreate the original hybrid by intercrossing. In addition, this approach resulted in a complete set of chromosome- substitution lines. Our method allows the selection of a single choice offspring from a segregating population and preservation of its heterozygous genotype by generating homozygous founder lines. © 2012 Nature America, Inc. All rights reserved. Source

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