Phenomic selection in wheat breeding: identification and optimisation of factors influencing prediction accuracy and comparison to genomic selection.

KEY MESSAGE: Phenomic selection is a promising alternative or complement to genomic selection in wheat breeding. Models combining spectra from different environments maximise the predictive ability of grain yield and heading date of wheat breeding lines. Phenomic selection (PS) is a recent breeding approach similar to genomic selection (GS) except that genotyping is replaced by near-infrared (NIR) spectroscopy. PS can potentially account for non-additive effects and has the major advantage of being low cost and high throughput. Factors influencing GS predictive abilities have been intensively studied, but little is known about PS. We tested and compared the abilities of PS and GS to predict grain yield and heading date from several datasets of bread wheat lines corresponding to the first or second years of trial evaluation from two breeding companies and one research institute in France. We evaluated several factors affecting PS predictive abilities including the possibility of combining spectra collected in different environments. A simple H-BLUP model predicted both traits with prediction ability from 0.26 to 0.62 and with an efficient computation time. Our results showed that the environments in which lines are grown had a crucial impact on predictive ability based on the spectra acquired and was specific to the trait considered. Models combining NIR spectra from different environments were the best PS models and were at least as accurate as GS in most of the datasets. Furthermore, a GH-BLUP model combining genotyping and NIR spectra was the best model of all (prediction ability from 0.31 to 0.73). We demonstrated also that as for GS, the size and the composition of the training set have a crucial impact on predictive ability. PS could therefore replace or complement GS for efficient wheat breeding programs.

Phenomic selection in wheat breeding: prediction of the genotype-by-environment interaction in multi-environment breeding trials.

KEY MESSAGE: Phenomic prediction of wheat grain yield and heading date in different multi-environmental trial scenarios is accurate. Modelling the genotype-by-environment interaction effect using phenomic data is a potentially low-cost complement to genomic prediction. The performance of wheat cultivars in multi-environmental trials (MET) is difficult to predict because of the genotype-by-environment interactions (G × E). Phenomic selection is supposed to be efficient for modelling the G × E effect because it accounts for non-additive effects. Here, phenomic data are near-infrared (NIR) spectra obtained from plant material. While phenomic selection has recently been shown to accurately predict wheat grain yield in single environments, its accuracy needs to be investigated for MET. We used four datasets from two winter wheat breeding programs to test and compare the predictive abilities of phenomic and genomic models for grain yield and heading date in different MET scenarios. We also compared different methods to model the G × E using different covariance matrices based on spectra. On average, phenomic and genomic prediction abilities are similar in all different MET scenarios. Better predictive abilities were obtained when G × E effects were modelled with NIR spectra than without them, and it was better to use all the spectra of all genotypes in all environments for modelling the G × E. To facilitate the implementation of phenomic prediction, we tested MET designs where the NIR spectra were measured only on the genotype-environment combinations phenotyped for the target trait. Missing spectra were predicted with a weighted multivariate ridge regression. Intermediate predictive abilities for grain yield were obtained in a sparse testing scenario and for new genotypes, which shows that phenomic selection is an efficient and practicable prediction method for dealing with G × E.

Protective role of the mitochondrial fusion protein OPA1 in hypertension.

