scholarly journals ForageGrassBase: Molecular resource for the forage grass Festuca pratensis Huds

2019 ◽  
Author(s):  
Jeevan Karloss Antony Samy ◽  
Odd Arne Rognli ◽  
Mallikarjuna Rao Kovi
Keyword(s):  
Draft Genome ◽  
Forage Yield ◽  
Grass Species ◽  
Comparative Genomic ◽  
Festuca Pratensis ◽  
Forage Grass ◽  
Forage Grasses ◽  
Genome Database ◽  
Genomic Resources ◽  
Link Type

AbstractBackgroundMeadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. F. pratensis is a diploid (2n =14) outbreeding species that belongs to the genus Festuca. Together with Lolium, they are the most important genera of forage grasses in temperate regions. F. pratensis has good winter survival, with high quality dry matter yields and persistency, and is suitable both for frequent-cutting conservation regimes and for grazing. It is a significant component of species-rich permanent pastures in the temperate regions, ensuring high forage yield under harsh climatic conditions where other productive forage grass species are unable to grow. However, genomic resources for F. Pratensis is not available so far.ResultsThe draft genome sequences of two F. pratensis genotypes “HF7/2” and “B14/16” are reported in this study. Here, using the draft genome, functional annotation datasets of two F. pratensis cultivars, we have constructed the F. pratensis genome database http://foragegrass.org/, the first open-access platform to provide comprehensive genomic resources related to this forage grass species. The current version of this database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes using Genome Browser (GBrowse). In addition, we have integrated comparative genomic tracks for F. pratensis genomes by mapping F.pratensis genome to the barley, rice, Brachypodium and maize genomes. We have integrated homologus search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadble data gives an user friendly access to F. pratensis genomic resouces. All data in the database were manually curated.ConclusionTo our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. It provides valuable resources for a range of research fields related to F. pratensis and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org. In the near future, we will expand the ForageGrassBase by adding genomic tools for other forage grass species, as soon as their genomes become available.

scholarly journals ForageGrassBase: molecular resource for the forage grass meadow fescue (Festuca pratensis Huds.)

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Jeevan Karloss Antony Samy ◽  
Odd Arne Rognli ◽  
Mallikarjuna Rao Kovi
Keyword(s):  
Draft Genome ◽  
Grass Species ◽  
Comparative Genomic ◽  
Festuca Pratensis ◽  
Forage Grass ◽  
Forage Grasses ◽  
Meadow Fescue ◽  
Crop Species ◽  
Genome Database ◽  
Genomic Resources

Abstract Meadow fescue (Festuca pratensis Huds.) is one of the most important forage grasses in temperate regions. It is a diploid (2n = 14) outbreeding species that belongs to the genus Festuca. Together with Lolium perenne, they are the most important genera of forage grasses. Meadow fescue has very high quality of yield with good winter survival and persistency. However, extensive genomic resources for meadow fescue have not become available so far. To address this lack of comprehensive publicly available datasets, we have developed functionally annotated draft genome sequences of two meadow fescue genotypes, ‘HF7/2’ and ‘B14/16’, and constructed the platform ForageGrassBase, available at http://foragegrass.org/, for data visualization, download and querying. This is the first open-access platform that provides extensive genomic resources related to this forage grass species. The current database provides the most up-to-date draft genome sequence along with structural and functional annotations for genes that can be accessed using Genome Browser (GBrowse), along with comparative genomic alignments to Arabidopsis, L. perenne, barley, rice, Brachypodium and maize genomes. We have integrated homologous search tool BLAST also for the users to analyze their data. Combined, GBrowse, BLAST and downloadable data gives a user-friendly access to meadow fescue genomic resources. To our knowledge, ForageGrassBase is the first genome database dedicated to forage grasses. The current forage grass database provides valuable resources for a range of research fields related to meadow fescue and other forage crop species, as well as for plant research communities in general. The genome database can be accessed at http://foragegrass.org.

Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 637-647 ◽  
Author(s):  
M A. Rouf Mian ◽  
Malay C Saha ◽  
Andrew A Hopkins ◽  
Zeng-Yu Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Tall Fescue ◽  
Related Species ◽  
Grass Species ◽  
Forage Grass ◽  
Forage Grasses ◽  
Cool Season ◽  
Phylogenetic Relations ◽  
Wide Range

Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca–Lolium species in the study. Tall wheatgrass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.Key words: phylogeny, EST-SSR, forage grasses, tall fescue.

scholarly journals Application of SCoT markers for accessing of genetic diversity of gramineous forage grass species

2021 ◽  
Vol 901 (1) ◽  
pp. 012038
Author(s):  
Yu M Mavlyutov ◽  
A O Shamustakimova ◽  
I A Klimenko
Keyword(s):  
Lolium Multiflorum ◽  
Molecular Genetic ◽  
Grass Species ◽  
Festuca Rubra ◽  
Festuca Pratensis ◽  
Forage Grass ◽  
Marker System ◽  
Scot Marker ◽  
Dna Profiles ◽  
Subsequent Identification

Abstract Using the SCoT marker system, 8 varieties of cereal grasses belonging to 5 species were analyzed: Festuca pratensis, Lolium perenne, Lolium multiflorum, Festuca rubra, Festulolium. Of the 10 tested SCoT markers, 7 informative markers were selected that reveal interspecies genetic polymorphism. According to the results of the analysis, DNA profiles characteristic of each studied species were obtained, and primers allowing to detect intervarietal differences for subsequent identification and molecular genetic passportization were selected.

Wind-mediated seed dispersal of invasive forage grasses from agricultural grasslands in Hokkaido, Japan

2019 ◽  
Vol 12 (02) ◽  
pp. 133-141
Author(s):  
Chika Egawa ◽  
Atsushi Shoji ◽  
Hiroyuki Shibaike
Keyword(s):  
Seed Dispersal ◽  
Poa Pratensis ◽  
Plant Cover ◽  
Kentucky Bluegrass ◽  
Dispersal Distance ◽  
Phleum Pratense ◽  
Grass Species ◽  
Forage Grass ◽  
Forage Grasses ◽  
Number Of Seeds

AbstractAlthough introduced pasture grasses are essential for forage production in current livestock farming, some species cause serious impacts on native biodiversity when naturalized. Information on the seed dispersal of invasive forage grasses from cultivated settings to surrounding environments can inform management efforts to prevent their naturalization. In this case study, we quantified the wind-mediated seed dispersal distance and amount of dispersed seed of invasive forage grasses from agricultural grasslands in Hokkaido, northern Japan. In total, 200 funnel seed traps were installed around three regularly mown grasslands and one unmown grassland where various forage grass species were grown in mixture. Seeds of each species dispersed outside the grasslands were captured from May to October 2017. Based on the trapped distances of seeds, the 99th percentile dispersal distance from the grasslands was estimated for six species, including timothy (Phleum pratense L.), orchardgrass (Dactylis glomerata L.), and Kentucky bluegrass (Poa pratensis L.). For two dominant species, P. pratense and D. glomerata, the numbers of seeds dispersed outside the field under mown and unmown conditions were determined under various plant cover situations. The estimated dispersal distances ranged from 2.3 m (P. pratense) to 31.5 m (P. pratensis), suggesting that areas within approximately 32 m of the grasslands are exposed to the invasion risk of some forage grass species. For both P. pratense and D. glomerata, the number of seeds dispersed outside the unmown grassland exceeded 100 seeds m−2 under high plant cover situations, while the number of seeds dispersed from the mown grasslands at the same plant cover level was less than one-third of that number. The results suggest that local land managers focus their efforts on frequent mowing of grasslands and monitoring of the areas within approximately 32 m of the grasslands to substantially reduce the naturalization of invasive forage grasses.

