Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome 1

Rice being a staple food crop of Kashmir valley, the focus is on enhancement of yield in order to meet the needs of ever-growing population.Identification of new parental lines is crucial for developing ecology-specific hybrids with ideal agronomic performance. Exploitation of heterosis in the form of hybrid rice technology can be one of the approaches to increase productivity in this crop, especially exploiting diversity among japonica lines can serve as an excellent route.A number of CMS lines suitable formountainous areas of Kashmir have been developed, however, the availability of promising restorer lines remains to be the major limitation for utilization of these lines.Identification of potential restorers acts as the main limiting factor for hybrid development in the Kashmir valley. Marker based screening for Rf3 and Rf4 fertility restorer genes can be helpful in rapid selection of restorer lines while dealing with the large quantity of genetic materials. In the present study, 100 rice germplasm were screened with the help of SSR markers, RM3148 and RM6100linked to Rf3 and Rf4 genes on chromosome 1 and 10, respectively. In total, 19 lines revealed the presence of both Rf3 and Rf4 genes. These lines amplified fertility restorer specific alleles for both the genes and may serve as potential restorers for obtaining heterotic rice hybrids. Further the germplasm lines were also evaluated for yield and quality traits.The present results would help in selection of suitable restorers along with preferred grain shape/size.

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Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽

10.1093/genetics/142.3.1021 ◽

1996 ◽

Vol 142 (3) ◽

pp. 1021-1031 ◽

Cited By ~ 3

Author(s):

Jianping Hu ◽

Beth Anderson ◽

Susan R Wessler

Keyword(s):

Gene Family ◽

Gene Families ◽

Chromosome 1 ◽

R Gene ◽

R Genes ◽

Helix Loop Helix ◽

Isolation And Characterization ◽

Undetermined Function ◽

Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

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EVOLUTION AND VARIATION OF RENIN GENES IN MICE

Genetics ◽

10.1093/genetics/108.3.651 ◽

1984 ◽

Vol 108 (3) ◽

pp. 651-667

Author(s):

Douglas P Dickinson ◽

Kenneth W Gross ◽

Nina Piccini ◽

Carol M Wilson

Keyword(s):

Gene Expression ◽

Submandibular Gland ◽

Regulation Of Gene Expression ◽

Inbred Strains ◽

Duplication Event ◽

Comparative Sequence Analysis ◽

Chromosome 1 ◽

Gene Encoding ◽

Prior Estimate ◽

Low Levels

ABSTRACT Inbred strains of mice carry Ren-1, a gene encoding the thermostable Renin-1 isozyme. Ren-1 is expressed at relatively low levels in mouse submandibular gland and kidney. Some strains also carry Ren-2, a gene encoding the thermolabile Renin-2 isozyme. Ren-2 is expressed at high levels in the mouse submandibular gland and at very low levels, if at all, in the kidney. Ren-1 and Ren-2 are closely linked on mouse chromosome 1, show extensive homology in coding and noncoding regions and provide a model for studying the regulation of gene expression. An investigation of renin genes and enzymatic activity in wild-derived mice identified several restriction site polymorphisms as well as putative variants in renin gene expression and protein structure. The number of renin genes carried by different subpopulations of wild-derived mice is consistent with the occurrence of a gene duplication event prior to the divergence of M. spretus (2.75-5.5 million yr ago). This conclusion is in agreement with a prior estimate based upon comparative sequence analysis of Ren-1 and Ren-2 from inbred laboratory mice.

