Marqueurs moléculaires et amélioration des plantes

Ce projet a pour but la création assistée par marqueurs d'une centaine de lignées "pseudo-isogéniques", chaque lignée ayant un fond génétique #sativa et un fragment introgressé #glaberrima d'environ 20 cM. La totalité des fragments introgressés devra couvrir l'ensemble du génome. La divergence ancienne (2 à 3 Ma) et l'isolement génétique des deux espèces cultivées de riz permet d'attendre un polymorphisme élevé, ce qui fait de ce croisement un matériel idéal pour une étude de cartographie par marqueurs moléculaires (PCR ciblée). La première étape sera la construction d'une carte génétique à base de marqueurs PCR-RFLP, sur la population BC1. L'obtention des lignées se fera par plusieurs croisements en retour successifs sur le parent #sativa, en choisissant à chaque étape les lignées dont la configuration allélique pour les marqueurs permet de garder les fragments recherchés. La dernière étape est une fixation par autofécondation. Les intérêts d'une telle approche sont multiples : utilisation en sélection, ressources génétiques expérimentales, étude et fixation des transgressions, approche "QTL" simplifiée et améliorée (fond génétique homogène ; multilocal), organisation du génome de #glaberrima vs sativa (recombinaisons ; domestication), cartographie comparée. (Résumé d'auteur

Aroma in rice : genetic analysis of a quantitative trait

Une nouvelle approche a permis de cartographier pour la première fois un gène majeur et 2 QTL contrôlant l'arôme du grain chez le riz. Elle impliquait la combinaison de deux techniques, la quantification des composés volatils des eaux de cuisson par CPG et la cartographie par marqueurs moléculaires. Quatre types de marqueurs moléculaires ont été utilisés (RFLP, RAPD, STS, isozymes). L'évaluation et la cartographie ont été faites sur une population d'haploïdes doublés qui conférait une évaluation précise du caractère en permettant l'analyse de grandes quantités de grains par génotype et a rendu possible la comparaison de la CPG et des tests sensitifs. La taille de population (135 lignées) fournissait une bonne précision de cartographie. Plusieurs marqueurs du chromosome 8 ont été trouvés liés à un gène majeur contrôlant la présence de 2-acétyl-1-pyrroline (AcPy), le composé principal de l'arôme du riz. De plus, nos résultats ont montré que la concentration en AcPy dans les plantes est régulée par au moins deux régions chromosomiques. Les estimations de fréquences de recombinaison du chromosome 8 ont été corrigées pour les fortes distorsions de ségrégation. Cette étude confirme que l'AcPy est le composé principal de l'arôme du riz. L'utilisation des marqueurs liés au gène majeur et aux QTL de l'AcPy en sélection assistée par marqueurs (en backcross) peut être envisagée. (Résumé d'auteur

Maximum-likelihood models for mapping genetic markers showing segregation distortion : 1. Backcross populations

Une approche du maximum de vraisemblance est utilisée pour estimer les fréquences de recombinaison entre des marqueurs présentant des distorsions de ségrégation dans des populations backcross. L'hypothèse faite ici est que les distorsions sont induites par des différences de viabilité entre gamètes ou zygotes dues à la présence d'un ou plusieurs allèles contre-sélectionnés. Nous montrons que l'estimateur de Bailey (1949) reste convergent donc efficace sous des conditions plus générales que celles définies par son auteur. Cet estimateur devrait donc être utilisé à la place de l'estimateur classique du maximum de vraisemblance. La question de la détection d'une liaison peut être affectée par les distorsions de ségrégation. (Résumé d'auteur

Insights into the genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and its molecular determinism in rice

This research and HN were funded by the Consultative Group for International Agricultural Research Program on rice-agrifood systems (CRP-RICE, 2017–2022), the French National Institute for Sustainable Development (IRD–France), and the International Join Laboratory (LMI-Rice 2) in Vietnam. Funding for some parts of this work was also provided through an SFC ODA GCRF award via the University of St Andrews, United Kingdom. The James Hutton Institute receives funding from the Rural and Environment Science and Analytical Services Division of the Scottish Government.Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F2 hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.Publisher PDFPeer reviewe

Identification of new sources of resistance to RHBV- rice hoja blanca virus

With the aim to find new sources of resistance to rice hoja blanca (white leaf) disease, transmitted by the insect Tagosodes orizicolus, 660 genotypes were evaluated under greenhouse and field conditions. Seven resistant genotypes were identified, and genomic studies were performed to demonstrate that the resistance in these sources is genetically different from that of Fedearroz 2000, which is currently the variety with the most resistance to hoja blanca. These new resistance sources constitute a resource that can be used to sustainably extend hoja blanca disease management throughout all of the rice-growing regions of tropical America. This is the first report of hoja blanca resistance in indica rice and different from that of Fedearroz 2000

Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines

<p>Abstract</p> <p>Background</p> <p>Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs.</p> <p>Results</p> <p>We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice <it>Oryza glaberrima </it>MG12 (acc. IRGC103544) in the genetic background of <it>Oryza sativa ssp. </it>tropical <it>japonica </it>(cv. Caiapó). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the <it>Rice stripe necrosis virus </it>was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11.</p> <p>Conclusions</p> <p>Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor underlying resistance to this virus. This population is a powerful breeding tool. It also helps in overcoming hybrid sterility barriers between species of rice.</p

Implementation and modeling of a femtosecond laser-activated streak camera

8 June 2017) A laser-activated streak camera was built to measure the duration of femtosecond electron pulses. The streak velocity of the device is 1.89 mrad/ps, which corresponds to a sensitivity of 34.9 fs/pixels. The streak camera also measures changes in the relative time of arrival between the laser and electron pulses with a resolution of 70 fs RMS. A full circuit analysis of the structure is presented to describe the streaking field and the general behavior of the device. We have developed a general mathematical model to analyze the streaked images. The model provides an accurate method to extract the pulse duration based on the changes of the electron beam profile when the streaking field is applied

Methylation in the CHH context allows to predict recombination in rice

DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics