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

African rices genome projects : GLASS and irigin : [P129]

The GLASS project (GLAberrima ASSembly), jointly between IRD and AfricaRice, aims to sequence de novo the two African NERICA parents, CG14 and TOG5681, representing the two opposite of the glaberrima variability. For that purpose we choose an hybrid approach combining the Illumina high-quality short reads and the PacificBioscience Long Reads technology. Tests were performed using Illumina data on TOG 5307 and TOG5681, using AbySS short-reads assembler, with 19x and 25x total data respectively. For TOG5307, we obtained 153'774 contigs (minimum size of 200b), mean size of 1.5 kb (N50 = 2.4kb, N90 = 637b). On TOG5681, we obtained 97'196 contigs (minimum size 200b), with a mean size of 2.8kb (N50 = 5kb, N90 = 1.3 kb). The overall assembly for each genome is of 0.56x for TOG5307 and of 0.69x for TOG5681. Just adding +6x of Illumina data almost doubled the assembly efficiency. PacBio data test on C2 and XL kits were also perfomed for CG14 data, providing respectively 143'456 and 99'488 contigs (mean size of 3140b and 3184b), with a 1.12x and 0.79x coverage. The C2 10x sequencing in PacBio for CG14 and TOG5681, and the 60x sequencing in Illumina for each is on the way. The annotation will be transfered from the Nipponbare MSU7.0 reference genome using tools such as QOD (Mancheron et al, 2010) and BLAST/BLAT based scripts. These sequences will be immediatly available for the whole community without restriction. The IRIGIN project from France Genomique (International RIce Genomic INitiative, http://irigin.org) is headed by IRD and CIRAD, and aimed to provide valuable genetic stocks genomic data in the frame of GriSP. African rice (300 O. glaberrima and 100 O. barthii) will be deeply resequenced (25x) and aligned on their reference (from the GLASS project). In the same time , NAMs population (indica x tropical japonica) from AfricaRice and CIAT will be genotyped (using low-coverage sequencing), to provide to the rice community the best genetic map ever created in plants, with the highest level of coverage ever seen. Thousand of terabytes of raw data and billions of polymorphic data will be gathered within this project, and will be distributed to the whole rice community as soon as possible. (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 : 2. F2 populations

Dans la génération F2, la sélection naturelle des gamètes et des zygotes peut affecter les linkages génétiques. Une équation mathématique qui prend toutes les probabibilités de linkage en compte est développée. L'intégration des marqueurs génétiques dominants et codominants permet d'obtenir une courbe de probabilité asymptotique. La comparaison de l'utilité et de la précision des modèles montre que la prise en compte des marqueurs dominants seuls ne donne pas assez d'information sur le cas de distorsions de ségrégation. L'estimation de la fraction de recombinaisons entre les marqueurs codominants est peu affectée par la sélection, ce qui n'est pas le cas pour les marqueurs dominant

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

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

SNP-based QTL mapping of 15 complex traits in barley under rain-fed and well-watered conditions by a mixed modeling approach

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint

The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives

Rice was the first crop to have a high-quality reference genome sequence and is now at the forefront of intense functional and evolutionary research for two reasons-its central role in world food security, and its status as a model system for grasses. A thorough characterization of the rice genome cannot be accomplished without a deep understanding of its evolutionary history. The genus Oryza contains two cultivated and 22 wild rice species that represent 10 distinct genome types embedded within a robust phylogeny spanning a ~15 million year time span. The genus contains an untapped reservoir of agriculturally important traits and a historical record of genomic changes (especially those related to domestication, polyploidy, speciation and adaption).The two main objectives of the 'Oryza Map Alignment Project' (OMAP) were to functionally characterize the rice genome from a comparative standpoint and to provide essential tools to leverage the novel genetic diversity from wild relatives for rice improvement. The objective of this review is to summarize our efforts towards developing the most comprehensive genus-wide set of publicly available BAC resources for the genus Oryza, the first of its kind among plants (and perhaps higher eukaryotes), and their applications

A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 50 end of the gene.Peer reviewe

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site