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Lee K, Bogdanova A, Missaoui A. Host Genetic Background Effect on Vertical Seed Transmission of Epichloë Endophyte Strains in Tall Fescue. MICROBIAL ECOLOGY 2023; 86:2618-2626. [PMID: 37470815 DOI: 10.1007/s00248-023-02270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) is a cool-season perennial grass widely grown for forage and turf. Tall fescue lives in association with a fungal endophyte that helps the grass overcome abiotic and biotic stressors. The endophyte is asexual and transmits vertically from the tall fescue plant to the next generation through the seed. Producers of endophyte-infected tall fescue must have endophyte infection in at least 70% of their seed. Therefore, endophyte seed transmission is vital in breeding and seed production. Transfer of endophytes from their native host to different backgrounds of elite tall fescue cultivars can lead to a low seed transmission of the endophyte to the seed. This study screened 23 previously uncharacterized endophyte strains for transmissibility when artificially inoculated into continental and Mediterranean-type host tall fescue. We found no correlation between the rate of successful inoculation and the seed transmission rate of the endophyte in the new host. Nor did the seed transmission rate of the endophyte strains in their native host correlate with the seed transmission rate of the endophyte in the new host. Five strains exhibited seed transmission above 70% in both Mediterranean and Continental host backgrounds and will be characterized further for potential use in cultivar development.
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Affiliation(s)
- Kendall Lee
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Ana Bogdanova
- Department of Biological Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Ali Missaoui
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
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2
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Islam MS, Chekhovskiy K, Saha MC. Dig up tall fescue plastid genomes for the identification of morphotype-specific DNA variants. BMC Genomics 2023; 24:586. [PMID: 37789301 PMCID: PMC10546690 DOI: 10.1186/s12864-023-09631-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species. Hexaploid tall fescue has three distinct morphotypes used either as forage or turf purposes. Its chloroplast genome is conserved due to it being maternally inherited to the next generation progenies. To identify morphotype-specific DNA markers and the genetic variations, plastid genomes of all three tall fescue morphotypes, i.e., Continental cv. Texoma MaxQ II, Rhizomatous cv. Torpedo, and Mediterranean cv. Resolute, have been sequenced using Illumina MiSeq sequencing platform. RESULTS The plastid genomes of Continental-, Rhizomatous-, and Mediterranean tall fescue were assembled into circular master molecules of 135,283 bp, 135,336 bp, and 135,324 bp, respectively. The tall fescue plastid genome of all morphotypes contained 77 protein-coding, 20 tRNAs, four rRNAs, two pseudo protein-coding, and three hypothetical protein-coding genes. We identified 630 SNPs and 124 InDels between Continental and Mediterranean, 62 SNPs and 20 InDels between Continental and Rhizomatous, and 635 SNPs and 123 InDels between Rhizomatous and Mediterranean tall fescue. Only four InDels in four genes (ccsA, rps18, accD, and ndhH-p) were identified, which discriminated Continental and Rhizomatous plastid genomes from the Mediterranean plastid genome. Here, we identified and reported eight InDel markers (NRITCHL18, NRITCHL35, NRITCHL43, NRITCHL65, NRITCHL72, NRITCHL101, NRITCHL104, and NRITCHL110) from the intergenic regions that can successfully discriminate tall fescue morphotypes. Divergence time estimation revealed that Mediterranean tall fescue evolved approximately 7.09 Mya, whereas the divergence between Continental- and Rhizomatous tall fescue occurred about 0.6 Mya. CONCLUSIONS To our knowledge, this is the first report of the assembled plastid genomes of Rhizomatous and Mediterranean tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of lawn and forage types of commercial varieties.
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Affiliation(s)
- Md Shofiqul Islam
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
- Genetics Laboratory, Indiana Crop Improvement Association, 7700 Stockwell Road, Lafayette, IN, 47909, USA.
- Department of Agronomy, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN, 47906, USA.
| | - Konstantin Chekhovskiy
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Malay C Saha
- Grass Genomics, Noble Research Institute LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
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Taleb MH, Majidi MM, Pirnajmedin F, Maibody SAMM. Plant functional trait responses to cope with drought in seven cool-season grasses. Sci Rep 2023; 13:5285. [PMID: 37002231 PMCID: PMC10066319 DOI: 10.1038/s41598-023-31923-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
In semi-arid and arid regions, the selection of suitable grass species with high-yield production, tolerance to drought stress, and potential for recovery from drought is of special importance. Despite extensive research in cool-season grasses, inter-species differences in post-drought recovery, persistence, survival, and summer dormancy and their relationship with drought tolerance need more investigation. In the present study, 28 diverse genotypes belonged to seven cool-season grass species, including Festuca arundinacea (tall fescue), Festuca pratensis (meadow fescue), Festuca ovina (sheep fescue), Festuca rubra (red fescue), Lolium perenne (perennial ryegrass), Lolium multiflorum (Italian ryegrass) and Lolium × hybridum were evaluated during 2016-2019 under three irrigation regimes (normal, mild, and intense drought stress). Then in the fourth year (on August 2019), irrigation was withheld at all previous irrigation regimes for two months during summer, and then species were re-irrigated to study the effect of prolonged drought conditions. A wide range of genetic diversity was detected in all the measured traits among and within species in response to different irrigation levels. Recurrent drought stress decreased forage productivity, post-drought recovery, and survival in all grass species. Among the studied species, tall fescue had higher forage production, drought tolerance, survival, recovery rate, and persistence. Sheep fescue had low forage production and recovery after drought. Drought tolerance (based on stress tolerance score, STS) was highly associated with forage yield and post-drought recovery and partially with summer dormancy under both mild and intense drought stress conditions. This indicated that selection based on higher STS would lead to choosing genotypes with better recovery after prolonged drought. Superior species and preferable genotypes for forage use from species Festuca arundinacea and for turf application from species Festuca arundinacea, Lolium perenne and Lolium × hybridum were identified across different water environments for future programs.
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Affiliation(s)
- Mohammad Hadi Taleb
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mohammad Mahdi Majidi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Fatemeh Pirnajmedin
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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Chen Y, Xiang Y, Hu Z, Gao Y, Zhang Y, Chen M, Khaldun ABM, Yan X, Fan J. Transcriptomic profiling revealed the role of 24-epibrassinolide in alleviating salt stress damage in tall fescue ( Festuca arundinacea). FRONTIERS IN PLANT SCIENCE 2022; 13:976341. [PMID: 36212305 PMCID: PMC9540362 DOI: 10.3389/fpls.2022.976341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Soil salinization is a major problem all over the world. The accumulation of salt in soil reduces the root water uptake and directly affects plant growth and metabolic activities. Brassinosteroid is a plant hormone that plays an important role in regulation of plant growth and physiological process, including promotion of cell expansion and elongation, signal transduction and stress response. Exogenous 24-epibrassinolide (EBL) has been proved to alleviate various environmental stress in plants. However, the role that EBL plays in salt stress response is still unknown in tall fescue (Festuca arundinacea). In this study, the physiology and molecular mechanisms regulated by exogenous EBL of salt stress response in tall fescue was investigated. Tall fescue plants were divided into four groups, including control (CK), NaCl solution (SALT), 24-epibrassinolide (EBL), NaCl solution + 24-epibrassinolide (SE). During the growth period of tall fescue, we found that electrolyte leakage (EL) and malondialdehyde (MDA) were decreased, chlorophyll (Chl) content and antioxidant enzyme activity were increased in leaves of tall fescue in SE group compared with SALT group, indicating that EBL improved the salt tolerance in grasses. Transcriptomic profiling analysis showed that after 12 h of treatments, 10,265, 13,830 and 10,537 differential genes were expressed in EBL, SALT, and SE groups compared with control, respectively. These differentially expressed genes (DEGs) mainly focused on binding, catalytic activity, cellular process, metabolic process, cellular anatomical entity. Moreover, most of the differential genes were expressed in the plant hormone signal transduction pathway. These results helped us to better understand the mechanism of exogenous 24-epibrassinolide to improve the salt tolerance of tall fescue.
