scholarly journals Unraveling Cuticle Formation, Structure, and Properties by Using Tomato Genetic Diversity

2021 ◽  
Vol 12 ◽  
Author(s):  
Johann Petit ◽  
Cécile Bres ◽  
Nicolas Reynoud ◽  
Marc Lahaye ◽  
Didier Marion ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Target Genes ◽  
Structure And Properties ◽  
Horticultural Crop ◽  
Cuticle Formation ◽  
Genomic Tools ◽  
Germplasm Diversity ◽  
Review Reports ◽  
High Quality Genome ◽  
Made In

The tomato (Solanum lycopersicum) fruit has a thick, astomatous cuticle that has become a model for the study of cuticle formation, structure, and properties in plants. Tomato is also a major horticultural crop and a long-standing model for research in genetics, fruit development, and disease resistance. As a result, a wealth of genetic resources and genomic tools have been established, including collections of natural and artificially induced genetic diversity, introgression lines of genome fragments from wild relatives, high-quality genome sequences, phenotype and gene expression databases, and efficient methods for genetic transformation and editing of target genes. This mini-review reports the considerable progresses made in recent years in our understanding of cuticle by using and generating genetic diversity for cuticle-associated traits in tomato. These include the synthesis of the main cuticle components (cutin and waxes), their role in the structure and properties of the cuticle, their interaction with other cell wall polymers as well as the regulation of cuticle formation. It also addresses the opportunities offered by the untapped germplasm diversity available in tomato and the current strategies available to exploit them.

scholarly journals Evaluation of AXIN1 and AXIN2 as targets of tankyrase inhibition in hepatocellular carcinoma cell lines

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenhui Wang ◽  
Pengyu Liu ◽  
Marla Lavrijsen ◽  
Shan Li ◽  
Ruyi Zhang ◽  
...  
Keyword(s):  
Cell Lines ◽  
Target Genes ◽  
Therapeutic Option ◽  
Carcinoma Cell Lines ◽  
Hepatocellular Carcinomas ◽  
Enhanced Expression ◽  
Mutant Lines ◽  
Substantial Interest ◽  
Support Tumor Growth ◽  
Made In

AbstractAXIN1 mutations are observed in 8–10% of hepatocellular carcinomas (HCCs) and originally were considered to support tumor growth by aberrantly enhancing β-catenin signaling. This view has however been challenged by reports showing neither a clear nuclear β-catenin accumulation nor clearly enhanced expression of β-catenin target genes. Here, using nine HCC lines, we show that AXIN1 mutation or siRNA mediated knockdown contributes to enhanced β-catenin signaling in all AXIN1-mutant and non-mutant lines, also confirmed by reduced signaling in AXIN1-repaired SNU449 cells. Both AXIN1 and AXIN2 work synergistically to control β-catenin signaling. While in the AXIN1-mutant lines, AXIN2 is solely responsible for keeping signaling in check, in the non-mutant lines both AXIN proteins contribute to β-catenin regulation to varying levels. The AXIN proteins have gained substantial interest in cancer research for a second reason. Their activity in the β-catenin destruction complex can be increased by tankyrase inhibitors, which thus may serve as a therapeutic option to reduce the growth of β-catenin-dependent cancers. At concentrations that inhibit tankyrase activity, some lines (e.g. HepG2, SNU398) were clearly affected in colony formation, but in most cases apparently independent from effects on β-catenin signaling. Overall, our analyses show that AXIN1 inactivation leads to enhanced β-catenin signaling in HCC cell lines, questioning the strong statements that have been made in this regard. Enhancing AXIN activity by tankyrase monotherapy provides however no effective treatment to affect their growth exclusively through reducing β-catenin signaling.

scholarly journals Rootstock-scion interaction:3. Effect on the composition of Cabernet Sauvignon wine

2019 ◽  
Vol 41 (1) ◽  
Author(s):  
Alberto Miele ◽  
Luiz Antenor Rizzon
Keyword(s):  
Genetic Diversity ◽  
Experimental Design ◽  
Volatile Compounds ◽  
Cabernet Sauvignon ◽  
Alcohol Content ◽  
Higher Alcohol ◽  
Dry Extract ◽  
Ph Values ◽  
Wine Composition ◽  
Made In

