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Fusarium crown and root rot is a severe fungal disease of tomato caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL). In this study, the genomic location of the FORL-resistance locus was determined using a set of molecular markers on chromosome 9 and an [F.sub.2] population derived from FORL-resistant inbred 'AV107-4' (Solanum lycopersicum) x susceptible 'L3708' (Solanum pimpinellifolium). Bioassay performed using Korean FORL strain KACC 40031 showed single dominant inheritance of FORL resistance in the [F.sub.2] population. In all, 13 polymerase chain reaction-based markers encompassing approximately 3.6-72.0 Mb of chromosome 9 were developed based on the Tomato-EXPEN 2000 map and SolCAP Tomato single nucleotide polymorphism array analysis. These markers were genotyped on 345 [F.sub.2] plants, and the FORL-resistance locus was found to be present on a pericentromeric region of suppressed chromosomal recombination in chromosome 9. The location of the FORL-resistance locus was further confirmed by testing these markers against diverse commercial tomato and stock cultivars resistant to FORL. A restriction fragment length polymorphism marker, PNU-D4, located at approximately 6.1 Mb of chromosome 9 showed the highest match with the resistance locus and was used for conducting high-resolution melting analysis for marker-assisted selection of FORL resistance. Key words: disease resistance, Fusarium crown and root rot, Fusarium oxysporum f. sp. radicis-lycopersici, molecular marker, Solanum lycopersicum. La pourriture fusarienne de la tige et des racines est une maladie fongique grave causee par le Fusarium oxysporum f. sp. radicis-lycopersici (FORL). Dans ce travail, la position genomique d'un locus de resistance au FORL a ete determinee a l'aide de marqueurs moleculaires situes sur le chromosome 9 et d'une population [F.sub.2] derivee du croisement entre la lignee fixee resistante 'AV107-4' (Solanum lycopersicum) et la lignee sensible 'L3708' (Solanum pimpinellifolium). Un bioessai realise a l'aide de la souche coreenne FORL KACC 40031 a montre une heredite monogenique dominante de la resistance au FORL au sein de cette population. En tout, 13 marqueurs PCR couvrant une region s'etendant approximativement entre 3,6 et 72,0 Mb du chromosome 9 ont ete developpes sur la base de la carte genetique TomatoEXPEN 2000 et de la puce de genotypage SolCAP SNP. Ces marqueurs ont ete genotypes sur 345 plantes [F.sub.2], et le locus de resistance au FORL a ete situe dans une region pericentromerique du chromosome 9 qui presente une suppression de la recombinaison. La position de ce locus de resistance a ete confirmee en utilisant ces marqueurs sur une collection de diverses varietes commerciales et sources de resistance au FORL. Un polymorphisme de longueur du fragment de restriction, PNU-D4, situe a environ 6,1 Mb sur le chromosome 9, a montre la plus forte association avec le locus de resistance et a ete utilise pour realiser des analyses de dissociation a haute resolution (<< high-resolution melting >>) pour des fins de selection assistee de la resistance au FORL. [Traduit par la Redaction] Mots-cles : resistance a la maladie, pourriture fusarienne de la tige et des racines, Fusarium oxysporum f. sp. radicis-lycopersici, marqueur moleculaire, Solanum lycopersicum., Introduction Fusarium oxysporum (Sacc.) Snyder & Hans., a soil-borne haploid fungal plant pathogen causes vascular wilt or root rot in various agricultural crops and ornamental plants (Olivain and Alabouvette 1997; [...]

A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of cereal EST-SSRs in ryegrass (Lolium spp.). A total of 165 cereal EST-SSRs were tested; a high rate of transferability (57%) and polymorphism (67% of functional EST-SSRs) was demonstrated between cereals and ryegrass. A total of 46 segregating loci derived from 37 EST-SSRs were mapped on an existing ryegrass genetic map. The mapped loci were uniformly distributed across all seven linkage groups without significant clustering at the distal regions of linkage groups. Sequences of ryegrass amplicons generated by randomly selected 16 EST-SSRs were aligned with reference sequences of cereal EST-SSRs. The SSR motifs and repeat lengths of the cereal EST-SSR markers were different from the majority of ryegrass amplicons. Furthermore, a majority of EST-SSRs amplified different flanking sequences of SSRs in ryegrass than the original cereal sequences. Our results suggest that the high degree of cereal EST-SSR transferability to ryegrass can be a useful enhancement to the molecular database of PCR-based markers but sequence analysis is essential before transferring genetic information using comparative mapping. Key words: Lolium, Poaceae, polymorphism, SSR marker, transferability, comparative mapping. La presence d'un grand nombre d'etiquettes de genes exprimes (EST) au sein des banques de sequences publiques ont permis de developper systematiquement des marqueurs microsatellites (SSR). Les EST-SSR derives de regions codantes conservees presentent une transportabilite importante aupres d'especes apparentees. Dans le present travail, les auteurs ont explore l'interet des EST-SSR developpes chez les cereales pour emploi chez le ray-grass (Lolium spp.). Un ensemble de 165 EST-SSR a ete teste. Des fortes proportions de transportabilite (57 %) et de polymorphisme (67% des EST-SSR fonctionnels) ont ete observees entre les cereales et le ray-grass. Au total, 47 locus en segregation, reveles a l'aide de 37 EST-SSR, ont ete positionnes sur une carte genetique du ray-grass. Les locus etaient egalement distribues sur les sept groupes de liaison sans groupement significatif aux extremites distales des groupes de liaison. Les sequences des amplicons obtenus chez le ray-grass a l'aide de 16 EST-SSR pris au hasard ont ete alignees avec les sequences de reference des EST-SSR chez les cereales. Les motifs et le degre de repetition des SSR chez les cereales etaient differents de ceux observes chez le ray-grass dans la majorite des cas. De plus, une majorite des regions amplifiees bordant les EST-SSR etaient differentes chez le ray-grass. Ces resultats suggerent que la grande transportabilite des EST-SSR chez le raygrass contribue a ameliorer la base de donnees moleculaires sur les marqueurs de type PCR mais que l'analyse des sequences est essentielle en vue de l'utilisation de l'information genetique pour de la cartographie comparee. Mots-cles : Lolium, poacees, polymorphisme, marqueur SSR, transportabilite, cartographie comparee. [Traduit par la Redaction], Introduction During the last two decades, a large number of expressed sequence tags (ESTs) have been generated in several cereal crop species. This information is an excellent resource for molecular [...]

Abstract Background Cultivated tomato (Solanum lycopersicum L.) has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP) discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market), OH9242 (processing), and PI114490 (cherry) were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α) used to define the confidence interval (CI), and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error) increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst) suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace), and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka) to synonymous substitutions (Ks) for 20 loci with multiple SNPs (≥ 4 per locus). Six of 20 loci showed ratios of Ka/Ks ≥ 0.9. Conclusion Array-based SFP discovery was an efficient method to identify a large number of molecular markers for genetics and breeding in elite tomato germplasm. Patterns of sequence variation across five major tomato groups provided insight into to the effect of human selection on genetic variation.

Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species. [ABSTRACT FROM AUTHOR]