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1.
Front Plant Sci ; 13: 950720, 2022.
Article in English | MEDLINE | ID: mdl-36003811

ABSTRACT

Across-season biomass assessment is crucial in the cultivar selection process to accurately evaluate the yield performance of lines under different growing conditions. However, it has been difficult to have an accurate, reliable, and repeated fresh biomass (FM) estimation of large populations of plants in the field without destructive harvesting, which incurs significant labor and operation costs. Sensor-based phenotyping platforms have advanced in the data collection of structural and vegetative information of plants, but the developed prediction models are still limited by low correlations at different growth stages and seasons. In this study, our objective was to develop and validate the global prediction models for across-season harvested fresh biomass (FM) yield based on the ground- and air-based sensor data including ground-based LiDAR, ground-based ultrasonic, and air-based multispectral camera to extract LiDAR plant volume (LV), LiDAR point density (LV_Den), height, and Normalized Difference Vegetative Index (NDVI). The study was conducted in a row-plot field trial with 480 rows (3 rows in a plot per cultivar) throughout the whole 2020 growing season up to the reproductive stage. We evaluated the performance of each plant parameter, their relationship, and the best subset prediction models using statistical stepwise selection at the row and plot levels through the seasonal and combined seasonal datasets. The best performing model: F M ~ L V ∗ L V _ D e n ∗ N D V I had a determination of coefficient R 2 of at least 0.9 in vegetative stages and 0.8 in the reproductive stage. Similar results can be achieved in a simpler model with just two LiDAR variables- F M ~ L V ∗ L V _ D e n . In addition, LV and LV_Den showed a robust correlation with FM on their own over seasons and growth stages, while NDVI only performed well in some seasons. The simpler model based on only LiDAR data can be widely applied over season without the need of additional sensor data and may thus make the in-field across-season biomass assessment more feasible and practical for fast and cost-effective development of higher biomass yield cultivars.

2.
Genes (Basel) ; 12(3)2021 02 25.
Article in English | MEDLINE | ID: mdl-33668850

ABSTRACT

Soil salinity is a major abiotic stress, limiting lentil productivity worldwide. Understanding the genetic basis of salt tolerance is vital to develop tolerant varieties. A diversity panel consisting of 276 lentil accessions was screened in a previous study through traditional and image-based approaches to quantify growth under salt stress. Genotyping was performed using two contrasting methods, targeted (tGBS) and transcriptome (GBS-t) genotyping-by-sequencing, to evaluate the most appropriate methodology. tGBS revealed the highest number of single-base variants (SNPs) (c. 56,349), and markers were more evenly distributed across the genome compared to GBS-t. A genome-wide association study (GWAS) was conducted using a mixed linear model. Significant marker-trait associations were observed on Chromosome 2 as well as Chromosome 4, and a range of candidate genes was identified from the reference genome, the most plausible being potassium transporters, which are known to be involved in salt tolerance in related species. Detailed mineral composition performed on salt-treated and control plant tissues revealed the salt tolerance mechanism in lentil, in which tolerant accessions do not transport Na+ ions around the plant instead localize within the root tissues. The pedigree analysis identified two parental accessions that could have been the key sources of tolerance in this dataset.


Subject(s)
Gene Expression Profiling/methods , Genomics/methods , Lens Plant/physiology , Quantitative Trait Loci , Salt Tolerance , Chromosome Mapping , Chromosomes, Plant/genetics , Gene Expression Regulation, Plant , Genome-Wide Association Study , Genotyping Techniques , Lens Plant/genetics , Plant Proteins/genetics , Polymorphism, Single Nucleotide , Sequence Analysis, DNA
3.
Front Plant Sci ; 11: 602313, 2020.
Article in English | MEDLINE | ID: mdl-33613582

ABSTRACT

Molecular characterization of genetically modified plants can provide crucial information for the development of detection and identification methods, to comply with traceability, and labeling requirements prior to commercialization. Detailed description of the genetic modification was previously a challenging step in the safety assessment, since it required the use of laborious and time-consuming techniques. In this study an accurate, simple, and fast method was developed for molecular characterization of genetically modified (GM) plants, following a user-friendly workflow for researchers with limited bioinformatic capabilities. Three GM events from a diverse array of crop species-perennial ryegrass, white clover, and canola-were used to test the approach that exploits long-read sequencing by the MinION device, from Oxford Nanopore Technologies. The method delivered a higher degree of resolution of the transgenic events within the host genome than has previously been possible with the standard Illumina short-range sequencing strategies. The flanking sequences, copy number, and presence of backbone sequences, and overall transgene insertion structure were determined for each of the plant genomes, with the additional identification of moderate-sized secondary insertions that would have previously been missed. The proposed workflow takes only about 1 week from DNA extraction to analyzed result, and the method will complement the existing approaches for molecular characterization of GM plants, since it makes the process faster, simpler, and more cost-effective.