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Affiliation(s)
- Yao Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yuanhang Xiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengrong Hu
- Hunan Tobacco Research Institute, Changsha, China
| | - Yang Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Youxin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Minghui Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Ansari HA, Ellison N, Stewart AV, Williams WM. Distribution patterns of rDNA loci in the Schedonorus- Lolium complex (Poaceae). COMPARATIVE CYTOGENETICS 2022; 16:39-54. [PMID: 35437460 PMCID: PMC8971122 DOI: 10.3897/compcytogen.v16.i1.79056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The Schedonorus-Lolium complex of the subtribe Loliinae (Poaceae) includes several economically important forage and turf grasses. This complex encompasses Lolium Linnaeus, 1753, Festuca Linnaeus, 1753 subgenus Schedonorus (P. Beauvois, 1824) Petermann, 1849 and Micropyropsis Romero Zarco et Cabezudo, 1983. New FISH results of 5S and 18S-26S rDNA sequences are presented for three species and the results are interpreted in a review of distribution patterns of 5S and 18S-26S rDNA sequences among other species in the complex. Micropyropsistuberosa Romero Zarco et Cabezudo, 1983 (2n = 2x = 14) displayed a distribution pattern of rDNA sequences identical to that of F.pratensis Hudson, 1762, supporting a close phylogenetic relationship at the bottom of the phylogenetic tree. "Loliummultiflorum" Lamarck, 1779 accessions sourced from Morocco showed a different pattern from European L.multiflorum and could be a unique and previously uncharacterised taxon. North African Festucasimensis Hochstetter ex A. Richard, 1851 had a marker pattern consistent with allotetraploidy and uniparental loss of one 18S-26S rDNA locus. This allotetraploid has previously been suggested to have originated from a hybrid with Festucaglaucescens (Festucaarundinaceavar.glaucescens Boissier, 1844). However, the distribution patterns of the two rDNA sequences in this allotetraploid do not align with F.glaucescens, suggesting that its origin from this species is unlikely. Furthermore, comparisons with other higher alloploids in the complex indicate that F.simensis was a potential donor of two sub-genomes of allohexaploid Festucagigantea (Linnaeus) Villars, 1787. In the overall complex, the proximal locations of both rDNA markers were conserved among the diploid species. Two types of synteny of the two markers could, to a considerable extent, distinguish allo- and autogamous Lolium species. The ancestral parentage of the three Festuca allotetraploids has not yet been determined, but all three appear to have been sub-genome donors to the higher allopolypoids of sub-genus Schedonorus. Terminal locations of both the markers were absent from the diploids but were very frequently observed in the polyploids.
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Affiliation(s)
- Helal Ahmad Ansari
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Nicholas Ellison
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Alan Vincent Stewart
- PGG Wrightson Seeds, Kimihia Research Centre, 1375 Springs Road, RD4, Lincoln 7674, New ZealandKimihia Research CentreLincolnNew Zealand
| | - Warren Mervyn Williams
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
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Tkach N, Nobis M, Schneider J, Becher H, Winterfeld G, Jacobs SWL, Röser M. Molecular Phylogenetics and Micromorphology of Australasian Stipeae (Poaceae, Subfamily Pooideae), and the Interrelation of Whole-Genome Duplication and Evolutionary Radiations in This Grass Tribe. FRONTIERS IN PLANT SCIENCE 2021; 11:630788. [PMID: 33552114 PMCID: PMC7862344 DOI: 10.3389/fpls.2020.630788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
The mainly Australian grass genus Austrostipa (tribe Stipeae) comprising approximately 64 species represents a remarkable example of an evolutionary radiation. To investigate aspects of diversification, macro- and micromorphological variation in this genus, we conducted molecular phylogenetic and scanning electron microscopy (SEM) analyses including representatives from most of Austrostipa's currently accepted subgenera. Because of its taxonomic significance in Stipeae, we studied the lemma epidermal pattern (LEP) in 34 representatives of Austrostipa. Plastid DNA variation within Austrostipa was low and only few lineages were resolved. Nuclear ITS and Acc1 yielded comparable groupings of taxa and resolved subgenera Arbuscula, Petaurista, and Bambusina in a common clade and as monophyletic. In most of the Austrostipa species studied, the LEP was relatively uniform (typical maize-like), but six species had a modified cellular structure. The species representing subgenera Lobatae, Petaurista, Bambusina as well as A. muelleri from subg. Tuberculatae were well-separated from all the other species included in the analysis. We suggest recognizing nine subgenera in Austrostipa (with number of species): Arbuscula (4), Aulax (2), Austrostipa (36), Bambusina (2), Falcatae (10), Lobatae (5), Longiaristatae (2), Petaurista (2) and the new subgenus Paucispiculatae (1) encompassing A. muelleri. Two paralogous sequence copies of Acc1, forming two distinct clades, were found in polyploid Austrostipa and Anemanthele. We found analogous patterns for our samples of Stipa s.str. with their Acc1 clades strongly separated from those of Austrostipa and Anemanthele. This underlines a previous hypothesis of Tzvelev (1977) that most extant Stipeae are of hybrid origin. We also prepared an up-to-date survey and reviewed the chromosome number variation for our molecularly studied taxa and the whole tribe Stipeae. The chromosome base number patterns as well as dysploidy and whole-genome duplication events were interpreted in a phylogenetic framework. The rather coherent picture of chromosome number variation underlines the enormous phylogenetic and evolutionary significance of this frequently ignored character.
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Affiliation(s)
- Natalia Tkach
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Julia Schneider
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| | - Hannes Becher
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Grit Winterfeld
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
| | | | - Martin Röser
- Department of Systematic Botany, Institute of Biology, Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle (Salle), Germany
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Decunta FA, Pérez LI, Malinowski DP, Molina-Montenegro MA, Gundel PE. A Systematic Review on the Effects of Epichloë Fungal Endophytes on Drought Tolerance in Cool-Season Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:644731. [PMID: 33841472 PMCID: PMC8025668 DOI: 10.3389/fpls.2021.644731] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/18/2021] [Indexed: 05/17/2023]
Abstract
Symptomless fungal endophytes in the genus Epichloë are repeatedly mentioned to increase tolerance of cool-season grasses to a wide range of environmental stress factors, mainly drought. However, the generality of this idea is challenged because (i) most studies have been conducted on two economically important forage grasses {tall fescue [Festuca arundinacea (Schreb.) Dumort] and perennial ryegrass (Lolium perenne L.)}, (ii) endophyte-mediated mechanisms and effects on plant responses to drought have shown to be highly variable across species, and that (iii) symbiosis incidence in plant populations occurring in extremely arid environments is usually low. We question this idea by reviewing the existing information about Epichloë fungal endophyte effects on drought tolerance in cool-season grasses. We combined standard review, vote counting, and calculation of effect sizes to synthesize the literature, identify information gaps, and guide future research. The total number of studies was higher for domesticated than for wild species, a ratio that was balanced when papers with data quality for effect size calculus were considered. After the drought, endophyte-infected plants accumulated more aboveground and belowground biomass than non-infected counterparts, while no effect on tillering was observed. However, these effects remained significant for wild (even on tillering) but not for domesticated species. Interestingly, despite the continuous effort in determining physiological mechanisms behind the endophyte effects, no studies evaluated plant fecundity as a measure of ecological fitness nor vital rates (such as survival) as to escalate individual-level variables to population. Together with the high variability in results, our work shows that generalizing a positive effect of fungal endophytes in plant tolerance to drought may be misleading. Future studies combining field surveys with manipulative experiments would allow us to unravel the role of fungal endophytes in plant adaptation by considering the evolutionary history of species and populations to the different ecological contexts.
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Affiliation(s)
- Facundo A. Decunta
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Buenos Aires, Argentina
- *Correspondence: Facundo A. Decunta
| | - Luis I. Pérez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Buenos Aires, Argentina
| | | | - Marco A. Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile
- Centro de Investigaciones y Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile
| | - Pedro E. Gundel
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Buenos Aires, Argentina
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
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8
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Shafiee P, Amini F, Mirzaghaderi G, Mortazavian SMM, Noori SAS. Karyotype Analysis in Six Species of Lolium and Festuca (Poaceae). CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Parisa Shafiee
- Department of Agronomy and Plant Breeding Sciences, University of Tehran, College of Aburaihan
| | - Fatemeh Amini
- Department of Agronomy and Plant Breeding Sciences, University of Tehran, College of Aburaihan
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan
| | | | - Seyed Ahmad Sadat Noori
- Department of Agronomy and Plant Breeding Sciences, University of Tehran, College of Aburaihan
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9
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Talukder SK, Bhamidimarri S, Chekhovskiy K, Saha MC. Mapping QTL for summer dormancy related traits in tall fescue (Festuca arundinacea Schreb.). Sci Rep 2020; 10:14539. [PMID: 32884044 PMCID: PMC7471293 DOI: 10.1038/s41598-020-71488-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/14/2020] [Indexed: 11/15/2022] Open
Abstract
Summer dormancy is an important stress avoidance mechanism of cool season perennial grasses to persist well under harsh summer conditions. QTL associated with summer-dormancy related traits in tall fescue has significant breeding implications. An F1 pseudo testcross population was developed by crossing a Mediterranean (103-2) to a Continental parent (R43-64). The population was genotyped using 2,000 SSR and DArT markers. Phenotyping was done in growth chambers and in two Oklahoma, USA locations. Total length of R43-64 and 103-2 maps were 1,956 cM and 1,535 cM, respectively. Seventy-seven QTL were identified in the male and 46 in the female parent maps. The phenotypic variability explained by the QTL ranged between 9.91 and 32.67%. Among all the QTL, five summer dormancy related putative QTL were identified in R43-64 linkage groups (LGs) 4, 5, 12, 20 and 22 and two in 103-2 LGs 5 and 17. All the putative summer dormant QTL regions in male map showed pleiotropic responses and epistatic interactions with other summer dormant and stress responsive QTL regions for plant height, new leaf and dry biomass weight. The flanking markers related to the QTL reported in this study will be useful to improve tall fescue persistence in dry areas through marker-assisted breeding.
