scholarly journals Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel

2012 ◽  
Vol 13 (4) ◽  
pp. r31 ◽  
Author(s):  
Marieke Simonis ◽  
Santosh S Atanur ◽  
Sam Linsen ◽  
Victor Guryev ◽  
Frans-Paul Ruzius ◽  
...  
Keyword(s):  
Recombinant Inbred ◽  
Genetic Basis ◽  
Recombinant Inbred Panel

scholarly journals Recombinant inbred lines derived from cultivars of pea for understanding the genetic basis of variation in breeders' traits

2018 ◽  
Vol 16 (5) ◽  
pp. 424-436 ◽  
Author(s):  
Carol Moreau ◽  
Maggie Knox ◽  
Lynda Turner ◽  
Tracey Rayner ◽  
Jane Thomas ◽  
...  
Keyword(s):  
Recombinant Inbred ◽  
Seed Weight ◽  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Field Trials ◽  
Genetic Maps ◽  
Genotypic Differences ◽  
Phenotypic Data ◽  
Growing Seasons ◽  
Randomized Field Trials

AbstractIn order to gain an understanding of the genetic basis of traits of interest to breeders, the pea varieties Brutus, Enigma and Kahuna were selected, based on measures of their phenotypic and genotypic differences, for the construction of recombinant inbred populations. Reciprocal crosses were carried out for each of the three pairs, and over 200 F2 seeds from each cross advanced to F13. Bulked F7 seeds were used to generate F8–F11 bulks, which were grown in triplicated plots within randomized field trials and used to collect phenotypic data, including seed weight and yield traits, over a number of growing seasons. Genetic maps were constructed from the F6 generation to support the analysis of qualitative and quantitative traits and have led to the identification of four major genetic loci involved in seed weight determination and at least one major locus responsible for variation in yield. Three of the seed weight loci, at least one of which has not been described previously, were associated with the marrowfat seed phenotype. For some of the loci identified, candidate genes have been identified. The F13 single seed descent lines are available as a germplasm resource for the legume and pulse crop communities.

scholarly journals Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 745-754 ◽  
Author(s):  
J Xiao ◽  
J Li ◽  
L Yuan ◽  
S D Tanksley
Keyword(s):  
Molecular Markers ◽  
Qtl Analysis ◽  
Recombinant Inbred ◽  
Quantitative Traits ◽  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Rflp Markers ◽  
Major Contributor ◽  
Significant Qtls

Abstract A set of 194 F7 lines derived from a subspecific rice cross showing strong F1 heterosis was backcrossed to the two parents. The materials (388 BC1F7 lines, 194 F8 lines, two parents, F1) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD > or = 2.0) was detected through 141 RFLP markers in the BC1F7 populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC1F7 populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC1F7 populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F8 population having phenotypic values superior to the F1 for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident.

scholarly journals Antipsychotic Behavioral Phenotypes in the Mouse Collaborative Cross Recombinant Inbred Inter-Crosses (RIX)

2020 ◽  
Vol 10 (9) ◽  
pp. 3165-3177
Author(s):  
Paola Giusti-Rodríguez ◽  
James G Xenakis ◽  
James J Crowley ◽  
Randal J Nonneman ◽  
Daniela M DeCristo ◽  
...  
Keyword(s):  
Body Weight ◽  
Recombinant Inbred ◽  
Mixed Models ◽  
Genetic Basis ◽  
Collaborative Cross ◽  
Typical Antipsychotic ◽  
Therapeutic Approaches ◽  
Orofacial Movements ◽  
Almost All ◽  
Vacuous Chewing