4.
Front Plant Sci ; 10: 1592, 2019.
Article in English | MEDLINE | ID: mdl-31921242

ABSTRACT

Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.

5.
Transgenic Res ; 27(5): 397-407, 2018 10.
Article in English | MEDLINE | ID: mdl-30030680

ABSTRACT

Alkaloid concentration of perennial ryegrass herbage is affected by endophyte strain and host plant genotype. However, previous studies suggest that associations between host and endophyte also depends on environmental conditions, especially those affecting nutrient reserves and that water-soluble carbohydrate (WSC) concentration of perennial ryegrass plants may influence grass-endophyte associations. In this study a single transgenic event, with altered expression of fructosyltransferase genes to produce high WSC and biomass, has been crossed into a range of cultivar backgrounds with varying Epichloë endophyte strains. The effect of the association between the transgenic trait and alkaloid production was assessed and compared with transgene free control populations. In the vast-majority of comparisons there was no significant difference between alkaloid concentrations of transgenic and non-transgenic plants within the same cultivar and endophyte backgrounds. There was no significant difference between GOI+ (gene of interest positive) and GOI- (gene of interest negative) populations in Janthritrem response. Peramine concentration was not different between GOI+ and GOI- for 10 of the 12 endophytes-cultivar combinations. Cultivar Trojan infected with NEA6 and Alto with SE (standard endophyte) exhibited higher peramine and lolitrem B (only for Alto SE) concentration, in the control GOI- compared with GOI+. Similarly, cultivar Trojan infected with NEA6 and Alto with NEA3 presented higher ergovaline concentration in GOI-. Differences in alkaloid concentration may be attributable to an indirect effect in the modulation of fungal biomass. These results conclude that the presence of this transgenic insertion, does not alter the risk (toxicity) of the endophyte-grass associations. Endophyte-host interactions are complex and further research into associations with high WSC plant should be performed in a case by case basis.


Subject(s)
Alkaloids/metabolism , Endophytes/metabolism , Epichloe/metabolism , Hexosyltransferases/genetics , Lolium/microbiology , Mycotoxins/metabolism , Animal Feed , Endophytes/physiology , Epichloe/physiology , Ergotamines/metabolism , Gene Expression Regulation, Plant , Heterocyclic Compounds, 2-Ring/metabolism , Hexosyltransferases/metabolism , Indole Alkaloids/metabolism , Lolium/genetics , Plant Proteins/genetics , Plants, Genetically Modified , Polyamines/metabolism
6.
Front Plant Sci ; 9: 1923, 2018.
Article in English | MEDLINE | ID: mdl-30671074

ABSTRACT

Implementation of molecular biotechnology, such as transgenic technologies, in forage species can improve agricultural profitability through achievement of higher productivity, better use of resources such as soil nutrients, water, or light, and reduced environmental impact. Development of detection and quantification techniques for genetically modified plants are necessary to comply with traceability and labeling requirements prior to regulatory approval for release. Real-time PCR has been the standard method used for detection and quantification of genetically modified events, and droplet digital PCR is a recent alternative technology that offers a higher accuracy. Evaluation of both technologies was performed using a transgenic high-energy forage grass as a case study. Two methods for detection and quantification of the transgenic cassette, containing modified fructan biosynthesis genes, and a selectable marker gene, hygromycin B phosphotransferase used for transformation, were developed. Real-time PCR was assessed using two detection techniques, SYBR Green I and fluorescent probe-based methods. A range of different agricultural commodities were tested including fresh leaves, tillers, seeds, pollen, silage and hay, simulating a broad range of processed agricultural commodities that are relevant in the commercial use of genetically modified pastures. The real-time and droplet digital PCR methods were able to detect both exogenous constructs in all agricultural products. However, a higher sensitivity and repeatability in transgene detection was observed with the droplet digital PCR technology. Taking these results more broadly, it can be concluded that the droplet digital PCR technology provides the necessary resolution for quantitative analysis and detection, allowing absolute quantification of the target sequence at the required limits of detection across all jurisdictions globally. The information presented here provides guidance and resources for pasture-based biotechnology applications that are required to comply with traceability requirements.