COLD HARDINESS OF FORAGE GRASSES GROWN ON THE CANADIAN PRAIRIES

1987 ◽  
Vol 67 (4) ◽  
pp. 1111-1115 ◽  
Author(s):  
A. E. LIMIN ◽  
D. B. FOWLER
Keyword(s):  
Triticum Aestivum ◽  
Cold Hardiness ◽  
Triticum Aestivum L ◽  
Grass Species ◽  
Forage Grass ◽  
Forage Grasses ◽  
Canadian Prairies ◽  
Seeding Date ◽  
Secale Cereale L ◽  
Cold Hardy

Cold hardiness ratings of 18 forage grass species, and cold hardy reference cultivars of winter wheat (Triticum aestivum L. ’Norstar’) and rye (Secale cereale L. ’Puma’), were compared to provide estimates of the winterkill risk for forage grasses established in the spring and fall on the Canadian prairies.Key words: Forage grasses, cold hardiness, seeding date, winter survival

scholarly journals The Strawberry DNA Testing Handbook

HortScience ◽  
2019 ◽  
Vol 54 (12) ◽  
pp. 2267-2270 ◽  
Author(s):  
Youngjae Oh ◽  
Jason D. Zurn ◽  
Nahla Bassil ◽  
Patrick P. Edger ◽  
Steven J. Knapp ◽  
...  
Keyword(s):  
Fragaria X Ananassa ◽  
Breeding Program ◽  
Dna Testing ◽  
Genome Database ◽  
Breeding Programs ◽  
Genomic Resources ◽  
Link Type ◽  
Strawberry Breeding

The availability of strawberry (Fragaria ×ananassa) genomic resources has increased dramatically in recent years. Some of these resources are readily applicable to strawberry breeding programs for use in DNA-informed breeding. Information about these tests and how to interpret them is dispersed through numerous manuscripts or in the laboratories that use them routinely. To assist breeders in identifying tests available to their breeding program and in implementing them in their program, a compendium of strawberry DNA tests was created. This compendium is available for download from the Genome Database for Rosaceae (https://www.rosaceae.org/organism/Fragaria/x-ananassa?pane=resource-4). This resource will be updated continually as old tests are modified and new tests are created.

Effect of plant age and cottony snow mold on winter survival of forage grasses

2002 ◽  
Vol 82 (4) ◽  
pp. 701-708 ◽  
Author(s):  
S. F. Hwang ◽  
D. A. Gaudet ◽  
G. D. Turnbull ◽  
K. F. Chang ◽  
R. J. Howard ◽  
...  
Keyword(s):  
Dry Matter ◽  
Forage Yield ◽  
Winter Survival ◽  
Grass Species ◽  
Dry Matter Yield ◽  
Forage Grasses ◽  
Snow Mold ◽  
Red Fescue ◽  
Mold Resistance ◽  
The Impact

The low temperature basidiomycete (LTB, syn. Copribus psychromorbidus Traquair), the causal agent of cottony snow mold, is a major constraint to forage grass survival and productivity in the parkland region of the Canadian prairies under prolonged snow cover (e.g., 160 d). Studies were conducted to establish the level of the snow mold resistance in seven grass species commonly grown in western Canada and to identify the seeding dates that permit grass plants to develop maximum levels of resistance to snow mold. Following attack by the LTB fungus, considerable variation in winter survival and forage yield was observed among the grass species. Smooth brome and meadow brome were most resistant, followed by timothy and creeping red fescue. Tall fescue and orchardgrass were the most susceptible. Controlled-environment and field studies demonstrated that orchardgrass seeded in late spring resulted in greater winter survival and dry matter yield than when seeded in July or August, both in snow mold inoculated and noninoculated treatments. Additional mortality and dry matter yield loss were linked to snow mold injury. These results demonstrated that snow mold injury could reduce winter survival and yield in first-year forage grasses, especially in orchardgrass, and early seeding could reduce the impact of winter stresses. Key words: Grass, orchardgrass, timothy, smooth bromegrass, meadow bromegrass, creeping red fescue

A Demonstration of a 1:1 Correspondence Between Chiasma Frequency and Recombination Using a Lolium perenne/Festuca pratensis Substitution

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 307-314 ◽  
Author(s):  
J King ◽  
L A Roberts ◽  
M J Kearsey ◽  
H M Thomas ◽  
R N Jones ◽  
...  
Keyword(s):  
Lolium Perenne ◽  
Chiasma Frequency ◽  
Chiasma Formation ◽  
Grass Species ◽  
Festuca Pratensis ◽  
Single Chromosome ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Frequency Counts

