Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments.

BACKGROUND: In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits were obtained through digital images measuring the root length at different depths. Two nearest-neighbor adjustments (M1 and M2) to model spatial variation were used for genetic parameter estimation and genomic prediction (GP). M1 and M2 used (co)variance structures and differed in the distance function to calculate between-neighbor correlations. M2 was the most developed adjustment, as accounted by the Euclidean distance between neighbors. RESULTS: The estimated heritabilities ([Formula: see text]) ranged from low to medium for root and above-ground traits. The genetic coefficient of variation ([Formula: see text]) ranged from 3.2 to 7.0% for above-ground and 4.7 to 10.4% for root traits, indicating good breeding potential for the measured traits. The highest [Formula: see text] observed for root traits revealed that significant genetic change in root development can be achieved through selection. We studied the genotype-by-water availability interaction, but no relevant interaction effects were detected. GP was assessed using leave-one-line-out (LOO) cross-validation. The predictive ability (PA) estimated as the correlation between phenotypes corrected by fixed effects and genomic estimated breeding values ranged from 0.33 to 0.49 for above-ground and 0.15 to 0.27 for root traits, and no substantial variance inflation in predicted genetic effects was observed. Significant differences in PA were observed in favor of M2. CONCLUSIONS: The significant [Formula: see text] and the accurate prediction of breeding values for above-ground and root traits revealed that developing genetically superior barley lines with improved root systems is possible. In addition, we found significant spatial variation in the experiment, highlighting the relevance of correctly accounting for spatial effects in statistical models. In this sense, the proposed nearest-neighbor adjustments are flexible approaches in terms of assumptions that can be useful for semi-field or field experiments.

Integrating a growth degree-days based reaction norm methodology and multi-trait modeling for genomic prediction in wheat.

Multi-trait and multi-environment analyses can improve genomic prediction by exploiting between-trait correlations and genotype-by-environment interactions. In the context of reaction norm models, genotype-by-environment interactions can be described as functions of high-dimensional sets of markers and environmental covariates. However, comprehensive multi-trait reaction norm models accounting for marker × environmental covariates interactions are lacking. In this article, we propose to extend a reaction norm model incorporating genotype-by-environment interactions through (co)variance structures of markers and environmental covariates to a multi-trait reaction norm case. To do that, we propose a novel methodology for characterizing the environment at different growth stages based on growth degree-days (GDD). The proposed models were evaluated by variance components estimation and predictive performance for winter wheat grain yield and protein content in a set of 2,015 F6-lines. Cross-validation analyses were performed using leave-one-year-location-out (CV1) and leave-one-breeding-cycle-out (CV2) strategies. The modeling of genomic [SNPs] × environmental covariates interactions significantly improved predictive ability and reduced the variance inflation of predicted genetic values for grain yield and protein content in both cross-validation schemes. Trait-assisted genomic prediction was carried out for multi-trait models, and it significantly enhanced predictive ability and reduced variance inflation in all scenarios. The genotype by environment interaction modeling via genomic [SNPs] × environmental covariates interactions, combined with trait-assisted genomic prediction, boosted the benefits in predictive performance. The proposed multi-trait reaction norm methodology is a comprehensive approach that allows capitalizing on the benefits of multi-trait models accounting for between-trait correlations and reaction norm models exploiting high-dimensional genomic and environmental information.

Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis.

KEY MESSAGE: Including additive and additive-by-additive epistasis in a NOIA parametrization did not yield orthogonal partitioning of genetic variances, nevertheless, it improved predictive ability in a leave-one-out cross-validation for wheat grain yield. Additive-by-additive epistasis is the principal non-additive genetic effect in inbred wheat lines and is potentially useful for developing cultivars based on total genetic merit; nevertheless, its practical benefits have been highly debated. In this article, we aimed to (i) evaluate the performance of models including additive and additive-by-additive epistatic effects for variance components (VC) estimation of grain yield in a wheat-breeding population, and (ii) to investigate whether including additive-by-additive epistasis in genomic prediction enhance wheat grain yield predictive ability (PA). In total, 2060 sixth-generation (F6) lines from Nordic Seed A/S breeding company were phenotyped in 21 year-location combinations in Denmark, and genotyped using a 15 K-Illumina-BeadChip. Three models were used to estimate VC and heritability at plot level: (i) "I-model" (baseline), (ii) "I + GA-model", extending I-model with an additive genomic effect, and (iii) "I + GA + GAA-model", extending I + GA-model with an additive-by-additive genomic effects. The I + GA-model and I + GA + GAA-model were based on the Natural and Orthogonal Interactions Approach (NOIA) parametrization. The I + GA + GAA-model failed to achieve orthogonal partition of genetic variances, as revealed by a change in estimated additive variance of I + GA-model when epistasis was included in the I + GA + GAA-model. The PA was studied using leave-one-line-out and leave-one-breeding-cycle-out cross-validations. The I + GA + GAA-model increased PA significantly (16.5%) compared to the I + GA-model in leave-one-line-out cross-validation. However, the improvement due to including epistasis was not observed in leave-one-breeding-cycle-out cross-validation. We conclude that epistatic models can be useful to enhance predictions of total genetic merit. However, even though we used the NOIA parameterization, the variance partition into orthogonal genetic effects was not possible.

