Indistinguishable patterns of recombination resulting from male and female meioses in Brassica napus (oilseed rape)

Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres

Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity in each generation through the formation of crossovers (COs). However, due to their importance in genome stability, COs are highly regulated in frequency and distribution. We previously demonstrated that this strict regulation of COs can be modified, both in terms of CO frequency and distribution, in allotriploid Brassica hybrids (2n = 3x = 29; AAC) resulting from a cross between Brassica napus (2n = 4x = 38; AACC) and Brassica rapa (2n = 2x = 20; AA). Using the recently updated B. napus genome now including pericentromeres, we demonstrated that COs occur in these cold regions in allotriploids, as close as 375 kb from the centromere. Reverse transcription quantitative PCR (RT-qPCR) of various meiotic genes indicated that Class I COs are likely involved in the increased recombination frequency observed in allotriploids. We also demonstrated that this modified recombination landscape can be maintained via successive generations of allotriploidy (odd ploidy level). This deregulated meiotic behavior reverts to strict regulation in allotetraploid (even ploidy level) progeny in the second generation. Overall, we provide an easy way to manipulate tight recombination control in a polyploid crop.

Fine mapping of meiotic crossovers in Brassica oleracea reveals patterns and variations depending on direction and combination of crosses

Meiotic recombination is crucial for assuring proper segregation of parental chromosomes and generation of novel allelic combinations. As this process is tightly regulated, identifying factors influencing rate, and distribution of meiotic crossovers (COs) is of major importance, notably for plant breeding programs. However, high-resolution recombination maps are sparse in most crops including the Brassica genus and knowledge about intraspecific variation and sex differences is lacking. Here, we report fine-scale resolution recombination landscapes for 10 female and 10 male crosses in Brassica oleracea, by analyzing progenies of five large four-way-cross populations from two reciprocally crossed F1s per population. Parents are highly diverse inbred lines representing major crops, including broccoli, cauliflower, cabbage, kohlrabi, and kale. We produced approximately 4.56T Illumina data from 1248 progenies and identified 15 353 CO across the 10 reciprocal crosses, 51.13% of which being mapped to <10 kb. We revealed fairly similar Mb-scale recombination landscapes among all cross combinations and between the sexes, and provided evidence that these landscapes are largely independent of sequence divergence. We evidenced strong influence of gene density and large structural variations on CO formation in B. oleracea. Moreover, we found extensive variations in CO number depending on the direction and combination of the initial parents crossed with, for the first time, a striking interdependency between these factors. These data improve our current knowledge on meiotic recombination and are important for Brassica breeders.

First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq

Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F₁ mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F₁ population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.

Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas

Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs.

Conserved patterns of chromosome pairing and recombination in Brassica napus crosses

The patterns of chromosome pairing and recombination in two contrasting Brassica napus F1 hybrids were deduced. One hybrid was from a winter oilseed rape (WOSR) x spring oilseed rape cross, the other from a resynthesized B. napus x WOSR cross. Segregation at 211 equivalent loci assayed in the population derived from each hybrid produced two collinear genetic maps. Alignment of the maps indicated that B. napus chromosomes behaved reproducibly as 19 homologous pairs and that the 19 distinct chromosomes of B. napus each recombined with unique chromosomes from the interspecific hybrid between Brassica rapa and Brassica oleracea. This result indicated that the genomes of the diploid progenitors of amphidiploid B. napus have remained essentially unaltered since the formation of the species and that the progenitor genomes were similar to those of modern-day B. rapa and B. oleracea. The frequency and distribution of crossovers were almost indistinguishable in the two populations, suggesting that the recombination machinery of B. napus could cope easily with different degrees of genetic divergence between homologous chromosomes. Efficient recombination in wide crosses will facilitate the introgression of novel alleles into oilseed rape from B. rapa and B. oleracea (via resynthesized B. napus) and reduce linkage drag.

Sex-specific crossover distributions and variations in interference level along Arabidopsis thaliana chromosome 4

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, >1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed.

Meiotic crossovers between homologous chromosomes ensure their proper segregation to generate ultimately gametes. They also create new allelic combinations which contribute to the diversity of traits among individuals. In all eukaryotes, the number and the localization of crossovers along chromosomes are not random. In addition, crossovers are not independent of each other: the occurrence of a crossover lowers the probability that another crossover arises in its vicinity. The mechanism of this phenomenon, called “crossover interference,” is one of the most challenging puzzles that geneticists have been faced with in the last century. In this paper, we precisely described the distribution of crossovers along Chromosome 4 of the model plant species Arabidopsis thaliana, separately in male and female meiosis. Interestingly, we observed that crossovers are 1.7 more numerous in male than in female meiosis, and this increase is especially marked at the ends of the chromosome. Moreover, our results provide the first evidence that the level of interference along a chromosome is not a constant and is correlated with the physical distance between crossovers. These results shed new light on the determinism of crossover localization and could have important outcomes on the relevance of current models of crossover interference.

Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm

The introgression of winter germplasm into spring canola (Brassica napus L.) represents a novel approach to improve seed yield of hybrid spring canola. In this study, quantitative trait loci (QTL) for seed yield and other traits were genetically mapped to determine the effects of genomic regions introgressed from winter germplasm into spring canola. Plant materials used comprised of two populations of doubled haploid (DH) lines having winter germplasm introgression from two related French winter cultivars and their testcrosses with a spring line used in commercial hybrids. These populations were evaluated for 2 years at two locations (Wisconsin, USA and Saskatchewan, Canada). Genetic linkage maps based on RFLP loci were constructed for each DH population. Six QTL were detected in the testcross populations for which the winter alleles increased seed yield. One of these QTL explained 11 and 19% of the phenotypic variation in the two Canadian environments. The winter allele for another QTL that increased seed yield was linked in coupling to a QTL allele for high glucosinolate content, suggesting that the transition of rapeseed into canola could have resulted in the loss of favorable seed yield alleles. Most QTL for which the introgressed allele decreased seed yield of hybrids mapped to genomic regions having homoeologous non-reciprocal transpositions. This suggests that allelic configurations created by these rearrangements might make an important contribution to genetic variation for complex traits in oilseed B. napus and could account for a portion of the heterotic effects in hybrids.

Genome-wide analysis of the frequency and distribution of crossovers at male and female meiosis in Sinapis alba L. (white mustard)

We present the first genetic linkage maps of Sinapis alba (white mustard) and a rigorous analysis of sex effects on the frequency and distribution of crossovers at meiosis in this species. Sex-averaged maps representing recombination in two highly heterozygous parents were aligned to give a consensus map consisting of 382 loci defined by restriction fragment length polymorphisms and arranged in 12 linkage groups with no unlinked markers. The loci were distributed in a near-random manner across the genome, and there was little evidence of segregation distortion. From these dense maps, a subset of spaced informative markers was used to establish recombination frequencies assayed separately in male and female gametes and derived from two distinct genetic backgrounds. Analyses of 746 gametes indicated that recombination frequencies were greater in male gametes, with the greatest differences near the ends of linkage groups. Genetic background had a lesser effect on recombination frequencies, with no discernible pattern in the distribution of such differences. The possible causes of sex differences in recombination frequency and the implications for plant breeding are discussed.

Recombination difference between sexes: a role for haploid selection

Why the autosomal recombination rate differs between female and male meiosis in most species has been a genetic enigma since the early study of meiosis. Some hypotheses have been put forward to explain this widespread phenomenon and, up to now, only one fact has emerged clearly: In species in which meiosis is achiasmate in one sex, it is the heterogametic one. This pattern, known as the Haldane-Huxley rule, is thought to be a side effect, on autosomes, of the suppression of recombination between the sex chromosomes. However, this rule does not hold for heterochiasmate species (i.e., species in which recombination is present in both sexes but varies quantitatively between sexes) and does not apply to species lacking sex chromosomes, such as hermaphroditic plants. In this paper, we show that in plants, heterochiasmy is due to a male-female difference in gametic selection and is not influenced by the presence of heteromorphic sex chromosomes. This finding provides strong empirical support in favour of a population genetic explanation for the evolution of heterochiasmy and, more broadly, for the evolution of sex and recombination.

Detection of chromosomal rearrangements derived from homologous recombination in four mapping populations of Brassica napus L

Genetic maps of Brassica napus were constructed from four segregating populations of doubled haploid lines. Each mapping population had the same male parent and used the same set of RFLP probes, facilitating the construction of a consensus map. Chromosomal rearrangements were identified in each population by molecular marker analysis and were classified as de novo homologous nonreciprocal transpositions (HNRTs), preexisting HNRTs, and homologous reciprocal transpositions (HRTs). Ninety-nine de novo HNRTs were identified by the presence of a few lines having duplication of a chromosomal region and loss of the corresponding homologous region. These de novo HNRTs were more prevalent in one population that had a resynthesized B. napus as a parent. Preexisting HNRTs were identified by fragment duplication or fragment loss in many DH lines due to the segregation of HNRTs preexisting in one of the parents. Nine preexisting HNRTs were identified in the three populations involving natural B. napus parents, which likely originated from previous homologous exchanges. The male parent had a previously described HRT between N7 and N16, which segregated in each population. These data suggest that chromosomal rearrangements caused by homologous recombination are widespread in B. napus. The effects of these rearrangements on allelic and phenotypic diversity are discussed.

RFLP linkage analysis and mapping genes controlling the fatty acid profile of Brassica juncea using reciprocal DH populations

An RFLP linkage map, comprising 300 linked and 16 unlinked loci, was constructed using reciprocal DH populations of Brassica juncea. The linked loci were organized into 18 linkage groups and seven unlinked segments, covering a total map distance of 1,564 cM. The A and B genomes were identified. The chi(2) test showed that 96.1% of the common intervals in the two populations differed non-significantly for recombination fractions, thus strongly suggesting the absence of sex-based differences for recombination fractions in B. juncea. Two QTLs, E(1a) and E(1b), significantly affected erucic acid content, and individually explained 53.7% and 32.1%, respectively, and collectively 85.8% of the phenotypic variation in the population. The QTLs E(1a) and E(1b) showed epistasis, and the full model including epistasis explained nearly all of the phenotypic variation in the population. The QTLs E(1a) and E(1b) were also associated with contents of oleic, linoleic and linolenic acids. Three additional QTLs (LN(2), LN(3) and LN(4)) significantly influenced linolenic acid content. The QTL LN(2) accounted for 35.4% of the phenotypic variation in the population. Epistatic interactions were observed between the QTLs E1a and LN(2). The stability of the detected QTLs across years and locations, and breeding strategies for improving the fatty acid profile of B. juncea, are discussed.

Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses

Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.Key words: coffee, mapping, sex differences, segregation distortion, recombination frequency.