A transcriptome map of perennial ryegrass (Lolium perenne L.)

Studer, Bruno; Byrne, Stephen; Nielsen, Rasmus Oestergaard; Panitz, Frank; Berthou, Christian; Islam, Shofiqul; Pfeifer, Matthias; Lübberstedt, Thomas; Asp, Torben

doi:10.1186/1471-2164-13-140

Cited by 62 publications

(75 citation statements)

References 95 publications

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“…The genetic linkage map based on single-nucleotide polymorphisms of expressed perennial ryegrass genes (Studer et al, 2012) served as a marker scaffold for the GenomeZipper. For this study, a total of 762 genederived markers (between 79 and 154 on each LG, 109 on average) have been located on the genetic linkage map.…”

Section: Input Data Analysismentioning

confidence: 99%

“…Suppression of recombination in centromeric regions leading to clustering of genes has been described in perennial ryegrass and meadow fescue Studer et al, 2012) and other grass species such as barley (Stein et al, 2007) and Brachypodium (Huo et al, 2011). However, these regions encompass substantial parts of chromosomes and genes (King et al, 2007), limiting the success of map-based cloning.…”

Section: The Perennial Ryegrass Genomezipper: a Useful Tool For Fine-mentioning

confidence: 99%

“…The genetic linkage map of expressed perennial ryegrass (Lolium perenne) genes (Studer et al, 2012) served as a scaffold for the GenomeZipper. In brief, the VrnA two-way pseudotestcross mapping population consisting of 184 F2 perennial ryegrass genotypes was used to map EST-derived single-nucleotide polymorphisms.…”

Section: Perennial Ryegrass Marker Scaffold and Unigenesmentioning

confidence: 99%

“…Until now, such genome-wide in silico comparative studies in forage and turf grass species have been limited by the availability of mapped marker sequences. However, a transcriptome-based genetic linkage map has recently become available for perennial ryegrass (Studer et al, 2012) with genome size of around 2.6 Gb (1C = 2,623 Mb [Kopecký et al, 2010]). This map contains 838 DNA markers spanning 750 centimorgan (cM) with an average marker distance of less than 0.9 cM, making it the most saturated genetic linkage map of perennial ryegrass to date.…”

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The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

et al. 2012

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Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genomewide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

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Section: Input Data Analysismentioning

confidence: 99%

Section: The Perennial Ryegrass Genomezipper: a Useful Tool For Fine-mentioning

confidence: 99%

Section: Perennial Ryegrass Marker Scaffold and Unigenesmentioning

confidence: 99%

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The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

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“…Genes from the least distant reference genome (in this case, B. distachyon) get highest priority for ordering, and subsequently, the additional reference genomes are overlaid onto this scaffold. Due to the absence of a high-quality genetic marker map of meadow fescue, genetic markers of L. perenne chromosome 4 were used as a scaffold to anchor the collinear segments from the model genomes (Studer et al, 2012).…”

Section: Assembly Of Chromosome 4f Sequences and Genome Zipper Analysismentioning

confidence: 99%

Flow Sorting and Sequencing Meadow Fescue Chromosome 4F

et al. 2013

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The analysis of large genomes is hampered by a high proportion of repetitive DNA, which makes the assembly of short sequence reads difficult. This is also the case in meadow fescue (Festuca pratensis), which is known for good abiotic stress resistance and has been used in intergeneric hybridization with ryegrasses (Lolium spp.) to produce Festulolium cultivars. In this work, we describe a new approach to analyze the large genome of meadow fescue, which involves the reduction of sample complexity without compromising information content. This is achieved by dissecting the genome to smaller parts: individual chromosomes and groups of chromosomes. As the first step, we flow sorted chromosome 4F and sequenced it by Illumina with approximately 503 coverage. This provided, to our knowledge, the first insight into the composition of the fescue genome, enabled the construction of the virtual gene order of the chromosome, and facilitated detailed comparative analysis with the sequenced genomes of rice (Oryza sativa), Brachypodium distachyon, sorghum (Sorghum bicolor), and barley (Hordeum vulgare). Using GenomeZipper, we were able to confirm the collinearity of chromosome 4F with barley chromosome 4H and the long arm of chromosome 5H. Several new tandem repeats were identified and physically mapped using fluorescence in situ hybridization. They were found as robust cytogenetic markers for karyotyping of meadow fescue and ryegrass species and their hybrids. The ability to purify chromosome 4F opens the way for more efficient analysis of genomic loci on this chromosome underlying important traits, including freezing tolerance. Our results confirm that next-generation sequencing of flow-sorted chromosomes enables an overview of chromosome structure and evolution at a resolution never achieved before.

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Nucleotide diversity of vernalization and flowering‐time‐related genes in a germplasm collection of meadow fescue (Festuca pratensis Huds. syn. Lolium pratense (Huds.) Darbysh.)

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Cogan

et al. 2013

Ecology and Evolution

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In plant species, control of flowering time is an important factor for adaptation to local natural environments. The Vrn1, CO, FT1 and CK2α genes are key components in the flowering-specific signaling pathway of grass species. Meadow fescue is an agronomically important forage grass species, which is naturally distributed across Europe and Western Asia. In this study, meadow fescue flowering-time-related genes were resequenced to assess nucleotide diversity in European and Western Asian subpopulations. Identified sequence polymorphisms were then converted into PCR-based molecular genetic markers, and a meadow fescue germplasm collection was genotyped to investigate global allelic variation. Lower nucleotide diversities were observed for the Vrn1 and CO orthologs, while relatively higher values were observed for the FT1 and casein kinase II α-subunit (CK2α) orthologs. The nucleotide diversity for FT1 orthologs in the Western Asian subpopulation was significantly higher than those of the European subpopulation. Similarly, significant differences in nucleotide diversity for the remaining genes were observed between several combinations of subpopulation. The global allele distribution pattern was consistent with observed level of nucleotide diversity. These results suggested that the degree of purifying selection acting on the genes differs according to geographical location. As previously shown for model plant species, functional specificities of flowering-time-related genes may also vary according to environmental conditions.

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A transcriptome map of perennial ryegrass (Lolium perenne L.)

Cited by 62 publications

References 95 publications

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

Flow Sorting and Sequencing Meadow Fescue Chromosome 4F

Nucleotide diversity of vernalization and flowering‐time‐related genes in a germplasm collection of meadow fescue (Festuca pratensis Huds. syn. Lolium pratense (Huds.) Darbysh.)

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