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Affiliation(s)
- Shyamal K Talukder
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- California Cooperative Rice Research Foundation, Rice Expt. Station, 955 Butte City Highway, Biggs, CA, USA
| | - Suresh Bhamidimarri
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
- Corteva Agriscience, 1040 Settler Rd., Connell, WA, USA
| | | | - Malay C Saha
- Noble Research Institute, LLC., 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA.
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10
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Svačina R, Sourdille P, Kopecký D, Bartoš J. Chromosome Pairing in Polyploid Grasses. FRONTIERS IN PLANT SCIENCE 2020; 11:1056. [PMID: 32733528 PMCID: PMC7363976 DOI: 10.3389/fpls.2020.01056] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Polyploids are species in which three or more sets of chromosomes coexist. Polyploidy frequently occurs in plants and plays a major role in their evolution. Based on their origin, polyploid species can be divided into two groups: autopolyploids and allopolyploids. The autopolyploids arise by multiplication of the chromosome sets from a single species, whereas allopolyploids emerge from the hybridization between distinct species followed or preceded by whole genome duplication, leading to the combination of divergent genomes. Having a polyploid constitution offers some fitness advantages, which could become evolutionarily successful. Nevertheless, polyploid species must develop mechanism(s) that control proper segregation of genetic material during meiosis, and hence, genome stability. Otherwise, the coexistence of more than two copies of the same or similar chromosome sets may lead to multivalent formation during the first meiotic division and subsequent production of aneuploid gametes. In this review, we aim to discuss the pathways leading to the formation of polyploids, the occurrence of polyploidy in the grass family (Poaceae), and mechanisms controlling chromosome associations during meiosis, with special emphasis on wheat.
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Affiliation(s)
- Radim Svačina
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Pierre Sourdille
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - David Kopecký
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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Zwyrtková J, Němečková A, Čížková J, Holušová K, Kapustová V, Svačina R, Kopecký D, Till BJ, Doležel J, Hřibová E. Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses. BMC PLANT BIOLOGY 2020; 20:280. [PMID: 32552738 PMCID: PMC7302162 DOI: 10.1186/s12870-020-02495-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/15/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Cultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species (Lolium) and diploid and hexaploid fescue species (Festuca). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species as well as one fescue and two ryegrass cultivars. RESULTS Partial genome sequences produced by Illumina sequencing technology were used for genome-wide comparative analyses with the RepeatExplorer pipeline. Retrotransposons were the most abundant repeat type in all seven grass species. The Athila element of the Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of the long terminal repeat (LTR) element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of fluorescence in situ hybridization (FISH) with a probe specific to the Fesreba element and immunostaining with centromeric histone H3 (CENH3) antibody showed their co-localization and indicated a possible role of Fesreba in centromere function. CONCLUSIONS Comparative repeatome analyses in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of the LTR element Fesreba. A new LTR element Fesreba was identified and found in abundance in centromeric regions of the fescues and ryegrasses. It may play a role in the function of their centromeres.
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Affiliation(s)
- Jana Zwyrtková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Alžběta Němečková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Veronika Kapustová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Radim Svačina
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - David Kopecký
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Bradley John Till
- Centro de Genómica Nutricional Agroacuícola, Las Heras 350, Temuco, Chile
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic
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12
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Freitas PP, Hampton JG, Rolston MP, Glare TR, Miller PP, Card SD. A Tale of Two Grass Species: Temperature Affects the Symbiosis of a Mutualistic Epichloë Endophyte in Both Tall Fescue and Perennial Ryegrass. FRONTIERS IN PLANT SCIENCE 2020; 11:530. [PMID: 32457777 PMCID: PMC7225326 DOI: 10.3389/fpls.2020.00530] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/07/2020] [Indexed: 05/12/2023]
Abstract
Many cool-season grasses form permanent, mutualistic symbioses with asexual Epichloë endophytes. These fungal symbionts often perform a protective role within the association as many strains produce secondary metabolites that deter certain mammalian and invertebrate herbivores. Although initially a serious issue for agriculture, due to mammalian toxins that manifested in major animal health issues, selected strains that provide abiotic stress protection to plants with minimal ill effects to livestock are now commercialized and routinely used to enhance pasture performance in many farming systems. These fungal endophytes and their grass hosts have coevolved over millions of years, and it is now generally accepted that most taxonomic groupings of Epichloë are confined to forming compatible associations (i.e., symptomless associations) with related grass genera within a tribe. The most desired compounds associated with Epichloë festucae var. lolii, an endophyte species associated with perennial ryegrass, are peramine and epoxy-janthitrems. No other major secondary metabolites with invertebrate bioactivity have been identified within this association. However, other agriculturally beneficial compounds, such as lolines, have been discovered in related endophyte species that form associations with fescue grasses. A rationale therefore existed to develop novel grass-endophyte associations between loline-producing endophytes originally isolated from tall fescue with elite cultivars of perennial ryegrass to achieve a wider spectrum of insect bioactivity. A suitable loline-producing endophyte strain of Epichloë sp. FaTG-3 was selected and inoculated into perennial ryegrass. We hypothesed that endophyte transmission frequency, endophyte mycelial biomass and endophyte-derived alkaloid production would differ between the original tall fescue host and the artificial association. Consistent with our hypothesis, our data strongly suggest that plant species significantly affected the plant-endophyte association. This effect became more apparent for transmission frequency and endophyte biomass as the plants matured. Overall, the viable endophyte infection frequency was greater in the tall fescue host than in perennial ryegrass, at all sampling dates. Additionally, temperature was found to be a significant factor affecting endophyte transmission frequency, endophyte mycelial biomass and alkaloid production. Implications for the development of novel grass-endophyte associations are discussed.
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Affiliation(s)
| | - John G. Hampton
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - M. Phil. Rolston
- Forage Science, AgResearch Limited, Lincoln Research Centre, Lincoln, New Zealand
- The Foundation for Arable Research, Christchurch, New Zealand
| | - Travis R. Glare
- Bio-Protection Research Centre, Lincoln University, Lincoln, New Zealand
| | - Poppy P. Miller
- Knowledge and Analytics, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Stuart D. Card
- Forage Science, AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
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13
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Ghariani S, Charfeddine A, Amari M, Chakroun M, Neila TF. Interspecific molecular variation of Tunisian complex Lolium perenne L. and Festuca arundinacea Schreb. based on the internal transcribed spacer locus (ITS). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:331-339. [PMID: 32158138 PMCID: PMC7036405 DOI: 10.1007/s12298-019-00749-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
To establish phylogenetic relationships and estimate the intra and interspecific divergence, the amplification and the sequencing of the internal transcribed spacers of ribosomal DNA (ITS = ITS1 + 5.8S + ITS2) were analyzed in Tunisian complex Lolium-Festuca DNA. These spacer regions have evolved mainly by point mutations. Results revealed a high level of polymorphism within studied species. Significant similarities were observed between these two species and showed the existence of an important phylogenetic relationship. Besides, this molecular approach has revealed two new clusterings, with a homologous ITS gene namely: Bromus hordeaceus and Hordeum murinum subsp. This could be explained by the conservation of an ancestral ITS gene in some fescue plants. Thus, Tunisian tall fescue and perennial ryegrass may derive from Bromus hordeaceus and Hordeum murinum subsp. Considerable morphology and bioclimatic distribution similarities were discovered in ITS sequences within the same species. This study can be of great help to identify suitable accessions that could be used in local fescue and ryegrass improvement program.