7.
Anal Biochem ; 418(2): 253-9, 2011 Nov 15.
Article in English | MEDLINE | ID: mdl-21867673

ABSTRACT

Current methods for measuring fructan levels in plant tissues are time-consuming and costly. They often involve multiple or sequential extractions, enzymatic or acid hydrolysis of fructan polymers, and multiple HPLC runs to quantify fructan-derived hexoses. Here we describe a new method that requires a single extraction step, followed by selective precipitation of fructans by acetone, acid hydrolysis of the precipitate, and a short (10 min) HPLC run to complete the procedure. We used perennial ryegrass samples to show that the new method has similar sensitivity, but better reproducibility, than a more complex method that is widely used. We have used the new method to study developmentally related changes in fructan levels in glasshouse-grown perennial ryegrass plants.


Subject(s)
Chromatography, High Pressure Liquid/methods , Fructans/analysis , Lolium/metabolism , Chemical Precipitation , Fructans/chemistry , Fructans/metabolism , Hydrolysis , Lolium/chemistry , Plant Extracts/analysis , Plant Extracts/chemistry , Plant Extracts/metabolism , Plant Leaves/chemistry , Plant Leaves/metabolism , Plant Roots/chemistry , Plant Roots/metabolism
8.
Theor Appl Genet ; 122(3): 609-22, 2011 Feb.
Article in English | MEDLINE | ID: mdl-20981402

ABSTRACT

Perennial ryegrass is a globally cultivated obligate outbreeding diploid species (2n = 2x = 14) which is subjected to periods of waterlogging stress due to flood irrigation during winter and the lead-up to summer. Reduction of oxygen supply to root systems due to waterlogging produces consequent deleterious effects on plant performance. Framework genetic maps for a large-scale genetic mapping family [F1(NA(x) × AU6)] were constructed containing 91 simple sequence repeat and 24 single nucleotide polymorphism genetic markers. Genetic trait dissection using both control and waterlogging treatments was performed in the glasshouse, a total of 143 maximally recombinant genotypes being selected from the overall sib-ship and replicated threefold in the trial. Analysis was performed for nine quantitative morphological traits measured 8 weeks after stress treatments were applied. A total of 37 quantitative trait loci (QTLs) were identified; 19 on the NA(x) parental genetic map, and 18 on the AU6 parental genetic map. Regions of particular interest were identified on linkage groups (LGs) 4 and 3 of the respective maps, which have been targeted for further analysis by selection of critical recombinants. This first study of genetic control of waterlogging tolerance in ryegrasses has important implications for breeding improvement of abiotic stress adaptation.


Subject(s)
Adaptation, Physiological/genetics , Floods , Lolium/anatomy & histology , Lolium/genetics , Quantitative Trait Loci/genetics , Quantitative Trait, Heritable , Chromosome Mapping , Inheritance Patterns/genetics , Lolium/growth & development , Phenotype , Recombination, Genetic/genetics , Stress, Physiological/genetics
9.
Plant Cell ; 22(10): 3357-73, 2010 Oct.
Article in English | MEDLINE | ID: mdl-20952635

ABSTRACT

Cinnamoyl CoA-reductase (CCR) and caffeic acid O-methyltransferase (COMT) catalyze key steps in the biosynthesis of monolignols, which serve as building blocks in the formation of plant lignin. We identified candidate genes encoding these two enzymes in perennial ryegrass (Lolium perenne) and show that the spatio-temporal expression patterns of these genes in planta correlate well with the developmental profile of lignin deposition. Downregulation of CCR1 and caffeic acid O-methyltransferase 1 (OMT1) using an RNA interference-mediated silencing strategy caused dramatic changes in lignin level and composition in transgenic perennial ryegrass plants grown under both glasshouse and field conditions. In CCR1-deficient perennial ryegrass plants, metabolic profiling indicates the redirection of intermediates both within and beyond the core phenylpropanoid pathway. The combined results strongly support a key role for the OMT1 gene product in the biosynthesis of both syringyl- and guaiacyl-lignin subunits in perennial ryegrass. Both field-grown OMT1-deficient and CCR1-deficient perennial ryegrass plants showed enhanced digestibility without obvious detrimental effects on either plant fitness or biomass production. This highlights the potential of metabolic engineering not only to enhance the forage quality of grasses but also to produce optimal feedstock plants for biofuel production.


