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Østrem L, Rapacz M, Larsen A, Marum P, Rognli OA. Chlorophyll a Fluorescence and Freezing Tests as Selection Methods for Growth Cessation and Increased Winter Survival in × Festulolium. FRONTIERS IN PLANT SCIENCE 2018; 9:1200. [PMID: 30177939 PMCID: PMC6109792 DOI: 10.3389/fpls.2018.01200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/26/2018] [Indexed: 05/30/2023]
Abstract
In a ×Festulolium population (FuRs0357) of parental origin Lolium perenne × Festuca pratensis, selection of freezing tolerance by freezing tests on whole plants (FT) and chlorophyll a (Chl-a) fluorimetry on frozen detached leaves (CF) was assessed in high and low directions during two cycles of selection. The original population went through two cycles of random mating. All selections and non-selected intercrossed generations of the original population were established in field trials at a coastal site and a continental site in Norway. At the coastal site, analyses of Chl-a fluorimetry parameters and leaf growth on individual plants in autumn and winter hardiness observed in field plots in spring showed that the first-generation selections for high freezing tolerance were associated with winter hardiness and early growth cessation. The second-generation FT-selections for high freezing tolerance were also associated with winter hardiness, whereas the CF-high selections diverged toward high photosynthetic activity. Both low selections were correlated with high photosynthetic activity. There were smaller variations between generations in unselected generations of the original population. Low accumulated leaf growth and early growth cessation were observed in the second-generation FT-selection for high freezing tolerance, whereas high normalized difference vegetation index (NDVI) were seen in Chl-a selections. Both selection methods distinguished diverging selections with significantly different high and low freezing tolerance, but selection efficiency was comparable only for the first selection cycle. Moreover, due to mixed ploidy level in the original population, selection by FT and CF generated diploid and tetraploid plants, respectively, which intensified the response of selection, particularly in the diploid selections. Total dry matter yield (DMY) (mean of three annual cuts for 3 years) of the FT-high selections was lower than for the CF-selections. At coastal sites, selection intensity using freezing tests on whole plants should be adapted to actual climate conditions, to obtain genotypes that balance photosynthetic activity during autumn and good winter hardiness, making them persistent and high yielding.
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Affiliation(s)
- Liv Østrem
- Department of Grassland and Livestock, Norwegian Institute of Bioeconomy Research (NIBIO), Hellevik i Fjaler, Norway
| | - Marcin Rapacz
- Department of Plant Physiology, University of Agriculture in Krakow, Krakow, Poland
| | | | | | - Odd A. Rognli
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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Harper J, Phillips D, Thomas A, Gasior D, Evans C, Powell W, King J, King I, Jenkins G, Armstead I. B chromosomes are associated with redistribution of genetic recombination towards lower recombination chromosomal regions in perennial ryegrass. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1861-1871. [PMID: 29635481 PMCID: PMC6019035 DOI: 10.1093/jxb/ery052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/10/2018] [Indexed: 05/26/2023]
Abstract
Supernumerary 'B' chromosomes are non-essential components of the genome present in a range of plant and animal species-including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.
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Affiliation(s)
- John Harper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dylan Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ann Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dagmara Gasior
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Caron Evans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Julie King
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Ian King
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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Velmurugan J, Mollison E, Barth S, Marshall D, Milne L, Creevey CJ, Lynch B, Meally H, McCabe M, Milbourne D. An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly. ANNALS OF BOTANY 2016; 118:71-87. [PMID: 27268483 PMCID: PMC4934400 DOI: 10.1093/aob/mcw081] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/28/2015] [Accepted: 02/17/2016] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS High density genetic linkage maps that are extensively anchored to assembled genome sequences of the organism in question are extremely useful in gene discovery. To facilitate this process in perennial ryegrass (Lolium perenne L.), a high density single nucleotide polymorphism (SNP)- and presence/absence variant (PAV)-based genetic linkage map has been developed in an F2 mapping population that has been used as a reference population in numerous studies. To provide a reference sequence to which to align genotyping by sequencing (GBS) reads, a shotgun assembly of one of the grandparents of the population, a tenth-generation inbred line, was created using Illumina-based sequencing. METHODS The assembly was based on paired-end Illumina reads, scaffolded by mate pair and long jumping distance reads in the range of 3-40 kb, with >200-fold initial genome coverage. A total of 169 individuals from an F2 mapping population were used to construct PstI-based GBS libraries tagged with unique 4-9 nucleotide barcodes, resulting in 284 million reads, with approx. 1·6 million reads per individual. A bioinformatics pipeline was employed to identify both SNPs and PAVs. A core genetic map was generated using high confidence SNPs, to which lower confidence SNPs and PAVs were subsequently fitted in a straightforward binning approach. KEY RESULTS The assembly comprises 424 750 scaffolds, covering 1·11 Gbp of the 2·5 Gbp perennial ryegrass genome, with a scaffold N50 of 25 212 bp and a contig N50 of 3790 bp. It is available for download, and access to a genome browser has been provided. Comparison of the assembly with available transcript and gene model data sets for perennial ryegrass indicates that approx. 570 Mbp of the gene-rich portion of the genome has been captured. An ultra-high density genetic linkage map with 3092 SNPs and 7260 PAVs was developed, anchoring just over 200 Mb of the reference assembly. CONCLUSIONS The combined genetic map and assembly, combined with another recently released genome assembly, represent a significant resource for the perennial ryegrass genetics community.
