scholarly journals Identification through fine mapping and verification using CRISPR/Cas9-targeted mutagenesis for a minor QTL controlling grain weight in rice

2020 ◽  
Author(s):  
Aye Nyein Chan ◽  
Lin-Lin Wang ◽  
Yu-Jun Zhu ◽  
Ye-Yang Fan ◽  
Jie-Yun Zhuang ◽  
...  
Keyword(s):  
Target Genes ◽  
Grain Weight ◽  
Targeted Mutagenesis ◽  
Gene Encoding ◽  
Minor Qtls ◽  
Causal Genes ◽  
Novel Alleles ◽  
Rice Improvement ◽  
A Minor ◽  
1000 Grain Weight

Abstract Key message A minor QTL for grain weight in rice, qTGW1.2b, was fine-mapped. Its casual gene OsVQ4 was confirmed through CRISPR/Cas9-targeted mutagenesis, exhibiting an effect that was larger than the original QTL effect. Abstract The CRISPR/Cas system exhibits a great potential for rice improvement, but the application was severely hindered due to insufficient target genes, especial the lack of validated genes underlying quantitative trait loci having small effects. In this study, a minor QTL for grain weight, qTGW1.2b, was fine-mapped into a 44.0 kb region using seven sets of near isogenic lines (NILs) developed from the indica rice cross (Zhenshan 97)3/Milyang 46, followed by validation of the causal gene using CRISPR/Cas9-targeted mutagenesis. In the NIL populations, 1000-grain weight of the Zhenshan 97 homozygous lines decreased by 0.9–2.0% compared with the Milyang 46 homozygous lines. A gene encoding VQ-motif protein, OsVQ4, was identified as the candidate gene based on parental sequence differences. The effect of OsVQ4 was confirmed by creating CRISPR/Cas9 knockout lines, whose 1000-grain weight decreased by 2.8–9.8% compared with the wild-type transgenic line and the recipient. These results indicate that applying genome editing system could create novel alleles with large phenotypic variation at minor QTLs, which is an effective way to validate causal genes of minor QTLs. Our study establishes a strategy for cloning minor QTLs, which could also be used to identify a large number of potential target genes for the application of CRISPR/Cas system.

A trait collection of spring groat barley

2018 ◽  
pp. 85-96
Author(s):  
I.A. Petukhova ◽  
V.K. Riabchun ◽  
V.A. Muzapharova ◽  
O.I. Padalka ◽  
T.A. Sheliakina ◽  
...  
Keyword(s):  
High Performance ◽  
Spring Barley ◽  
Vegetation Period ◽  
Grain Weight ◽  
Starting Material ◽  
Economic Traits ◽  
The Czech Republic ◽  
Science And Education ◽  
New Varieties ◽  
1000 Grain Weight

The goal of our research was to form a collection of groats barley, to search, to select and to evaluate starting material of spring barley for a set of valuable economic traits, technological properties and culinary qualities of barley groats. Results and Discussion. Basing on to the results of assessments, we identified selected 55 spring barley accessions, which were characterized by 17 traits and 75 expression levels. The collection includes accessions from 11 countries; the largest number of accessions (59) are from Ukraine; 39 – from Russia; 10 - from Belarus; 10 - from Germany; 6 - from France; 5 - from Kazakhstan; 4 - from Canada; 3 - from the Czech Republic; 2 – from Great Britain; 1 accesson is from Serbia; and 1 - from Austria. Accessions combining high levels of expression of different traits are the most valuable. They include the following accessions: Doridnyi, Vodohrai, Sviatomykhailivskyi, Svarozhych, Soka, Іlot (UKR). Naked accessions include: Akhilles (UKR), Mayskiy, Oskar, Golozyornyy 1, Omskiy Golozyornyy 1 (RUS), CDC Alamo, CDC Candle (CAN). These varieties can be starting material for creation of new modern high-performance spring groats barley varieties. Ten valuable accessions registered with the NCPGRU (Sovіra, Doridnyi, Soka, Vodohrai, Partner, Yukatan, Avhii, Svarozhych, Baskak, and Virtuoz) were included in the trait groats collection. Conclusions. Basing on the results of multiyear studies, we formed the trait collection of spring groats barley comprising 140 accessions from 11 countries. The collection includes 55 reference accessions that cover 17 traits (plant height, vegetation period, ear length, grain weight per ear, 1000-grain weight, grain shape, grain evenness, vitreousness, culinary qualities of barley groats, etc.) characterized by 75 levels of their expression. The collection is of considerable value for science and education. The accessions selected allow improving the efficiency of breeding to create new varieties with high technological and culinary properties as well as with a set of valuable economic characteristics.

