A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency

Abstract

Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.

Keywords: Brassica napus; allotriploidy; genetic mapping; plant breeding; polyploidy; recombination rate and distribution.

Figure 1

Production of (a) AnAr diploid, (b) AnArCn allotriploid and (c) AnArCnCo allotetraploid hybrids sharing the same A genotype and their derived progenies.

Figure 2

Chromosome pairing at metaphase I in pollen mother cells of (a) the allotriploid AnArCn, (b,c) the synthetic B. napus ChEM ArArCoCo-S0 and (d) the allotetraploid AnArCnCo hybrid. C chromosomes are labeled in red via the use of the Bob014O06 BAC clone (GISH-like). Univalents are indicated by a * and A–C bivalents by an arrow. Chromosomes were counterstained with DAPI. Scale bars represent 5 μm.

Figure 3

Homologous recombination landscape in diploid, allotriploid and allotetraploid hybrids. The first circle represents the 10 chromosomes of B. rapa cv. Chiifu v1.5. Within the second circle, the gene and transposable element (TE) densities along each A chromosome are mentioned, with black rectangles indicating the putative centromere positions [53]. In the inner circle, the recombination rates (cM/Mb) of AnAr (2x), AnArCn (3x) and AnArCnCo (4x) are shown as red, blue and green lines, respectively. Significant differences within an interval are highlighted in peach, light blue and purple for 2x vs. 3x, 4x vs. 3x, or 4x and 2x vs. 3x, respectively. Above the recombination landscape, the physical position of each polymorph SNP used for these comparisons is indicated.

Figure 4

Recombination and introgression patterns along the ten A chromosomes of the allotriploid (AnArCn) and allotetraploid (AnArCnCo) hybrids. For each A chromosome (A01 to A10), the distribution of the recombination (in cM/Mb, indicated by lines) and average size of introgressions (in Mb, represented by dots) at each marker position in the progeny of allotriploid (blue) and allotetraploid hybrid (green) are presented for all A chromosomes. Below each graph, the physical positions of polymorph SNPs along each B. napus cv. Darmor-bzh v10 chromosome are indicated. The position of pericentromeres and centromeres (inferred in this study) are illustrated as light gray and black boxes, respectively.

Figure 5

Characterization of introgressions in the AnArCn and AnArCnCo populations. (a) Size of introgressions, (b) number of introgressions. White triangle indicates mean. (c) Correlation between the relative introgression size and their relative position from the centromere (Cen.) to the telomere (Tel.) analyzed in the progeny of the AnArCn hybrid (blue) and AnArCnCo hybrid (green). Regression lines are indicated in red.

Figure 6

Crossover localization in a pericentromeric region carrying a QTL conferring resistance to Leptosphaeria maculans. (a) Recombination rate (in cM/Mb, as lines) and the average size of introgression (in Mb, as dots) along the A01 chromosome, for the AnArCn (green) and AnArCnCo (blue) hybrids. The resistance QTL is represented by a purple box with its borders delimited by purple dashed lines. The different possible haplotypes found in the backcross progeny of (b) the AnArCn (131 plants) or (c) the AnArCnCo hybrids (213 plants) are displayed, with the homozygous B. napus cv. Darmor regions in green and the introgressed regions of B. rapa cv. Chiifu in blue. A 4.96 Mb region surrounding the centromere and deprived of markers is highlighted in gray. Red stars symbolize the crossover positions.