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Affiliation(s)
- Salma Ghariani
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Amina Charfeddine
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Marwen Amari
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
| | - Mohamed Chakroun
- Laboratoire des Productions Animales et Fourragères, Institut National de Recherche Agronomique de la Tunisie, Université de Carthage, Rue Hédi Karray, 2049 Ariana, Tunisia
| | - Trifi-Farah Neila
- Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 Tunis, Tunisia
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14
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Ebrahimzadegan R, Houben A, Mirzaghaderi G. Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds. Sci Rep 2019; 9:19989. [PMID: 31882680 PMCID: PMC6934454 DOI: 10.1038/s41598-019-56383-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022] Open
Abstract
Here, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (-B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran
| | - Andreas Houben
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, 6617715175, Sanandaj, Iran.
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15
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Kruse J, Dietrich W, Zimmermann H, Klenke F, Richter U, Richter H, Thines M. Ustilago species causing leaf-stripe smut revisited. IMA Fungus 2018; 9:49-73. [PMID: 30018872 PMCID: PMC6048562 DOI: 10.5598/imafungus.2018.09.01.05] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/12/2018] [Indexed: 12/02/2022] Open
Abstract
Leaf-stripe smuts on grasses are a highly polyphyletic group within Ustilaginomycotina, occurring in three genera, Tilletia, Urocystis, and Ustilago. Currently more than 12 Ustilago species inciting stripe smuts are recognised. The majority belong to the Ustilago striiformis-complex, with about 30 different taxa described from 165 different plant species. This study aims to assess whether host distinct-lineages can be observed amongst the Ustilago leaf-stripe smuts using nine different loci on a representative set. Phylogenetic reconstructions supported the monophyly of the Ustilago striiformis-complex that causes leaf-stripe and the polyphyly of other leaf-stripe smuts within Ustilago. Furthermore, smut specimens from the same host genus generally clustered together in well-supported clades that often had available species names for these lineages. In addition to already-named lineages, three new lineages were observed, and described as new species on the basis of host specificity and molecular differences: namely Ustilago jagei sp. nov. on Agrostis stolonifera, U. kummeri sp. nov. on Bromus inermis, and U. neocopinata sp. nov. on Dactylis glomerata.
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Affiliation(s)
- Julia Kruse
- Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | | | - Horst Zimmermann
- Cluster for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
| | | | - Udo Richter
- Traubenweg 8, 06632 Freyburg / Unstrut, Germany
| | | | - Marco Thines
- Goethe University Frankfurt am Main, Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,Cluster for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
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16
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Talukder SK, Azhaguvel P, Chekhovskiy K, Saha MC. Molecular discrimination of tall fescue morphotypes in association with Festuca relatives. PLoS One 2018; 13:e0191343. [PMID: 29342197 PMCID: PMC5771633 DOI: 10.1371/journal.pone.0191343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/03/2018] [Indexed: 11/18/2022] Open
Abstract
Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species used as forage and turf, and in conservation plantings. There are three morphotypes in hexaploid tall fescue: Continental, Mediterranean and Rhizomatous. This study was conducted to develop morphotype-specific molecular markers to distinguish Continental and Mediterranean tall fescues, and establish their relationships with other species of the Festuca genus for genomic inference. Chloroplast sequence variation and simple sequence repeat (SSR) polymorphism were explored in 12 genotypes of three tall fescue morphotypes and four Festuca species. Hypervariable chloroplast regions were retrieved by using 33 specifically designed primers followed by sequencing the PCR products. SSR polymorphism was studied using 144 tall fescue SSR primers. Four chloroplast (NFTCHL17, NFTCHL43, NFTCHL45 and NFTCHL48) and three SSR (nffa090, nffa204 and nffa338) markers were identified which can distinctly differentiate Continental and Mediterranean morphotypes. A primer pair, NFTCHL45, amplified a 47 bp deletion between the two morphotypes is being routinely used in the Noble Research Institute's core facility for morphotype discrimination. Both chloroplast sequence variation and SSR diversity showed a close association between Rhizomatous and Continental morphotypes, while the Mediterranean morphotype was in a distant clade. F. pratensis and F. arundinacea var. glaucescens, the P and G1G2 genome donors, respectively, were grouped with the Continental clade, and F. mairei (M1M2 genome) grouped with the Mediterranean clade in chloroplast sequence variation, while both F. pratensis and F. mairei formed independent clade in SSR analysis. Age estimation based on chloroplast sequence variation indicated that the Continental and Mediterranean clades might have been colonized independently during 0.65 ± 0.06 and 0.96 ± 0.1 million years ago (Mya) respectively. The findings of the study will enhance tall fescue breeding for persistence and productivity.
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Affiliation(s)
| | - Perumal Azhaguvel
- Noble Research Institute, LLC, Ardmore, OK, United States of America
| | | | - Malay C. Saha
- Noble Research Institute, LLC, Ardmore, OK, United States of America
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17
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Missaoui AM, Malinowski DP, Pinchak WE, Kigel J. Insights into the Drought and Heat Avoidance Mechanism in Summer-Dormant Mediterranean Tall Fescue. FRONTIERS IN PLANT SCIENCE 2017; 8:1971. [PMID: 29204152 PMCID: PMC5698279 DOI: 10.3389/fpls.2017.01971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 11/01/2017] [Indexed: 05/11/2023]
Abstract
Summer dormancy is an evolutionary response that some perennial cool-season grasses adopted as an avoidance strategy to escape summer drought and heat. It is correlated with superior survival after severe summer droughts in many perennial grass species originating from Mediterranean environments. Understanding the genetic mechanism and environmental determinants of summer dormancy is important for interpreting the evolutionary history of seasonal dormancy and for the development of genomic tools to improve the efficiency of genetic selection for this important trait. The objectives of this research are to assess morphological and biochemical attributes that seem to be specific for the characterization of summer dormancy in tall fescue, and to validate the hypothesis that genes underlying stem determinacy might be involved in the mechanism of summer dormancy. Our results suggest that vernalization is an important requirement in the onset of summer dormancy in tall fescue. Non-vernalized tall fescue plants do not exhibit summer dormancy as vernalized plants do and behave more like summer-active types. This is manifested by continuation of shoot growth and high root activity in water uptake during summer months. Therefore, summer dormancy in tall fescue should be tested only in plants that underwent vernalization and are not subjected to water deficit during summer months. Total phenolic concentration in tiller bases (antioxidants) does not seem to be related to vernalization. It is most likely an environmental response to protect meristems from oxidative stress. Sequence analysis of the TFL1 homolog CEN gene from tall fescue genotypes belonging to summer-dormant and summer-active tall fescue types showed a unique deletion of three nucleotides specific to the dormant genotypes. Higher tiller bud numbers in dormant plants that were not allowed to flower and complete the reproductive cycle, confirmed that stem determinacy is a major component in the mechanism of summer dormancy. The number of variables identified in these studies as potential players in summer dormancy in tall fescue including vernalization, TFL1/CEN, water status, and protection from oxidative stress are a further confirmation that summer dormancy is a quantitative trait controlled by several genes with varying effects and prone to genotype by environment interactions.
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Affiliation(s)
- Ali M. Missaoui
- Institute of Plant Breeding Genetics and Genomics, The University of Georgia, Athens, GA, United States
| | | | | | - Jaime Kigel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
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18
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Shinozuka H, Hettiarachchige IK, Shinozuka M, Cogan NOI, Spangenberg GC, Cocks BG, Forster JW, Sawbridge TI. Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host. Sci Rep 2017; 7:9024. [PMID: 28831055 PMCID: PMC5567365 DOI: 10.1038/s41598-017-07886-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/10/2017] [Indexed: 11/22/2022] Open
Abstract
Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes or other plant species. In this report, evidence for ancient horizontal transfer of a fungal nuclear gene, encoding a ß-1,6-glucanase enzyme for fungal cell wall degradation, into an angiosperm lineage is presented for the first time. The gene was identified from de novo sequencing and assembly of the genome and transcriptome of perennial ryegrass, a cool-season grass species. Molecular analysis confirmed the presence of the complete gene in the genome of perennial ryegrass. No corresponding sequence was found in other plant species, apart from members of the Poeae sub-tribes Loliinae and Dactylidinae. Evidence suggests that a common ancestor of the two sub-tribes acquired the gene from a species ancestral to contemporary grass-associated fungal endophytes around 9-13 million years ago. This first report of horizontal transfer of a nuclear gene from a taxonomically distant eukaryote to modern flowering plants provides evidence for a novel adaptation mechanism in angiosperms.
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Affiliation(s)
- Hiroshi Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia.
