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

Deciphering the genome structure and paleohistory of _Theobroma cacao_

We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution

Development of microsatelllte markers for the genetic analysis of Crinipellis perniciosa.

Witches' broom disease of cacao (Theobroma cacao L.), caused by Crinipellis perniciosa (Stahel) Singer, is the most importam disease of cacao in the cacao growing areas of South America and Caribbean Tslands. Very little is known about the genetic biology of the pathogen population, and this infonnation is very importam to the host improvement programs and deployment of resistant planting material. A collaborative America Countries intemational program was initiated to identify and describe the genetic diversity of Crinipellis perniciosa in South America. Microsatellites (SSR) constitute highly infonnative genetic markers for popuJation genetic studies due to their co-dominant and multiallelic nature and distribution in the genome. SSR primers were searched in the C.perniciosa genome data base and designed as potential candidates to define an efficient, standardized, molecular fingerprinting protocol for this pathogen. These primers have been evaluated for reliability, widespread disttibution across the C.perniciosa genome and their ability to discriminate isolates ofthis fungus. The final objective here is to study the diversity structure ofthe C. perniciosa population from the main cacao growing area in South America countries. Preliminary results are reported

Dernières avancées dans le séquençage du génome de Theobroma Cacao Criollo : nouvel assemblage, annotations et outils

Le 26 décembre 2010, le Consortium international pour le séquençage du génome du cacaoyer (International Cocoa Genome Sequencing Consortium -ICGS) a publié dans Nature Genetics la première séquence du génome de Theobroma cacao L. Le génotype choisi, le B97-61/B2, est une variété de Criollo qui apporte un arôme fin au chocolat. Cette première séquence comportait 76% de la couverture du génome et 67% de l'assemblage a été ancré dans une carte génétique à haute densité. Au cours de l'année qui vient de s'écouler, de nouveaux progrès ont été faits sur l'assemblage, l'annotation du génome et l'identification de familes de gènes. De plus, de nouveaux outils ont été développés pour Înieux exploiter la séquence. Un navigateur de génome a été cré pour permettre aux utilisateurs d'accéder à la séquence, de visualiser leurs antions (structure des gènes, fonction putative du gène, analyse génomiques comparatives, expression des gènes dans différents tissus/conditions, etc.) et interroger les données avec plusieurs sources biologiques, effectuer une comparaison de séquence et lancer une recherche par mots-clés. L'assemblage actuel représente 87,1% de la taile estimée du génome (430 Mb). Cet assemblage semble couvrir une très large proportion de l'euchromatine du génome de T cacao, permettant de récupérer 97,8% des ressources sur les unigènes (38 737 unigènes assemblés à partir de 715 457 séquences EST) dans l'assemblage du génome. Les annotations ont révélé 28 798 gènes codants de protéines panni lesquels 86,1% pourient être ancrés dans une carte génétique à haute densité. Seulement 20% du génome se composait d'éléments transposables, soit un pourcentage significativement inférieur à comparer à d'autres génomes de taille similaire. Cette séquence de génome va faciliter une meilleure compréhension de l'élaboration des caractéristiques et accélèrera la sélection de T. cacao par une sélection assistée par marqueurs efficace et l'exploitation des ressources génétiques. Le navigateur de génome est disponible gratuitement sur le site web suivant: httpJ/cocoagendb.cirad_fr (Résumé d'auteur

A genetically anchored physical framework for Theobroma cacao cv. Matina 1-6

<p>Abstract</p> <p>Background</p> <p>The fermented dried seeds of <it>Theobroma cacao </it>(cacao tree) are the main ingredient in chocolate. World cocoa production was estimated to be 3 million tons in 2010 with an annual estimated average growth rate of 2.2%. The cacao bean production industry is currently under threat from a rise in fungal diseases including black pod, frosty pod, and witches' broom. In order to address these issues, genome-sequencing efforts have been initiated recently to facilitate identification of genetic markers and genes that could be utilized to accelerate the release of robust <it>T. cacao </it>cultivars. However, problems inherent with assembly and resolution of distal regions of complex eukaryotic genomes, such as gaps, chimeric joins, and unresolvable repeat-induced compressions, have been unavoidably encountered with the sequencing strategies selected.</p> <p>Results</p> <p>Here, we describe the construction of a BAC-based integrated genetic-physical map of the <it>T. cacao </it>cultivar Matina 1-6 which is designed to augment and enhance these sequencing efforts. Three BAC libraries, each comprised of 10× coverage, were constructed and fingerprinted. 230 genetic markers from a high-resolution genetic recombination map and 96 Arabidopsis-derived conserved ortholog set (COS) II markers were anchored using pooled overgo hybridization. A dense tile path consisting of 29,383 BACs was selected and end-sequenced. The physical map consists of 154 contigs and 4,268 singletons. Forty-nine contigs are genetically anchored and ordered to chromosomes for a total span of 307.2 Mbp. The unanchored contigs (105) span 67.4 Mbp and therefore the estimated genome size of <it>T. cacao </it>is 374.6 Mbp. A comparative analysis with <it>A. thaliana, V. vinifera</it>, and <it>P. trichocarpa </it>suggests that comparisons of the genome assemblies of these distantly related species could provide insights into genome structure, evolutionary history, conservation of functional sites, and improvements in physical map assembly. A comparison between the two <it>T. cacao </it>cultivars Matina 1-6 and Criollo indicates a high degree of collinearity in their genomes, yet rearrangements were also observed.</p> <p>Conclusions</p> <p>The results presented in this study are a stand-alone resource for functional exploitation and enhancement of <it>Theobroma cacao </it>but are also expected to complement and augment ongoing genome-sequencing efforts. This resource will serve as a template for refinement of the <it>T. cacao </it>genome through gap-filling, targeted re-sequencing, and resolution of repetitive DNA arrays.</p

Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers

Background and Aims The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Methods Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. Key Results and ConclusionsWe determine the closest diploid progenitors of the triploid 'Cavendish' and 'Gros Michel' subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. 'Cavendish', 'Plantain' and 'Mutika- Lujugira'), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference. (Résumé d'auteur

Deciphering the genome structure of Theobroma cacao (W107)

Theobroma cacao L., is a diploid tree fruit species, originated from the South American rainforests, and constitutes an important source of incomes for farmers of tropical countries. We produced a high quality draft genome sequence corresponding to a 16,7X genome coverage of a criollo genotype. The assembly corresponds to 76% of the estimated genome size of the T. cacao genotype B97-61/B2 (430 Mbp). This assembly appears to cover a very large proportion of the euchromatin of the T. cacao genome, allowing to recover 97.8% of the unigene resource (38,737 unigenes assembled from 715,457 EST sequences) in the genome assembly. Annotations revealed 28,798 protein-coding genes among which 82% could be anchored in a high density genetic map. Only 20% of the genome consisted in transposable elements, a significantly lower percentage compared to other genome of similar size. This first cocoa genome sequence was the support for several genome analyses revealing specific extension of some gene families. The comparative mapping of genes involved in disease resistance and quality traits, localised in the genome sequence, and QTLs related to these traits highlighted several co-localisations between them and candidate genes potentially involved in useful cocoa trait variations. This genome sequence will facilitate a better understanding of trait elaboration and will accelerate T. cacao breeding through efficient marker assisted selection and exploitation of genetic resources. A genome browser allows to access freely to the cocoa sequence data at the following website : http://cocoagendb.cirad.fr. (Texte intégral