124 research outputs found
Use of genetic markers for the detection of off-types for DUS phenotypic traits in the inbreeding crop, barley
Detection of crop off-types is of interest for
multiple uses, including the assessment of uniformity
for new plant variety applications during distinctness,
uniformity and stability (DUS) testing for the awarding
of plant breeders’ rights (PBR). Here, we investigate
whether genetic markers, in this case Kompetitive
Allele-Specific PCR (KASP), can be used for the identification
off-types for phenotypes assessed for DUS in
the inbreeding cereal crop, barley (Hordeum vulgare).
To demonstrate proof of principle, KASP markers diagnostic
for phenotypic expression of nine DUS phenotypes,
and DNA from two barley varieties (‘Pelican’ and
‘Felicie’) carrying contrasting alleles at each marker
were used. We found that for the majority of markers,
it was possible to robustly call alleles down to template
DNA concentrations of 2 ng, but not ≤ 0.2 ng. When
used in mixtures of DNA consisting of ‘Felicie’ DNA
spiked with different concentrations of ‘Pelican’ DNA,
robust allele calling was possible in DNA mixtures
down to 18 ng:2 ng. Collectively, this demonstrates that
where diagnostic markers are available, molecular identification
of a single off-type for a given DUS trait
within a bulk of ten individuals should be possible. We
validated this assumption, with all of the diagnostic
genetic markers investigated found to robustly detect
DUS off-types at a frequency of 10% in DNA extracted
from tissue collected from pools of 10 individuals. Ultimately,
this work demonstrates that, where diagnostic
polymorphisms are known for DUS traits, KASP
markers should be able to robustly detect off-types or
cross-contamination within DNA samples from a diploid
inbred species down to 10%. While just two varieties
that contrasted for the eight DUS targeted were
investigated in this study, as the markers used are diagnostic
for their relevant phenotype (or a proportion of
the variation observed for that phenotype), in theory the
approach should be valid for any variety studied—
although the introduction of novel alleles via spontaneous
mutation or more exotic germplasm pools may
mean that marker sets would need to be periodically
added to or updated. However, we nevertheless demonstrate
the principle that, for a subset of DUS traits,
molecular markers can now be robustly used as a tool
towards determining all three components of the DUS
testing process in barley. These results are relevant for
the assessment of varietal uniformity by crop breeders,
crop testing authorities and germplasm maintenance, as
well as highlighting the potential use of bulk samples
rather than individual plant samples for assessment of
distinctness by molecular methods
CWITools: A Python3 Data Analysis Pipeline for the Cosmic Web Imager Instruments
The Palomar Cosmic Web Imager (PCWI) and Keck Cosmic Web Imager (KCWI) are integral-field spectrographs on the Hale 5m telescope at Palomar Observatory and the Keck-2 10m telescope at W. M. Keck Observatory, respectively. In recent years, these instruments have been increasingly used to conduct survey work; in particular focused on the circumgalactic and intergalactic media at high redshift. Extracting faint signals from three-dimensional IFU data is a complex task which can become prohibitively difficult for large samples without the proper tools. We present CWITools, a package written in Python3 for the analysis of PCWI and KCWI data. CWITools is designed to provide a pipeline between the output of the standard instrument data reduction pipelines and scientific products such as surface brightness maps, spectra, velocity maps, as well as a wide array of associated models and measurements. While the package is designed specifically for PCWI and KCWI data, the package is open source and can be adapted to accommodate any three-dimensional integral field spectroscopy data. Here, we describe this pipeline, the methodology behind individual steps and provide example applications
A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene
We used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene
Seed storage proteins of faba bean (Vicia faba L): current status and prospects for genetic improvement
Faba bean (Vicia faba L.) is one of the foremost candidate crops for simultaneously increasing both sustainability and global supply of plant protein. On a dry matter basis, its seeds contain about 29% protein of which more than 80% consists of globulin storage proteins (vicilin and legumin). However, to achieve optimum utilization of this crop for human and animal nutrition, both protein content and quality have to be improved. Though initial investigations on the heritability of these traits indicated the possibility for genetic improvement, little has been achieved so far, partly due to the lack of genetic information coupled with the complex relationship between protein content and grain yield. This review reports on the current knowledge on Vicia faba seed storage proteins, their structure, composition, and genetic control, and highlights key areas for further improvement of the content and composition of Vicia faba seed storage proteins on the basis of recent advances in Vicia faba genome knowledge and genetic tools
Genetic variation at flowering time loci in wild and cultivated barley
The worldwide spread of barley cultivation required adaptation to agricultural environments far distant from those found in its centre of domestication. An important component of this adaptation is the timing of flowering, achieved predominantly in response to day length and temperature. Here, we use a collection of cultivars, landraces and wild barley accessions to investigate the origins and distribution of allelic diversity at four major flowering time loci, mutations at which have been under selection during the spread of barley cultivation into Europe. Our findings suggest that while mutant alleles at the PPD-H1 and PPD-H2 photoperiod loci occurred pre-domestication, the mutant vernalization non-responsive alleles utilized in landraces and cultivars at the VRN-H1 and VRN-H2 loci occurred post-domestication. The transition from wild to cultivated barley is associated with a doubling in the number of observed multi-locus flowering-time haplotypes, suggesting that the resulting phenotypic variation has aided adaptation to cultivation in the diverse ecogeographic locations encountered. Despite the importance of early-flowering alleles during the domestication of barley in Europe, we show that novel VRN alleles associated with early flowering in wild barley have been lost in domesticates, highlighting the potential of wild germplasm as a source of novel allelic variation for agronomic traits
