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1.
Ecol Evol ; 14(4): e11294, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38633520

ABSTRACT

Flowering time is an important phenological trait in plants and a critical determinant of the success of pollination and fruit or seed development, with immense significance for agriculture as it directly affects crop yield and overall food production. Shifts in the growth season, changes in the growth season duration and changes in the production rate are environmental processes (potentially linked to climate change) that can lead to changes in flowering time in the long-term due to selection. In contrast, biomass loss (due to, for example, herbivory or diseases) can have profound consequences for plant mass production and food security. We model the effects of these environmental processes on the flowering time evolutionarily stable strategy (ESS) of annual plants and the potential consequences for reproductive output. Our model recapitulates previous theoretical results linked to climate change and light competition and makes novel predictions about the effects of biomass loss on the evolution of flowering time. Our analysis elucidates how both the magnitude and direction of the evolutionary response can depend on whether biomass loss occurs during the earlier vegetative phase or during the later reproductive phase and on whether or not plants are adapted to grow in dense, competitive environments. Specifically, light competition generates an asymetric effect of mass loss on flowering time even when loss is indiscriminate (equal rates), with vegetative mass loss having a stronger effect on flowering time (resulting in greater ESS change) and final reproductive output.

2.
Plant Physiol ; 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38630859

ABSTRACT

Thousands of barley (Hordeum vulgare L.) mutants have been isolated over the last century, and many are stored in gene banks across various countries. In the present work, we developed a pipeline to efficiently identify causal mutations in barley. The pipeline is also efficient for mutations located in centromeric regions. Through bulked-segregant analyses using whole genome sequencing of pooled F2 seedlings, we mapped two mutations and identified a limited number of candidate genes. We applied the pipeline on F2-mapping populations made from xan-j.59 (unknown mutation) and xan-l.82 (previously known). The Xantha-j (xan-j) gene was identified as encoding chlorophyll synthase, which catalyzes the last step in the chlorophyll biosynthetic pathway: the addition of a phytol moiety to the propionate side chain of chlorophyllide. Key amino-acid residues in the active site, including the binding sites of the isoprenoid and chlorophyllide substrates, were analyzed in an AlphaFold2-generated structural model of the barley chlorophyll synthase. Three allelic mutants, xan-j.19, xan-j.59, and xan-j.64 were characterized. While xan-j.19 is a one-base pair deletion and xan-j.59 is a nonsense mutation, xan-j.64 causes an S212F substitution in chlorophyll synthase. Our analyses of xan-j.64 and treatment of growing barley with clomazone, an inhibitor of chloroplastic isoprenoid biosynthesis, suggest that binding of the isoprenoid substrate is a prerequisite for the stable maintenance of chlorophyll synthase in the plastid. We further suggest that chlorophyll synthase is a sensor for coordinating chlorophyll and isoprenoid biosynthesis.

3.
BMJ Open ; 14(4): e081835, 2024 Apr 19.
Article in English | MEDLINE | ID: mdl-38643010

ABSTRACT

INTRODUCTION: Rare diseases (RDs) collectively impact over 30 million people in Europe. Most individual conditions have a low prevalence which has resulted in a lack of research and expertise in this field, especially regarding genetic newborn screening (gNBS). There is increasing recognition of the importance of incorporating patients' needs and general public perspectives into the shared decision-making process regarding gNBS. This study is part of the Innovative Medicine Initiative project Screen4Care which aims at shortening the diagnostic journey for RDs by accelerating diagnosis for patients living with RDs through gNBS and the use of digital technologies, such as artificial intelligence and machine learning. Our objective will be to assess expecting parent's perspectives, attitudes and preferences regarding gNBS for RDs in Italy and Germany. METHODS AND ANALYSIS: A mixed method approach will assess perspectives, attitudes and preferences of (1) expecting parents seeking genetic consultation and (2) 'healthy' expecting parents from the general population in two countries (Germany and Italy). Focus groups and interviews using the nominal group technique and ranking exercises will be performed (qualitative phase). The results will inform the treatment of attributes to be assessed via a survey and a discrete choice experiment (DCE). The total recruitment sample will be 2084 participants (approximatively 1000 participants in each country for the online survey). A combination of thematic qualitative and logit-based quantitative approaches will be used to analyse the results of the study. ETHICS AND DISSEMINATION: This study has been approved by the Erlangen University Ethics Committee (22-246_1-B), the Freiburg University Ethics Committee (23-1005 S1-AV) and clinical centres in Italy (University of FerraraCE: 357/2023/Oss/AOUFe and Hospedale Bambino Gesu: No.2997 of 2 November 2023, Prot. No. _902) and approved for data storage and handling at the Uppsala University (2022-05806-01). The dissemination of the results will be ensured via scientific journal publication (open access).


