A major quantitative trait locus on chromosome A9, BnaPh1, controls homoeologous recombination in Brassica napus

Abstract

Ensuring faithful homologous recombination in allopolyploids is essential to maintain optimal fertility of the species. Variation in the ability to control aberrant pairing between homoeologous chromosomes in Brassica napus has been identified. The current study exploited the extremes of such variation to identify genetic factors that differentiate newly resynthesised B. napus, which is inherently unstable, and established B. napus, which has adapted to largely control homoeologous recombination. A segregating B. napus mapping population was analysed utilising both cytogenetic observations and high-throughput genotyping to quantify the levels of homoeologous recombination. Three quantitative trait loci (QTL) were identified that contributed to the control of homoeologous recombination in the important oilseed crop B. napus. One major QTL on BnaA9 contributed between 32 and 58% of the observed variation. This study is the first to assess homoeologous recombination and map associated QTLs resulting from deviations in normal pairing in allotetraploid B. napus. The identified QTL regions suggest candidate meiotic genes that could be manipulated in order to control this important trait and further allow the development of molecular markers to utilise this trait to exploit homoeologous recombination in a crop.

Keywords: Brassica; cytogenetics; homoeologous recombination; meiosis; polyploidy.

Fig. 1

Examples of chromosome spreads from Brassica napus SGDH lines. Chromosome spreads of meiocytes at late diakinesis/MI examined by FISH (left image of each pair) with 45S rDNA (green) and BoB061G14 (red), and GISH (right image of each pair) with labelled C genome (red), DAPI‐stained A genome (blue). Homoeologous bivalents and quadrivalents (arrows), multivalents (stars) and a univalent whose partner is in a multivalent (triangles) are highlighted. (a) SG‐261, a single C9 in a bivalent with an extra A10; (b) SG‐5, two AG CGS bivalents, one AG CG bivalent, one multivalent (A10 C9 A9 C8 C8 A9 C9 A10); (c) SG‐235, two A1 C1 homoeologous bivalents orientated with both A1 facing the same pole and both C1 facing the other, one A3 A3 C3 C3 quadrivalent; (d) SG‐25, one AG AG CG CG quadrivalent, one multivalent (C8 C8 A9 C9 C9) with univalent A9. The 45S rDNA signal on A9 in (b–d) is not visible at this exposure. Bar, 5 μm.

Fig. 2

Diagrams illustrating meiotic configurations resulting from synaptic partner switches from homologues to homoeologues in Brassica napus SGDH lines. Synaptic partner switches (SPS) (upper diagram), MI configuration (lower diagram). A genome chromosomes (blue), C genome chromosomes (red), centromeres (solid circles). Chromosomes consist of two chromatids (not shown). The minimum number of crossovers (CO) (black crosses) required in each synapsed region is shown. The allocated score is in the adjacent text box. (a–g) Two pairs of chromosomes with homoeology in one arm and one SPS. (a) One SPS but no CO in a region of synapsis between homoeologues results in two homologous bivalents and this has no score. (b–g) One SPS accompanied by one CO (one SPSC) with the outcome at MI depending on the presence/absence of COs in the other switched/not switched regions. (b) AC bivalent with A and C univalents. (c) two AC bivalents. (d) AAC trivalent and C univalent. (e) ACC trivalent and A univalent. (f) chain quadrivalent AACC. (g) ring quadrivalent AACC. (h) An example of two SPSC between three homoeologous chromosome pairs with additional COs resulting in one multivalent and a univalent as in Fig. 1(d). (i) An example of three SPSC with additional COs between four chromosome pairs with homoeology as in Fig. 1(b).

Fig. 3

Correlation of cytogenetic and SNP array measurements of homoeologous recombination. The scatterplot shows the correlation of the rate of HeR measured using cytogenetics and reciprocal SNP marker gain/loss. The distribution of scores for each analysis is shown in the graphs above and to the right of the scatterplot (x‐axis SNP scoring, y‐axis cytogenetic scoring) and the correlation statistic (r) is indicated.

Fig. 4

Distribution of events across the Brassica napus genome. The number of reciprocal and deletion/duplication events in the testcross lines measured using the Brassica SNP array is shown. Blue bars represent the reciprocal events, purple bars show the events where only the deletion or duplication of the SNP allele could be identified.

Fig. 5

Map positions of QTL controlling homoeologous pairing events in Brassica napus. The outer circle represents the physical length of the chromosomes (A genome in blue, C genome in red), the inner circle (green) the genetic linkage groups, the position of the markers on the physical chromosomes is shown by the linked grey lines. The positions of the QTL loci are shown by coloured blocks, with the colours representing the different phenotypes used to identify loci; purple – HeR only, blue – HeR and cytogenetics, and yellow – common to all phenotypes. The synteny between B. napus meiosis genes are shown as connecting lines across the centre of the circle, those genes with only two orthologues are shown in red.