Directional gene conversion and homogenization of rDNA shapes evolution in Brassica

Brassica napus (AACC, oilseed rape) is an allotetraploid species derived from the putative progenitor diploid species B.rapa (AA) and B. oleracea (CC). To assess the influence of intensive breeding conditions on the evolution of the B. napus genome, Kovarik et al. employ cytogenetic and genomic approaches to analyze rDNA structure in 21 cultivars of B. napus.

Southern blot hybridization of genomic DNA from several B. napus cultivars.

(A) Southern blot hybridization of genomic DNA from several B. napus cultivars. In the left panel the blot was hybridized with the 26S probe. After stripping the blot was rehybridized with the A-genome-specific IGS probe (B). ‘C’, C-genome bands; ‘A’, A-genome bands; ‘A*’ indicates an IGS family amplified in a subset of B. napus cultivars. (C) Example of a Southern hybridization of the C-genome-specific IGS probe. Note strong hybridization of the probe to ‘Yudal’ DNA. (D) The radioactivity of bands was quantified using a Phosphorimager and homeologue gene number expressed as a proportion of C-genome rDNA to total rDNA. Numbers below indicate two major chloroplast haplotypes identified by Cifuentes et al. (2010). In the same study, the B. napus cultivars were divided into groups with low (–), intermediate (±) and high (+) frequency of homeologue chromosome pairing in meiosis (symbols towards the bottom).

The B. napus cultivars differ in degree and direction of rDNA homogenization; the prevalent direction of gene conversion (towards the A genome) correlates with the direction of expression dominance, indicating that gene activity may be required for interlocus gene conversion.

Reference

Sochorová, J., Coriton, O., Kuderová, A., Lunerová, J., Chèvre, A.-M., & Kovařík, A. (2016). Gene conversion events and variable degree of homogenization of rDNA loci in cultivars of Brassica napus. Annals of Botany, 119(1), 13–26. https://doi.org/10.1093/aob/mcw187