Hypertension is associated with excessive reactive oxygen species (ROS) production in vascular cells. Mitochondria undergo fusion and fission, a process playing a role in mitochondrial function. OPA1 is essential for mitochondrial fusion. Loss of OPA1 is associated with ROS production and cell dysfunction. We hypothesized that mitochondria fusion could reduce oxidative stress that defect in fusion would exacerbate hypertension. Using (a) Opa1 haploinsufficiency in isolated resistance arteries from Opa1+/- mice, (b) primary vascular cells from Opa1+/- mice, and (c) RNA interference experiments with siRNA against Opa1 in vascular cells, we investigated the role of mitochondria fusion in hypertension. In hypertension, Opa1 haploinsufficiency induced altered mitochondrial cristae structure both in vascular smooth muscle and endothelial cells but did not modify protein level of long and short forms of OPA1. In addition, we demonstrated an increase of mitochondrial ROS production, associated with a decrease of superoxide dismutase 1 protein expression. We also observed an increase of apoptosis in vascular cells and a decreased VSMCs proliferation. Blood pressure, vascular contractility, as well as endothelium-dependent and -independent relaxation were similar in Opa1+/- , WT, L-NAME-treated Opa1+/- and WT mice. Nevertheless, chronic NO-synthase inhibition with L-NAME induced a greater hypertension in Opa1+/- than in WT mice without compensatory arterial wall hypertrophy. This was associated with a stronger reduction in endothelium-dependent relaxation due to excessive ROS production. Our results highlight the protective role of mitochondria fusion in the vasculature during hypertension by limiting mitochondria ROS production.

Metabolomic Profiling of Angiotensin-II-Induced Abdominal Aortic Aneurysm in Ldlr-/- Mice Points to Alteration of Nitric Oxide, Lipid, and Energy Metabolisms.

Aneurysm is the second-most common disease affecting the aorta worldwide after atherosclerosis. While several clinical metabolomic studies have been reported, no study has reported deep metabolomic phenotyping in experimental animal models of aortic aneurysm. We performed a targeted metabolomics study on the blood and aortas of an experimental mice model of aortic aneurysm generated by high-cholesterol diet and angiotensin II in Ldlr-/- mice. The mice model showed a significant increase in media/lumen ratio and wall area, which is associated with lipid deposition within the adventitia, describing a hypertrophic remodeling with an aneurysm profile of the abdominal aorta. Altered aortas showed increased collagen remodeling, disruption of lipid metabolism, decreased glucose, nitric oxide and lysine metabolisms, and increased polyamines and asymmetric dimethylarginine (ADMA) production. In blood, a major hyperlipidemia was observed with decreased concentrations of glutamine, glycine, taurine, and carnitine, and increased concentrations of the branched amino acids (BCAA). The BCAA/glycine and BCAA/glutamine ratios discriminated with very good sensitivity and specificity between aneurysmatic and non-aneurysmatic mice. To conclude, our results reveal that experimental induction of aortic aneurysms causes a profound alteration in the metabolic profile in aortas and blood, mainly centered on an alteration of NO, lipid, and energetic metabolisms.

Cardiac Overexpression of PDE4B Blunts ß-Adrenergic Response and Maladaptive Remodeling in Heart Failure.

BACKGROUND: The cyclic AMP (adenosine monophosphate; cAMP)-hydrolyzing protein PDE4B (phosphodiesterase 4B) is a key negative regulator of cardiac ß-adrenergic receptor stimulation. PDE4B deficiency leads to abnormal Ca2+ handling and PDE4B is decreased in pressure overload hypertrophy, suggesting that increasing PDE4B in the heart is beneficial in heart failure. METHODS: We measured PDE4B expression in human cardiac tissues and developed 2 transgenic mouse lines with cardiomyocyte-specific overexpression of PDE4B and an adeno-associated virus serotype 9 encoding PDE4B. Myocardial structure and function were evaluated by echocardiography, ECG, and in Langendorff-perfused hearts. Also, cAMP and PKA (cAMP dependent protein kinase) activity were monitored by Förster resonance energy transfer, L-type Ca2+ current by whole-cell patch-clamp, and cardiomyocyte shortening and Ca2+ transients with an Ionoptix system. Heart failure was induced by 2 weeks infusion of isoproterenol or transverse aortic constriction. Cardiac remodeling was evaluated by serial echocardiography, morphometric analysis, and histology. RESULTS: PDE4B protein was decreased in human failing hearts. The first PDE4B-transgenic mouse line (TG15) had a ≈15-fold increase in cardiac cAMP-PDE activity and a ≈30% decrease in cAMP content and fractional shortening associated with a mild cardiac hypertrophy that resorbed with age. Basal ex vivo myocardial function was unchanged, but ß-adrenergic receptor stimulation of cardiac inotropy, cAMP, PKA, L-type Ca2+ current, Ca2+ transients, and cell contraction were blunted. Endurance capacity and life expectancy were normal. Moreover, these mice were protected from systolic dysfunction, hypertrophy, lung congestion, and fibrosis induced by chronic isoproterenol treatment. In the second PDE4B-transgenic mouse line (TG50), markedly higher PDE4B overexpression, resulting in a ≈50-fold increase in cardiac cAMP-PDE activity caused a ≈50% decrease in fractional shortening, hypertrophy, dilatation, and premature death. In contrast, mice injected with adeno-associated virus serotype 9 encoding PDE4B (1012 viral particles/mouse) had a ≈50% increase in cardiac cAMP-PDE activity, which did not modify basal cardiac function but efficiently prevented systolic dysfunction, apoptosis, and fibrosis, while attenuating hypertrophy induced by chronic isoproterenol infusion. Similarly, adeno-associated virus serotype 9 encoding PDE4B slowed contractile deterioration, attenuated hypertrophy and lung congestion, and prevented apoptosis and fibrotic remodeling in transverse aortic constriction. CONCLUSIONS: Our results indicate that a moderate increase in PDE4B is cardioprotective and suggest that cardiac gene therapy with PDE4B might constitute a new promising approach to treat heart failure.