Study onGenetic Variability, Heritability and Genetic Advance for Seed Yield and Component Traits in Rice

2017 ◽  
Vol 4 (03) ◽  
Author(s):  
PUNIT KUMAR ◽  
VICHITRA KUMAR ARYA ◽  
PRADEEP KUMAR ◽  
LOKENDRA KUMAR ◽  
JOGENDRA SINGH
Keyword(s):  
Grain Yield ◽  
Plant Height ◽  
Seed Yield ◽  
Flag Leaf ◽  
Grain Weight ◽  
Major Influence ◽  
Genetic Advance ◽  
Component Traits ◽  
Biological Yield ◽  
1000 Grain Weight

A study on genetic variability, heritability and genetic advance for seed yield and component traits was made in 40 genotypes of riceduring kharif 2011-2012 at SHIATS, Allahabad. The analysis of variance showed highly significant differences among the treatments for all the 13 traits under study.The genotypes namely CN 1446-5-8-17-1-MLD4 and CR 2706 recorded highest mean performance for panicles per hill and grain yield. The highest genotypic and phenotypic variances (VG and VP) were recorded for spikelets per panicle (3595.78 and 3642.41) followed by biological yield (355.72 and 360.62) and plant height (231.48 and 234.35).High heritability (broad sense) coupled with high genetic advance was observed for plant height, flag leaf length, panicles per hill, tillers per hill, days to maturity, spikelet’s per panicle, biological yield, harvest index, 1000 grain weight and grain yield, indicating that selection will be effective based on these traits because they were under the influence of additive and additive x additive type of gene action. Highest coefficient of variation (PCV and GCV) was recorded for tillers per hill (18.42% and 17.23%), panicle per hill (19.76 % and 18.68%), spikelet’s per panicle (34.30 and34.07 %), biological yield (28.31 % and 28.12 %), 1000 grain weight (15.57 % and 15 31 %) and grain yield (46.66% and 23.54 %), indicating that these traits are under the major influence of genetic control, therefore the above mentioned traits contributed maximum to higher grain yield compared to other traits, indicating grain yield improvement through the associated traits.

The effect of seed rate and growing season on four oat cultivars: II. Culm morphology and panicle conformation

1968 ◽  
Vol 70 (3) ◽  
pp. 405-410 ◽  
Author(s):  
I. T. Jones ◽  
J. D. Hayes
Keyword(s):  
Relative Length ◽  
Field Trials ◽  
Grain Weight ◽  
Seed Rate ◽  
Total Height ◽  
Growing Seasons ◽  
Length Increase ◽  
Total Plant ◽  
Oat Cultivars ◽  
1000 Grain Weight

SUMMARYThe effects of low and high seed rates on height, culm and panicle morphology of four oat cultivars grown in field trials in two growing seasons were investigated. Significant differences were detected between cultivars in the number of extended culm internodes, panicle whorls initiated, total height, length of panicle and individual internodes. Differences in seed rate had no effect on the number of culm internodes, but high seed rate significantly reduced the whorl number in the panicle, total plant height, length of panicle and the three upper internodes. The fourth internode remained unaffected, but the lowermost internode showed a relative length increase at high seed rate. The interaction of cultivar x seed rate was significant for total height, and for the length of the central internodes, but the length of the panicle was similarly affected in all cultivars.Panicle conformation was markedly affected by seed rate; high population density caused a reduction in number of grain-bearing whorls, and reduced the number of spikelets and total grain weight per whorl, and 1000 grain weight particularly in the lowermost whorls. The percentage of husk in the grain was increased slightly at high seed rate. The effect of seed rate on culm and panicle morphology is discussed in relation to the development of stiffer-strawed oats.

scholarly journals Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae

2020 ◽  
Author(s):  
Seungwoo Cha ◽  
Chang Pyo Hong ◽  
Hyun Ah Kang ◽  
Ji-Sook Hahn
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Target Genes ◽  
Gene Encoding ◽  
Metabolic Switch ◽  
Differential Activation ◽  
N Terminus ◽  
Activation Mechanisms ◽  
In Trans ◽  
Separate Activation