Subject(s)
Neonatal Screening , Patient Preference , Infant, Newborn , Humans , Artificial Intelligence , Rare Diseases/diagnosis , Rare Diseases/genetics , Focus Groups
4.
Hereditas ; 161(1): 11, 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38454479

ABSTRACT

BACKGROUND: Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS: Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION: Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.


Subject(s)
Hordeum , Hordeum/genetics , Plant Breeding , Mutagenesis , Genomics
5.
BMC Med Ethics ; 24(1): 83, 2023 10 12.
Article in English | MEDLINE | ID: mdl-37828462

ABSTRACT

BACKGROUND: New disease-modifying ways to treat Parkinson's disease (PD) may soon become a reality with intracerebral transplantation of cell products produced from human embryonic stem cells (hESCs). The aim of this study was to assess what factors influence preferences of patients with PD regarding stem-cell based therapies to treat PD in the future. METHODS: Patients with PD were invited to complete a web-based discrete choice experiment to assess the importance of the following attributes: (i) type of treatment, (ii) aim of treatment, (iii) available knowledge of the different types of treatments, (iv) effect on symptoms, and (v) risk for severe side effects. Latent class conditional logistic regression models were used to determine preference estimates and heterogeneity in respondents' preferences. RESULTS: A substantial difference in respondents' preferences was observed in three latent preference patterns (classes). "Effect on symptoms" was the most important attribute in class 1, closely followed by "type of treatment," with medications as preferred to other treatment alternatives. Effect on symptoms was also the most important attribute in class 2, with treatment with hESCs preferred over other treatment alternatives. Likewise for class 3, that mainly focused on "type of treatment" in the decision-making. Respondents' class membership was influenced by their experience in treatment, side effects, and advanced treatment therapy as well as religious beliefs. CONCLUSIONS: Most of the respondents would accept a treatment with products emanating from hESCs, regardless of views on the moral status of embryos. Preferences of patients with PD may provide guidance in clinical decision-making regarding treatments deriving from stem cells.


Subject(s)
Choice Behavior , Parkinson Disease , Humans , Parkinson Disease/therapy , Patient Preference , Logistic Models , Embryonic Stem Cells
6.
BMC Rheumatol ; 7(1): 17, 2023 Jul 03.
Article in English | MEDLINE | ID: mdl-37400929

ABSTRACT

AIM: Early assessment of patient preferences has the potential to support shared decisions in personalized precision medicine for patients with rheumatoid arthritis (RA). The aim of this study was to assess treatment preferences of patients with RA (< 5 years) with previous experience of inadequate response to first-line monotherapy. METHOD: Patients were recruited (March-June 2021) via four clinics in Sweden. Potential respondents (N = 933) received an invitation to answer a digital survey. The survey included an introductory part, a discrete choice experiment (DCE) and demographic questions. Each respondent answered 11 hypothetical choice questions as part of the DCE. Patient preferences and preference heterogeneity were estimated using random parameter logit models and latent class analysis models. RESULTS: Patients (n = 182) assessed the most important treatment attributes out of physical functional capacity, psychosocial functional capacity, frequency of mild side effects and likelihood of severe side effects. In general, patients preferred a greater increase in functional capacity and decreased side effects. However, a substantial preference heterogeneity was identified with two underlying preference patterns. The most important attribute in the first pattern was the 'likelihood of getting a severe side effect'. Physical functional capacity was the most important attribute in the second pattern. CONCLUSION: Respondents focused their decision-making mainly on increasing their physical functional capacity or decreasing the likelihood of getting a severe side effect. These results are highly relevant from a clinical perspective to strengthen communication in shared decision making by assessing patients' individual preferences for benefits and risks in treatment discussions.