Subject(s)
Aldehyde Oxidoreductases/metabolism , Lignin/biosynthesis , Lolium/enzymology , Methyltransferases/metabolism , Plant Proteins/metabolism , Aldehyde Oxidoreductases/genetics , Gene Expression Regulation, Plant , Lolium/genetics , Methyltransferases/genetics , Molecular Sequence Data , Plant Proteins/genetics , Plants, Genetically Modified/enzymology , Plants, Genetically Modified/genetics , RNA Interference , RNA, Plant/genetics
10.
Plant Mol Biol ; 72(3): 343-55, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19943086

ABSTRACT

Perennial ryegrass is an obligate outbreeding pasture grass of the Poaceae family, with a two-locus (S and Z) gametophytic self-incompatibility (SI) mechanism. This system has provided a major obstacle to targeted varietal development, and enhanced knowledge is expected to support more efficient breeding strategies. Comparative genetics and physical mapping approaches have been developed to permit molecular cloning of the SI genes. SI gene-linked genetic markers based on heterologous cDNA restriction fragment length polymorphisms (RFLPs) and homologous genomic DNA-derived simple sequence repeats (SSRs) were converted to single nucleotide polymorphism (SNP) format for efficient genotyping. Genetic mapping identified the location of SI loci and demonstrated macrosynteny between related grass species. S- and Z-linked bacterial artificial chromosome (BAC) clones were sequenced using massively parallel pyrosequencing technology to provide the first physical mapping data for Poaceae SI loci. The sequence assembly process suggested a lower prevalence of middle repetitive sequences in the Z locus region and hence precedence for positional cloning strategy. In silico mapping using data from rice, Brachypodium distachyon and Sorghum revealed high sequence conservation in the vicinity of the Z locus region between SI and self-compatible (SC) grass species. Physical mapping identified a total of nine genes encoded in the Z locus region. Expression profiling and nucleotide diversity assessment identified two Z-linked genes, LpTC116908 and LpDUF247, as plausible candidates for the male and female determinants of the S-Z SI system.


Subject(s)
Chromosome Mapping , Cloning, Molecular/methods , Genes, Plant , Lolium/genetics , Chromosomes, Artificial, Bacterial , Chromosomes, Plant , Expressed Sequence Tags , Gene Expression Profiling , Gene Library , Genetic Linkage , Genetic Markers , Genotype , Physical Chromosome Mapping , Polymorphism, Single Nucleotide , Reproduction/genetics , Sequence Analysis, DNA
11.
Theor Appl Genet ; 120(3): 607-19, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19865805

ABSTRACT

Allotetraploid (2n = 4x = 32) white clover (Trifolium repens L.) is the most commonly cultivated legume component of temperate pastures, sown in swards with a companion grass species. Genetic control of growth performance of white clover on saline land is highly important for dairy industries, due to increasing soil salinity problems. The objective of this study was to identify quantitative trait loci (QTLs) for salinity tolerance in terms of vegetative growth under stress. Two parental genetic maps consisting of 213 and 159 marker loci and spanning 1,973.0 and 1,837.6 cM, respectively, were constructed using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers from a two-way pseudo-test cross F(1) population derived from pair-crossing of the Haifa(2) and LCL(2) genotypes. A total of 8 unique genomic regions on 8 linkage groups (LGs) of the Haifa(2) parental map and 6 unique regions on 5 LGs in the LCL(2) parental map were associated with plant growth under salt stress and relative growth under stress, as compared to control conditions. The results of this study indicate that salt tolerance in white clover is controlled by multiple QTLs, some at common locations, but each of limited magnitude. Location of these QTLs provides the genetic basis and potential for pyramiding of salt tolerance genes in breeding improvement.


