scholarly journals Reference transcriptome assembly and annotation for perennial ryegrass

Genome ◽  
2017 ◽  
Vol 60 (12) ◽  
pp. 1086-1088 ◽  
Author(s):  
Hiroshi Shinozuka ◽  
Noel O.I. Cogan ◽  
German C. Spangenberg ◽  
John W. Forster
Keyword(s):  
Perennial Ryegrass ◽  
Transcriptome Assembly ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Grass Species ◽  
Rna Seq ◽  
Pasture Grass ◽  
Tissue Samples ◽  
Genome Sequence Assembly ◽  
Transcriptome Resource

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 931 547 255 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.

Assessment of gene flow using tetraploid genotypes of perennial ryegrass (Lolium perenne L.)

2004 ◽  
Vol 55 (4) ◽  
pp. 389 ◽  
Author(s):  
K. V. Cunliffe ◽  
A. C. Vecchies ◽  
E. S. Jones ◽  
G. A. Kearney ◽  
J. W. Forster ◽  
...  
Keyword(s):  
Gene Flow ◽  
Seed Production ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Grass Species ◽  
Numerical Representation ◽  
Pasture Grass ◽  
Important Species ◽  
Lolium Perenne L ◽  
Total Seed

Ryegrass species are among the most important species in sown pastures, turf settings, and weed populations worldwide. Perennial ryegrass (Lolium perenne L.) is an outcrossing, wind-pollinated grass. Recent research has demonstrated the feasibility of developing transgenic perennial ryegrass varieties. In order to model the consequences of gene flow from transgenic grass genotypes in a field situation, the model non-transgenic trait of fertility among autotetraploid genotypes was chosen. Gene flow over distance and direction from a donor plot to surrounding sexually compatible recipient plants was studied. Reproductive isolation was achieved through the fertility barrier that arises between tetraploid and diploid ryegrass genotypes, despite the presence of diploid plants in a meadow situation. Fertility was used as an indication of effective gene flow over distance and direction. Measures of the fertility of recipient plants included total seed production (TSP), floret site utilisation (FSU), and relative fertility of recipient plants as a percentage of those within the donor plot (RF%). A leptokurtic distribution for gene flow was identified, with differences in the rate of decline over distance depending on direction. Simple sequence repeat (SSR) polymorphism was used to identify the paternity of progeny plants. The proportional representation of parents among the progeny was not significantly different from that expected due to the numerical representation of the different donor parent genotypes. The results of this research will have important implications for risk analysis prior to the field release of transgenic ryegrasses, fescues, and other pasture grass species, and for seed production in terms of cultivar purity and optimum isolation distance.

Persistence of perennial ryegrass, tall fescue and cocksfoot following annual sowings: influence of grass species, ryegrass cultivar and pasture age on yield, composition and density

2021 ◽  
Vol 17 ◽  
Author(s):  
Tom Maxwell ◽  
Grant Edwards ◽  
Katherine Tozer ◽  
Gerald Cosgrove
Keyword(s):  
Perennial Ryegrass ◽  
Tall Fescue ◽  
Grass Species ◽  
Botanical Composition ◽  
Release Date ◽  
Confounding Effect ◽  
Pasture Grass ◽  
Age Cohort ◽  
Tiller Density ◽  
Pasture Age

Persistence is an important component of perennial pasture-grass productivity. Defining traits that affect persistence is essential for improving pasture longevity through plant breeding and for identifying persistence traits that should be included in cultivar ranking indices. Compared with conventional longitudinal studies, where a single sowing is monitored over time, repeated annual sowings allow the effects on persistence of sowing year and the ensuing interactions between environment and age of pasture to be identified. An experiment was commenced in 2015 under sheep grazing in Canterbury and in 2016 under cattle grazing in Waikato, where eight cultivars of perennial ryegrass representing different ploidy, flowering date, and cultivar age (release date), and one cultivar each of tall fescue and cocksfoot were sown in four randomised complete blocks in autumn each year. This paper reports interim data on spring and autumn pasture yield, composition, and density of 3-year-old, 2-year-old and 1-year-old pastures exposed to the same environmental conditions within the same, single year. There were significant effects on yield, botanical composition, basal cover and tiller density due to cultivar, pasture age, and their interaction. When the confounding effect of year-to-year variation was removed by comparing each age cohort in the same year, the underlying differences among grass species and cultivars, and ages of pasture, is starting to reveal the nature of this influence on pasture persistence.