- Dairy Futures Cooperative Research Centre, Bundoora, Australia.
| | - Inoka K Hettiarachchige
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - German C Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Benjamin G Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - John W Forster
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Timothy I Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, La Trobe University, Bundoora, Victoria, 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, 3086, Australia
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19
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Ekanayake PN, Kaur J, Tian P, Rochfort SJ, Guthridge KM, Sawbridge TI, Spangenberg GC, Forster JW. Genomic and metabolic characterisation of alkaloid biosynthesis by asexual Epichloë fungal endophytes of tall fescue pasture grasses. Genome 2017; 60:496-509. [PMID: 28177829 DOI: 10.1139/gen-2016-0173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Symbiotic associations between tall fescue grasses and asexual Epichloë fungal endophytes exhibit biosynthesis of alkaloid compounds causing both beneficial and detrimental effects. Candidate novel endophytes with favourable chemotypic profiles have been identified in germplasm collections by screening for genetic diversity, followed by metabolite profile analysis in endogenous genetic backgrounds. A subset of candidates was subjected to genome survey sequencing to detect the presence or absence and structural status of known genes for biosynthesis of the major alkaloid classes. The capacity to produce specific metabolites was directly predictable from metabolic data. In addition, study of duplicated gene structure in heteroploid genomic constitutions provided further evidence for the origin of such endophytes. Selected strains were inoculated into meristem-derived callus cultures from specific tall fescue genotypes to perform isogenic comparisons of alkaloid profile in different host backgrounds, revealing evidence for host-specific quantitative control of metabolite production, consistent with previous studies. Certain strains were capable of both inoculation and formation of longer-term associations with a nonhost species, perennial ryegrass (Lolium perenne L.). Discovery and primary characterisation of novel endophytes by DNA analysis, followed by confirmatory metabolic studies, offers improvements of speed and efficiency and hence accelerated deployment in pasture grass improvement programs.
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Affiliation(s)
- Piyumi N Ekanayake
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Jatinder Kaur
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Pei Tian
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Simone J Rochfort
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,b School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Kathryn M Guthridge
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Timothy I Sawbridge
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,b School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - German C Spangenberg
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,b School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - John W Forster
- a Agriculture Victoria, Biosciences Research, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia.,b School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia.,c Molecular Plant Breeding Cooperative Research Centre, Victorian AgriBiosciences Centre, La Trobe Research and Development Park, Bundoora, Victoria 3083, Australia.,d Dairy Futures Cooperative Research Centre, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
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Guan X, Yuyama N, Stewart A, Ding C, Xu N, Kiyoshi T, Cai H. Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:584. [PMID: 28484473 PMCID: PMC5399756 DOI: 10.3389/fpls.2017.00584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/31/2017] [Indexed: 05/04/2023]
Abstract
To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR) markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA) revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3), with a few lines that instead grouped with L. multiflorum (C4) or Lolium rigidum (C6). Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.
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Affiliation(s)
- Xuanli Guan
- Department of Plant Genetics, Breeding and Seed Science, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
- Laboratory of Crop Heterosis and Utilization, Ministry of EducationBeijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of AgricultureBeijing, China
| | - Nana Yuyama
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed AssociationNasushiobara, Japan
| | | | - Chenglong Ding
- Institute of Livestock Science, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Nengxiang Xu
- Institute of Livestock Science, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Takako Kiyoshi
- Forage Crop Biotechnology Research Team, National Institute of Livestock and Grassland ScienceNasushiobara, Japan
| | - Hongwei Cai
- Department of Plant Genetics, Breeding and Seed Science, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
- Laboratory of Crop Heterosis and Utilization, Ministry of EducationBeijing, China
- Beijing Key Laboratory of Crop Genetic Improvement and Genome, Ministry of AgricultureBeijing, China
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed AssociationNasushiobara, Japan
- *Correspondence: Hongwei Cai
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Munday JS, Finch SC, Vlaming JB, Sutherland BL, Fletcher LR. Pathological changes seen in horses in New Zealand grazing Mediterranean tall fescue (Lolium arundinaceum) infected with selected endophytes (Epichloë coenophiala) causing equine fescue oedema. N Z Vet J 2016; 65:147-151. [PMID: 27750516 DOI: 10.1080/00480169.2016.1248516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AIM To investigate whether Mediterranean tall fescue (Lolium arundinaceum (Schreb.) Darbysh. (syn Festuca arundinacea)) infected with selected fungal endophytes (Epichloë coenophiala (formerly Neotyphodium coenophialum)) caused equine fescue oedema when grown in New Zealand, and to examine the pathological changes associated with this intoxication. METHODS Horses were grazed on Mediterranean tall fescue that was infected with the endophytes AR542 (n=2), or AR584 (n=3), or Mediterranean tall fescue that was endophyte-free (n=2). Blood samples were taken up to 7 days after the start of feeding to detect changes in concentrations of total protein in serum and packed cell volume. Any horse showing clinical evidence of disease was subject to euthanasia and necropsy. RESULTS Within 6 days, both horses grazing fescue infected with AR542 became depressed and lethargic. One horse grazing fescue infected with endophyte AR584 became depressed within a 5-day feeding period while another horse in this group died shortly after being removed from the AR584 pasture. The third horse in this group did not develop clinical signs within the 5-day feeding period. However, haemoconcentration and hypoproteinaemia was detected in all horses grazing Mediterranean tall fescue that was infected by AR542 or AR584 endophyte. No abnormalities were observed in horses grazing fescue that was endophyte-free. Necropsy examination was performed on two horses grazing fescue infected with AR542 and one horse grazing fescue infected with AR584. All three horses had marked oedema of the gastrointestinal tract. Histologically, the oedema was accompanied by large numbers of eosinophils, but no necrosis. CONCLUSIONS Horses grazing Mediterranean tall fescue that was infected by AR542 or AR584 developed hypoproteinaemia and haemoconcentration, most likely due to leakage of plasma proteins into the gastrointestinal tract. This suggests that these selected endophytes produce a compound that is toxic to horses, although the toxic principle is currently unknown. CLINICAL RELEVANCE Mediterranean tall fescue that is infected by AR542 or AR584 should not be fed to horses in New Zealand. This intoxication should be considered in horses in which a rapid onset of hypoproteinaemia and haemoconcentration is detected. This intoxication should also be considered if marked gastrointestinal oedema is observed.
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Affiliation(s)
- J S Munday
- a Pathobiology, Institute of Veterinary, Animal and Biomedical Sciences , Massey University , Private Bag 11222, Palmerston North 4442 , New Zealand
| | - S C Finch
- b Ruakura Research Centre , AgResearch Ltd. , Private Bag 3123, Hamilton , New Zealand
| | - J B Vlaming
- a Pathobiology, Institute of Veterinary, Animal and Biomedical Sciences , Massey University , Private Bag 11222, Palmerston North 4442 , New Zealand.,c Lincoln Research Centre , AgResearch Ltd. , Private Bag 4749, Christchurch , New Zealand
| | - B L Sutherland
- c Lincoln Research Centre , AgResearch Ltd. , Private Bag 4749, Christchurch , New Zealand
| | - L R Fletcher
- b Ruakura Research Centre , AgResearch Ltd. , Private Bag 3123, Hamilton , New Zealand.,c Lincoln Research Centre , AgResearch Ltd. , Private Bag 4749, Christchurch , New Zealand
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22
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Saikkonen K, Phillips TD, Faeth SH, McCulley RL, Saloniemi I, Helander M. Performance of Endophyte Infected Tall Fescue in Europe and North America. PLoS One 2016; 11:e0157382. [PMID: 27284909 PMCID: PMC4902185 DOI: 10.1371/journal.pone.0157382] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/27/2016] [Indexed: 11/18/2022] Open
Abstract
Human assisted plant invasions from Europe to North America have been more common than the reverse. We tested endophyte-mediated performance of tall fescue in parallel three year experiments in Europe and the USA using endophyte infected and uninfected wild and cultivated plants. Experimental plants were subjected to nutrient and water treatments. Whereas endophyte infection increased tall fescue performance in general, the effects of endophytes on plant growth and reproduction varied among plant origins under different environmental conditions. Naturally endophyte-free Finnish cultivar ‘Retu’ performed equally well as ‘Kentucky-31’ in both geographic locations. All Eurasian origin plants performed well in the US. In Finland, plants established well and both cultivars survived over the first winter. However, winter mortality of ‘Kentucky-31’ plants was higher, particularly in fertilized soils in the subsequent winters. Our results suggest that tall fescue ecotype ‘Kentucky-31’ that flourishes in North America is poorly adapted to Northern European conditions.
