Homoeologous exchanges in allopolyploids: how Brassica napus established self‐control!

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Commentary

Homoeologous exchanges in

allopolyploids: how Brassica

napus established self-control!

The fertility of sexually reproductive organisms relies on their ability to produce viable and healthy gametes that contain balanced haploid sets of chromosomes. This occurs during meiosis and in most organisms, correct chromosome segregation of maternal and paternal homologous chromosomes requires formation of meiotic crossovers (COs), i.e. reciprocal exchange of large DNA fragments between chromosomes. Combined with sister-chromatid cohe-sion, COs hold the homologous chromosomes together, allowing them to segregate faithfully. This process is more intricate in allopolyploid species because of the presence of very similar, but not identical, chromosomes (called homoeologues) inherited from the original parent species. In allopolyploids, COs between homoeo-logues must be controlled to avoid chromosome mis-segregation resulting in aneuploidy, and to thus ensure fertility. In the recently published article in New Phytologist, Higgins et al. (2021; https:// doi.org/10.1111/nph.16986) identified regions from oilseed rape genome that contribute to this control.

‘. . . this could ultimately represent an important

break-through to introduce diversity from wild relatives into

crops.’

Oilseed rape (Brassica napus; AACC; 2n= 38) is a recent allotetraploid species that originated from interspecific natural hybridization between domesticated forms of B. oleracea (CC, 2n= 18) and B. rapa (AA, 2n = 20) c. 2000–7500 years ago (Chalhoub et al., 2014; Lu et al., 2019). Brassica napus behaves almost completely like a diploid species during meiosis, with the vast majority of COs being formed between pairs of homologous chromosomes (Grandont et al., 2014). This does not preclude a small number of COs forming erratically between homoeologous chromosomes (Higgins et al., 2018). However, their frequency remains very low in stabilized varieties compared to that measured in resynthesized B. napus (i.e. those derived from an artificial hybridization between B. oleracea and B. rapa accessions) in which 30–45% of pollen mother cells show allosyndetic bivalents/mul-tivalents associations between A and C chromosomes indicating

that reciprocal exchanges of genetic material occur between homoeologous chromosomes during prophase I of meiosis (Szad-kowski et al., 2010). Following chromosome segregation, these exchanges can fix in the next generations, where they can be detected as the simultaneous loss/duplication of corresponding homoeologous regions (Gaeta et al., 2007; Nicolas et al., 2007; Higgins et al., 2018). Resynthesized B. napus lineages can be propagated for several generations, regardless of increased genomic instability and reduced fertility (Xiong & Pires, 2011; Rousseau-Gueutin et al., 2017). It is likely that oilseed rape originated among such highly unstable lineages through selection and/or evolution of genes or alleles that reduce CO formation between homoeologous chromosomes and therefore increase fitness.

Higgins et al. (2021) reasoned that any factor that would have been selected during B. napus evolution to reduce CO formation between homoeologues should also reduce the number of meiotic associations and the resulting homoeologous exchanges in a segregating population derived from a cross between a newly resynthesized line (i.e. that does not contain the selected genes/ alleles) and a stabilized variety (i.e. that on the contrary carries the genes/alleles; Fig. 1). This basic premise turned out to be true and Higgins et al. (2021) were able to map three reliable quantitative trait loci (QTLs) that affect the number of chiasmatic associations and/or exchanges of chromosome segments between homoeo-logues in a segregating population similar to the one described earlier. Interestingly, the low number of Pairing homoeologous loci identified in B. napus is consistent with that observed in allopolyploid bread wheat (Triticum aestivum L.: 2n= 6x = 42; AABBDD genome) where only two main loci, Ph1 and Ph2, control homoeologous recombination (Martın et al., 2017; Serra et al., 2021). Another similarity between the two species is that one locus proves to be far more efficient than the others: Ph1 in wheat and BnaPh1 in oilseed rape.

BnaPh1, the QTL located on chromosome BnaA9, was detected with the three data sets Higgins et al. (2021) used (i.e. Reciprocal Exchange, Deletion/Duplication, Synaptic Partner Switch accompanied by at least one CO) highlighting its robustness. This QTL represented 32–58% of the variation of the traits, depending on the data sets, with the repressive allele being contributed by the stabilized/cultivated variety. This QTL locates in a homoeologous position compared to PrBn that was found on chromosome BnaC9 (Liu et al., 2006) suggesting that the two loci could be two different homoeologous alleles playing the same role in two different genetic backgrounds (Darmor and PSA12). This also raises the question whether these two QTLs correspond to genes that prevent homoeologous synapsis or, on the contrary, genes that do not affect synapsis but prevent homoeologous COs. This dual effect was raised for Ph1 and it was shown that Ph1 rather prevents homoeologous COs to be resolved (Martın et al., 2017).

This article is a Commentary on Higgins et al. (2021), doi 10.1111/nph.16986

Ó 2021 The Authors

New PhytologistÓ 2021 New Phytologist Foundation

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Since Higgins et al. (2021) used a high-density single nucleotide polymorphism (SNP) array and mapped their QTLs on a saturated genetic map of> 21 000 SNPs, they achieved a coverage that allowed the physical location of the three QTLs. The region around BnaPh1 remains quite large (12.8 Mb) and includes hundreds of genes. As is customary in such situations, they proposed candidate genes under-lying the QTL interval, based on their involvement in meiosis but with no guarantee that the causal factor is among these ‘usual suspects’. Nevertheless, some lessons can be drawn from these data. For example, none of the candidates identified by Higgins et al. (2021) are directly involved in the main CO pathway (Class I COs) that was recently shown to mainly contribute to homoeologous CO formation in B. napus (Gonzalo et al., 2019). This contrasts with the Ph1 locus of wheat that encodes a duplicated copy of ZIP4 (Martin et al., 2017), a protein that serves as a hub and coordinates the formation of class I COs (Pyatnitskaya et al., 2019). This difference suggests that the control of CO formation between homoeologues is different in wheat and oilseed rape (discussed in Grandont et al., 2014).