7.
Front Genet ; 14: 1213815, 2023.
Article in English | MEDLINE | ID: mdl-37470037

ABSTRACT

Many induced mutants are available in barley (Hordeum vulgare L.). One of the largest groups of induced mutants is the Erectoides (ert) mutants, which is characterized by a compact and upright spike and a shortened culm. One isolated mutant, ert-k.32, generated by X-ray treatment and registered in 1958 under the named "Pallas", was the first ever induced barley mutant to be released on the market. Its value was improved culm strength and enhanced lodging resistance. In this study, we aimed to identify the casual gene of the ert-k.32 mutant by whole genome sequencing of allelic ert-k mutants. The suggested Ert-k candidate gene, HORVU.MOREX.r3.6HG0574880, is located in the centromeric region of chromosome 6H. The gene product is an alpha/beta hydrolase with a catalytic triad in the active site composed of Ser-167, His-261 and Asp-232. In comparison to proteins derived from the Arabidopsis genome, ErtK is most similar to a thioesterase with de-S-acylation activity. This suggests that ErtK catalyzes post-translational modifications by removing fatty acids that are covalently attached to cysteine residues of target proteins involved in regulation of plant architecture and important commercial traits such as culm stability and lodging resistance.

9.
J Agric Food Chem ; 71(18): 6967-6977, 2023 May 10.
Article in English | MEDLINE | ID: mdl-37104658

ABSTRACT

Flavonoid compounds like anthocyanins and proanthocyanidins are important plant secondary metabolites having wide biological activities for humans. In this study, the molecular function of the Ant13 locus, which is one of the key loci governing flavonoid synthesis in barley, was determined. It was found that Ant13 encodes a WD40-type regulatory protein, which is required for transcriptional activation of a set of structural genes encoding enzymes of flavonoid biosynthesis at the leaf sheath base (colored by anthocyanins) and in grains (which accumulate proanthocyanidins). Besides its role in flavonoid biosynthesis, pleiotropic effects of this gene in plant growth were revealed. The mutants deficient in the Ant13 locus showed similar germination rates but a decreased rate of root and shoot growth and yield-related parameters in comparison to the parental cultivars. This is the seventh Ant locus (among 30) for which molecular functions in flavonoid biosynthesis regulation have been determined.


Subject(s)
Hordeum , Proanthocyanidins , Humans , Anthocyanins/metabolism , Proanthocyanidins/metabolism , Hordeum/genetics , Hordeum/metabolism , Flavonoids/metabolism , Transcription Factors/genetics , Gene Expression Regulation, Plant , Plant Proteins/genetics , Plant Proteins/metabolism
10.
Dev World Bioeth ; 23(4): 344-357, 2023 Dec.
Article in English | MEDLINE | ID: mdl-36269885

ABSTRACT

As genomic research becomes commonplace across the world, there is an increased need to coordinate practices among researchers, especially with regard to data sharing. One such way is an international code of conduct. In September 2020, an expert panel consisting of representatives from various fields convened to discuss a draft proposal formed via a synthesis of existing professional codes and other recommendations. This article presents an overview and analysis of the main issues related to international genomic research that were discussed by the expert panel, and the results of the discussion and follow up responses by the experts. As a result, the article presents as an annex a proposal for an international code of conduct for data sharing in genomics that is meant to establish best practices.


