Devenir des génomes et des gènes dans un contexte polyploïde: cas du colza (Brassica napus L.)

Thèse soutenue à AGROCAMPUS-OUEST sous le sceau de l'Université Européenne de Bretagne. - Publication autorisée par le jury Annexes : Bibliogr. (217-237 p.)Allopolyploidy plays a key role in Angiosperm speciation and biodiversity. Allopolyploid species are good models to understand how genes and genome redundancy are managed at the confrontation of two genomes in resynthesized plants from known progenitors. Progenitors of oilseed rape (Brassica napus (AACC, 2n=38) are close to B. rapa (AA, 2n=20) and B. oleracea (CC, 2n=18). Homoeologous recombination (between parental genomes) is detected after some generations of resynthesized B. napus, while gene expression is strongly modified as early as in F1 hybrids. This work focused on the magnitude of structural modifications at onset of polyploid formation and their consequences on homoeologous gene expression. Using cytogenetic approach, we studied the first meiosis of F1 hybrids (AC genome) and their derived S0 plants (AACC genome) obtained through somatic doubling or using its female unreduced gametes. Homoeologous recombination in their progrenies was studied by molecular approach, focusing on two highly syntenic homoeologous chromosomes (A1 and C1) to maximize homoeologous recombination probability. We finally studied gene expression in homoeologous regions on A1 and C1 where recombination occurred and modulates their copy number. We showed that the first meiosis of B. napus blends genomes (Szadkowski et al., 2010), in a magnitude that depend upon polyploid formation pathways and cytoplasm. These genetic rearrangements bias homoeologous gene expression even at heterozygous stage. My results provide new clues to understand genetic and gene expression instability in young polyploid species like B. napus.L’allopolyploïdie (plusieurs lots de génomes apparentés dans un individu) joue un rôle majeur dans la spéciation et la biodiversité des Angiospermes contemporaines. Les espèces allopolyploïdes permettent d’aborder les mécanismes de régulation de la redondance d’information génétique lors de la confrontation de deux génomes proches. On peut pour cela utiliser des hybrides polyploïdes synthétisés de novo à partir des espèces parentales préalablement identifiées. Le colza (Brassica napus AACC, 2n=38) est issu du croisement entre B. rapa (AA, 2n=20) et B. oleracea (CC, 2n=18). Au cours des premières générations de colzas synthétiques, on observe de la recombinaison entre régions homéologues (mêmes régions sur chaque génome), alors que des modifications fonctionnelles se mettent en place dès la confrontation des deux génomes dans l’hybride F1 (génome AC). L’objectif de ce travail est de déterminer l’importance relative des modifications structurales et leurs conséquences fonctionnelles dans les toutes premières générations après hybridation. Nous avons étudié par analyses cytogénétique et génétique la stabilité de la première méiose d’hybrides F1 (génome AC) et des S0 (génome AACC) correspondantes issus de gamètes non réduits ou de doublement somatique. Nous avons focalisé cette étude sur les deux chromosomes homéologues les plus synténiques (A1 et C1) pour maximiser la probabilité de recombinaison homéologue. Nous avons enfin étudié les conséquences des remaniements faisant varier le nombre de copies de gènes homéologues sur leur niveau d’expression. Nous montrons que la polyploïdie soumet la première génération de colzas synthétiques à une phase de forte restructuration des génomes A et C, les gamètes transmis n’étant pas équivalents selon le mode de formation du polyploïde et le cytoplasme (Szadkowski et al., 2010). Nous montrons également que ces restructurations à l’état hétérozygote semblent dicter le niveau d’expression des copies de gènes homéologues. Cette étude devrait permettre de mieux comprendre la phase d’instabilité précédant la stabilisation d’une jeune espèce allopolyploïde telle que le colza

Homoeolog expression bias and expression level dominance in allopolyploid cotton

Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we explored gene expression patterns in interspecific hybrid F-1, and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up-or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F1 hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection

New natural organic–inorganic pH indicators: Synthesis and characterization of pro-ecological hybrid pigments based on anthraquinone dyes and mineral supports

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Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding.

International audienceIn this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability

First meioses of Brassica napus are genome blenders

First meioses of Brassica napus are genome blenders. Plant and Animal Genomes Conferenc

Screening a priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors

Screening a priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors. Effectome meeting 201

La première méiose des colzas resynthetisés, un mixeur de génome

Chromosomal reshuffling occurs during meiosis in newly created polyploid species in Brassica, contributing to differentiation of parental genomes in the hybrid. In newly synthesized Brassica napus, studies have shown little effect of the very first meiosis in genomic restructuring. However, the frequent and non random fixation of translocations (HNRTs) in early generations of re-synthesized B. napus suppose a major role of the first meiosis in chromosome rearrangements. To study homeologous pairing and remodelling at the creation of the polyploidy, homeologous pair of chromosomes A1-C1 provide an appropriate model, being completely collinear in macrosynteny in B. napus and its progenitors and being the most rearranged pair in natural B. napus haploids.On multiple lineages of synthetic B.napus, we aimed to : (i) Establish the frequent pairing of A1-C1 during the first meiosis of neo-polyploids; (ii) Assess precisely the impact of this meiosis on the nature, the size and the frequency of rearrangements generated on A1 and C1; (iii) Determine the effect of A1-C1 rearrangements on the perturbation of regular meiotic behaviour in contrasted progeny. (i) Various S0 (colchicines doubled hybrids) lineages of resynthesized B. napus have been created from 4 different diploid parents to test genetic background as long as a reciprocal cross to test maternal cytoplasmic effect. By using BAC-FISH (Fluorescent In Situ Hybridisation) approach at meiosis of the first generation S0, it is possible to detect implication of A1-C1 in abnormal chromosome pairing. Evidence for A-C pairing at first meiosis exist, and this work will determine the A1-C1 pairing ability of the progenitors structure. (ii) To assess the impact of first meiosis on genome remodelling in gametes, crosses were performed between the 4 amphidiploids (S0) and a natural B. napus (92 ind. for each). We identified a contrasted behaviour of the B. rapa cytoplasm population, but all had highly frequent inherited chromosomes rearrangements using molecular markers from A1 and C1, and their nature (translocation vs. deletion) will be discussed on a subset of contrasted individuals using BAC FISH differentiating homeologous regions. (iii) By establishing the meiotic behaviour of this subset of plants, we will validate the effect of A1-C1 homogenisation on further genome instability. These data will bring new insight on genome restructuration in polyploids after genome duplication

Genome-wide association mapping of loci involved in Potato virus Y resistance and tolerance in pepper germplasm

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