In a previous study, Higgins et al. (2018) reported that few COs (1–2% of total COs) can still form between homoeologues in

B. napus, which hardly ever happens in wheat (Martin et al., 2017). However, several studies (reviewed in Martinez-Perez et al., 2001) reported the presence of synaptic partner switches at zygotene in wheat, the number of which decreases as meiosis progresses. As explained earlier by Jenkins & Rees (1991), this pattern may indicate either that ‘the synaptic multivalents were “undone”, eliminated by the dissolution and reassembly of the synaptonemal complex before pachytene [. . .] or that they were not consolidated by chiasmata (i.e. crossovers), the latter being localized strictly within segments of homologous pairs of chromosomes’. The presence of synaptic multivalents was also reported in B. napus (Grandont et al., 2014) and it remains to be understood how BnaPh1 limits CO formation between homoeologues (e.g. rejec-tion or dissolurejec-tion or nonconsolidarejec-tion of early inter-homoeologue recombination intermediates). In this regard, it must be empha-sized that, contrary to wheat and some other allopolyploid species, the homoeologous synaptic and chiasmatic associations that are rare in euploid B. napus (AACC) become dominant in allohaploids (AC) (Grandont et al., 2014). This indicates either that BnaPh1 is haplo-insufficient or that it does not specifically oppose the

Brassica rapa AA; 2n=20 Brassica oleracea CC; 2n=18 Nascentorresynthesized Brassica napus AACC; 2n=38 . . . Brassica napus AACC; 2n=38 Selection and fixation of BnaPh1 ( ) F1 hybrid DH progeny . . .

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--QT L m a p p in g BnaPh1 -/-BnaPh1 -/-BnaPh1 +/+ BnaPh1 +/+ BnaPh1

+/-Fig. 1 Schematic representation of logic behind the QTL mapping approach implemented by Higgins et al. (2021; https://doi.org/10.1111/nph.16986) in the recently published article in New Phytologist. Nascent or resynthesized oilseed rape tolerates homoeologous exchanges (HEs) that the selection of BnaPh1 during the evolution of Brassica napus helps to reduce. Assuming that the selected BnaPh1 allele is dominant, the hybrid between neo- and stabilized B. napus exhibits a normal meiosis where only homologous chromosomes synapse and recombine. In the doubled-haploid (DH) progeny derived from this hybrid, BnaPh1 segregates, either decreasing or increasing inter-homoeologue associations that further resolve into inter-homoeologue exchanges. Higgins et al. (2021) used these variables for QTL detection.

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formation of early recombination intermediates and COs between homoeologues. Therefore, BnaPh1 would rather help promote the maturation of recombination intermediates between the two homologues in the euploid lines, but it does not prevent COs between homoeologues in haploid lines.

The BnaPh1 interval does not contain genes involved in the mismatch repair system either. BnaPh1 is therefore not equivalent to the Ph2 locus of wheat, which was recently demonstrated to encode MSH7 (MutS Homologue 7; Serra et al., 2021), one of the proteins that is thought to mediate the recognition, excision and repair of DNA lesions and/or mispairs (Culligan & Hays, 2000). Although the regions around the minor QTLs (BnaA3 and BnaC7) identified by Higgins et al. (2021) include genes encoding another MutS Homologue protein, MSH3, it is uncertain whether these genes may be causal for the QTLs. First, MSH3 protein has an affinity for loop-outs of various sizes (Culligan & Hays, 2000 and references cited therein), rather than for base/base mismatches. Second, the two QTLs showed opposite effects on CO formation between homoeologues (i.e. the two homoeologous alleles con-tributed by the established variety reduced and increased inter-homoeologue COs, respectively). Once again, and despite an apparent similarity in the genetic architecture that controls CO formation between homoeologues in wheat and oilseed rape, the molecular underpinnings seems to be different.

Is this discrepancy really a surprise? We think not. Evolution is opportunistic and, as described earlier, there may be several solutions to ensure meiotic adaptations to polyploidy. The work presented by Higgins et al. (2021) is therefore an important step forward to identify new genes involved in homoeologous recom-bination in plants. In addition to improving our understanding of this basic phenomenon, this could ultimately represent an important breakthrough to introduce diversity from wild relatives into crops.

Acknowledgements

The Institut Jean-Pierre Bourgin (IJPB) benefits from the support of Saclay Plant Sciences– SPS (ANR-17-EUR-0007).

ORCID

Pierre Sourdille https://orcid.org/0000-0002-1027-2224 Eric Jenczewski https://orcid.org/0000-0001-7821-5384 Pierre Sourdille1* and Eric Jenczewski2 1_{Genetics, Diversity & Ecophysiology of Cereals, INRAE,} Universite Clermont-Auvergne, Clermont-Ferrand, 63000 France; 2_{Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite} Paris-Saclay, Versailles, 78000 France (**Author for correspondence: email [email protected])

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Key words: chromosome synapsis, crossover, homoeologous exchanges, homoeologous recombination, Ph1, Ph2, PrBn.

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