scholarly journals Profiling the Lolium perenne Microbiome: From Seed to Seed

2020 ◽  
Vol 4 (3) ◽  
pp. 281-289 ◽  
Author(s):  
Ian Tannenbaum ◽  
Jatinder Kaur ◽  
Ross Mann ◽  
Timothy Sawbridge ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Grass Species ◽  
Growth Media ◽  
Dairy Farmers ◽  
Pasture Grass ◽  
Core Microbiome ◽  
Operational Taxonomic Units ◽  
Bacterial Microbiome ◽  
Seed Transmissibility

Lolium perenne (perennial ryegrass) is a common temperate pasture grass species and is favored by dairy farmers. Commercially, the known association with the mutualistic endophytic fungus Epichloë festucae subsp. lolii is used to enhance insect resistance of host plants. Knowledge of other members of the microbiome and their functions are limited. Sequencing of the V4 region of the 16S ribosomal RNA gene was used to examine the bacterial microbiome of perennial ryegrass (Alto) seed (generation 1 [G1]), subsequent mature plants grown in soil and sand, and seed (generation 2 [G2]) from crosses of these mature plants. The G1 microbiome was dominated by the class Gammaproteobacteria. The mature plant microbiomes were far more diverse, comprising up to 37 classes inclusive of Gammaproteobacteria. Different growth media yielded different microbiome profiles in mature plants. The G2 microbiome, similar to the G1 microbiome, was dominated by Gammaproteobacteria as the primary constituent, with additional supplementation from class Bacilli. This suggests the continuation of a core microbiome which persists from seed through plant maturation to seed. This study sheds new light on the hereditability of perennial ryegrass bacterial microbiomes and has identified some operational taxonomic units of potential commercial significance due to their seed transmissibility, and their roles are currently being explored.

Targeted genotyping-by-sequencing permits cost-effective identification and discrimination of pasture grass species and cultivars

2016 ◽  
Vol 129 (5) ◽  
pp. 991-1005 ◽  
Author(s):  
Luke W. Pembleton ◽  
Michelle C. Drayton ◽  
Melissa Bain ◽  
Rebecca C. Baillie ◽  
Courtney Inch ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Cost Effective ◽  
Grass Species ◽  
Pasture Grass

scholarly journals Plant virus interaction mechanisms and joint pathways in mosaic disease of Small Cardamom (Elettaria cardamomum maton) by RNA-Sec

2020 ◽  
Vol 35 (1-2) ◽  
Author(s):  
Sarika Jaiswal ◽  
Aamir Khan ◽  
Johnson George K ◽  
Rahul Singh Jasrotia ◽  
U B Angadi ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Mosaic Disease ◽  
Whole Genome Sequence ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Web Resource ◽  
Elettaria Cardamomum ◽  
Molecular Events ◽  
Genomic Resource

Small cardamom (Elettaria cardamomum), is one of the costliest spices across the globe. It is grown in limited coastal tropical countries. It is widely exported agri-produce with global turnover of > 10 billion USD. It is majorly affected by the mosaic or marble disease and hence warrants the deep study at molecular level. Till now, there is no availability of whole genome sequence along with any genomic resources. Under such cases, RNA seq approach can be a rapid and economical alternative to gather the information at genomic level. De novo transcriptome assembly was carried out using Illumina Hiseq data. Analysis revealed a total of 5317 differentially expressed genes, 2267 transcription factors, >100 pathways and 175,952 genic region putative markers. Gene regulatory network analysis was performed to see the molecular events playing role in marble disease. We report the first transcriptomic results that shows the disease mechanism mediated by perturbation in auxin homeostasis and ethylene signaling. These events lead to senescence. We also developed the web-genomic resource, SCMVTDb which houses putative molecular markers, candidate genes and transcript information. Such web resource can be used in small cardamom germplasm improvement against mosaic disease in endeavour of its increased productivity.