Subject(s)
Genomics , Information Dissemination , Humans , Research Personnel
11.
BMC Med Ethics ; 23(1): 124, 2022 12 03.
Article in English | MEDLINE | ID: mdl-36463154

ABSTRACT

BACKGROUND: Parkinson's disease (PD) has been considered to be one of the most promising target diseases for forthcoming cell-based therapy. The aim of this study is to explore the views of individuals with cryopreserved embryos on using human embryonic stem cells for treating PD. METHODS: The study was performed as a qualitative, semi-structured interview study in June-October 2020. Participants were recruited at a private fertility clinic located in one of the larger Swedish cities. The clinic provides both publicly financed and privately financed IVF-treatments. All interviews were performed by telephone and analyzed using thematic content analysis. Five main categories emerged from 27 sub-categories. RESULTS: In total, 18 interviews were performed with 22 individuals, as either a couple (n = 16) or separately (n = 6). Participants had different views on what a cryopreserved embryo is. Some participants addressed cryopreserved embryos as 'a lump of cells', and some in terms of their 'unborn child'. Conditions for donation of cryopreserved embryos for cell-based treatment in PD were: not losing control of what is happening to the embryo, that donating must be voluntary and based on informed consent with time for reflection, that reimbursement, equality and transparency. CONCLUSIONS: Using cryopreserved embryos to treat PD is associated with fundamental ethical and practical issues. This study shows that IVF couples with left-over embryos may be supportive but there is a need for future research to assess people's views on using cryopreserved embryos for cell-based treatment in PD on a more aggregated level.


Subject(s)
Parkinson Disease , Humans , Parkinson Disease/therapy , Sweden , Cell- and Tissue-Based Therapy , Embryo, Mammalian , Fertilization in Vitro
12.
BMC Med Ethics ; 23(1): 138, 2022 12 22.
Article in English | MEDLINE | ID: mdl-36550460

ABSTRACT

BACKGROUND: The use of human embryonic stem cells (ES cells) for the development of medical therapies is surrounded with moral concerns. The aim of this study was to assess the public's attitudes toward the use of ES cells for treatment of Parkinson's disease (PD) and other diseases, what factors are most important to consider when using ES cells for drug development, and if there is an association between religious beliefs and attitudes toward using ES cells for medical treatment. METHODS: A randomly selected sample of the Swedish public, aged 18-87-years-old, completed an online survey (n = 467). The survey assessed socio-demographics, religious views, perceived moral status of the embryo, and attitudes toward using ES cells for medical treatment of PD and other diseases. Adjusted odds ratios (ORs) and 95% confidence intervals (CI) for positive vs. negative attitude toward using ES cells for drug development were computed using logistic regression. RESULTS: The respondents were positive about using ES for treatment; specifically, 70% totally agreed that it is acceptable to use ES cells for treatment of PD, while 40% totally agreed that it is acceptable to use ES cells for treatment but induced pluripotent cells is just as efficient. Religion being of little importance in one's life was associated with a positive attitude toward using ES cells for treatment of PD (adjusted OR 6.39, 95% CI 2.78-14.71). The importance of being able "to access new, effective treatments against diseases that do not have any treatment available" was ranked as the most important factor to consider when using ES cells for drug development. CONCLUSION: Most respondents are positive about using ES cells for drug development, and making effective treatments accessible to those who do not have any. However, these attitudes are influenced by the specific disorder that the drug development is intended for, as well as the religious views and perceived moral status of the early embryo.


Subject(s)
Human Embryonic Stem Cells , Humans , Adolescent , Young Adult , Adult , Middle Aged , Aged , Aged, 80 and over , Sweden , Attitude , Religion , Morals , Surveys and Questionnaires
13.
BMC Med Ethics ; 23(1): 102, 2022 10 19.
Article in English | MEDLINE | ID: mdl-36261826

ABSTRACT

BACKGROUND: Human embryonic stem cells (hESC) as a source for the development of advanced therapy medicinal products are considered for treatment of Parkinson's disease (PD). Research has shown promising results and opened an avenue of great importance for patients who currently lack a disease modifying therapy. The use of hESC has given rise to moral concerns and been the focus of often heated debates on the moral status of human embryos. Approval for marketing is still pending. OBJECTIVE: To Investigate the perspectives and concerns of patients with PD, patients being the directly concerned stakeholders in the ethical discussion. METHODS: Qualitative semi-structured interviews related to this new therapy in seventeen patients from two Swedish cities. RESULTS: The participants expressed various interests related to the use of human embryos for development of medicinal therapies; however, overall, they were positive towards the use of hESC for treatment of PD. It was deemed important that the donating woman or couple made the choice to donate embryos voluntarily. Furthermore, there were concerns that the industry does not always prioritise the patient over profit; thus, transparency was seen as important.