Phenomic Selection: A New and Efficient Alternative to Genomic Selection.

Recently, it has been proposed to switch molecular markers to near-infrared (NIR) spectra for inferring relationships between individuals and further performing phenomic selection (PS), analogous to genomic selection (GS). The PS concept is similar to genomic-like omics-based (GLOB) selection, in which molecular markers are replaced by endophenotypes, such as metabolites or transcript levels, except that the phenomic information obtained for instance by near-infrared spectroscopy (NIRS ) has usually a much lower cost than other omics. Though NIRS has been routinely used in breeding for several decades, especially to deal with end-product quality traits, its use to predict other traits of interest and further make selections is new. Since the seminal paper on PS , several publications have advocated the use of spectral acquisition (including NIRS and hyperspectral imaging) in plant breeding towards PS , potentially providing a scope of what is possible. In the present chapter, we first come back to the concept of PS as originally proposed and provide a classification of selected papers related to the use of phenomics in breeding. We further provide a review of the selected literature concerning the type of technology used, the preprocessing of the spectra, and the statistical modeling to make predictions. We discuss the factors that likely affect the efficiency of PS and compare it to GS in terms of predictive ability. Finally, we propose several prospects for future work and application of PS in the context of plant breeding.

Author's reply (in reference to letter to editor proposed by Etem Caliskan, Catherine J. Pachuk, Louis P. Perrault, Maximilian Y Emmert and entitled: preservation solutions to improve graft patency: The devil is in the detail).

Not applicable.

Combining Crop Growth Modeling With Trait-Assisted Prediction Improved the Prediction of Genotype by Environment Interactions.

Plant breeders evaluate their selection candidates in multi-environment trials to estimate their performance in contrasted environments. The number of genotype/environment combinations that can be evaluated is strongly constrained by phenotyping costs and by the necessity to limit the evaluation to a few years. Genomic prediction models taking the genotype by environment interactions (GEI) into account can help breeders identify combination of (possibly unphenotyped) genotypes and target environments optimizing the traits under selection. We propose a new prediction approach in which a secondary trait available on both the calibration and the test sets is introduced as an environment specific covariate in the prediction model (trait-assisted prediction, TAP). The originality of this approach is that the phenotyping of the test set for the secondary trait is replaced by crop-growth model (CGM) predictions. So there is no need to sow and phenotype the test set in each environment which is a clear advantage over the classical trait-assisted prediction models. The interest of this approach, called CGM-TAP, is highest if the secondary trait is easy to predict with CGM and strongly related to the target trait in each environment (and thus capturing GEI). We tested CGM-TAP on bread wheat with heading date as secondary trait and grain yield as target trait. Simple CGM-TAP model with a linear effect of heading date resulted in high predictive abilities in three prediction scenarios (sparse testing, or prediction of new genotypes or of new environments). It increased predictive abilities of all reference GEI models, even those involving sophisticated environmental covariates.