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Affiliation(s)
- Kari Saikkonen
- Natural Resources Institute Finland (Luke), Turku, Finland
- * E-mail:
| | - Timothy D. Phillips
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stanley H. Faeth
- Department of Biology, University of North Carolina, Greensboro, North Carolina, United States of America
| | - Rebecca L. McCulley
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky, United States of America
| | - Irma Saloniemi
- Department of Biology, University of Turku, Turku, Finland
| | - Marjo Helander
- Natural Resources Institute Finland (Luke), Turku, Finland
- Department of Biology, University of Turku, Turku, Finland
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23
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Cheng Y, Ma X, Zhou K, Humphreys MW, Zhang XQ. Phylogenetic analysis of Festuca–Lolium complex using SRAP markers. GENETIC RESOURCES AND CROP EVOLUTION 2016; 63:7-18. [PMID: 0 DOI: 10.1007/s10722-015-0324-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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24
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Hume DE, Ryan GD, Gibert A, Helander M, Mirlohi A, Sabzalian MR. Epichloë Fungal Endophytes for Grassland Ecosystems. SUSTAINABLE AGRICULTURE REVIEWS 2016. [DOI: 10.1007/978-3-319-26777-7_6] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Sun X, Xie Y, Bi Y, Liu J, Amombo E, Hu T, Fu J. Comparative study of diversity based on heat tolerant-related morpho-physiological traits and molecular markers in tall fescue accessions. Sci Rep 2015; 5:18213. [PMID: 26666506 PMCID: PMC4678371 DOI: 10.1038/srep18213] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/09/2015] [Indexed: 11/28/2022] Open
Abstract
Heat stress is a critical challenge to tall fescue (Festuca arundinacea Schreb.) in many areas of the globe and variations in genetic structure and functional traits is for the efficient breeding programs on developing heat tolerant cultivars. Tolerant-related morpho-physiological traits and simple sequence repeat (SSR) markers were employed to survey genetic diversity in greenhouse and growth chamber trials. 100 tall fescue accessions, including 8 commercial cultivars and 92 natural genotypes, showed a high variation in phenotypic performance under heat stress. Based on standardized heat tolerant-related morpho-physiological data, all tall fescue accessions were clustered into five groups. The accessions with similar heat tolerance were likely to be clustered in the same group. The highest genetic diversity was obtained for accessions from Africa judged by Nei’s gene diversity (0.2640) and PIC (0.2112). All grass accessions could be divided into three major groups based on SSR markers, which was partially congruous to the geographical regions and history of introduction. A low correlation was found between morpho-physiological traits and SSR markers by Mantel test. The patterns in morpho-physiological trait variations and genetic diversity associated with heat tolerance were useful to design breeding programs for developing heat stress resistance in tall fescue.
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Affiliation(s)
- Xiaoyan Sun
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.,Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Yan Xie
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Yufang Bi
- Key Laboratory of High Efficent Processing of Bamboo, China National Bamboo Research Center, Hangzhou 310012, Zhejiang Province, China
| | - Jianping Liu
- The Key Laboratory of Horticultural Plant Genetic and Improvement of Jiangxi, Institute of Biology and Resources, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Tao Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
| | - Jinmin Fu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430074, Hubei, P.R. China
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26
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McGranahan DA, Burgdorf R, Kirkman KP. Epichloae infection in a native South African grass, Festuca costata Nees. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:914-921. [PMID: 25619128 DOI: 10.1111/plb.12307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 06/04/2023]
Abstract
Fungal endophytes have been documented in almost all terrestrial plant groups. Although the endophyte infection syndrome in agronomic cultivars is well studied, relatively little work addresses questions of spatial ecology and fire effects on epichloae endophyte infection in native grasses, and none, to our knowledge, in sub-Saharan Africa. We sampled seven populations of the native Festuca costata Nees along the spline of the Drakensberg range in South Africa at several spatial scales, including both recently burned and unburned stands. We tested epichloae presence and prevalence with immunoblot assays, PCR and genetic sequencing. We found epichloae endophytes were present and prevalent (38-98% infection rates depending on location). Variation in infection rates occurred primarily among locations, but also among bunches. There was little evidence that endophyte infection rates varied with fire. Novel evidence of epichloae infection of a native Festuca in South Africa opens the door to several new research questions, from the phylogenetic relationship between epichloae of sub-Saharan Africa and other continents to the ecological advantages or disadvantages that endophytes confer upon their hosts, especially in a fire-prone ecosystem vulnerable to global environmental change.
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Affiliation(s)
- D A McGranahan
- School of Natural Resource Sciences - Range Science, North Dakota State University, Fargo, ND, USA
| | - R Burgdorf
- Plant Pathology, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - K P Kirkman
- Grassland Science, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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27
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Hochbach A, Schneider J, Röser M. A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA. Mol Phylogenet Evol 2015; 87:14-27. [DOI: 10.1016/j.ympev.2015.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 03/06/2015] [Accepted: 03/12/2015] [Indexed: 01/18/2023]
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28
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Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. AOB PLANTS 2015; 7:plv046. [PMID: 25940204 PMCID: PMC4480051 DOI: 10.1093/aobpla/plv046] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/21/2015] [Indexed: 05/08/2023]
Abstract
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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Affiliation(s)
- Jeffery M Saarela
- Botany Section, Research and Collections, Canadian Museum of Nature, PO Box 3443 Stn. D, Ottawa, ON, Canada K1P 3P4
| | - William P Wysocki
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Craig F Barrett
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA 90032-8201, USA
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jerrold I Davis
- Section of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
| | - Lynn G Clark
- Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, USA
| | - Scot A Kelchner
- Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dustin R Mayfield
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
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Czaban A, Sharma S, Byrne SL, Spannagl M, Mayer KFX, Asp T. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation. BMC Genomics 2015; 16:249. [PMID: 25886302 PMCID: PMC4389671 DOI: 10.1186/s12864-015-1447-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/06/2015] [Indexed: 01/18/2023] Open
Abstract
Background The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium-Festuca complex show very diverse phenotypes, and many of them are related to agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity. Results We have generated de novo transcriptome assemblies for four species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some of the differences between the more stress tolerant Festuca, and the less stress tolerant Lolium species. Conclusions Our data presents a comprehensive transcriptome sequence comparison between species from the Lolium-Festuca complex, with the identification of potential candidate genes underlying some important phenotypical differences within the complex (such as VRN2). The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them. It is likely that the knowledge of the genomes will be largely transferable between species within the complex. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1447-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adrian Czaban
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.
| | - Sapna Sharma
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Stephen L Byrne
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany.
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, Slagelse, 4200, Denmark.
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Bednarskaya IA, Popov VN, Dugar YN, Akinina GE, Dolgova TA. Issr analysis of some species of angustifoliate fescue. CYTOL GENET+ 2014. [DOI: 10.3103/s0095452714060024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Griffin PC, Hoffmann AA. Limited genetic divergence among Australian alpine Poa tussock grasses coupled with regional structuring points to ongoing gene flow and taxonomic challenges. ANNALS OF BOTANY 2014; 113:953-65. [PMID: 24607721 PMCID: PMC3997636 DOI: 10.1093/aob/mcu017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/27/2014] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS While molecular approaches can often accurately reconstruct species relationships, taxa that are incompletely differentiated pose a challenge even with extensive data. Such taxa are functionally differentiated, but may be genetically differentiated only at small and/or patchy regions of the genome. This issue is considered here in Poa tussock grass species that dominate grassland and herbfields in the Australian alpine zone. METHODS Previously reported tetraploidy was confirmed in all species by sequencing seven nuclear regions and five microsatellite markers. A Bayesian approach was used to co-estimate nuclear and chloroplast gene trees with an overall dated species tree. The resulting species tree was used to examine species structure and recent hybridization, and intertaxon fertility was tested by experimental crosses. KEY RESULTS Species tree estimation revealed Poa gunnii, a Tasmanian endemic species, as sister to the rest of the Australian alpine Poa. The taxa have radiated in the last 0·5-1·2 million years and the non-gunnii taxa are not supported as genetically distinct. Recent hybridization following past species divergence was also not supported. Ongoing gene flow is suggested, with some broad-scale geographic structure within the group. CONCLUSIONS The Australian alpine Poa species are not genetically distinct despite being distinguishable phenotypically, suggesting recent adaptive divergence with ongoing intertaxon gene flow. This highlights challenges in using conventional molecular taxonomy to infer species relationships in recent, rapid radiations.