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Affiliation(s)
- Janaki Velmurugan
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland University College Dublin, School of Agriculture and Food Science, Dublin, Ireland
| | - Ewan Mollison
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland Information and Computational Sciences Group, James Hutton Institute, Errol Road, Invergowrie, Dundee, UK Division of Plant Sciences, University of Dundee at the James Hutton Institute, Errol Road, Invergowrie, Dundee, UK
| | - Susanne Barth
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland
| | - David Marshall
- Information and Computational Sciences Group, James Hutton Institute, Errol Road, Invergowrie, Dundee, UK
| | - Linda Milne
- Information and Computational Sciences Group, James Hutton Institute, Errol Road, Invergowrie, Dundee, UK
| | | | - Bridget Lynch
- University College Dublin, School of Agriculture and Food Science, Dublin, Ireland
| | - Helena Meally
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland
| | - Matthew McCabe
- Teagasc, Animal and Grassland Research and Innovation Centre, Grange, Ireland
| | - Dan Milbourne
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland
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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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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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King J, Thomas A, James C, King I, Armstead I. A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis. BMC Genomics 2013. [PMID: 23819624 DOI: 10.1186/1471‐2164‐14‐437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. RESULTS A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. CONCLUSIONS DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.
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King J, Thomas A, James C, King I, Armstead I. A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis. BMC Genomics 2013; 14:437. [PMID: 23819624 PMCID: PMC3704433 DOI: 10.1186/1471-2164-14-437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/19/2013] [Indexed: 01/28/2023] Open
Abstract
Background Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. Results A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. Conclusions DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.
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Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 2012; 7:e44684. [PMID: 22984541 PMCID: PMC3439404 DOI: 10.1371/journal.pone.0044684] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
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Rodríguez-Suárez C, Giménez MJ, Gutiérrez N, Avila CM, Machado A, Huttner E, Ramírez MC, Martín AC, Castillo A, Kilian A, Martín A, Atienza SG. Development of wild barley (Hordeum chilense)-derived DArT markers and their use into genetic and physical mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:713-22. [PMID: 22048641 DOI: 10.1007/s00122-011-1741-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 10/18/2011] [Indexed: 05/24/2023]
Abstract
Diversity arrays technology (DArT) genomic libraries were developed from H. chilense accessions to support robust genotyping of this species and a novel crop comprising H. chilense genome (e.g., tritordeums). Over 11,000 DArT clones were obtained using two complexity reduction methods. A subset of 2,209 DArT markers was identified on the arrays containing these clones as polymorphic between parents and segregating in a population of 92 recombinant inbred lines (RIL) developed from the cross between H. chilense accessions H1 and H7. Using the segregation data a high-density map of 1,503 cM was constructed with average inter-bin density of 2.33 cM. A subset of DArT markers was also mapped physically using a set of wheat-H. chilense chromosome addition lines. It allowed the unambiguous assignment of linkage groups to chromosomes. Four segregation distortion regions (SDRs) were found on the chromosomes 2H(ch), 3H(ch) and 5H(ch) in agreement with previous findings in barley. The new map improves the genome coverage of previous H. chilense maps. H. chilense-derived DArT markers will enable further genetic studies in ongoing projects on hybrid wheat, seed carotenoid content improvement or tritordeum breeding program. Besides, the genetic map reported here will be very useful as the basis to develop comparative genomics studies with barley and model species.
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Affiliation(s)
- C Rodríguez-Suárez
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo. 4084, 14080, Córdoba, Spain
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