Cardiopulmonary bypass and internal thoracic artery: Can roller or centrifugal pumps change vascular reactivity of the graft? The IPITA study: A randomized controlled clinical trial.

BACKGROUND: Cardiopulmonary bypass (CPB) induces a systemic inflammatory response (SIRS) and affects the organ vascular bed. Experimentally, the lack of pulsatility alters myogenic tone of resistance arteries and increases the parietal inflammatory response. The purpose of this study was to compare the vascular reactivity of the internal thoracic arteries (ITAs) due to the inflammatory response between patients undergoing coronary artery bypass grafting (CABG) under CPB with a roller pump or with a centrifugal pump. METHODS: Eighty elective male patients undergoing CABG were selected using one or two internal thoracic arteries under CPB with a roller pump (RP group) or centrifugal pump (CFP group). ITA samples were collected before starting CPB (Time 1) and before the last coronary anastomosis during aortic cross clamping (Time 2). The primary endpoint was the endothelium-dependent relaxation of ITAs investigated using wire-myography. The secondary endpoint was the parietal inflammatory response of arteries defined by the measurements of superoxide levels, leukocytes and lymphocytes rate and gene expression of inflammatory proteins using. Terminal complement complex activation (SC5b-9) and neutrophil activation (elastase) analysis were performed on arterial blood at the same times. RESULTS: Exposure time of ITAs to the pump flow was respectively 43.3 minutes in the RP group and 45.7 minutes in the CFP group. Acetylcholine-dependent relaxation was conserved in the two groups whatever the time. Gene expression of C3 and C4a in the artery wall decreased from Time 1 to Time 2. No oxidative stress was observed in the graft. There was no difference between the groups concerning the leukocytes and lymphocytes rate. SC5b-9 and elastase increased between Time 1 and Time 2. CONCLUSION: Endothelium-dependent relaxation of the internal thoracic arteries was preserved during CPB whatever the type of pump used. The inflammatory response observed in the blood was not found in the graft wall within this time frame. TRIAL REGISTRATION: Name of trial study protocol: IPITA Registration number (ClinicalTrials.gov): NCT04168853.

Do storage solutions protect endothelial function of arterialized vein graft in an experimental rat model?

BACKGROUND: This study aims to compare the effects of storage solutions commonly used in coronary artery bypass grafting on the vascular reactivity in vein graft interposed in arterial position in syngeneic rats. METHODS: Twenty-seven male Lewis rats were sacrified to sample a vein graft implanted 6 weeks ago into abdominal aorta position. The vein grafts were inferior venae cavae initially pretreated with heparinized saline solution (HS) or autologous heparinized blood (AHB) or our referent solution, GALA. The endothelial functionality, the in situ Reactive Oxygen Species (ROS) levels and the histological characteristics were conducted from segments of arterialized vein graft. RESULTS: At 6 weeks, graft thrombosis occurred respectively in 22% of AHB group, 62.5% in the HS group and 82.5% in the GALA group. In each group, significative intimal hyperplasia was observed. After 6 weeks, an endothelium-remodeling layer associated with an increase of wall thickness was observed in each group. Endothelium-dependent tone was reduced in the vein graft regardless of the group. No difference was observed concerning the ROS in vein graft between the different groups. In distal aortic sections, ROS levels were increased in HS and GALA groups. CONCLUSIONS: Storage solutions used in this experimental model of vein graft implanted in arterial position cause graft injury and a complete disappearance of vascular reactivity. GALA solution did not reduce intimal risk hyperplasia when the vein graft was exposed to arterial flow in a rat model.

Potential for Local Fertilization: A Benthocosm Test of Long-Term and Short-Term Effects of Mussel Excretion on the Plankton.