Abstract Schizophrenia is an idiopathic disorder that affects approximately 1% of the human population, and presents with persistent delusions, hallucinations, and disorganized behaviors. Antipsychotics are the standard pharmacological treatment for schizophrenia, but are frequently discontinued by patients due to inefficacy and/or side effects. Chronic treatment with the typical antipsychotic haloperidol causes tardive dyskinesia (TD), which manifests as involuntary and often irreversible orofacial movements in around 30% of patients. Mice treated with haloperidol develop many of the features of TD, including jaw tremors, tongue protrusions, and vacuous chewing movements (VCMs). In this study, we used genetically diverse Collaborative Cross (CC) recombinant inbred inter-cross (RIX) mice to elucidate the genetic basis of antipsychotic-induced adverse drug reactions (ADRs). We performed a battery of behavioral tests in 840 mice from 73 RIX lines (derived from 62 CC strains) treated with haloperidol or placebo in order to monitor the development of ADRs. We used linear mixed models to test for strain and treatment effects. We observed highly significant strain effects for almost all behavioral measurements investigated (P < 0.001). Further, we observed strong strain-by-treatment interactions for most phenotypes, particularly for changes in distance traveled, vertical activity, and extrapyramidal symptoms (EPS). Estimates of overall heritability ranged from 0.21 (change in body weight) to 0.4 (VCMs and change in distance traveled) while the portion attributable to the interactions of treatment and strain ranged from 0.01 (for change in body weight) to 0.15 (for change in EPS). Interestingly, close to 30% of RIX mice exhibited VCMs, a sensitivity to haloperidol exposure, approximately similar to the rate of TD in humans chronically exposed to haloperidol. Understanding the genetic basis for the susceptibility to antipsychotic ADRs may be possible in mouse, and extrapolation to humans could lead to safer therapeutic approaches for schizophrenia.

scholarly journals Genetic dissection of heterosis of indica–japonica by introgression line, recombinant inbred line and their testcross populations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenqing Yang ◽  
Fan Zhang ◽  
Sundus Zafar ◽  
Junmin Wang ◽  
Huajin Lu ◽  
...  
Keyword(s):  
Grain Yield ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Introgression Line ◽  
Successful Implementation ◽  
Genetic Dissection ◽  
Single Nucleotide ◽  
Panicle Number ◽  
Main Effect

AbstractThe successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) (japonica) and IR2061 (indica), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F1s (TCF1s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF1s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phenotypic variations of four traits of RILs and XSILs, TCF1s and absolute mid-parent heterosis in two locations. Furthermore, overdominance and underdominance were detected to play predominant effects on most traits in this study, suggesting overdominance and underdominance as well as epistasis are the main genetic bases of heterosis in rice. Some M-QTLs exhibiting positive overdominance effects such as qPN1.2, qPN1.5 and qPN4.3 for increased panicle number per plant, qGYP9 and qGYP12.1 for increased grain yield per plant, and qTGW3.4 and qTGW8.2 for enhanced 1000-grain weight would be highly valuable for breeding to enhance grain yield of hybrid rice by marker-assisted selection.

scholarly journals Antipsychotic behavioral phenotypes in the mouse Collaborative Cross recombinant inbred inter-crosses (RIX)

2019 ◽  
Author(s):  
Paola Giusti-Rodríguez ◽  
James G. Xenakis ◽  
James J. Crowley ◽  
Randal J. Nonneman ◽  
Daniela M. DeCristo ◽  
...  
Keyword(s):  
Body Weight ◽  
Recombinant Inbred ◽  
Mixed Models ◽  
Genetic Basis ◽  
Collaborative Cross ◽  
Typical Antipsychotic ◽  
Therapeutic Approaches ◽  
Orofacial Movements ◽  
Almost All ◽  
Vacuous Chewing

