Standard deviation and absolute bias for QTL estimates in the new method.

<p><i>a</i>: additive effect; <i>d</i>: dominant effect; and <i>var</i>: residual variance.</p

Multi-QTL Mapping for Quantitative Traits Using Epistatic Distorted Markers

<div><p>The interaction between segregation distortion loci (SDL) has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL) mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F₂ individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (<i>P</i> = 2.94e-4).</p></div

Simulated parameters in all the Monte Carlo simulation experiments.

<p>Simulated parameters in all the Monte Carlo simulation experiments.</p

Additional file 2: Dataset_S1. of A heuristic model for computational prediction of human branch point sequence

(FASTA 146 kb

Additional file 1: Table S1. of A heuristic model for computational prediction of human branch point sequence

The formulas of 15 scoring measures (Score0-Score14) and corresponding values for P j , Q j  ∈ [0, 1], j = 1, 2, 3. Table S2. The endpoints (5′- and 3′-) of the shortened AGEZ and corresponding branch sites labeled by their positons relative to the 3’ss for each intron in Additional file 2: Dataset S1 when L = 9. Table S3. The endpoints (5′- and 3′-) of the shortened AGEZ and corresponding branch sites labeled by their positons relative to the 3’ss for each intron in Additional file 3: Dataset S2 when L = 9. Table S4. The relative frequencies of nucleotides at each position for BPSs in Additional file 2: Dataset S1 and corresponding information content (IC). Table S5. The relative frequencies of nucleotides at each position for BPSs in Additional file 3: Dataset S2 and corresponding information content (IC). Table S6. The relative frequencies of nucleotides at each position for 252,302 human BPSs predicted by sequencing method. Table S7. The results of 15 scoring measures (Score0-Score14) for BPS prediction on Additional file 2:Dataset S1 and Additional file 3: Dataset S2. Table S8. The relative frequencies of nucleotides at each position for genome-wide predicted BPSs and corresponding information content (IC) (DOCX 44 kb

for QTL parameters in the paired <i>t</i> test between the old and new methods.

<p><i>p</i>: QTL position; <i>a</i>: additive effect of QTL; <i>d</i>: dominant effect of QTL; <i>var</i>: residual variance. The <i>dashed line</i> represents the critical value at the 0.05 level of significance.</p

Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

<div><p>The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F₁ crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F₁ hybrids, and all these F₁ phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F₁ hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.</p></div

Elite restorer and sterile lines and hybrid combinations.

<p>Elite restorer and sterile lines and hybrid combinations.</p

Effect of QTL heritability on mapping QTL in the NCII.

<p>Power of QTL detection (a); false positive rate (b); and average (c) and standard deviation (d) of absolute bias between estimated and true effects.</p

Germ cell apoptosis in FST288-treated mice ovaries.

<p>Ovaries at 17.5 dpc were cultured alone (as a control) or with 500 ng/mL FST288 for 4 days prior to apoptosis assay (TUNEL). After culture ovaries were fixed and sectioned, a TUNEL assay was performed on the sections. No significant difference in oocyte apoptosis was observed between control and FST288-treated ovaries (A-D, arrows; TUNEL-positive oocytes). Populations of apoptotic oocytes and total oocytes per section in each treatment group were quantified (E and F). Scale bars: 40 μm (A-D).</p