Abstract The interaction among rootstock, scion and environment may induce different responses to the grapevine physiology and consequently to the grape and wine composition. The vineyards of Serra Gaúcha, Brazil, are established in soils that may have different physicochemical attributes. Furthermore, the grapevines are grafted on a wide diversity of rootstocks. Therefore, this study aimed to determine their effect on the wine composition of the Cabernet Sauvignon (CS) grafted on Rupestris du Lot, 101-14 Mgt, 3309 C, 420A Mgt, 5BB K, 161-49 C, SO4, Solferino, 1103 P, 99 R, 110 R, Gravesac, Fercal, Dogridge and Isabel, featuring some genetic diversity altogether. The experimental design was in randomized blocks, with 15 treatments, three replicates and 10 vines per plot. The grapes were harvested at maturity for three years, and then wines were made in glass recipients of 20 L. When alcoholic and malolactic fermentations were over, the wine analyses were performed on twenty-five variables related to alcohol, acidity, dry extract, polyphenols and volatile compounds. The main results show that all variables were affected year by year, some of them by the rootstock and a few by the interaction between rootstock and year. The rootstock effect was observed mainly on variables related to alcohol, acidity and ashes. Results show that the CS/101-14 Mgt wine had higher alcohol content than CS/Dogridge and CS/Isabel wines, which was probably due to the 101-14 Mgt rootstock favoring an early grape ripening. However, higher pH values were observed in the CS/Rupestris du Lot, CS/5BB K and CS/Gravesac than CS/420A Mgt, CS/110 R and CS/Isabel wines. These results show that there is a diversity of rootstocks that can be used by the growers due to the Cabernet Sauvignon wine composition similarities.

Structure and Properties of Polysilsesquioxanes and Copolymers for Ultra-Low Dielectric Films

2003 ◽  
Vol 766 ◽  
Author(s):  
Do Y. Yoon ◽  
Hyun Wook Ro ◽  
Eun Su Park ◽  
Jin-Kyu Lee ◽  
Hie-Joon Kim ◽  
...  
Keyword(s):  
Copper Interconnects ◽  
Dielectric Constants ◽  
Dielectric Films ◽  
Structure And Properties ◽  
Structure Property ◽  
Detailed Structure ◽  
Low Dielectric ◽  
Structure Property Relationships ◽  
Mechanical Modulus ◽  
Made In

AbstractPolysilsesquioxanes (PSSQs) with the empirical formula (RSiO3/2)n have become very important as low-dielectric insulators for copper interconnects in the next-generation logic devices, but the detailed structure-property relationships were completely lacking. We have investigated the microstructure and functional properties of PSSQs with varying alkyl substituents and also PSSQ copolymers. As a result, significant advances have been made in the scientific understanding of PSSQ structures and significant improvements of key properties such as the crack resistance, mechanical modulus and hardness, and incorporation of nanometer-sized (<4 nm) porosity for ultra-low dielectric constants (<2.0).

The structure and properties of welded joints in niobium made in a controlled helium atmosphere

1987 ◽  
Vol 1 (7) ◽  
pp. 618-620
Author(s):  
G A Petrunin ◽  
A M Lyubchik ◽  
N F Chugai ◽  
E A Asnis ◽  
M M Nerodenko
Keyword(s):  
Welded Joints ◽  
Structure And Properties ◽  
Helium Atmosphere ◽  
Made In

scholarly journals Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits

2018 ◽  
Author(s):  
Heather E. Wheeler ◽  
Sally Ploch ◽  
Alvaro N. Barbeira ◽  
Rodrigo Bonazzola ◽  
Angela Andaleon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Complex Traits ◽  
Target Gene ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Nucleic Acid Binding ◽  
Expression Of Genes ◽  
Gene Associations ◽  
Made In