Abstract Gcr1, an important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1U and Gcr1S, produced from un-spliced and spliced transcripts, respectively. In this study, by generating strains expressing only Gcr1U or Gcr1S using the CRISPR/Cas9 system, we elucidate differential activation mechanisms of these two isoforms. The Gcr1U monomer forms an active complex with its coactivator Gcr2 homodimer, whereas Gcr1S acts as a homodimer without Gcr2. The USS domain, 55 residues at the N-terminus existing only in Gcr1U, inhibits dimerization of Gcr1U and even acts in trans to inhibit Gcr1S dimerization. The Gcr1S monomer inhibits the metabolic switch from fermentation to respiration by directly binding to the ALD4 promoter, which can be restored by overexpression of the ALD4 gene, encoding a mitochondrial aldehyde dehydrogenase required for ethanol utilization. Gcr1U and Gcr1S regulate almost the same target genes, but show unique activities depending on growth phase, suggesting that these isoforms play differential roles through separate activation mechanisms depending on environmental conditions.

scholarly journals Evolution of a major virion protein of the giant pandoraviruses from an inactivated bacterial glycoside hydrolase

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Mart Krupovic ◽  
Natalya Yutin ◽  
Eugene Koonin
Keyword(s):  
Glycoside Hydrolase ◽  
Carbohydrate Binding ◽  
Virion Protein ◽  
Gene Encoding ◽  
Dna Viruses ◽  
Virus Particles ◽  
Major Increase ◽  
A Minor ◽  
Particle Shapes ◽  
Icosahedral Capsid

Abstract The diverse viruses in the phylum Nucleocytoviricota (also known as NLCDVs, Nucleo-cytoplasmic Large DNA Viruses) typically possess large icosahedral virions. However, in several families of Nucleocytoviricota, the icosahedral capsid was replaced by irregular particle shapes, most notably, the amphora-like virions of pandoraviruses and pithoviruses, the largest known virus particles in the entire virosphere. Pandoraviruses appear to be the most highly derived viruses in this phylum because their evolution involved not only the change in the virion shape, but also, the actual loss of the gene encoding double-jelly roll major capsid protein (DJR MCP), the main building block of icosahedral capsids in this virus assemblage. Instead, pandoravirus virions are built of unrelated abundant proteins. Here we show that the second most abundant virion protein of pandoraviruses, major virion protein 2 (MVP2), evolved from an inactivated derivative of a bacterial glycoside hydrolase of the GH16 family. The ancestral form of MVP2 was apparently acquired early in the evolution of the Nucleocytoviricota, to become a minor virion protein. After a duplication in the common ancestor of pandoraviruses and molliviruses, one of the paralogs displaces DJR MCP in pandoraviruses, conceivably, opening the way for a major increase in the size of the virion and the genome. Exaptation of a carbohydrate-binding protein for the function of the MVP is a general trend in virus evolution and might underlie the transformation of the virion shape in other groups of the Nucleocytoviricota as well.

scholarly journals Exploiting the GTEx resources to decipher the mechanisms at GWAS loci

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alvaro N. Barbeira ◽  
◽  
Rodrigo Bonazzola ◽  
Eric R. Gamazon ◽  
Yanyu Liang ◽  
...  
Keyword(s):  
Complex Traits ◽  
Target Genes ◽  
Genome Wide Association Study ◽  
Data Driven ◽  
Functional Interpretation ◽  
Transcriptome Regulation ◽  
Genome Wide ◽  
Causal Genes ◽  
Dose Dependent ◽  
Single Approach

AbstractThe resources generated by the GTEx consortium offer unprecedented opportunities to advance our understanding of the biology of human diseases. Here, we present an in-depth examination of the phenotypic consequences of transcriptome regulation and a blueprint for the functional interpretation of genome-wide association study-discovered loci. Across a broad set of complex traits and diseases, we demonstrate widespread dose-dependent effects of RNA expression and splicing. We develop a data-driven framework to benchmark methods that prioritize causal genes and find no single approach outperforms the combination of multiple approaches. Using colocalization and association approaches that take into account the observed allelic heterogeneity of gene expression, we propose potential target genes for 47% (2519 out of 5385) of the GWAS loci examined.