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Associations between Amplification (1q) and Prior Cancer in a Real-World De Novo Myeloma Cohort

JNCI Cancer Spectrum ◽

10.1093/jncics/pkaa111 ◽

2021 ◽

Author(s):

Elizabeth B Lamont ◽

Andrew J Yee ◽

Stuart L Goldberg ◽

David S Siegel ◽

Andrew D Norden

Keyword(s):

Real World ◽

Fluorescent In Situ Hybridization ◽

De Novo ◽

Chromosome 1 ◽

Second Malignancies ◽

Cancer History ◽

Screening Strategies ◽

Cytogenetic Testing

Abstract Genomic biomarkers inform treatment in multiple myeloma (MM) making patient clinical data a potential window into MM biology. We evaluated de novo MM patients for associations between specific MM cytogenetic patterns and prior cancer history. Analyzing a MM real-world dataset (RWD), we identified a cohort of 1,769 patients with fluorescent in-situ hybridization (FISH) cytogenetic testing at diagnosis. Fully 241 patients (0.14) had histories of prior cancer(s). Amplification of the long arm of chromosome 1 [amp(1q)] varied by prior cancer history (0.31 with prior cancer vs 0.24 without; p = .02). No other MM translocations, amplifications, or deletions were associated with prior cancers. Amp(1q) and cancer history remained strongly associated in a logistic regression adjusting for patient demographic and disease attributes. The results merit follow-up regarding carcinogenic treatment effects and screening strategies for second malignancies. Broadly the findings suggest analyses of patient-level phenotypic-genomic RWD may accelerate cancer research through hypothesis generating studies.

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Identification of Quantitative Trait Loci Influencing Traits Related to Energy Balance in Selection and Inbred Lines of Mice

Genetics ◽

10.1093/genetics/152.2.699 ◽

1999 ◽

Vol 152 (2) ◽

pp. 699-711 ◽

Cited By ~ 1

Author(s):

D E Moody ◽

D Pomp ◽

M K Nielsen ◽

L D Van Vleck

Keyword(s):

Quantitative Trait Loci ◽

Energy Balance ◽

Heat Loss ◽

Quantitative Trait ◽

Subcutaneous Fat ◽

High Heat ◽

Chromosome 1 ◽

Direct Calorimetry ◽

Resource Population ◽

Trait Loci

Abstract Energy balance is a complex trait with relevance to the study of human obesity and maintenance energy requirements of livestock. The objective of this study was to identify, using unique mouse models, quantitative trait loci (QTL) influencing traits that contribute to variation in energy balance. Two F2 resource populations were created from lines of mice differing in heat loss measured by direct calorimetry as an indicator of energy expenditure. The HB F2 resource population originated from a cross between a noninbred line selected for high heat loss and an inbred line with low heat loss. Evidence for significant QTL influencing heat loss was found on chromosomes 1, 2, 3, and 7. Significant QTL influencing body weight and percentage gonadal fat, brown fat, liver, and heart were also identified. The LH F2 resource population originated from noninbred lines of mice that had undergone divergent selection for heat loss. Chromosomes 1 and 3 were evaluated. The QTL for heat loss identified on chromosome 1 in the HB population was confirmed in the LH population, although the effect was smaller. The presence of a QTL influencing 6-wk weight was also confirmed. Suggestive evidence for additional QTL influencing heat loss, percentage subcutaneous fat, and percentage heart was found for chromosome 1.

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From Benign Inflammatory Dermatosis to Cutaneous Lymphoma. DNA Copy Number Imbalances in Mycosis Fungoides versus Large Plaque Parapsoriasis

Medicina ◽

10.3390/medicina57050502 ◽

2021 ◽

Vol 57 (5) ◽

pp. 502

Author(s):

Georgiana Gug ◽

Caius Solovan

Keyword(s):