Subject(s)
Human Embryonic Stem Cells , Parkinson Disease , Female , Humans , Parkinson Disease/therapy , Embryo, Mammalian , Qualitative Research
14.
Int J Mol Sci ; 23(19)2022 Sep 21.
Article in English | MEDLINE | ID: mdl-36232362

ABSTRACT

Increased salinity is one of the major consequences of climatic change affecting global crop production. The early stages in the barley (Hordeum vulgare L.) life cycle are considered the most critical phases due to their contributions to final crop yield. Particularly, the germination and seedling development are sensitive to numerous environmental stresses, especially soil salinity. In this study, we aimed to identify SNP markers linked with germination and seedling development at 150 mM NaCl as a salinity treatment. We performed a genome-wide association study (GWAS) using a panel of 208 intermedium-spike barley (H. vulgare convar. intermedium (Körn.) Mansf.) accessions and their genotype data (i.e., 10,323 SNPs) using the genome reference sequence of "Morex". The phenotypic results showed that the 150 mM NaCl salinity treatment significantly reduced all recorded germination and seedling-related traits compared to the control treatment. Furthermore, six accessions (HOR 11747, HOR 11718, HOR 11640, HOR 11256, HOR 11275 and HOR 11291) were identified as the most salinity tolerant from the intermedium-spike barley collection. GWAS analysis indicated that a total of 38 highly significantly associated SNP markers under control and/or salinity traits were identified. Of these, two SNP markers on chromosome (chr) 1H, two on chr 3H, and one on chr 4H were significantly linked to seedling fresh and dry weight under salinity stress treatment. In addition, two SNP markers on chr 7H were also significantly associated with seedling fresh and dry weight but under control condition. Under salinity stress, one SNP marker on chr 1H, 5H and 7H were detected for more than one phenotypic trait. We found that in most of the accessions exhibiting the highest salinity tolerance, most of the salinity-related QTLs were presented. These results form the basis for detailed studies, leading to improved salt tolerance breeding programs in barley.


Subject(s)
Hordeum , Genome-Wide Association Study , Germination/genetics , Hordeum/genetics , Plant Breeding , Salt Tolerance/genetics , Seedlings/genetics , Sodium Chloride/pharmacology , Soil
15.
Nature ; 606(7912): 113-119, 2022 06.
Article in English | MEDLINE | ID: mdl-35585233

ABSTRACT

Cultivated oat (Avena sativa L.) is an allohexaploid (AACCDD, 2n = 6x = 42) thought to have been domesticated more than 3,000 years ago while growing as a weed in wheat, emmer and barley fields in Anatolia1,2. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.


Subject(s)
Avena , Edible Grain , Genome, Plant , Avena/genetics , Diploidy , Edible Grain/genetics , Genome, Plant/genetics , Mosaicism , Plant Breeding , Tetraploidy
16.
Plants (Basel) ; 11(7)2022 Mar 26.
Article in English | MEDLINE | ID: mdl-35406869

ABSTRACT

Wheat (Triticum aestivum L.) is one of the major staple crops in the world and is used to prepare a range of foods. The development of new varieties with wider variation in grain composition could broaden their use. We characterized grains and flours from oil-accumulating transgenic wheat expressing the oat (Avena sativa L.) endosperm WRINKLED1 (AsWRI1) grown under field conditions. Lipid and starch accumulation was determined in developing caryopses of AsWRI1-wheat and X-ray microtomography was used to study grain morphology. The developing caryopses of AsWRI1-wheat grains had increased triacylglycerol content and decreased starch content compared to the control. Mature AsWRI1-wheat grains also had reduced weight, were wrinkled and had a shrunken endosperm and X-ray tomography revealed that the proportion of endosperm was decreased while that of the aleurone was increased. Grains were milled to produce two white flours and one bran fraction. Mineral and lipid analyses showed that the flour fractions from the AsWRI1-wheat were contaminated with bran, due to the effects of the changed morphology on milling. This study gives a detailed analysis of grains from field grown transgenic wheat that expresses a gene that plays a central regulatory role in carbon allocation and significantly affects grain composition.

