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201.
Background
Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows.Methods
Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect.Results
For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects.Conclusions
Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.Electronic supplementary material
The online version of this article (doi:10.1186/s12711-015-0124-6) contains supplementary material, which is available to authorized users. 相似文献202.
Lucie Emilie Schmaltz Cédric Juillet Joost Marius Tinbergen Yvonne Ingje Verkuil Joslyn Corstiaan Elbert Wouter Hooijmeijer Theunis Piersma 《Population Ecology》2015,57(4):613-624
The ruff Philomachus pugnax, a lekking shorebird wintering in Africa and breeding across northern Eurasia, declined severely in its western range. Based on a capture-mark-resighting programme (2004–2011) in the westernmost staging area in Friesland (the Netherlands), we investigated changes in apparent annual survival in relation to age and sex to explore potential causes of decline. We also related temporal variation in apparent survival to environmental factors. We used the Capture-Mark-Recapture multievent statistical framework to overcome biases in survival estimates after testing for hidden heterogeneity of detection. This enabled the estimation of the probability to belong to high or low detectability classes. Apparent survival varied between years but was not related to weather patterns along the flyway, or to flood levels in the Sahel. Over time, a decline in apparent survival is suggested. Due to a short data series and flag loss in the last period this cannot be verified. Nevertheless, the patterns in sex-specific detectability and survival lead to new biological insights. Among highly detectable birds, supposedly most reliant on Friesland, males survived better than females ( = 0.74, range 0.51–0.93; = 0.51, range 0.24–0.81). Among low detectable birds, the pattern is reversed ( = 0.64, range 0.37–0.89; = 0.73, range 0.48–0.93). Probably the staging population contains a mixture of sex-specific migration strategies. A loss of staging females could greatly affect the dynamics of the western ruff population. Further unravelling of these population processes requires geographically extended demographic monitoring and the use of tracking devices. 相似文献
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Jamieson C Maclean JK Brown CI Campbell RA Gillen KJ Gillespie J Kazemier B Kiczun M Lamont Y Lyons AJ Moir EM Morrow JA Pantling J Rankovic Z Smith L 《Bioorganic & medicinal chemistry letters》2011,21(2):805-811
Starting from compound 1, we utilized biostructural data to successfully evolve an existing series into a new chemotype with a promising overall profile, exemplified by 19. 相似文献
207.
De Savi C Pape A Sawyer Y Milne D Davies C Cumming JG Ting A Lamont S Smith PD Tart J Page K Moore P 《Bioorganic & medicinal chemistry letters》2011,21(11):3301-3306
A new achiral class of N-hydroxyformamide inhibitor of both ADAM-TS4 and ADAM-TS5, 2 has been discovered through modification of the complex P1 group present in historical inhibitors 1. This structural change improved the DMPK properties and greatly simplified the synthesis whilst maintaining excellent cross-MMP selectivity profiles. Investigation of structure-activity and structure-property relationships in the P1 group resulted in both ADAM-TS4 selective and mixed ADAM-TS4/5 inhibitors. This led to the identification of a pre-clinical candidate with excellent bioavailability across three species and predicting once daily dosing kinetics. 相似文献
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Zhang YK Plattner JJ Freund YR Easom EE Zhou Y Gut J Rosenthal PJ Waterson D Gamo FJ Angulo-Barturen I Ge M Li Z Li L Jian Y Cui H Wang H Yang J 《Bioorganic & medicinal chemistry letters》2011,21(2):644-651
A series of boron-containing benzoxaborole compounds was designed and synthesized for a structure-activity relationship investigation surrounding 7-(HOOCCH2CH2)-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (1) with the goal of discovering a new antimalarial treatment. Compound 1 demonstrates the best potency (IC50 = 26 nM) against Plasmodium falciparum and has good drug-like properties, with low molecular weight (206.00), low ClogP (0.86) and high water solubility (750 μg/mL at pH 7). 相似文献
209.
Bordon Y 《Nature reviews. Immunology》2011,11(5):300-301
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