Mycosis Fungoides ◽

Copy Number ◽

Snp Array ◽

Chromosome 1 ◽

Copy Number Alterations ◽

Dna Copy Number ◽

Large Plaque ◽

Inflammatory Dermatosis ◽

Fresh Frozen ◽

Dna Copy Number Alterations

Background and Objectives: Mycosis fungoides (MF) and large plaque parapsoriasis (LPP) evolution provide intriguing data and are the cause of numerous debates. The diagnosis of MF and LPP is associated with confusion and imprecise definition. Copy number alterations (CNAs) may play an essential role in the genesis of cancer out of genes expression dysregulation. Objectives: Due to the heterogeneity of MF and LPP and the scarcity of the cases, there are an exceedingly small number of studies that have identified molecular changes in these pathologies. We aim to identify and compare DNA copy number alterations and gene expression changes between MF and LPP to highlight the similarities and the differences between these pathologies. Materials and Methods: The patients were prospectively selected from University Clinic of Dermatology and Venereology Timișoara, Romania. From fresh frozen skin biopsies, we extracted DNA using single nucleotide polymorphism (SNP) data. The use of SNP array for copy number profiling is a promising approach for genome-wide analysis. Results: After reviewing each group, we observed that the histograms generated for chromosome 1–22 were remarkably similar and had a lot of CNAs in common, but also significant differences were seen. Conclusions: This study took a step forward in finding out the differences and similarities between MF and LPP, for a more specific and implicitly correct approach of the case. The similarity between these two pathologies in terms of CNAs is striking, emphasizing once again the difficulty of approaching and differentiating them.

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Low Glucose Mediated Fluconazole Tolerance in Cryptococcus neoformans

Journal of Fungi ◽

10.3390/jof7060489 ◽

2021 ◽

Vol 7 (6) ◽

pp. 489

Author(s):

Somanon Bhattacharya ◽

Natalia Kronbauer Oliveira ◽

Anne G. Savitt ◽

Vanessa K. A. Silva ◽

Rachel B. Krausert ◽

...

Keyword(s):

Cryptococcus Neoformans ◽

Mitochondrial Function ◽

Efflux Pump ◽

Nile Red ◽

Fold Increase ◽

Growth Conditions ◽

Chromosome 1 ◽

Normal Glucose ◽

Low Glucose ◽

Synthetic Media

Chronic meningoencephalitis is caused by Cryptococcus neoformans and is treated in many parts of the world with fluconazole (FLC) monotherapy, which is associated with treatment failure and poor outcome. In the host, C. neoformans propagates predominantly under low glucose growth conditions. We investigated whether low glucose, mimicked by growing in synthetic media (SM) with 0.05% glucose (SMlowglu), affects FLC-resistance. A > 4-fold increase in FLC tolerance was observed in seven C. neoformans strains when minimum inhibitory concentration (MIC) was determined in SMlowglu compared to MIC in SM with normal (2%) glucose (SMnlglu). In SMlowglu, C. neoformans cells exhibited upregulation of efflux pump genes AFR1 (8.7-fold) and AFR2 (2.5-fold), as well as decreased accumulation (2.6-fold) of Nile Red, an efflux pump substrate. Elevated intracellular ATP levels (3.2-fold and 3.4-fold), as well as decreased mitochondrial reactive oxygen species levels (12.8-fold and 17-fold), were found in the presence and absence of FLC, indicating that low glucose altered mitochondrial function. Fluorescence microscopy revealed that mitochondria of C. neoformans grown in SMlowglu were fragmented, whereas normal glucose promoted a reticular network of mitochondria. Although mitochondrial membrane potential (MMP) was not markedly affected in SMlowglu, it significantly decreased in the presence of FLC (12.5-fold) in SMnlglu, but remained stable in SMlowglu-growing C. neoformans cells. Our data demonstrate that increased FLC tolerance in low glucose-growing C. neoformans is the result of increased efflux pump activities and altered mitochondrial function, which is more preserved in SMlowglu. This mechanism of resistance is different from FLC heteroresistance, which is associated with aneuploidy of chromosome 1 (Chr1).