The FLASHES Survey I: Integral Field Spectroscopy of the CGM around 48 QSOs
We present the pilot study component of the Fluorescent Lyman-Alpha
Structures in High-z Environments (FLASHES) Survey; the largest integral-field
spectroscopy survey to date of the circumgalactic medium at . We
observed 48 quasar fields between 2015 and 2018 with the Palomar Cosmic Web
Imager (Matuszewski et al. 2010). Extended HI Lyman- emission
is discovered around 42/48 of the observed quasars, ranging in projected,
flux-weighted radius from 21-71 proper kiloparsecs (pkpc), with 26 nebulae
exceeding in effective diameter. The circularly averaged
surface brightness radial profile peaks at a maximum of
( adjusted for
cosmological dimming) and luminosities range from
to
. The emission appears to have a highly
eccentric morphology and a maximum covering factor of ( for giant
nebulae). On average, the nebular spectra are red-shifted with respect to both
the systemic redshift and Ly peak of the quasar spectrum. The
integrated spectra of the nebulae mostly have single or double-peaked line
shapes with global dispersions ranging from to
, though the individual (Gaussian) components of lines
with complex shapes mostly appear to have dispersions
, and the flux-weighted velocity centroids of the lines
vary by thousands of with respect to the systemic QSO
redshifts. Finally, the root-mean-square velocities of the nebulae are found to
be consistent with gravitational motions expected in dark matter halos of mass
. We compare these results to existing
surveys at both higher and lower redshift
Elevated temperature drives a shift from selfing to outcrossing in the insect pollinated legume, faba bean (Vicia faba)
Climate change can threaten the reproductive success of plants, both directly, through physiological damage during increasingly extreme weather events, and indirectly, through disruption of plant–pollinator interactions. To explore how plant–pollinator interactions are modified by extreme weather, we exposed faba bean (Vicia faba) plants to elevated temperature for 5 d during flowering, simulating a heatwave. We then moved the plants to flight cages with either bumblebees or no pollinators, or to two field sites, where plants were enclosed in mesh bags or pollinated by wild insect communities. We used a morphological marker to quantify pollen movement between experimental plants. There was a substantial increase in the level of outcrossing by insect pollinators following heat stress. Proportion outcrossed seed increased from 17 % at control temperature to 33 % following heat stress in the flight cages, and from 31 % to 80 % at one field site, but not at the other (33 % to 32 %). Abiotic stress can dramatically shift the relative contributions of cross- and self-pollination to reproduction in an insect pollinated plant. The resulting increases in gene flow have broad implications for genetic diversity and functioning of ecosystems, and may increase resilience by accelerating the selection of more stress-tolerant genotypes
Molecular and phenotypic characterization of the alternative seasonal growth habit and flowering time in barley (Hordeum vulgare ssp. vulgare L.)
Barley can be classified into three major agronomic types, based on its seasonal growth habit (SGH): spring, winter and alternative. Winter varieties require exposure to vernalization to promote subsequent flowering and are autumn-sown. Spring varieties proceed to flowering in the absence of vernalization and are sown in the spring. The ‘alternative’ (also known as ‘facultative’) SGH is only loosely defined and can be sown in autumn or spring. Here, we investigate the molecular genetic basis of alternative barley. Analysis of the major barley vernalization (VRN-H1, VRN-H2) and photoperiod (PPD-H1, PPD-H2) response genes in a collection of 386 varieties found alternative SGH to be characterized by specific allelic combinations. Spring varieties possessed spring loci at one or both of the vernalization response loci, combined with long-day non-responsive ppd-H1 alleles and wild-type alleles at the short-day photoperiod response locus, PPD-H2. Winter varieties possessed winter alleles at both vernalization loci, in combination with the mutant ppd-H2 allele conferring delayed flowering under short-day photoperiods. In contrast, all alternative varieties investigated possessed a single spring allele (either at VRN-H1 or at VRN-H2) combined with mutant ppd-H2 alleles. This allelic combination is found only in alternative types and is diagnostic for alternative SGH in the collection studied. Analysis of flowering time under controlled environment found alternative varieties flowered later than spring control lines, with the difference most pronounced under short-day photoperiods. This work provides genetic characterization of the alternative SGH phenotype, allowing precise manipulation of SGH and flowering time within breeding programmes, and provides the molecular tools for classification of all three SGH categories within national variety registration processes
Evaluation of Claviceps purpurea isolates on wheat reveals complex virulence and host susceptibility relationships
Ergot of cereals, caused by Claviceps purpurea, results in yield loss and downgrading of infested grain because of toxic alkaloids in the sclerotia. Resistant wheat genotypes are known, but their effectiveness against different C. purpurea isolates over geographic regions
has not been studied. The objective of this study was to examine the pathogenic variability among isolates of C. purpurea on wheat lines differing in resistance. Under controlled environmental conditions, 41 single spore isolates of C. purpurea were obtained from Canadian
and UK collections and inoculated onto a set of wheat genotypes composed of durum wheat lines ‘Melita’, ‘Kyle’ and 9260B-173A, and hexaploid spring wheat lines ‘Cadillac’, ‘Vista’, ‘Kenya Farmer’, ‘Lee’ and HY630. Honeydew production and weight of sclerotia produced
per spike were assessed. There were significant differences among the wheat genotypes for overall reactions to the pathogen isolates, and among pathogen isolates for geographic origin and host origin. Twenty virulence phenotypes were identified using the honeydew
production data, and 23 virulence phenotypes identified using the sclerotial weight data from the 41 isolates. The existence of different virulence phenotypes indicates that variability in virulence exists in populations of C. purpurea, and knowledge of virulence phenotypes is necessary to effectively breed for resistant commercial lines
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