ABSTRACTSchizophrenia is an idiopathic disorder that affects approximately 1% of the human population, and presents with persistent delusions, hallucinations, and disorganized behaviors. Antipsychotics are the standard pharmacological treatment for schizophrenia, but are frequently discontinued by patients due to inefficacy and/or side effects. Chronic treatment with the typical antipsychotic haloperidol causes tardive dyskinesia (TD), which manifests as involuntary and often irreversible orofacial movements in around 30% of patients. Mice treated with haloperidol develop many of the features of TD, including jaw tremors, tongue protrusions, and vacuous chewing movements (VCMs). In this study, we used genetically diverse Collaborative Cross (CC) recombinant inbred inter-cross (RIX) mice to elucidate the genetic basis of antipsychotic-induced adverse drug reactions (ADRs). We performed a battery of behavioral tests in 840 mice from 73 RIX lines (derived from 62 CC strains) treated with haloperidol or placebo in order to monitor the development of ADRs. We used linear mixed models to test for strain and treatment effects. We observed highly significant strain effects for almost all behavioral measurements investigated (p<0.001). Further, we observed strong strain-by-treatment interactions for most phenotypes, particularly for changes in distance traveled, vertical activity, and extrapyramidal symptoms (EPS). Estimates of overall heritability ranged from 0.21 (change in body weight) to 0.4 (VCMs and change in distance traveled) while the portion attributable to the interactions of treatment and strain ranged from 0.01 (for change in body weight) to 0.15 (for change in EPS). Interestingly, close to 30% of RIX mice exhibited VCMs, a sensitivity to haloperidol exposure, approximately similar to the rate of TD in humans chronically exposed to haloperidol. Understanding the genetic basis for the susceptibility to antipsychotic ADRs may be possible in mouse, and extrapolation to humans could lead to safer therapeutic approaches for schizophrenia.

scholarly journals Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations

2021 ◽  
Vol 12 ◽  
Author(s):  
Jianing You ◽  
Hang Liu ◽  
Surong Wang ◽  
Wei Luo ◽  
Lulu Gou ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Snp Array ◽  
Spike Density ◽  
Kernel Length ◽  
Trait Loci

Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson’s correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.

scholarly journals Systems genetic analysis of binge-like eating in a C57BL/6J x DBA/2J-F2 cross

2020 ◽  
Author(s):  
Emily J. Yao ◽  
Richard K. Babbs ◽  
Julia C. Kelliher ◽  
Kimberly P. Luttik ◽  
M. Imad Damaj ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Binge Eating ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Genetic Basis ◽  
Strain Differences ◽  
Inbred Strains ◽  
Recombinant Inbred Strains ◽  
Chromosome 6 ◽  
Trait Locus

ABSTRACTObjectiveBinge eating is a heritable quantitative trait associated with eating disorders (ED) and refers to the rapid consumption of a large quantity of energy-dense food that is associated with loss of control, anxiety, and depression. Binge Eating Disorder is the most common ED in adults in the US; however, the genetic basis is unknown. We previously identified robust mouse inbred strain differences between C57BL/6J and DBA/2J in binge-like eating (BLE) of sweetened palatable food (PF) in an intermittent access, conditioned place preference paradigm.MethodsTo map the genetic basis of BLE, we phenotyped and genotyped 128 C57BL/6J x DBA/2J-F2 mice.ResultsWe identified a quantitative trait locus (QTL) on chromosome 13 influencing progressive changes in body weight across training days (LOD = 5.5; 26-39 cM). We also identified two sex-combined QTLs influencing PF intake on chromosome 5 (LOD = 5.6; 1.5-LOD interval = 21-28 cM) and 6 (LOD = 5.3; 1.5-LOD interval = 50-59 cM). Furthermore, sex-specific analyses revealed that the chromosome 6 locus was driven by males (1.5-LOD interval: 52-59 cM) and identified a female-selective QTL for BLE on chromosome 18 (LOD = 4.1; 1.5-LOD interval: 23-35 cM). Systems genetic analysis of the chromosome 6 locus for BLE using GeneNetwork legacy trait datasets from BXD recombinant inbred strains identified Adipor2 and Plxnd1 as two positional, functional, biological candidate genes.DiscussionWe identified genetic loci influencing BLE. Future studies will phenotype BXD recombinant inbred strains to fine map loci and support candidate gene nomination and validation.

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