Subject(s)
Quantitative Trait Loci/genetics , Salt Tolerance/genetics , Stress, Physiological/genetics , Trifolium/genetics , Biomass , Chromosome Mapping , Phenotype , Quantitative Trait, Heritable , Salt Tolerance/drug effects , Sodium Chloride/pharmacology , Stress, Physiological/drug effects , Trifolium/drug effects , Trifolium/growth & development
12.
BMC Plant Biol ; 9: 62, 2009 May 19.
Article in English | MEDLINE | ID: mdl-19450286

ABSTRACT

BACKGROUND: Qualitative pathogen resistance in both dicotyledenous and monocotyledonous plants has been attributed to the action of resistance (R) genes, including those encoding nucleotide binding site--leucine rich repeat (NBS-LRR) proteins and receptor-like kinase enzymes. This study describes the large-scale isolation and characterisation of candidate R genes from perennial ryegrass. The analysis was based on the availability of an expressed sequence tag (EST) resource and a functionally-integrated bioinformatics database. RESULTS: Amplification of R gene sequences was performed using template EST data and information from orthologous candidate using a degenerate consensus PCR approach. A total of 102 unique partial R genes were cloned, sequenced and functionally annotated. Analysis of motif structure and R gene phylogeny demonstrated that Lolium R genes cluster with putative ortholoci, and evolved from common ancestral origins. Single nucleotide polymorphisms (SNPs) predicted through resequencing of amplicons from the parental genotypes of a genetic mapping family were validated, and 26 distinct R gene loci were assigned to multiple genetic maps. Clusters of largely non-related NBS-LRR genes were located at multiple distinct genomic locations and were commonly found in close proximity to previously mapped defence response (DR) genes. A comparative genomics analysis revealed the co-location of several candidate R genes with disease resistance quantitative trait loci (QTLs). CONCLUSION: This study is the most comprehensive analysis to date of qualitative disease resistance candidate genes in perennial ryegrass. SNPs identified within candidate genes provide a valuable resource for mapping in various ryegrass pair cross-derived populations and further germplasm analysis using association genetics. In parallel with the use of specific pathogen virulence races, such resources provide the means to identify gene-for-gene mechanisms for multiple host pathogen-interactions and ultimately to obtain durable field-based resistance.


Subject(s)
Chromosome Mapping , Immunity, Innate , Lolium/genetics , Quantitative Trait Loci , Computational Biology , DNA, Plant/genetics , Databases, Genetic , Expressed Sequence Tags , Genes, Plant , Genetic Linkage , Genome, Plant , Genomics , Lolium/immunology , Phylogeny , Plant Diseases/genetics , Sequence Alignment
13.
Genome ; 51(11): 905-11, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18956023

ABSTRACT

Computational analysis has been used to align the genetic map of white clover (Trifolium repens L.) with the draft genome sequence of the model legume species Medicago truncatula Gaertn. In silico comparison based on white clover expressed sequence tags that contain simple sequence repeat loci revealed substantial macrosynteny between the genomes of these two species, which are closely related within the Trifolieae tribe of the Fabaceae family. Six of the eight homoeologous chromosome groups (HGs) of allotetraploid white clover show predominant relationships with single M. truncatula (Mt) chromosomes, while the two remaining groups may have participated in an evolutionary reciprocal translocation event. On this basis, a new chromosome nomenclature system for allotetraploid white clover is proposed such that HG A = 3, HG B = 8, HG C = 7, HG D = 4, HG E = 1, HG F = 2, HG G = 5, and HG H = 6. A rationalized linkage map ordering system has also been demonstrated. Improved knowledge of the relationships between agricultural and model forage legume genomes will facilitate prediction of gene location for key agronomic traits for pasture production.


Subject(s)
Medicago truncatula/classification , Medicago truncatula/genetics , Trifolium/classification , Trifolium/genetics , Chromosome Mapping , DNA, Plant/genetics , Evolution, Molecular , Expressed Sequence Tags , Genome, Plant , Minisatellite Repeats , Phylogeny , Polyploidy , Species Specificity , Terminology as Topic
14.
Mol Genet Genomics ; 280(4): 293-304, 2008 Oct.
Article in English | MEDLINE | ID: mdl-18642031

ABSTRACT

The combination of homologous, homoeologous and paralogous classes of sequence variation presents major challenges for SNP discovery in outbreeding allopolyploid species. Previous in vitro gene-associated SNP discovery studies in the allotetraploid forage legume white clover (Trifolium repens L.) were vulnerable to such effects, leading to prohibitive levels of attrition during SNP validation. Identification of T. occidentale and T. pallescens as the putative diploid progenitors of white clover has permitted discrimination of the different sequence variant categories. Amplicons from selected abiotic stress tolerance-related genes were obtained using mapping family parents and individuals from each diploid species. Following cloning, progenitor comparison allowed tentative assignment of individual haplotypes to one or other sub-genome, as well as to gene copies within sub-genomes. A high degree of coincidence and identity between SNPs and HSVs was observed. Close similarity was observed between the genome of T. occidentale and one white clover sub-genome, but the affinity between T. pallescens and the other sub-genome was weaker, suggesting that a currently uncharacterised taxon may be the true second progenitor. Selected validated SNPs were attributed to individual sub-genomes by assignment to and naming of homoeologous linkage groups, providing the basis for improved genetic trait-dissection studies. The approach described in this study is broadly applicable to a range of allopolyploid taxa of equivocal ancestry.


