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Genomic prediction (GP) is expected to become a powerful technology for accelerating the genetic improvement of complex crop traits. Several GP models have been proposed to enhance their applications in plant breeding, including environmental effects and genotype-by-environment interactions (G×E). In this study, we proposed a two-step model for plant biomass prediction wherein environmental information and growth-related traits were considered. First, the growth-related traits were predicted by GP. Second, the biomass was predicted from the GP-predicted values and environmental data using machine learning or crop growth modeling. We applied the model to a 2-year-old field trial dataset of recombinant inbred lines of japonica rice and evaluated the prediction accuracy with training and testing data by cross-validation performed over two years. Therefore, the proposed model achieved an equivalent or a higher correlation between the observed and predicted values (0.53 and 0.65 for each year, respectively) than the model in which biomass was directly predicted by GP (0.40 and 0.65 for each year, respectively). This result indicated that including growth-related traits enhanced accuracy of biomass prediction. Our findings are expected to contribute to the spread of the use of GP in crop breeding by enabling more precise prediction of environmental effects on crop traits.

It has been reported that vitamin D regulates the immune system. However, whether vitamin D repletion modulates inflammatory responses in lymphocytes from dialysis patients is unclear. In the clinical trial, thirty-two (32) dialysis patients with 25 vitamin D ≤ 20ng/mL were randomized to receive either supplementation of cholecalciferol 100,000 UI/week/3 months (16 patients) or placebo (16 patients). In the in vitro study, B and T lymphocytes from 12 healthy volunteers (HV) were incubated with or without uremic serum in the presence or absence of 25 or 1,25 vitamin D. We evaluated the intracellular expression of IL-6, IFN-γ TLR7, TLR9, VDR, CYP27b1 and CYP24a1 by flow cytometry. We observed a reduction in the expression of TLR7, TLR9, INF-γ and CYP24a1 and an increase in VDR and CYP27b1 expression in patients which were supplemented with cholecalciferol, whereas no differences were found in the placebo group. Uremic serum increased the intracellular expression of IL-6, IFN-γ, TLR7, TLR9, VDR, CYP27b1 and CYP24a1. Treatment with 25 or 1,25 vitamin D decreased IL-6 and TLR9. CYP24a1 silencing plus treatment with 25 and/or 1,25 vitamin D had an additional reduction effect on IL-6, IFN-γ, TLR7 and TLR9 expression. This is the first study showing that cholecalciferol repletion has an anti-inflammatory effect and improves vitamin D intracellular regulatory enzymes on lymphocytes from dialysis patients.