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Constructing Large-Scale Genetic Maps Using an Evolutionary Strategy Algorithm

Genetics ◽

10.1093/genetics/165.4.2269 ◽

2003 ◽

Vol 165 (4) ◽

pp. 2269-2282

Author(s):

D Mester ◽

Y Ronin ◽

D Minkov ◽

E Nevo ◽

A Korol

Keyword(s):

Discrete Optimization ◽

High Performance ◽

Large Scale ◽

Simulated Data ◽

Real Data ◽

Genetic Maps ◽

Chromosome 1 ◽

Evolutionary Strategy ◽

Group A ◽

The One

Abstract This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with ∼50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

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New homozygous gpt delta transgenic rat strain improves an efficiency of the in vivo mutagenicity assay

Genes and Environment ◽

10.1186/s41021-021-00195-1 ◽

2021 ◽

Vol 43 (1) ◽

Author(s):

Kenichi Masumura ◽

Tomoko Ando ◽

Akiko Ukai ◽

Sho Fujiwara ◽

Shigeo Yokose ◽

...

Keyword(s):

Bone Marrow ◽

Gene Mutation ◽

Point Mutations ◽

Chromosome 1 ◽

Transgenic Rat ◽

Target Tissue ◽

Sequencing Analysis ◽

Rat Strain ◽

Packaging Efficiency

Abstract Background Gene mutation assays in transgenic rodents are useful tools to investigate in vivo mutagenicity in a target tissue. Using a lambda EG10 transgene containing reporter genes, gpt delta transgenic mice and rats have been developed to detect point mutations and deletions. The transgene is integrated in the genome and can be rescued through an in vitro packaging reaction. However, the packaging efficiency is lower in gpt delta rats than in mice, because of the transgene in gpt delta rats being heterozygous and in low copy number. To improve the packaging efficiency, we herein describe a newly developed homozygous gpt delta rat strain. Results The new gpt delta rat has a Wistar Hannover background and has been successfully maintained as homozygous for the transgene. The packaging efficiency in the liver was 4 to 8 times higher than that of existing heterozygous F344 gpt delta rats. The frequency of gpt point mutations significantly increased in the liver and bone marrow of N-nitroso-N-ethylurea (ENU)- and benzo[a]pyrene (BaP)-treated rats. Spi− deletion frequencies significantly increased in the liver and bone marrow of BaP-treated rats but not in ENU-treated rats. Whole genome sequencing analysis identified ≥ 30 copies of lambda EG10 transgenes integrated in rat chromosome 1. Conclusions The new homozygous gpt delta rat strain showed a higher packaging efficiency, and could be useful for in vivo gene mutation assays in rats.

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Gain/Amplification of Chromosome Arm 1q21 in Multiple Myeloma

Cancers ◽

10.3390/cancers13020256 ◽

2021 ◽

Vol 13 (2) ◽

pp. 256

Author(s):

Ichiro Hanamura

Keyword(s):

Multiple Myeloma ◽

Hematological Malignancy ◽

Treatment Approach ◽

Current Knowledge ◽

Chromosome 1 ◽

Plasma Cell Neoplasm ◽

Chromosome Arm ◽

Cell Neoplasm ◽

Prognostic Implications ◽

Tandem Duplications

Multiple myeloma (MM), a plasma cell neoplasm, is an incurable hematological malignancy characterized by complex genetic and prognostic heterogeneity. Gain or amplification of chromosome arm 1q21 (1q21+) is the most frequent adverse chromosomal aberration in MM, occurring in 40% of patients at diagnosis. It occurs in a subclone of the tumor as a secondary genomic event and is more amplified as the tumor progresses and a risk factor for the progression from smoldering multiple myeloma to MM. It can be divided into either 1q21 gain (3 copies) or 1q21 amplification (≥4 copies), and it has been suggested that the prognosis is worse in cases of amplification than gain. Trisomy of chromosome 1, jumping whole-arm translocations of chromosome1q, and tandem duplications lead to 1q21+ suggesting that its occurrence is not consistent at the genomic level. Many studies have reported that genes associated with the malignant phenotype of MM are situated on the 1q21 amplicon, including CKS1B, PSMD4, MCL1, ANP32E, and others. In this paper, we review the current knowledge regarding the clinical features, prognostic implications, and the speculated pathology of 1q21+ in MM, which can provide clues for an effective treatment approach to MM patients with 1q21+.

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