Subject(s)
Genes, Plant/physiology , Phylogeny , Polymorphism, Single Nucleotide , Stress, Physiological/genetics , Trifolium/genetics , Base Sequence , Breeding , Molecular Sequence Data , Sequence Alignment
15.
Mol Genet Genomics ; 278(5): 585-97, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17647019

ABSTRACT

Development of accurate high-throughput molecular marker systems such as SNPs permits evaluation and selection of favourable gene variants to accelerate elite varietal production. SNP discovery in perennial ryegrass has been based on PCR amplification and sequencing of multiple amplicons designed to scan all components of the transcriptional unit. Full-length genes (with complete intron-exon structure and promoter information) corresponding to well-defined biochemical functions such as lignin biosynthesis and oligosaccharide metabolism are ideal for complete SNP haplotype determination. Multiple SNPs at regular intervals across the transcriptional unit were detected within and between the heterozygous parents and validated in the progeny of the F (1)(NA(6) x AU(6)) genetic mapping family. Haplotype structures in the parental genotypes were defined and haplotypic abundance, structure and variation were assessed in diverse germplasm sources. Decay of LD to r (2) values of c. 0.2 typically occurs over 500-3,000 bp, comparable with gene length and with little apparent variation between diverse, ecotypic and varietal population sub-groups. Similar patterns were revealed as limited blocks of intragenic LD. The results are compatible with the reproductive biology of perennial ryegrass and the effects of large ancestral population size. This analysis provides crucial information to validate strategies for correlation of haplotypic diversity and phenotypic variation through association mapping.


Subject(s)
Linkage Disequilibrium , Lolium/genetics , Polymorphism, Single Nucleotide , Chromosomes, Plant , Cloning, Molecular , Crosses, Genetic , Exons , Genes, Plant , Haplotypes , Models, Genetic , Models, Statistical , Phenotype , Polymerase Chain Reaction
16.
Genome ; 49(8): 919-30, 2006 Aug.
Article in English | MEDLINE | ID: mdl-17036067

ABSTRACT

White clover (Trifolium repens L.) is an important temperate pasture legume that plays a key role as a companion to grass species, such as perennial ryegrass (Lolium perenne L.). Due to the outbreeding nature of white clover, cultivars are highly heterogeneous. Genetic diversity was assessed using 16 elite cultivars from Europe, North and South America, Australia, and New Zealand. Fifteen simple sequence repeat markers that detect single, codominant polymorphic genetic loci were selected for the study. The genetic relationships among individuals were compared using phenetic clustering, and those among cultivars were compared using nonmetric multidimensional scaling. Intrapopula tion variability exceeded interpopulation variability, with substantial overlap among populations and weak interpopula tion differentiation. No obvious or significant differentiation was observed on the basis of morphology or geographic origin of the cultivars. The number of parental genotypes used to derive each cultivar was not a major determinant of genome-wide genetic diversity. The outcomes of this assessment of genetic variation in elite white clover germplasm pools have important implications for the feasibility of molecular marker-based cultivar discrimination, and will be used to assist the design of linkage disequilibrium mapping strategies for marker-trait association.


Subject(s)
Trifolium/genetics , Base Sequence , DNA Primers/genetics , DNA, Plant/genetics , Genetic Variation , Genotype , Minisatellite Repeats , Polymorphism, Genetic
17.
Genome ; 49(6): 572-83, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16936837

