Association of Two Marker Loci With Chromosome 1 in Cotton: LL and duplicate locus lp1

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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Epistatic Control of Non-Mendelian Inheritance in Mouse Interspecific Crosses

Genetics ◽

10.1093/genetics/143.4.1739 ◽

1996 ◽

Vol 143 (4) ◽

pp. 1739-1752 ◽

Cited By ~ 2

Author(s):

Xavier Montagutelli ◽

Rowena Turner ◽

Joseph H Nadeau

Keyword(s):

X Chromosome ◽

Genetic Basis ◽

Mendelian Inheritance ◽

The Other ◽

Interspecific Crosses ◽

Chromosome 2 ◽

Mus Spretus ◽

F1 Hybrid ◽

Strong Deviation ◽

Marker Loci

Abstract Strong deviation of allele frequencies from Mendelian inheritance favoring Mus spretus-derived alleles has been described previously for X-linked loci in four mouse interspecific crosses. We reanalyzed data for three of these crosses focusing on the location of the gene(s) controlling deviation on the X chromosome and the genetic basis for incomplete deviation. At least two loci control deviation on the X chromosome, one near Xist (the candidate gene controlling X inactivation) and the other more centromerically located. In all three crosses, strong epistasis was found between loci near Xist and marker loci on the central portion of chromosome 2. The mechanism for this deviation from Mendelian expectations is not yet known but it is probably based on lethality of embryos carrying particular combinations of alleles rather than true segregation distortion during oogenesis in F1 hybrid females.

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Bayesian Inference of Recent Migration Rates Using Multilocus Genotypes

Genetics ◽

10.1093/genetics/163.3.1177 ◽

2003 ◽

Vol 163 (3) ◽

pp. 1177-1191 ◽

Cited By ~ 13

Author(s):

Gregory A Wilson ◽

Bruce Rannala

Keyword(s):

Probability Distributions ◽

Gray Wolf ◽

Data Sets ◽

Genotype Data ◽

Migration Rates ◽

Multilocus Genotypes ◽

Monte Carlo Techniques ◽

Inbreeding Coefficients ◽

Genotype Frequencies ◽

Marker Loci

Abstract A new Bayesian method that uses individual multilocus genotypes to estimate rates of recent immigration (over the last several generations) among populations is presented. The method also estimates the posterior probability distributions of individual immigrant ancestries, population allele frequencies, population inbreeding coefficients, and other parameters of potential interest. The method is implemented in a computer program that relies on Markov chain Monte Carlo techniques to carry out the estimation of posterior probabilities. The program can be used with allozyme, microsatellite, RFLP, SNP, and other kinds of genotype data. We relax several assumptions of early methods for detecting recent immigrants, using genotype data; most significantly, we allow genotype frequencies to deviate from Hardy-Weinberg equilibrium proportions within populations. The program is demonstrated by applying it to two recently published microsatellite data sets for populations of the plant species Centaurea corymbosa and the gray wolf species Canis lupus. A computer simulation study suggests that the program can provide highly accurate estimates of migration rates and individual migrant ancestries, given sufficient genetic differentiation among populations and sufficient numbers of marker loci.

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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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