Genomic prediction with haplotype blocks in wheat

Haplotype blocks might carry additional information compared to single SNPs and have therefore been suggested for use as independent variables in genomic prediction. Studies in different species resulted in more accurate predictions than with single SNPs in some traits but not in others. In addition, it remains unclear how the blocks should be built to obtain the greatest prediction accuracies. Our objective was to compare the results of genomic prediction with different types of haplotype blocks to prediction with single SNPs in 11 traits in winter wheat. We built haplotype blocks from marker data from 361 winter wheat lines based on linkage disequilibrium, fixed SNP numbers, fixed lengths in cM and with the R package HaploBlocker. We used these blocks together with data from single-year field trials in a cross-validation study for predictions with RR-BLUP, an alternative method (RMLA) that allows for heterogeneous marker variances, and GBLUP performed with the software GVCHAP. The greatest prediction accuracies for resistance scores for B. graminis, P. triticina, and F. graminearum were obtained with LD-based haplotype blocks while blocks with fixed marker numbers and fixed lengths in cM resulted in the greatest prediction accuracies for plant height. Prediction accuracies of haplotype blocks built with HaploBlocker were greater than those of the other methods for protein concentration and resistances scores for S. tritici, B. graminis, and P. striiformis. We hypothesize that the trait-dependence is caused by properties of the haplotype blocks that have overlapping and contrasting effects on the prediction accuracy. While they might be able to capture local epistatic effects and to detect ancestral relationships better than single SNPs, prediction accuracy might be reduced by unfavorable characteristics of the design matrices in the models that are due to their multi-allelic nature.

Genomic Prediction Can Provide Precise Estimates of the Genotypic Value of Barley Lines Evaluated in Unreplicated Trials

Genomic prediction has been established in breeding programs to predict the genotypic values of selection candidates without phenotypic data. First results in wheat showed that genomic predictions can also prove useful to select among material for which phenotypic data are available. In such a scenario, the selection candidates are evaluated with low intensity in the field. Genome-wide effects are estimated from the field data and are then used to predict the genotypic values of the selection candidates. The objectives of our simulation study were to investigate the correlations r(y, g) between genomic predictions y and genotypic values g and to compare these with the correlations r(p, g) between phenotypic values p and genotypic values g. We used data from a yield trial of 250 barley lines to estimate variance components and genome-wide effects. These parameters were used as basis for simulations. The simulations included multiple crossing schemes, population sizes, and varying sizes of the components of the masking variance. The genotypic values g of the selection candidates were obtained by genetic simulations, the phenotypic values p by simulating evaluation in the field, and the genomic predictions y by RR-BLUP effect estimation from the phenotypic values. The correlations r(y, g) were greater than the correlations r(p, g) for all investigated scenarios. We conclude that using genomic predictions for selection among candidates tested with low intensity in the field can proof useful for increasing the efficiency of barley breeding programs.

Dynamics and interactions of cobalamin and folate status during advanced aging - a longitudinal study in a community-dwelling cohort with multiple follow-ups

BACKGROUND

Older people are reported to be prone to imbalances between cobalamin and folate status with possible adverse effects on health. This longitudinal study investigates dynamics and interactions of cobalamin and folate status in a cohort of community-dwelling older adults by considering possible influencing factors.

METHODS

In total, 332 subjects ≥ 60 years were investigated over a mean observation period of 12 years. Data collection included serum cobalamin, folate and creatinine, dietary intakes of cobalamin, folate and alcohol, use of supplements, body composition, smoking behavior, and diseases. Linear mixed-effects models with repeated measurements were used to investigate the influence of variables on serum cobalamin and folate.

RESULTS

At baseline, median cobalamin intake exceeded the dietary reference value (DRV), while median folate intake was considerably below DRV. In most subjects, serum concentrations of both vitamins were within reference ranges. For serum cobalamin, apart from supplement use (Parameter estimate [95% confidence interval]: 130.17 [53.32, 207.01]), the main positive predictor was serum folate (4.63 [2.64, 6.62]). For serum folate, serum creatinine (10.85 [4.85, 16.86]), use of supplements (7.86 [5.05, 10.67]), serum cobalamin (0.01 [< 0.01, 0.01]), and dietary folate intake (0.02 [0.01, 0.03]) were positive predictors. No main effects of age, sex, body composition, alcohol intake or smoking were found after adjusting for simultaneous inference.

CONCLUSIONS

Advancing age, per se, is no risk factor for a decline in serum concentrations of cobalamin or folate in subjects ≥ 60 years. Suboptimal folate intake may limit the function of folate regarding the supply of methyl groups for methylation of cobalamin and subsequent creatine biosynthesis. The positive association of serum creatinine with folate deserves further exploration with regard to its possible relevance for maintaining energy dependent functional integrity in the course of ageing.

Prediction of Means and Variances of Crosses With Genome-Wide Marker Effects in Barley

Background: The expected genetic variance is an important criterion for the selection of crossing partners which will produce superior combinations of genotypes in their progeny. The advent of molecular markers has opened up new vistas for obtaining precise predictors for the genetic variance of a cross, but fast prediction methods that allow plant breeders to select crossing partners based on already available data from their breeding programs without complicated calculations or simulation of breeding populations are still lacking. The main objective of the present study was to demonstrate the practical applicability of an analytical approach for the selection of superior cross combinations with experimental data from a barley breeding program. We used genome-wide marker effects to predict the yield means and genetic variances of 14 DH families resulting from crosses of four donor lines with five registered elite varieties with the genotypic information of the parental lines. For the validation of the predicted parameters, the analytical approach was extended by the masking variance as a major component of phenotypic variance. The predicted parameters were used to fit normal distribution curves of the phenotypic values and to conduct an Anderson-Darling goodness-of-fit test for the observed phenotypic data of the 14 DH families from the field trial. Results: There was no evidence that the observed phenotypic values deviated from the predicted phenotypic normal distributions in 13 out of 14 crosses. The correlations between the observed and the predicted means and the observed and predicted variances were r = 0.95 and r = 0.34, respectively. After removing two crosses with downward outliers in the phenotypic data, the correlation between the observed and predicted variances increased to r = 0.76. A ranking of the 14 crosses based on the sum of predicted mean and genetic variance identified the 50% best crosses from the field trial correctly. Conclusions: We conclude that the prediction accuracy of the presented approach is sufficiently high to identify superior crosses even with limited phenotypic data. We therefore expect that the analytical approach based on genome-wide marker effects is applicable in a wide range of breeding programs.

Prediction of hybrid performance in maize with a ridge regression model employed to DNA markers and mRNA transcription profiles

Background

Ridge regression models can be used for predicting heterosis and hybrid performance. Their application to mRNA transcription profiles has not yet been investigated. Our objective was to compare the prediction accuracy of models employing mRNA transcription profiles with that of models employing genome-wide markers using a data set of 98 maize hybrids from a breeding program.

Results

We predicted hybrid performance and mid-parent heterosis for grain yield and grain dry matter content and employed cross validation to assess the prediction accuracy. Prediction with a ridge regression model using random effects for mRNA transcription profiles resulted in similar prediction accuracies than employing the model to DNA markers. For hybrids, of which none of the parental inbred lines was part of the training set, the ridge regression model did not reach the prediction accuracy that was obtained with a model using transcriptome-based distances.

Conclusion

We conclude that mRNA transcription profiles are a promising alternative to DNA markers for hybrid prediction, but further studies with larger data sets are required to investigate the superiority of alternative prediction models.