A critical evaluation of the effect of population size and phenotypic measurement on QTL detection and localization using a large F2 murine mapping population

Li, Xinmin; Quigg, Richard J.; Zhou, Jiang; Xu, Shizhong; Masinde, Godfred; Mohan, Subburaman; Baylink, David J.

doi:10.1590/s1415-47572006000100030

Cited by 28 publications

(14 citation statements)

References 18 publications

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“…An attempt was made to produce at least 300 F 2 offspring from these F 1 matings. This sample size was expected to be a reasonable compromise between the labor-intensive difficulties associated with the phenotyping process (see below) and the achievement of an acceptable level of statistical power for the detection of QTL (18). With a sample size of 300, the statistical power to detect a QTL that contributes 5% of the total variation in a trait is 0.98 if its effects are entirely additive or 0.90 if there is complete dominance (22).…”

Section: Animalsmentioning

confidence: 99%

Quantitative trait loci for physical activity traits in mice

Lightfoot

Turner

Pomp

et al. 2008

Physiological Genomics

141

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The genomic locations and identities of the genes that regulate voluntary physical activity are presently unknown. The purpose of this study was to search for quantitative trait loci (QTL) that are linked with daily mouse running wheel distance, duration, and speed of exercise. F(2) animals (n = 310) derived from high active C57L/J and low active C3H/HeJ inbred strains were phenotyped for 21 days. After phenotyping, genotyping with a fully informative single-nucleotide polymorphism panel with an average intermarker interval of 13.7 cM was used. On all three activity indexes, sex and strain were significant factors, with the F(2) animals similar to the high active C57L/J mice in both daily exercise distance and duration of exercise. In the F(2) cohort, female mice ran significantly farther, longer, and faster than male mice. QTL analysis revealed no sex-specific QTL but at the 5% experimentwise significance level did identify one QTL for duration, one QTL for distance, and two QTL for speed. The QTL for duration (DUR13.1) and distance (DIST13.1) colocalized with the QTL for speed (SPD13.1). Each of these QTL accounted for approximately 6% of the phenotypic variance, whereas SPD9.1 (chromosome 9, 7 cM) accounted for 11.3% of the phenotypic variation. DUR13.1, DIST13.1, SPD13.1, and SPD9.1 were subsequently replicated by haplotype association mapping. The results of this study suggest a genetic basis of voluntary activity in mice and provide a foundation for future candidate gene studies.

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Section: Animalsmentioning

confidence: 99%

Quantitative trait loci for physical activity traits in mice

Lightfoot

Turner

Pomp

et al. 2008

Physiological Genomics

141

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“…, where VP1 and VP2 are the variances of the isogenic parental strains and VF1 and VF2 are the variances of the F1 and F2 offspring (25,35).…”

Section: Massett Unpublished Observations)mentioning

confidence: 99%

Quantitative trait loci for exercise training responses in FVB/NJ and C57BL/6J mice

