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.

Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat

2011 ◽  
Vol 9 (2) ◽  
pp. 243-246 ◽  
Author(s):  
Agata Gadaleta ◽  
Angelica Giancaspro ◽  
Silvana Zacheo ◽  
Domenica Nigro ◽  
Stefania Lucia Giove ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Phylogenetic Trees ◽  
Plant Genome ◽  
Phylogenetic Relations ◽  
Diversity Assessment ◽  
Wide Range ◽  
Genomic Ssr ◽  
High Level ◽  
Expressed Sequence

Microsatellite markers (simple sequence repeats, SSRs) are used for a wide range of crop genetic and breeding applications, including genetic diversity assessment, phylogenetic analysis, genotypic profiling and marker-assisted selection. Genomic SSR (gSSR) have attracted more attention because of abundance in plant genome, reproducibility, high level of polymorphism and codominant inheritance. Recently, the availability of data for expressed sequence tags (EST), has given more emphasis to EST-derived SSRs, which belong to the transcribed regions of DNA, and are expected to be more conserved and have a higher transferability rate across species than gSSR markers. In the present study, several gSSR and EST-SSR markers were investigated for their transferability and level of DNA polymorphism in different ancestral tetraploid and diploid Triticum and Aegilops species. The same gSSR and EST-SSR markers were also evaluated for their applicability in the phylogenetic analysis of wheat. Both gSSR and EST-SSR markers showed differences for the average transferability rate and the number of alleles/locus. Phylogenetic trees based on gSSR and EST-SSR markers were in accordance with phylogenetic relations based on cytogenetic and molecular analyses.

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.

scholarly journals Natural variation of physiological traits, molecular markers, and chlorophyll catabolic genes associated with heat tolerance in perennial ryegrass accessions

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jing Zhang ◽  
Hui Li ◽  
Yiwei Jiang ◽  
Huibin Li ◽  
Zhipeng Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Perennial Ryegrass ◽  
Physiological Traits ◽  
Grass Species ◽  
Cool Season ◽  
Catabolic Genes ◽  
Heat Tolerant ◽  
Cool Season Grass

Abstract Background Identification of genetic diversity in heat tolerance and associated traits is of great importance for improving heat tolerance in cool-season grass species. The objectives of this study were to determine genetic variations in heat tolerance associated with phenotypic and physiological traits and to identify molecular markers associated with heat tolerance in a diverse collection of perennial ryegrass (Lolium perenne L.). Results Plants of 98 accessions were subjected to heat stress (35/30 °C, day/night) or optimal growth temperature (25/20 °C) for 24 d in growth chambers. Overall heat tolerance of those accessions was ranked by principal component analysis (PCA) based on eight phenotypic and physiological traits. Among these traits, electrolyte leakage (EL), chlorophyll content (Chl), relative water content (RWC) had high correlation coefficients (− 0.858, 0.769, and 0.764, respectively) with the PCA ranking of heat tolerance. We also found expression levels of four Chl catabolic genes (CCGs), including LpNYC1, LpNOL, LpSGR, and LpPPH, were significant higher in heat sensitive ryegrass accessions then heat tolerant ones under heat stress. Furthermore, 66 pairs of simple sequence repeat (SSR) markers were used to perform association analysis based on the PCA result. The population structure of ryegrass can be grouped into three clusters, and accessions in cluster C were relatively more heat tolerant than those in cluster A and B. SSR markers significantly associated with above-mentioned traits were identified (R2 > 0.05, p < 0.01)., including two pairs of markers located on chromosome 4 in association with Chl content and another four pairs of markers in association with EL. Conclusion The result not only identified useful physiological parameters, including EL, Chl content, and RWC, and their associated SSR markers for heat-tolerance breeding of perennial ryegrass, but also highlighted the involvement of Chl catabolism in ryegrass heat tolerance. Such knowledge is of significance for heat-tolerance breeding and heat tolerance mechanisms in perennial ryegrass as well as in other cool-season grass species.

scholarly journals Natural Variation of Physiological Traits, Molecular Markers, and Chlorophyll Catabolic Genes Associated With Heat Tolerance in Perennial Ryegrass Accessions

2020 ◽  
Author(s):  
Bin Xu ◽  
Jing Zhang ◽  
Hui Li ◽  
Yiwei Jiang ◽  
Huibin Li ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Perennial Ryegrass ◽  
Principal Component ◽  
Physiological Traits ◽  
Grass Species ◽  
Cool Season ◽  
Catabolic Genes ◽  
Cool Season Grass

Abstract Background: Identification of genetic diversity in heat tolerance and associated traits is of great importance for improving heat tolerance in cool-season grass species. The objectives of this study were to determine genetic variations in heat tolerance associated with phenotypic and physiological traits and to identify molecular markers associated with heat tolerance in a diverse collection of perennial ryegrass (Lolium perenne L.). Results: Plants of 98 accessions were subjected to heat stress (35/30 ℃, day/night) or optimal growth temperature (25/20 ℃) for 24 d in growth chambers. Overall heattolerance of those accessions was ranked by principal component analysis (PCA) based on eight phenotypic and physiological traits. Among these traits, electrolyte leakage (EL), chlorophyll content (Chl), relative water content (RWC) had high correlation coefficients (−0.858, 0.769, and 0.764, respectively) with the PCA ranking of heat tolerance. We also found expression levels of four Chl catabolic genes (CCGs), including LpNYC1, LpNOL, LpSGR, and LpPPH, were closely related to the heat tolerance of ryegrass accessions. Furthermore, 66 pairs of simple sequence repeat (SSR) markers were used to perform association analysis based on the PCA result. The population structure of ryegrass can be grouped into three clusters, and accessions in cluster C were relatively more heat tolerant than those in cluster A and B. SSR markers significantly associated with above-mentioned traits were identified (R2>0.05, p<0.01)., including two pairs of markers located on chromosome 4 in association with Chl content and another four pairs of markers in association with EL.Conclusion:The result not only identified useful physiological parameters, including EL, Chl content, and RWC, and their associated SSR markers for heat-tolerance breeding of perennial ryegrass, but also highlighted the involvement of Chl catabolism in ryegrass heat tolerance. Such knowledge is of significance for heat-tolerance breeding and heat tolerance mechanisms in perennial ryegrass as well as in other cool-season grass species.

scholarly journals Natural variation of physiological traits, molecular markers, and chlorophyll catabolic genes associated with heat tolerance in perennial ryegrass accessions

2020 ◽  
Author(s):  
Jing Zhang ◽  
Hui Li ◽  
Yiwei Jiang ◽  
Huibin Li ◽  
Zhipeng Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Perennial Ryegrass ◽  
Physiological Traits ◽  
Grass Species ◽  
Cool Season ◽  
Catabolic Genes ◽  
Heat Tolerant ◽  
Cool Season Grass

Abstract Background: Identification of genetic diversity in heat tolerance and associated traits is of great importance for improving heat tolerance in cool-season grass species. The objectives of this study were to determine genetic variations in heat tolerance associated with phenotypic and physiological traits and to identify molecular markers associated with heat tolerance in a diverse collection of perennial ryegrass (Lolium perenne L.).Results: Plants of 98 accessions were subjected to heat stress (35/30 ℃, day/night) or optimal growth temperature (25/20 ℃) for 24 d in growth chambers. Overall heat tolerance of those accessions was ranked by principal component analysis (PCA) based on eight phenotypic and physiological traits. Among these traits, electrolyte leakage (EL), chlorophyll content (Chl), relative water content (RWC) had high correlation coefficients (−0.858, 0.769, and 0.764, respectively) with the PCA ranking of heat tolerance. We also found expression levels of four Chl catabolic genes (CCGs), including LpNYC1, LpNOL, LpSGR, and LpPPH, were significant higher in heat sensitive ryegrass accessions then heat tolerant ones under heat stress. Furthermore, 66 pairs of simple sequence repeat (SSR) markers were used to perform association analysis based on the PCA result. The population structure of ryegrass can be grouped into three clusters, and accessions in cluster C were relatively more heat tolerant than those in cluster A and B. SSR markers significantly associated with above-mentioned traits were identified (R2>0.05, p <0.01)., including two pairs of markers located on chromosome 4 in association with Chl content and another four pairs of markers in association with EL.Conclusion: The result not only identified useful physiological parameters, including EL, Chl content, and RWC, and their associated SSR markers for heat-tolerance breeding of perennial ryegrass, but also highlighted the involvement of Chl catabolism in ryegrass heat tolerance. Such knowledge is of significance for heat-tolerance breeding and heat tolerance mechanisms in perennial ryegrass as well as in other cool-season grass species.

Tall fescue genomic SSR markers: development and transferability across multiple grass species

2006 ◽  
Vol 113 (8) ◽  
pp. 1449-1458 ◽  
Author(s):  
Malay C. Saha ◽  
John D. Cooper ◽  
M. A. Rouf Mian ◽  
Konstantin Chekhovskiy ◽  
Gregory D. May
Keyword(s):  
Ssr Markers ◽  
Tall Fescue ◽  
Grass Species ◽  
Genomic Ssr

Tall fescue EST-SSR markers with transferability across several grass species

2004 ◽  
Vol 109 (4) ◽  
pp. 783-791 ◽  
Author(s):  
Malay C. Saha ◽  
M. A. Rouf Mian ◽  
Imad Eujayl ◽  
John C. Zwonitzer ◽  
Liangjiang Wang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Tall Fescue ◽  
Grass Species

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.

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

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