AbstractRegulation of gene expression is an important mechanism through which genetic variation can affect complex traits. A substantial portion of gene expression variation can be explained by both local (cis) and distal (trans) genetic variation. Much progress has been made in uncovering cis-acting expression quantitative trait loci (cis-eQTL), but trans-eQTL have been more difficult to identify and replicate. Here we take advantage of our ability to predict the cis component of gene expression coupled with gene mapping methods such as PrediXcan to identify high confidence candidate trans-acting genes and their targets. That is, we correlate the cis component of gene expression with observed expression of genes in different chromosomes. Leveraging the shared cis-acting regulation across tissues, we combine the evidence of association across all available GTEx tissues and find 2356 trans-acting/target gene pairs with high mappability scores. Reassuringly, trans-acting genes are enriched in transcription and nucleic acid binding pathways and target genes are enriched in known transcription factor binding sites. Interestingly, trans-acting genes are more significantly associated with selected complex traits and diseases than target or background genes, consistent with percolating trans effects. Our scripts and summary statistics are publicly available for future studies of trans-acting gene regulation.

scholarly journals (17) TRAP Markers Help Categorizea Pelargonium Collection

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1067C-1067
Author(s):  
Rose Palumbo ◽  
Wai-Foong Hong ◽  
Jinguo Hu ◽  
Charles Krause ◽  
David Tay ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Throughput ◽  
Target Genes ◽  
Large Population ◽  
Ornamental Plants ◽  
Ornamental Plant ◽  
High Quality ◽  
Target Region ◽  
Future Studies ◽  
Loss Of Genetic Diversity

The Ornamental Plant Germplasm Center (OPGC) maintains a collection of herbaceous ornamental plants in order to protect future breeders from a loss of genetic diversity. The current Pelargonium collection includes ≈870 accessions. Our preliminary studies showed that TRAP (Target Region Amplified Polymorphism) has promise for analyzing the variation in our collection, and so we have expanded the study to analyze the entire Pelargonium collection. We have used the same primers for this screening of the Pelargonium collection as were used on sunflowers, and TRAP results run on a sequencing gel showed 90–150 bands that segregate the population into groups of similar accessions. In order to facilitate analysis of OPGC's large population, we have converted the method to a high throughput technique that efficiently analyzed the entire population. We used a 96-well DNA extraction kit from Qiagen that produced high quality DNA in spite of the high phenol levels in some Pelargonium species. Also, the use of labeled primers allowed analysis of the gels to be aided by a computer. These results produce a categorization of the collection that, combined with morphology and taxonomy, will form the basis for future studies that will use target genes specific to Pelargonium.

scholarly journals An Evolution From a Predominant K1 Allelic Variant to MAD20 of msp1 Gene Between 2015 to 2019 in Metehara, Southeast Ethiopia

2021 ◽  
Author(s):  
Abeba Reda ◽  
Alebachew Messele ◽  
Hussein Mohammed ◽  
Ashenafi Assefa ◽  
Lemu Golassa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Target Genes ◽  
Temporal Dynamics ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Cross Sectional Study ◽  
Cross Sectional ◽  
Southeast Ethiopia ◽  
Parasite Populations ◽  
Msp1 Gene

Abstract Background: The complexity and quantity of parasite populations circulating in a specific location are reflected in the genetic diversity of malaria parasites (s). Between 2015 and 2019, this study in Metehara, South east, Ethiopia. set out to investigate the temporal dynamics of genetic diversity and multiplicity as a result of evolutionary change in the genes that contribute to Plasmodium falciparum infection elimination. Method: Between 2015 and 2019, a cross-sectional study was carried out. from eighty-three dry blood spots from malaria patients who were screened for P. falciparum mono-infection by QPCR. From this seventy confirmed P. falciparum were genotyping to merozoite surface protein 1,2 and glutamate-rich protein using nested PCR.Result: Between 2015 and 2019, seventy (84.3%) of the isolates were successfully genotyped for all three target genes in both years. In 2015 and 2019, the allelic distributions of the three genes differed significantly (P= 0.001). Overall, the most common allelic families for msp1 and msp2 were K1 and FC27 respectively. For glurp, eight distinct genotypes were identified. In 2015, the genotyping of msp1, msp2 and glurp was 25 (86.2%), 25 (86.2%) and 24 (82.2%) respectively. K1, MAD20 and RO33 all have 19(65.5%), 3(10.3%) and 3(10.3%) msp1 allelic families respectively. In 2019 the genes were 30 (73.2%), 39 (95.1%) and 30 (73.2%). K1, MAD20, and RO33 were genotyped for 6 (14.6 percent), 18 (43.9 percent) and 6 (14.6 percent) genotyping respectively. Over all the multiplicity of infection was 1.67 (95 percent CI 1.54-1.74) and the heterozygosity index for msp1, msp2, and glurp was 0.48, 0.70, and 0.55 respectively.Conclusion: This study provides current information on the genetic diversity of P. falciparum populations in Metehara over five-year intervals, The progression of the dominant K1 variant from 2015 to MAD20 variant in 2019 was observed in this study.