Mussel aquaculture has expanded worldwide and it is important to assess its impact on the water column and the planktonic food web to determine the sustainability of farming practices. Mussel farming may affect the planktonic food web indirectly by excreting bioavailable nutrients in the water column (a short-term effect) or by increasing nutrient effluxes from biodeposit-enriched sediments (a long-term effect). We tested both of these indirect effects in a lagoon by using plankton-enclosing benthocosms that were placed on the bottom of a shallow lagoon either inside of a mussel farm or at reference sites with no history of aquaculture. At each site, half of the benthocosms were enriched with seawater that had held mussels (excretion treatment), the other half received non-enriched seawater as a control treatment. We monitored nutrients ([PO43-] and [NH4+]), dissolved oxygen and plankton components (bacteria, the phytoplankton and the zooplankton) over 5 days. We found a significant relationship between long-term accumulation of mussel biodeposits in sediments, water-column nutrient concentrations and plankton growth. Effects of mussel excretion were not detected, too weak to be significant given the spatial and temporal variability observed in the lagoon. Effects of mussels on the water column are thus likely to be coupled to benthic processes in such semi-enclosed water bodies.

Genetic dysfunction of serotonin 2A receptor hampers response to antidepressant drugs: A translational approach.

Pharmacological studies have yielded valuable insights into the role of the serotonin 2A (5-HT2A) receptor in major depressive disorder (MDD) and antidepressant drugs (ADs) response. However, it is still unknown whether genetic variants in the HTR2A gene affect the therapeutic outcome of ADs and the mechanism underlying the regulation of such response remains poorly described. In this context, a translational human-mouse study offers a unique opportunity to address the possibility that variations in the HTR2A gene may represent a relevant marker to predict the efficacy of ADs. In a first part of this study, we investigated in depressed patients the effect of three HTR2A single nucleotide polymorphisms (SNPs), selected for their potential functional consequences on 5-HT2A receptor (rs6313, rs6314 and rs7333412), on response and remission rates after 3 months of antidepressant treatments. We also explored the consequences of the constitutive genetic inactivation of the 5-HT2A receptor (i.e. in 5-HT2A(-/-) mice) on the activity of acute and prolonged administration of SSRIs. Our clinical data indicate that GG patients for the rs7333412 SNP were less prone to respond to ADs than AA/AG patients. In the preclinical study, we demonstrated that the 5-HT2A receptor exerts an inhibitory influence on the neuronal activity of the serotonergic system after acute administration of SSRIs. However, while the chronic administration of the SSRIs escitalopram or fluoxetine elicited a progressive increased in the firing rate of 5-HT neurons in 5-HT2A(+/+) mice, it failed to do so in 5-HT2A(-/-) mutants. These electrophysiological impairments were associated with a decreased ability of the chronic administration of fluoxetine to stimulate hippocampal plasticity and to produce antidepressant-like activities. Genetic loss of the 5-HT2A receptor compromised the activity of chronic treatment with SSRIs, making this receptor a putative marker to predict ADs response.

Dose-dependent response of a benthic system to biodeposition from suspended blue mussel (Mytilus edulis) culture.

This study reports the results of a field experiment using benthic mesocosms that examined dose-dependent effects of mussel biodeposition on the benthic environment. Mesocosms were placed in the natural sea bottom and subjected to one of eight levels of biodeposition (from 0 to 1400 mussels m⁻²). Most analyses indicated non-linear (i.e., threshold) effects. Sediment characteristics changed significantly between 200 and 400 mussels m⁻² as did multivariate community structure. Community structure effects were characterised by changes in abundances of species that are very sensitive or tolerant to organic loading. The multivariate AZTI Marine Biotic Index (M-AMBI) indicated that the benthic status changed from High to Good in all mesocosms receiving biodeposits. Sediments acted as a sink for oxygen (O2), but results suggest O2 sediment demand was not sensitive enough to evaluate organic loading impacts. Results from this and improved experiments can be used to determine the environmental carrying capacity of sites for bivalve culture.