Search

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931547 255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48 713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling, and identification of candidate genes for multiple biological functions. Key words: Lolium, pasture, RNA-Seq, unigene, candidate gene, breeding. Résumé : Une approche RNA-Seq a été employée pour générer une ressources transcriptomique exhaustive pour le ray-grass anglais, une importante espèce fourragère tempérée. Au total, 931547 255 lectures ont été obtenues à partir de 19 librairies correspondant à 19 tissus distincts, incluant à la fois des stades végétatifs et reproductifs du développement. L'assemblage des données a généré un jeu de référence final composé de 48 713 contig et scaffold. Cette ressource transcriptomique permettra de supporter l'assemblage de séquences génomiques complètes, la génomique comparée, les méthodes de génotypage par séquençage (GBS) fondées sur l'échantillonnage des transcrits ainsi que l'identification de gènes candidats pour de nombreuses fonctions biologiques. [Traduit par la Rédaction] Mots-clés : Lolium, pâturage, RNA-Seq, unigène, gène candidat, sélection., Introduction Perennial ryegrass (Lolium perenne L.) is a globally important pasture grass of temperate livestock production systems. Perennial ryegrass is a member of the Pooideae (cool-season) sub-family of the grass [...]

Assignment or exclusion of an individual to specific populations or cultivars based on molecular genetic markers provides an attractive approach for varietal identification at the individual level in cross-pollinated plant species. The objectives of this study were (i) to explore the molecular diversity and relationships between Australasian perennial ryegrass (Lolium perenne L.) populations; (ii) to investigate accuracy of assignment of individuals to different types of populations including ecotypic, nonrestricted--and restricted-based cultivars; and (iii) to determine the effect of variable number of SSR loci and different statistical analysis methods on assignment accuracy. Eight forage perennial ryegrass populations comprising 48 individual plants per population were genotyped with 29 simple sequence repeat (SSR) marker loci. The number of alleles per locus ranged from 3.72 to 6.76. The mean observed heterozygosity varied from 0.419 to 0.538. Various genetic distance estimates and clustering methods obtained results consistent with breeding history. Genetic variation among (8.7%) and within populations (91.3%) was significant. Accuracy of individual assignment differed by population type, and it was higher (>90%) for restricted-based cultivars than for ecotypic and nonrestricted-based populations. These results indicate that SSR marker profiles can be effectively used to assign individuals for outbreeding populations such as perennial ryegrass. The approach used in this study may be useful for ryegrass germplasm management issues such as cultivar identification at the individual level.

Computational analysis has been used to align the genetic map of white clover (Trifolium repens L.) with the draft genome sequence of the model legume species Medicago truncatula Gaertn. In silico comparison based on white clover expressed sequence tags that contain simple sequence repeat loci revealed substantial macrosynteny between the genomes of these two species, which are closely related within the Trifolieae tribe of the Fabaceae family. Six of the eight homoeologous chromosome groups (HGs) of allotetraploid white clover show predominant relationships with single M. truncatula (Mt) chromosomes, while the two remaining groups may have participated in an evolutionary reciprocal translocation event. On this basis, a new chromosome nomenclature system for allotetraploid white clover is proposed such that HG A = 3, HG B = 8, HG C = 7, HG D = 4, HG E = 1, HG F = 2, HG G = 5, and HG H = 6. A rationalized linkage map ordering system has also been demonstrated. Improved knowledge of the relationships between agricultural and model forage legume genomes will facilitate prediction of gene location for key agronomic traits for pasture production. Key words: comparative genetics, Trifolium repens, legumes, in silico, evolution, linkage groups, allopolyploid. Des analyses bioinformatiques ont ete faites pour aligner la carte genetique du trefle blanc (Trifolium repens L.) avec la version preliminaire de la sequence genomique de la legumineuse modele Medicago truncatula Gaertn. Des analyses in silico realisees avec des etiquettes de sequences exprimees du trefle blanc qui contiennent des microsatellites ont revele une macrosyntenie substantielle entre les genomes de ces deux especes, lesquelles sont tres proches au sein de la tribu des trifoliees de la famille des fabacees. Six des huit groupes chromosomiques homeologues (GH) de l'allotetraploide qu'est le trefle blanc ont montre une parente predominante avec un seul chromosome du M. truncatula, tandis que les deux autres groupes ont possiblement participe a une translocation reciproque survenue au cours de l'evolution. Sur cette base, une nouvelle nomenclature chromosomique pour le trefle blanc allotetraploide est proposee selon laquelle HG A = 3, HG B = 8, HG C = 7, HG D = 4, HG E = 1, HG F = 2, HG G = 5 et HG H =6. Un systeme rationalise pour definir l'ordre sur la carte genetique est egalement illustre. Une connaissance amelioree des relations entre les genomes de legumineuses cultivees et modeles facilitera la prediction de l'emplacement des genes pour des caracteres agronomiques cles en production fourragere. Mots-cles : genetique comparee, Trifolium repens, legumineuses, in silico, evolution, groupes de liaison, allopolyploide. [Traduit par la Redaction], Introduction The legume family (Fabaceae) is highly diverse and provides the second most important global food and forage source after grasses (Graham and Vance 2003). The Papilinoideae subfamily of the [...]

Abstract: White clover (Trifolium repens L.) is an important temperate pasture legume that plays a key role as a companion to grass species, such as perennial ryegrass (Lolium perenne L.). [...]

Abstract: The causative organism of crown rust in ryegrasses (Puccinia coronata f.sp. lolii) is an obligate biotroph that causes significant economic losses within the temperate grazing industries of dairy, meat, [...]

Ref.: Genome, 49: 572-583. Please note that during the preparation of the above manuscript, the table containing details of primer sequences inadvertently incorporated information in 2 instances from 2 distinct [...]