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Affiliation(s)
- Philippa C. Griffin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ary A. Hoffmann
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
- Pest and Environmental Adaptation Research Group, Department of Zoology, University of Melbourne, Parkville 3010, Victoria, Australia
- Long Term Ecological Research Network, http://www.ltern.org.au/
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32
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Blaner A, Schneider J, Röser M. Phylogenetic relationships in the grass family (Poaceae) based on the nuclear single copy locus topoisomerase 6 compared with chloroplast DNA. SYST BIODIVERS 2014. [DOI: 10.1080/14772000.2014.890137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Shinozuka H, Hand ML, Cogan NOI, Spangenberg GC, Forster JW. Nucleotide diversity of vernalization and flowering-time-related genes in a germplasm collection of meadow fescue (Festuca pratensis Huds. syn. Lolium pratense (Huds.) Darbysh.). Ecol Evol 2013; 3:4415-26. [PMID: 24340183 PMCID: PMC3856742 DOI: 10.1002/ece3.828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/09/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022] Open
Abstract
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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Affiliation(s)
- Hiroshi Shinozuka
- Biosciences Research Division, Department of Environment and Primary Industries, AgriBio, The Centre for AgriBioscience 5 Ring Road, La Trobe University Research and Development Park, Bundoora, Victoria, 3083, Australia ; Dairy Futures Cooperative Research Centre Bundoora, Victoria, 3086, Australia
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Ekanayake PN, Rabinovich M, Guthridge KM, Spangenberg GC, Forster JW, Sawbridge TI. Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement. BMC Evol Biol 2013; 13:270. [PMID: 24330497 PMCID: PMC4028799 DOI: 10.1186/1471-2148-13-270] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/06/2013] [Indexed: 04/09/2023] Open
Abstract
Background Tall fescue and meadow fescue are important as temperate pasture grasses, forming mutualistic associations with asexual Neotyphodium endophytes. The most frequently identified endophyte of Continental allohexaploid tall fescue is Neotyphodium coenophialum, while representatives of two other taxa (FaTG-2 and FaTG-3) have been described as colonising decaploid and Mediterranean hexaploid tall fescue, respectively. In addition, a recent study identified two other putatively novel endophyte taxa from Mediterranean hexaploid and decaploid tall fescue accessions, which were designated as uncharacterised Neotyphodium species (UNS) and FaTG-3-like respectively. In contrast, diploid meadow fescue mainly forms associations with the endophyte taxon Neotyphodium uncinatum, although a second endophyte taxon, termed N. siegelii, has also been described. Results Multiple copies of the translation elongation factor 1-a (tefA) and β-tubulin (tub2) ‘house-keeping’ genes, as well as the endophyte-specific perA gene, were identified for each fescue-derived endophyte taxon from whole genome sequence data. The assembled gene sequences were used to reconstruct evolutionary relationships between the heteroploid fescue-derived endophytes and putative ancestral sub-genomes derived from known sexual Epichloë species. In addition to the nuclear genome-derived genes, the complete mitochondrial genome (mt genome) sequence was obtained for each of the sequenced endophyte, and phylogenetic relationships between the mt genome protein coding gene complements were also reconstructed. Conclusions Complex and highly reticulated evolutionary relationships between Epichloë-Neotyphodium endophytes have been predicted on the basis of multiple nuclear genes and entire mitochondrial protein-coding gene complements, derived from independent assembly of whole genome sequence reads. The results are consistent with previous studies while also providing novel phylogenetic insights, particularly through inclusion of data from the endophyte lineage-specific gene, as well as affording evidence for the origin of cytoplasmic genomes. In particular, the results obtained from the present study imply the possible occurrence of at least two distinct E. typhina progenitors for heteropoid taxa, as well the ancestral contribution of an endophyte species distinct from (although related to) contemporary E. baconii to the extant hybrid species. Furthermore, the present study confirmed the distinct taxonomic status of the newly identified fescue endophyte taxa, FaTG-3-like and UNS, which are consequently proposed to be renamed FaTG4 and FaTG5, respectively.
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Affiliation(s)
| | | | | | | | - John W Forster
- Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3086, Australia.
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Cuyeu R, Rosso B, Pagano E, Soto G, Fox R, Ayub ND. Genetic diversity in a world germplasm collection of tall fescue. Genet Mol Biol 2013. [PMID: 23885206 DOI: 10.1590/s1415‐47572013005000021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.
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Affiliation(s)
- Romina Cuyeu
- Instituto de Genética Ewald A. Favret, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Provincia de Buenos Aires, Argentina
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Cuyeu R, Rosso B, Pagano E, Soto G, Fox R, Ayub ND. Genetic diversity in a world germplasm collection of tall fescue. Genet Mol Biol 2013; 36:237-42. [PMID: 23885206 PMCID: PMC3715290 DOI: 10.1590/s1415-47572013005000021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 03/20/2013] [Indexed: 12/02/2022] Open
Abstract
Festuca arundinacea Schreb., commonly known as tall fescue, is a major forage crop in temperate regions. Recently, a molecular analysis of different accessions of a world germplasm collection of tall fescue has demonstrated that it contains different species from the genus Festuca and allowed their rapid classification into the three major morphotypes (Continental, Mediterranean and Rhizomatous). In this study, we explored the genetic diversity of 161 accessions of Festuca species from 29 countries, including 28 accessions of INTA (Argentina), by analyzing 15 polymorphic SSR markers by capillary electrophoresis. These molecular markers allowed us to detect a total of 214 alleles. The number of alleles per locus varied between 5 and 24, and the values of polymorphic information content ranged from 0.627 to 0.840. In addition, the accessions analyzed by flow cytometry showed different ploidy levels (diploid, tetraploid, hexaploid and octaploid), placing in evidence that the world germplasm collection consisted of multiple species, as previously suggested. Interestingly, almost all accessions of INTA germplasm collection were true hexaploid tall fescue, belonging to two eco-geographic races (Continental and Mediterranean). Finally, the data presented revealed an ample genetic diversity of tall fescue showing the importance of preserving the INTA collection for future breeding programs.
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Affiliation(s)
- Romina Cuyeu
- Instituto de Genética Ewald A. Favret, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Provincia de Buenos Aires, Argentina
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Hand ML, Spangenberg GC, Forster JW, Cogan NOI. Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex. G3 (BETHESDA, MD.) 2013; 3:607-616. [PMID: 23550121 PMCID: PMC3618348 DOI: 10.1534/g3.112.005264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 01/28/2013] [Indexed: 11/22/2022]
Abstract
Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL-psaI intergenic region, however, revealed a "hot-spot" of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses.
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Affiliation(s)
- Melanie L Hand
- Department of Primary Industries, Biosciences Research Division, AgriBio, the Centre for AgriBioscience, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3086, Australia
| | - German C Spangenberg
- Department of Primary Industries, Biosciences Research Division, AgriBio, the Centre for AgriBioscience, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3086, Australia
| | - John W Forster
- Department of Primary Industries, Biosciences Research Division, AgriBio, the Centre for AgriBioscience, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria 3083, Australia
- La Trobe University, Bundoora, Victoria 3086, Australia
| | - Noel O I Cogan
- Department of Primary Industries, Biosciences Research Division, AgriBio, the Centre for AgriBioscience, La Trobe University Research and Development Park, Bundoora, Victoria 3083, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria 3083, Australia
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Young HA, Sarath G, Tobias CM. Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass. BMC PLANT BIOLOGY 2012; 12:117. [PMID: 22834676 PMCID: PMC3492167 DOI: 10.1186/1471-2229-12-117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/11/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Karyotypes can provide information about taxonomic relationships, genetic aberrations, and the evolutionary origins of species. However, differentiation of the tiny chromosomes of switchgrass (Panicum virgatum L.) and creation of a standard karyotype for this bioenergy crop has not been accomplished due to lack of distinguishing features and polyploidy. RESULTS A cytogenetic study was conducted on a dihaploid individual (2n = 2X = 18) of switchgrass to establish a chromosome karyotype. Size differences, condensation patterns, and arm-length ratios were used as identifying features and fluorescence in-situ hybridization (FISH) assigned 5S and 45S rDNA loci to chromosomes 7 and 2 respectively. Both a maize CentC and a native switchgrass centromeric repeat (PviCentC) that shared 73% sequence identity demonstrated a strong signal on chromosome 3. However, only the PviCentC probe labeled the centromeres of all chromosomes. Unexpected PviCentC and 5S rDNA hybidization patterns were consistent with severe reduction or total deletion of these repeats in one subgenome. These patterns were maintained in tetraploid and octoploid individuals. The 45S rDNA repeat produced the expected number of loci in dihaploid, tetraploid and octoploid individuals. Differences observed at the 5S rDNA loci between the upland and lowland ecotypes of switchgrass provided a basis for distinguishing these subpopulations. CONCLUSION Collectively, these results provide a quantitative karyotype of switchgrass chromosomes. FISH analyses indicate genetic divergence between subgenomes and allow for the classification of switchgrass plants belonging to divergent genetic pools. Furthermore, the karyotype structure and cytogenetic analysis of switchgrass provides a framework for future genetic and genomic studies.