Autoregulated Expression of Schizosaccharomyces pombe Meiosis-Specific Transcription Factor Mei4 and a Genome-Wide Search for Its Target Genes

Genetics ◽  
2000 ◽  
Vol 154 (4) ◽  
pp. 1497-1508 ◽  
Author(s):  
Hiroko Abe ◽  
Chikashi Shimoda
Keyword(s):  
Transcription Factor ◽  
Schizosaccharomyces Pombe ◽  
Target Genes ◽  
Northern Blotting ◽  
Forkhead Transcription Factor ◽  
Gene Encoding ◽  
Putative Promoter Region ◽  
Cis Acting ◽  
A Genome ◽  
Genome Wide Search

Abstract The Schizosaccharomyces pombe mei4+ gene encoding a forkhead transcription factor is necessary for the progression of meiosis and sporulation. We searched for novel meiotic genes, the expression of which is dependent on Mei4p, since only the spo6+ gene has been assigned to its targets. Six known genes responsible for meiotic recombination were examined by Northern blotting, but none were Mei4 dependent for transcription. We determined the important cis-acting element, designated FLEX, to which Mei4p can bind. The S. pombe genome sequence database (The Sanger Centre, UK) was scanned for the central core heptamer and its flanking 3′ sequence of FLEX composed of 17 nucleotides, and 10 candidate targets of Mei4 were selected. These contained a FLEX-like sequence in the 5′ upstream nontranslatable region within 1 kb of the initiation codon. Northern blotting confirmed that 9 of them, named mde1+ to mde9+, were transcriptionally induced during meiosis and were dependent on mei4+. Most mde genes have not been genetically defined yet, except for mde9+, which is identical to spn5+, which encodes one of the septin family of proteins. mde3+ and a related gene pit1+ encode proteins related to Saccharomyces cerevisiae Ime2. The double disruptant frequently produced asci having an abnormal number and size of spores, although it completed meiosis. We also found that the forkhead DNA-binding domain of Mei4p binds to the FLEX-like element in the putative promoter region of mei4 and that the maximum induction level of mei4 mRNA required functional mei4 activity. Furthermore, expression of a reporter gene driven by the authentic mei4 promoter was induced in vegetative cells by ectopic overproduction of Mei4p. These results suggest that mei4 transcription is positively autoregulated.

scholarly journals SfnR2 Regulates Dimethyl Sulfide-Related Utilization inPseudomonas aeruginosaPAO1

2018 ◽  
Vol 201 (4) ◽  
Author(s):  
Benjamin R. Lundgren ◽  
Zaara Sarwar ◽  
Kyle S. Feldman ◽  
Joseph M. Shoytush ◽  
Christopher T. Nomura
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Target Genes ◽  
Dimethyl Sulfide ◽  
Sulfur Compound ◽  
Main Function ◽  
Gene Encoding ◽  
Content Type ◽  
First Results ◽  
Terrestrial Environments ◽  
Initial Activation

ABSTRACTDimethyl sulfide (DMS) is a volatile sulfur compound produced mainly from the degradation of dimethylsulfoniopropionate (DMSP) in marine environments. DMS undergoes oxidation to form dimethyl sulfoxide (DMSO), dimethyl sulfone (DMSO2), and methanesulfonate (MSA), all of which occur in terrestrial environments and are accessible for consumption by various microorganisms. The purpose of the present study was to determine how the enhancer-binding proteins SfnR1 and SfnR2 contribute to the utilization of DMS and its derivatives inPseudomonas aeruginosaPAO1. First, results from cell growth experiments showed that deletion of eithersfnR2orsfnG, a gene encoding a DMSO2-monooxygenase, significantly inhibits the ability ofP. aeruginosaPAO1 to use DMSP, DMS, DMSO, and DMSO2as sulfur sources. Deletion of thesfnR1ormsuEDCgenes, which encode a MSA desulfurization pathway, did not abolish the growth ofP. aeruginosaPAO1 on any sulfur compound tested. Second, data collected from β-galactosidase assays revealed that themsuEDC-sfnR1operon and thesfnGgene are induced in response to sulfur limitation or nonpreferred sulfur sources, such as DMSP, DMS, and DMSO, etc. Importantly, SfnR2 (and not SfnR1) is essential for this induction. Expression ofsfnR2is induced under sulfur limitation but independently of SfnR1 or SfnR2. Finally, the results of this study suggest that the main function of SfnR2 is to direct the initial activation of themsuEDC-sfnR1operon in response to sulfur limitation or nonpreferred sulfur sources. Once expressed, SfnR1 contributes to the expression ofmsuEDC-sfnR1,sfnG, and other target genes involved in DMS-related metabolism inP. aeruginosaPAO1.IMPORTANCEDimethyl sulfide (DMS) is an important environmental source of sulfur, carbon, and/or energy for microorganisms. For various bacteria, includingPseudomonas,Xanthomonas, andAzotobacter, DMS utilization is thought to be controlled by the transcriptional regulator SfnR. Adding more complexity, some bacteria, such asAcinetobacter baumannii,Enterobacter cloacae, andPseudomonas aeruginosa, possess two, nonidentical SfnR proteins. In this study, we demonstrate that SfnR2 and not SfnR1 is the principal regulator of DMS metabolism inP. aeruginosaPAO1. Results suggest that SfnR1 has a supportive but nonessential role in the positive regulation of genes required for DMS utilization. This study not only enhances our understanding of SfnR regulation but, importantly, also provides a framework for addressing gene regulation through dual SfnR proteins in other bacteria.