Massett

Fan

Berk

2009

Physiological Genomics

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Massett MP, Fan R, Berk BC. Quantitative trait loci for exercise training responses in FVB/NJ and C57BL/6J mice. Physiol Genomics 40: 15-22, 2009. First published September 29, 2009 doi:10.1152/physiolgenomics.00116.2009.-The genetic factors determining the magnitude of the response to exercise training are poorly understood. The aim of this study was to identify quantitative trait loci (QTL) associated with adaptation to exercise training in a cross between FVB/NJ (FVB) and C57BL/6J (B6) mice. Mice completed an exercise performance test before and after a 4-wk treadmill running program, and changes in exercise capacity, expressed as work (kg ⅐ m), were calculated. Changes in work in F2 mice averaged 1.51 Ϯ 0.08 kg ⅐ m (94.3 Ϯ 7.3%), with a range of Ϫ1.67 to ϩ4.55 kg ⅐ m. All F2 mice (n ϭ 188) were genotyped at 20-cM intervals with 103 single nucleotide polymorphisms (SNPs), and genomewide linkage scans were performed for pretraining, posttraining, and change in work. Significant QTL for pretraining work were located on chromosomes 14 at 4.0 cM [3.72 logarithm of odds (LOD)] and 19 at 34.4 cM (3.63 LOD). For posttraining work significant QTL were located on chromosomes 3 at 60 cM (4.66 LOD) and 14 at 26 cM (4.99 LOD). Suggestive QTL for changes in work were found on chromosomes 11 at 44.6 cM (2.30 LOD) and 14 at 36 cM (2.25 LOD). When pretraining work was used as a covariate, a potential QTL for change in work was identified on chromosome 6 at 68 cM (3.56 LOD). These data indicate that one or more QTL determine exercise capacity and training responses in mice. Furthermore, these data suggest that the genes that determine pretraining work and training responses may differ. treadmill running; genetic factors LOW EXERCISE CAPACITY or cardiorespiratory fitness is comparable to elevated systolic blood pressure, obesity, diabetes, and smoking as a risk factor and predictor of future disease (33,47). Improving cardiorespiratory fitness through increased physical activity can significantly reduce the risk of all-cause mortality (8), regardless of the level of initial fitness (22). However, there is a high degree of individual variation in the responses to exercise training. For example, there are some individuals who might not show an increase in maximal oxygen consumption (V O 2max ) in response to endurance training (9, 12). Consequently, identifying the genetic factors modulating the adaptations to exercise may provide insight into individual differences in responses to training. However, the genetic factors determining the magnitude of the response to exercise are poorly understood.Initial studies investigating the genetic basis for exercise capacity and training responses focused on familial resemblance and heritability of performance phenotypes. Results from cross-sectional, twin, and prospective studies indicate that the heritability for training-induced changes in V O 2max and submaximal power output ranges from 25% to 50% (11). Heritability estimates from family studies also vary between 25% and 50%, depending...

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“…To obviate this limitation, the map resolution and hence QTL detection power, were improved by integrating the two BC2 maps. Other factors, such as the phenotypic measurement accuracy and marker density, also contributed to the QTL detection and localization [34].…”

Section: Discussionmentioning

confidence: 99%

Revealing QTLs Associated with Fatty Acid Composition and Compactness on an Integrated Linkage Map Of Oil Palm Interspecific Backcross 2 (BC2)

Yaakub

Kamaruddin

Singh

et al. 2019

Preprint

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Background Molecular breeding has opened new avenues for crop improvement with the potential for faster progress. As oil palm is the major producer of vegetable oil in the world, its improvement, such as developing compact planting materials and improving its oil’s fatty acid composition, is important. Results This study sought to identify the QTLs associated with fatty acid composition and vegetative traits for compactness in the crop. It integrated two separate interspecific backcross two (BC2) mapping populations to improve the genetic resolution and evaluate the consistency of the QTLs identified. A total of 1,963 markers (1,814 SNPs and 149 SSRs) spanning a total map length of 1793 cM was integrated into a consensus map. The QTL analysis observed 19 and 10 significant genomic loci associated with FAC and compactness, respectively. Conclusions A few genomic regions were revealed to be major loci influencing FAC and compactness. It is hoped that the QTLs identified will be useful tools for marker-assisted selection, accelerate the process of identifying desirable genotypes for breeding.

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A critical evaluation of the effect of population size and phenotypic measurement on QTL detection and localization using a large F2 murine mapping population

Cited by 28 publications

References 18 publications

Quantitative trait loci for physical activity traits in mice

Quantitative trait loci for physical activity traits in mice

Quantitative trait loci for exercise training responses in FVB/NJ and C57BL/6J mice

Revealing QTLs Associated with Fatty Acid Composition and Compactness on an Integrated Linkage Map Of Oil Palm Interspecific Backcross 2 (BC2)

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