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Affiliation(s)
- Hugh A Young
- Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Gautam Sarath
- USDA Central-East Regional Biomass Center, 137 Keim Hall, East Campus, UNL, Lincoln, NE, 68583, USA
| | - Christian M Tobias
- Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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Gundel PE, Helander M, Casas C, Hamilton CE, Faeth SH, Saikkonen K. Neotyphodium fungal endophyte in tall fescue (Schedonorus phoenix): a comparison of three Northern European wild populations and the cultivar Kentucky-31. FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0173-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hand ML, Cogan NOI, Forster JW. Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb). BMC Genomics 2012; 13:219. [PMID: 22672128 PMCID: PMC3444928 DOI: 10.1186/1471-2164-13-219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/15/2012] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) provide essential tools for the advancement of research in plant genomics, and the development of SNP resources for many species has been accelerated by the capabilities of second-generation sequencing technologies. The current study aimed to develop and use a novel bioinformatic pipeline to generate a comprehensive collection of SNP markers within the agriculturally important pasture grass tall fescue; an outbreeding allopolyploid species displaying three distinct morphotypes: Continental, Mediterranean and rhizomatous. RESULTS A bioinformatic pipeline was developed that successfully identified SNPs within genotypes from distinct tall fescue morphotypes, following the sequencing of 414 polymerase chain reaction (PCR) - generated amplicons using 454 GS FLX technology. Equivalent amplicon sets were derived from representative genotypes of each morphotype, including six Continental, five Mediterranean and one rhizomatous. A total of 8,584 and 2,292 SNPs were identified with high confidence within the Continental and Mediterranean morphotypes respectively. The success of the bioinformatic approach was demonstrated through validation (at a rate of 70%) of a subset of 141 SNPs using both SNaPshot™ and GoldenGate™ assay chemistries. Furthermore, the quantitative genotyping capability of the GoldenGate™ assay revealed that approximately 30% of the putative SNPs were accessible to co-dominant scoring, despite the hexaploid genome structure. The sub-genome-specific origin of each SNP validated from Continental tall fescue was predicted using a phylogenetic approach based on comparison with orthologous sequences from predicted progenitor species. CONCLUSIONS Using the appropriate bioinformatic approach, amplicon resequencing based on 454 GS FLX technology is an effective method for the identification of polymorphic SNPs within the genomes of Continental and Mediterranean tall fescue. The GoldenGate™ assay is capable of high-throughput co-dominant SNP allele detection, and minimises the problems associated with SNP genotyping in a polyploid by effectively reducing the complexity to a diploid system. This SNP collection may now be refined and used in applications such as cultivar identification, genetic linkage map construction, genome-wide association studies and genomic selection in tall fescue. The bioinformatic pipeline described here represents an effective general method for SNP discovery within outbreeding allopolyploid species.
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Affiliation(s)
- Melanie L Hand
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, VIC 3083, Australia
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Genotypic and chemotypic diversity of Neotyphodium endophytes in tall fescue from Greece. Appl Environ Microbiol 2012; 78:5501-10. [PMID: 22660705 DOI: 10.1128/aem.01084-12] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epichloid endophytes provide protection from a variety of biotic and abiotic stresses for cool-season grasses, including tall fescue. A collection of 85 tall fescue lines from 15 locations in Greece, including both Continental and Mediterranean germplasm, was screened for the presence of native endophytes. A total of 37 endophyte-infected lines from 10 locations were identified, and the endophytes were classified into five distinct groups (G1 to G5) based on physical characteristics such as colony morphology, growth rate, and conidial morphology. These classifications were supported by phylogenetic analyses of housekeeping genes tefA and tubB, and the endophytes were further categorized as Neotyphodium coenophialum isolates (G1, G4, and G5) or Neotyphodium sp. FaTG-2 (Festuca arundinacea taxonomic group 2 isolates (G2 and G3). Analyses of the tall fescue matK chloroplast genes indicated a population-wide, host-specific association between N. coenophialum and Continental tall fescue and between FaTG-2 and Mediterranean tall fescue that was also reflected by differences in colonization of host tillers by the native endophytes. Genotypic analyses of alkaloid gene loci combined with chemotypic (chemical phenotype) profiles provided insight into the genetic basis of chemotype diversity. Variation in alkaloid gene content, specifically the presence and absence of genes, and copy number of gene clusters explained the alkaloid diversity observed in the endophyte-infected tall fescue, with one exception. The results from this study provide insight into endophyte germplasm diversity present in living tall fescue populations.
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Hand ML, Cogan NOI, Forster JW. Molecular characterisation and interpretation of genetic diversity within globally distributed germplasm collections of tall fescue (Festuca arundinacea Schreb.) and meadow fescue (F. pratensis Huds.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1127-37. [PMID: 22222441 DOI: 10.1007/s00122-011-1774-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 12/15/2011] [Indexed: 05/20/2023]
Abstract
Allohexaploid tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum [Schreb.] Darbysh.) is an agriculturally important grass cultivated for pasture and turf world-wide. Genetic improvement of tall fescue could benefit from the use of non-domesticated germplasm to diversify breeding populations through the incorporation of novel and superior allele content. However, such potential germplasm must first be characterised, as three major morphotypes (Continental, Mediterranean and rhizomatous) with varying degrees of hybrid interfertility are commonly described within this species. As hexaploid tall fescue is also a member of a polyploid species complex that contains tetraploid, octoploid and decaploid taxa, it is also possible that germplasm collections may have inadvertently sampled some of these sub-species. In this study, 1,040 accessions from the publicly available United States Department of Agriculture tall fescue and meadow fescue germplasm collections were investigated. Sequence of the chloroplast genome-located matK gene and the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) permitted attribution of accessions to the three previously known morphotypes and also revealed the presence of tall fescue sub-species of varying ploidy levels, as well as other closely related species. The majority of accessions were, however, identified as Continental hexaploid tall fescue. Analysis using 34 simple sequence repeat markers was able to further investigate the level of genetic diversity within each hexaploid tall fescue morphotype group. At least two genetically distinct sub-groups of Continental hexaploid tall fescue were identified which are probably associated with palaeogeographic range expansion of this morphotype. This work has comprehensively characterised a large and complex germplasm collection and has identified genetically diverse accessions which may potentially contribute valuable alleles at agronomic loci for tall fescue cultivar improvement programs.
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Affiliation(s)
- Melanie L Hand
- Biosciences Research Division, Department of Primary Industries, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, VIC, 3083, Australia
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Kaur S, Francki MG, Forster JW. Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:125-38. [PMID: 21831136 DOI: 10.1111/j.1467-7652.2011.00644.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An understanding of nature and extent of nucleotide sequence variation is required for programmes of discovery and characterization of single nucleotide polymorphisms (SNPs), which provide the most versatile class of molecular genetic marker. A majority of higher plant species are polyploids, and allopolyploidy, because of hybrid formation between closely related taxa, is very common. Mutational variation may arise both between allelic (homologous) sequences within individual subgenomes and between homoeologous sequences among subgenomes, in addition to paralogous variation between duplicated gene copies. Successful SNP validation in allopolyploids depends on differentiation of the sequence variation classes. A number of biological factors influence the feasibility of discrimination, including degree of gene family complexity, inbreeding or outbreeding reproductive habit, and the level of knowledge concerning progenitor diploid species. In addition, developments in high-throughput DNA sequencing and associated computational analysis provide general solutions for the genetic analysis of allopolyploids. These issues are explored in the context of experience from a range of allopolyploid species, representing grain (wheat and canola), forage (pasture legumes and grasses), and horticultural (strawberry) crop. Following SNP discovery, detection in routine genotyping applications also presents challenges for allopolyploids. Strategies based on either design of subgenome-specific SNP assays through homoeolocus-targeted polymerase chain reaction (PCR) amplification, or detection of incremental changes in nucleotide variant dosage, are described.
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Affiliation(s)
- Sukhjiwan Kaur
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Victoria, Australia
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