17.
Hum Mutat ; 43(6): 717-733, 2022 06.
Article in English | MEDLINE | ID: mdl-35178824

ABSTRACT

Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.


Subject(s)
Genomics , Rare Diseases , Exome , Genetic Association Studies , Genomics/methods , Humans , Phenotype , Rare Diseases/diagnosis , Rare Diseases/genetics
18.
Plants (Basel) ; 10(12)2021 Dec 20.
Article in English | MEDLINE | ID: mdl-34961296

ABSTRACT

MADS-box transcription factors are crucial regulators of inflorescence and flower development in plants. Therefore, the recent interest in this family has received much attention in plant breeding programs due to their impact on plant development and inflorescence architecture. The aim of this study was to investigate the role of HvMADS-box genes in lateral spikelet development in barley (Hordeum vulgare L.). A set of 30 spike-contrasting barley lines were phenotypically and genotypically investigated under controlled conditions. We detected clear variations in the spike and spikelet development during the developmental stages among the tested lines. The lateral florets in the deficiens and semi-deficiens lines were more reduced than in two-rowed cultivars except cv. Kristina. Interestingly, cv. Kristina, int-h.43 and int-i.39 exhibited the same behavior as def.5, def.6, semi-def.1, semi-def.8 regarding development and showed reduced lateral florets size. In HOR1555, HOR7191 and HOR7041, the lateral florets continued their development, eventually setting seeds. In contrast, lateral florets in two-rowed barley stopped differentiating after the awn primordia stage giving rise to lateral floret sterility. At harvest, the lines tested showed large variation for all central and lateral spikelet-related traits. Phylogenetic analysis showed that more than half of the 108 MADS-box genes identified are highly conserved and are expressed in different barley tissues. Re-sequence analysis of a subset of these genes showed clear polymorphism in either SNPs or in/del. Variation in HvMADS56 correlated with altered lateral spikelet morphology. This suggests that HvMADS56 plays an important role in lateral spikelet development in barley.

19.
PLoS One ; 16(11): e0255262, 2021.
Article in English | MEDLINE | ID: mdl-34793465

ABSTRACT

The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.


Subject(s)
Bacterial Proteins/genetics , Bacteriophages/genetics , Gene Expression Regulation, Bacterial , Genetic Variation , Rhodobacter capsulatus/virology , Gene Transfer Techniques
20.
Planta ; 254(1): 9, 2021 Jun 20.
Article in English | MEDLINE | ID: mdl-34148131

ABSTRACT

MAIN CONCLUSION: Both mutant ert-c.1 and ert-d.7 carry T2-T3 translocations in the Ert-c gene. Principal coordinate analyses revealed the translocation types and translocation breakpoints. Mutant ert-d.7 is an Ert-c Ert-d double mutant. Mutations in the Ert-c and Ert-d loci are among the most common barley mutations affecting plant architecture. The mutants have various degrees of erect and compact spikes, often accompanied with short and stiff culms. In the current study, complementation tests, linkage mapping, principal coordinate analyses and fine mapping were conducted. We conclude that the original ert-d.7 mutant does not only carry an ert-d mutation but also an ert-c mutation. Combined, mutations in Ert-c and Ert-d cause a pyramid-dense spike phenotype, whereas mutations in only Ert-c or Ert-d give a pyramid and dense phenotype, respectively. Associations between the Ert-c gene and T2-T3 translocations were detected in both mutant ert-c.1 and ert-d.7. Different genetic association patterns indicate different translocation breakpoints in these two mutants. Principal coordinate analysis based on genetic distance and screening of recombinants from all four ends of polymorphic regions was an efficient way to narrow down the region of interest in translocation-involved populations. The Ert-c gene was mapped to the marker interval of 2_0801to1_0224 on 3HL near the centromere. The results illuminate a complex connection between two single genes having additive effects on barley spike architecture and will facilitate the identification of the Ert-c and Ert-d genes.


Subject(s)
Hordeum , Base Sequence , Chromosome Mapping , Hordeum/genetics , Mutation , Phenotype
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