Abstract A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line (2n = 2x = 14). The chromatin of F. pratensis and L. perenne can be distinguished by genomic in situ hybridization (GISH), and it is therefore possible to visualize the substituted F. pratensis chromosome in the L. perenne background and to study chiasma formation in a single marked bivalent. Recombination occurs freely in the F. pratensis/L. perenne bivalent, and chiasma frequency counts give a predicted map length for this bivalent of 76 cM. The substituted F. pratensis chromosome was also mapped with 104 EcoRI/Tru91 and HindIII/Tru91 amplified fragment length polymorphisms (AFLPs), generating a marker map of 81 cM. This map length is almost identical to the map length of 76 cM predicted from the chiasma frequency data. The work demonstrates a 1:1 correspondence between chiasma frequency and recombination and, in addition, the absence of chromatid interference across the Festuca and Lolium centromeres.

Genome analysis reveals that the correct name of type strain Adlercreutzia caecicola DSM 22242T is Parvibacter caecicola Clavel et al. 2013

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Dominic A. Stoll ◽  
Nicolas Danylec ◽  
Christina Grimmler ◽  
Sabine E. Kulling ◽  
Melanie Huch
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Content Type ◽  
Link Type ◽  
Genome Wide ◽  
Average Amino Acid Identity ◽  
Biochemical Analyses

The strain Adlercreutzia caecicola DSM 22242T (=CCUG 57646T=NR06T) was taxonomically described in 2013 and named as Parvibacter caecicola Clavel et al. 2013. In 2018, the name of the strain DSM 22242T was changed to Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 due to taxonomic investigations of the closely related genera Adlercreutzia, Asaccharobacter and Enterorhabdus within the phylum Actinobacteria . However, the first whole draft genome of strain DSM 22242T was published by our group in 2019. Therefore, the genome was not available within the study of Nouioui et al. (2018). The results of the polyphasic approach within this study, including phenotypic and biochemical analyses and genome-based taxonomic investigations [genome-wide average nucleotide identity (gANI), alignment fraction (AF), average amino acid identity (AAI), percentage of orthologous conserved proteins (POCP) and genome blast distance phylogeny (GBDP) tree], indicated that the proposed change of the name Parvibacter caecicola to Adlercreutzia caecicola was not correct. Therefore, it is proposed that the correct name of Adlercreutzia caecicola (Clavel et al. 2013) Nouioui et al. 2018 strain DSM 22242T is Parvibacter caecicola Clavel et al. 2013.

Reclassification of Parvularcula flava as Aquisalinus luteolus nom. nov. and emended description of the genus Aquisalinus

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Jun-Jie Ying ◽  
Zhi-Cheng Wu ◽  
Yuan-Chun Fang ◽  
Lin Xu ◽  
Cong Sun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Parvularcula flava was proposed as a novel member of genus Parvularcula in 2016. Some time earlier, Aquisalinus flavus has been proposed as a novel species of a novel genus named Aquisalinus . When comparing the 16S rRNA gene sequences of type strains P. flava NH6-79T and A. flavus D11M-2T, they showed 97.9 % sequence identity, much higher than the sequence identities 92.7–94.3 % between P. flava NH6-79T and type strains in the genus Parvularcula , indicating that the later proposed novel taxon Parvularcula flava need reclassification. The phylogenetic trees based on 16S rRNA gene sequences and genome sequences both showed that P. flava NH6-79T and A. flavus D11M-2T formed a separated branch away from strains in the genera Parvularcula , Marinicaulis and Amphiplicatus . The average amino acid identity and average nucleotide identity values of P. flava NH6-79T and A. flavus D11M-2T were 87.9 and 85.0 %, respectively, much higher than the values between P. flava NH6-79T and other closely related type strains (54.3 %–58.1 % and 68.6–70.4 %, respectively). P. flava NH6-79T and A. flavus D11M-2T also contained summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) and C16 : 0 as major fatty acids, distinguishing them from other closely related taxa. Based on the results of the phylogenetic, comparative genomic and phenotypic analyses, Parvularcula flava should be reclassified as Aquisalinus luteolus nom. nov. and the description of genus Aquisalinus is emended.

Sign in / Sign up

Export Citation Format

Share Document