scholarly journals XBP-1 Regulates a Subset of Endoplasmic Reticulum Resident Chaperone Genes in the Unfolded Protein Response

2003 ◽  
Vol 23 (21) ◽  
pp. 7448-7459 ◽  
Author(s):  
Ann-Hwee Lee ◽  
Neal N. Iwakoshi ◽  
Laurie H. Glimcher
Keyword(s):  
Endoplasmic Reticulum ◽  
Unfolded Protein Response ◽  
Target Genes ◽  
Gene Profiling ◽  
Minor Role ◽  
Compensatory Mechanism ◽  
Unfolded Protein ◽  
The Unfolded Protein Response ◽  
A Minor ◽  
Protein Response

ABSTRACT The mammalian unfolded protein response (UPR) protects the cell against the stress of misfolded proteins in the endoplasmic reticulum (ER). We have investigated here the contribution of the UPR transcription factors XBP-1, ATF6α, and ATF6β to UPR target gene expression. Gene profiling of cell lines lacking these factors yielded several XBP-1-dependent UPR target genes, all of which appear to act in the ER. These included the DnaJ/Hsp40-like genes, p58IPK, ERdj4, and HEDJ, as well as EDEM, protein disulfide isomerase-P5, and ribosome-associated membrane protein 4 (RAMP4), whereas expression of BiP was only modestly dependent on XBP-1. Surprisingly, given previous reports that enforced expression of ATF6α induced a subset of UPR target genes, cells deficient in ATF6α, ATF6β, or both had minimal defects in upregulating UPR target genes by gene profiling analysis, suggesting the presence of compensatory mechanism(s) for ATF6 in the UPR. Since cells lacking both XBP-1 and ATF6α had significantly impaired induction of select UPR target genes and ERSE reporter activation, XBP-1 and ATF6α may serve partially redundant functions. No UPR target genes that required ATF6β were identified, nor, in contrast to XBP-1 and ATF6α, did the activity of the UPRE or ERSE promoters require ATF6β, suggesting a minor role for it during the UPR. Collectively, these results suggest that the IRE1/XBP-1 pathway is required for efficient protein folding, maturation, and degradation in the ER and imply the existence of subsets of UPR target genes as defined by their dependence on XBP-1. Further, our observations suggest the existence of additional, as-yet-unknown, key regulators of the UPR.

scholarly journals Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis

2019 ◽  
Author(s):  
Jing Yang ◽  
Amanda McGovern ◽  
Paul Martin ◽  
Kate Duffus ◽  
Xiangyu Ge ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
T Cells ◽  
Complex Disease ◽  
Target Genes ◽  
Disease Risk ◽  
Association Studies ◽  
Dna Interaction ◽  
Genome Wide Association Studies ◽  
Causal Genes

AbstractGenome-wide association studies have identified genetic variation contributing to complex disease risk. However, assigning causal genes and mechanisms has been more challenging because disease-associated variants are often found in distal regulatory regions with cell-type specific behaviours. Here, we collect ATAC-seq, Hi-C, Capture Hi-C and nuclear RNA-seq data in stimulated CD4+ T-cells over 24 hours, to identify functional enhancers regulating gene expression. We characterise changes in DNA interaction and activity dynamics that correlate with changes gene expression, and find that the strongest correlations are observed within 200 kb of promoters. Using rheumatoid arthritis as an example of T-cell mediated disease, we demonstrate interactions of expression quantitative trait loci with target genes, and confirm assigned genes or show complex interactions for 20% of disease associated loci, including FOXO1, which we confirm using CRISPR/Cas9.

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