scholarly journals The Use of Genomic Information for the Conservation of Animal Genetic Diversity

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3208
Author(s):  
J. Kor Oldenbroek
Keyword(s):  
Genetic Diversity ◽  
Genetic Distances ◽  
Small Populations ◽  
Genomic Information ◽  
Conservation Genomics ◽  
Rare Alleles ◽  
Genomic Regions ◽  
Made In

The conservation of genetic diversity, both among and within breeds, is a costly process. Therefore, choices between breeds and animals within breeds are unavoidable, either for conservation in vitro (gene banks) or in vivo (maintaining small populations alive). Nowadays, genomic information on breeds and individual animals is the standard for the choices to be made in conservation. Genomics may accurately measure the genetic distances among breeds and the relationships among animals within breeds. Homozygosity at loci and at parts of chromosomes is used to measure inbreeding. In addition, genomics can be used to detect potentially valuable rare alleles and haplotypes, their carriers in these breeds and can facilitate in vivo or in vitro conservations of these genomic regions.

scholarly journals Genome-wide development of miRNA-based SSR markers in Cleistogenes songorica with their transferability analysis to gramineae and non- gramineae species

2019 ◽  
Author(s):  
Gisele Kanzana ◽  
Yufei Zhang ◽  
Tiantian Ma ◽  
Wenxian Liu ◽  
Fan Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Target Genes ◽  
Stress Conditions ◽  
Biotic And Abiotic Stress ◽  
Marker Assisted Breeding ◽  
Map Construction ◽  
Expected Heterozygosity ◽  
Genome Wide ◽  
Precursor Mirnas

AbstractSSR markers are commonly used for many genetic applications, such as map construction, fingerprinting and genetic diversity analysis due to their high reproducibility, levels of polymorphism and abundance. As endogenous, small RNAs, miRNAs have essential roles in plant development and gene expression under diverse stress conditions, including various biotic and abiotic stress conditions. In the present study, we predicted 110 pre-miRNAs sequences from 287 precursor miRNAs and used them as queries for SSR marker development. Among 110 primer pairs, 85 were successfully amplified and examined for transferability to other gramineae and non-gramineae species. The results showed that all 82 primer pairs yielded unambiguous and strong amplification, and across the 23 studied Cleistogenes accessions, a total of 385 alleles were polymorphic. The number of alleles produced per primer varied from 3 to 11, with an average of 4.69 per locus. The expected heterozygosity (He) ranged from 0.44 to 0.88, with an average of 0.74 per locus, and the PIC (Polymorphism Information Content) values ranged from 0.34 to 0.87, with an average of 0.69 per locus. In this study, 1422 miRNA target genes were predicted and analyzed using the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. The results showed that this miRNA-based microsatellite marker system can be very useful for genetic diversity and marker-assisted breeding studies.

scholarly journals Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing

2020 ◽  
Author(s):  
N Tanaka ◽  
M Shenton ◽  
Y Kawahara ◽  
M Kumagai ◽  
H Sakai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Target Genes ◽  
Association Studies ◽  
Heading Date ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Flowering Genes ◽  
Food Research ◽  
Flowering Regulation

Abstract The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole-genome resequencing of these 50 accessions and obtained a total of 2,145,095 single nucleotide polymorphism (SNPs) and 317,832 insertion–deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+, to examine the haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed genome-wide association studies (GWAS) for agronomical traits using the JRC and another core collection, the World Rice Core Collection (WRC), comprising 69 accessions also provided by the NARO genebank. In leaf blade width, a strong peak close to NAL1, a key gene for the regulation of leaf width, and, in heading date, a peak near HESO1 involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC + WRC. Thus, JRC and JRC + WRC are suitable populations for GWAS of particular traits.

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