Non‐random distribution of extensive chromosome rearrangements in Brassica napus depends on genome organization

• Published in: The Plant journal : for cell and molecular biology 2012-05, Vol.70 (4), p.691-703
• Main Authors: Nicolas, Stéphane D., Monod, Hervé, Eber, Frédérique, Chèvre, Anne‐Marie, Jenczewski, Eric
• Format: Article
• Language: English
• Subjects: Adenylate cyclase; Agricultural sciences; Biological and medical sciences; Brassica napus; Brassica napus - classification; Brassica napus - genetics; Cell cycle, cell proliferation; Cell division; Cell physiology; Centromeres; Chromosome Mapping; Chromosome rearrangements; Chromosomes; Chromosomes, Plant - genetics; Crosses, Genetic; Diploids; Diploidy; Evolution; Evolution, Molecular; Fertility; Fertility - genetics; Flowers & plants; Fundamental and applied biological sciences. Psychology; Gene Rearrangement; Genetic distance; Genetic diversity; Genetic Loci - genetics; Genetic Variation; Genic rearrangement. Recombination. Transposable element; genome evolution; genome rearrangement; Genome, Plant - genetics; Genomes; Genomics; Haploidy; homeologous recombination; Life Sciences; Linkage Disequilibrium; Mathematical models; Meiosis; Meiosis - genetics; meiotic recombination; Models, Genetic; Molecular and cellular biology; Molecular genetics; Phylogeny; Plant biology; Plant physiology and development; Polyploidy; Statistical analysis; structural variation
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2012.04914.x

Summary Chromosome rearrangements are common, but their dynamics over time, mechanisms of occurrence and the genomic features that shape their distribution and rate are still poorly understood. We used allohaploid Brassica napus (AC, n = 19) as a model to analyze the effect of genomic features on the formation and diversity of meiotically driven chromosome rearrangements. We showed that allohaploid B. napus meiosis leads to extensive new structural diversity. Almost every allohaploid offspring carried a unique combination of multiple rearrangements throughout the genome, and was thus structurally differentiated from both its haploid parent and its sister plants. This large amount of genome reshuffling was remarkably well‐tolerated in the heterozygous state, as neither male nor female fertility were strongly reduced, and meiosis behavior was normal in most cases. We also used a quantitative statistical model, which accounted for 75% of the observed variation in rearrangement rates, to show that the distribution of meiotically driven chromosome rearrangements was not random but was shaped by three principal genomic features. In descending order of importance, the rate of marker loss increased strongly with genetic distance from the centromere, the degree of collinearity between chromosomes, and the genome of origin (A