ABSTRACT

The causative organism of crown rust in ryegrasses (Puccinia coronata f.sp. lolii) is an obligate biotroph that causes significant economic losses within the temperate grazing industries of dairy, meat, and wool production. This study reports on the development, transferability, and utility of gene-associated simple sequence repeat (SSR) molecular markers for crown rust. Analysis of 1,100 expressed sequence tag (EST) sequences from a urediniospore-derived cDNA library detected 55 SSR loci. The majority of EST-SSR arrays contained perfect trinucleotide repeats with consistently low repeat numbers, and the motifs (ACC)n and (CAT)n were most commonly represented. DNA extraction from single pustules, in conjunction with multiple displacement amplification, provided the basis for PCR-based screening to evaluate genetic marker performance. An example of the identification of intraspecific genetic diversity was obtained from the analysis of 16 P. coronata isolates originating from the United Kingdom, Australia, New Zealand, and Japan. A subset of 12 robust EST-SSR markers was informative for determination of pathogen diversity within and between these localities. It was also demonstrated that crown rust EST-SSR markers were capable of cross-amplification in closely related fungal taxa (Puccinia spp.) and filamentous fungi within the Ascomycota.


Subject(s)
Expressed Sequence Tags , Fungi/genetics , Lolium/microbiology , Minisatellite Repeats , Plant Diseases/genetics , Base Sequence , DNA, Complementary/analysis , DNA, Fungal/classification , Fungi/classification , Fungi/pathogenicity , Genetic Markers , Genetic Variation , Genome, Fungal , Molecular Sequence Data , Nucleic Acid Amplification Techniques/methods , Phylogeny , Polymerase Chain Reaction/methods , Sequence Homology, Nucleic Acid
18.
Mol Genet Genomics ; 276(2): 101-12, 2006 Aug.
Article in English | MEDLINE | ID: mdl-16708235

ABSTRACT

Molecular genetic marker development in perennial ryegrass has largely been dependent on anonymous sequence variation. The availability of a large-scale EST resource permits the development of functionally-associated genetic markers based on SNP variation in candidate genes. Genic SNP loci and associated haplotypes are suitable for implementation in molecular breeding of outbreeding forage species. Strategies for in vitro SNP discovery through amplicon cloning and sequencing have been designed and implemented. Putative SNPs were identified within and between the parents of the F(1)(NA(6) x AU(6)) genetic mapping family and were validated among progeny individuals. Proof-of-concept for the process was obtained using the drought tolerance-associated LpASRa2 gene. SNP haplotype structures were determined and correlated with predicted amino acid changes. Gene-length LD was evaluated across diverse germplasm collections. A survey of SNP variation across 100 candidate genes revealed a high frequency of SNP incidence (c. 1 per 54 bp), with similar proportions in exons and introns. A proportion (c. 50%) of the validated genic SNPs were assigned to the F(1)(NA(6) x AU(6)) genetic map, showing high levels of coincidence with previously mapped RFLP loci. The perennial ryegrass SNP resource will enable genetic map integration, detailed LD studies and selection of superior allele content during varietal development.


Subject(s)
Expressed Sequence Tags , Genes, Plant/genetics , Lolium/genetics , Polymorphism, Single Nucleotide , Quantitative Trait Loci/genetics , Breeding , Cloning, Molecular , Exons/genetics , Genetic Markers , Introns , Plant Proteins/genetics , Sequence Analysis, DNA
19.
J Healthc Inf Manag ; 18(4): 56-60, 2004.
Article in English | MEDLINE | ID: mdl-15537135

ABSTRACT

With the increased interest in evidence-based medicine, Internet access and the growing emphasis on national standards, there is an increased challenge for teaching institutions and nursing services to teach and implement standards. At the same time, electronic clinical documentation tools have started to become a common format for recording nursing notes. The major aim of this paper is to ascertain and assess the availability of clinical nursing tools based on the NANDA, NOC and NIC standards. Faculty at 20 large nursing schools and directors of nursing at 20 hospitals were interviewed regarding the use of nursing standards in clinical documentation packages, not only for teaching purposes but also for use in hospital-based systems to ensure patient safety. A survey tool was utilized that covered questions regarding what nursing standards are being taught in the nursing schools, what standards are encouraged by the hospitals, and teaching initiatives that include clinical documentation tools. Information was collected on how utilizing these standards in a clinical or hospital setting can improve the overall quality of care. Analysis included univariate and bivariate analysis. The consensus between both groups was that the NANDA, NOC and NIC national standards are the most widely taught and utilized. In addition, a training initiative was identified within a large university where a clinical documentation system based on these standards was developed utilizing handheld devices.


Subject(s)
Nursing Records/standards , Nursing/standards , Interviews as Topic , Nursing Diagnosis , Outcome Assessment, Health Care , United States
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