scholarly journals Developing Heterotic Groups for Successful Hybrid Breeding in Perennial Ryegrass

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1410
Author(s):  
Maximilian Vogt ◽  
Steven Yates ◽  
Timothy Sykes ◽  
Wilbert Luesink ◽  
Michael Koch ◽  
...  
Keyword(s):  
Perennial Ryegrass ◽  
Genotyping By Sequencing ◽  
Breeding Program ◽  
Hybrid Breeding ◽  
Yield Potential ◽  
Grass Species ◽  
Heterotic Groups ◽  
Growing Seasons ◽  
Synthetic Varieties ◽  
Genetically Improved

Perennial ryegrass (Lolium perenne L.), an important forage grass species in temperate regions, is genetically improved by population breeding. Although valued for their broad genetic base, the resulting synthetic varieties only partially exploit heterosis. Hybrid breeding offers opportunities to fix beneficial heterotic patterns more effectively and, hence, to increase the yield potential. A suspected bottleneck in the production of perennial ryegrass hybrids is the genetic intermixture of existing germplasm, impeding the definition of heterotic groups. In this study, selected parental populations of a diploid and tetraploid cytoplasmic male sterility (CMS)-based hybrid breeding program were characterized using genotyping-by-sequencing (GBS). Hybrid populations, derived from 26 parental combinations of the tetraploid breeding program, were tested for yield performance and compared to synthetic varieties at five sites over four growing seasons. The hybrids significantly outperformed the synthetics by 4.15% on average for total dry matter yield. Additionally, GBS revealed the existence of sub-populations within the tetraploid CMS germplasm. This sub-population structure represents the untapped potential that could be exploited for heterosis to further increase biomass yields. Here, we show that CMS hybrids generate substantial yield gains in perennial ryegrass and provide a method to further improve hybrid breeding, using GBS to select for heterotic groups.

scholarly journals Sequence-based genetic mapping of Cynodon dactylon Pers. reveals new insights into genome evolution in Poaceae

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Tilin Fang ◽  
Hongxu Dong ◽  
Shuhao Yu ◽  
Justin Q. Moss ◽  
Charles H. Fontanier ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genetic Map ◽  
First Generation ◽  
Cynodon Dactylon ◽  
Warm Season ◽  
Genotyping By Sequencing ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Genome Sequence Assembly ◽  
New Cultivars

AbstractBermudagrass (Cynodon dactylon Pers.) is an important warm-season perennial used extensively for turf, forage, soil conservation and remediation worldwide. However, limited genomic information has hindered the application of molecular tools towards understanding genome evolution and in breeding new cultivars. We genotype a first-generation selfed population derived from the tetraploid (4x = 36) ‘A12359’ using genotyping-by-sequencing. A high-density genetic map of 18 linkage groups (LGs) is constructed with 3,544 markers. Comparative genomic analyses reveal that each of nine homeologous LG pairs of C. dactylon corresponds to one of the first nine chromosomes of Oropetium thomaeum. Two nested paleo-ancestor chromosome fusions (ρ6-ρ9-ρ6, ρ2-ρ10-ρ2) may have resulted in a 12-to-10 chromosome reduction. A segmental dissemination of the paleo-chromosome ρ12 (ρ1-ρ12-ρ1, ρ6-ρ12-ρ6) leads to the 10-to-9 chromosome reduction in C. dactylon genome. The genetic map will assist in an ongoing whole genome sequence assembly and facilitate marker-assisted selection (MAS) in developing new cultivars.

Stability and Yield of Cool-Season Pasture Grass Species Grown at Five Irrigation Levels

Crop Science ◽  
2002 ◽  
Vol 42 (3) ◽  
pp. 890 ◽  
Author(s):  
Blair L. Waldron ◽  
Kay H. Asay ◽  
Kevin B. Jensen
Keyword(s):  
Grass Species ◽  
Cool Season ◽  
Pasture Grass ◽  
Irrigation Levels
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