Genomic prediction for grain yield and micro-environmental sensitivity in winter wheat.

Individuals within a common environment experience variations due to unique and non-identifiable micro-environmental factors. Genetic sensitivity to micro-environmental variation (i.e. micro-environmental sensitivity) can be identified in residuals, and genotypes with lower micro-environmental sensitivity can show greater resilience towards environmental perturbations. Micro-environmental sensitivity has been studied in animals; however, research on this topic is limited in plants and lacking in wheat. In this article, we aimed to (i) quantify the influence of genetic variation on residual dispersion and the genetic correlation between genetic effects on (expressed) phenotypes and residual dispersion for wheat grain yield using a double hierarchical generalized linear model (DHGLM); and (ii) evaluate the predictive performance of the proposed DHGLM for prediction of additive genetic effects on (expressed) phenotypes and its residual dispersion. Analyses were based on 2,456 advanced breeding lines tested in replicated trials within and across different environments in Denmark and genotyped with a 15K SNP-Illumina-BeadChip. We found that micro-environmental sensitivity for grain yield is heritable, and there is potential for its reduction. The genetic correlation between additive effects on (expressed) phenotypes and dispersion was investigated, and we observed an intermediate correlation. From these results, we concluded that breeding for reduced micro-environmental sensitivity is possible and can be included within breeding objectives without compromising selection for increased yield. The predictive ability and variance inflation for predictions of the DHGLM and a linear mixed model allowing heteroscedasticity of residual variance in different environments (LMM-HET) were evaluated using leave-one-line-out cross-validation. The LMM-HET and DHGLM showed good and similar performance for predicting additive effects on (expressed) phenotypes. In addition, the accuracy of predicting genetic effects on residual dispersion was sufficient to allow genetic selection for resilience. Such findings suggests that DHGLM may be a good choice to increase grain yield and reduce its micro-environmental sensitivity.

Sustained virological response to direct-acting antiviral regimens reduces the risk of hepatocellular carcinoma in HIV/HCV-coinfected patients with cirrhosis.

Objectives: To assess the impact of all-oral direct-acting antiviral agent (DAA) regimens on the risk of hepatocellular carcinoma (HCC) in HIV/HCV-coinfected patients with cirrhosis. Methods: This was a multicentre prospective cohort study recruiting HIV/HCV-coinfected patients with a new diagnosis of compensated cirrhosis. Patients were followed up until HCC, death or the censoring date (March 2017). The primary endpoint was the emergence of HCC. The incidence rate (IR) (95% CI) of HCC in different groups was computed. Time-to-event analyses were performed to identify predictors of HCC emergence. Results: The study included 495 HIV/HCV-coinfected patients with cirrhosis. After a median (IQR) follow-up of 59 (27-84) months, 22 (4.4%; 95% CI 2.6-6.3) patients developed an HCC. The IR (95% CI) of HCC was 0.93 (0.06-1.42) per 100 person-years (PY). Three hundred and three (61%) patients achieved sustained virological response (SVR) during follow-up, 79 after interferon (IFN)-based regimens and 224 after an all-oral DAA regimen. The IR (95% CI) of HCC after all-oral DAA was 0.35 (0.14-0.85) per 100 PY whereas it was 1.79 (1.11-2.88) per 100 PY in the remaining cohort (P = 0.0005). When only patients with SVR were considered, the IR (95% CI) of HCC after all-oral DAA was 0.32 (0.12-0.86) whereas it was 0 per 100 PY among those with SVR after IFN-based therapies (P = 0.27). Achieving SVR with an all-oral DAA regimen during follow-up was independently associated with a lower risk of HCC emergence (subhazard ratio 0.264; 95% CI 0.070-0.991; P = 0.049). Conclusions: SVR with all-oral DAA regimens reduces the risk of HCC in HIV/HCV-coinfected patients with compensated cirrhosis.

Hepatocellular carcinoma after sustained virological response with interferon-free regimens in HIV/hepatitis C virus-coinfected patients.

OBJECTIVE: To assess the possible association between the use of direct antiviral agents (DAA) and the risk of hepatocellular carcinoma (HCC) in HIV/hepatitis C virus (HCV)-coinfected patients. METHODS: The GEHEP-002 cohort recruits HCC cases in HIV-infected patients from 32 centers from Spain. Three analyses were performed: the proportion of HCC cases after sustained virological response (SVR) and the evolution of this proportion over time, the frequency of HCC after SVR in HIV/HCV-coinfected patients with cirrhosis, and the probability of HCC recurrence after curative therapies among those undergoing HCV therapy. RESULTS: Forty-two (13%) out of 322 HCC cases in HIV/HCV-coinfected patients occurred after SVR. Twenty-eight (10%) out of 279 HCC cases diagnosed during the years of use of IFN-based regimens occurred after SVR whereas this occurred in 14 (32.6%) out of the 43 HCC cases diagnosed in the all-oral DAA period (P < 0.0001). One thousand, three hundred and thirty-seven HIV/HCV-coinfected patients with cirrhosis achieved SVR in the cohort. The frequency of HCC after SVR declined from 15% among those cured with pegylated-IFN with ribavirin to 1.62 and 0.87% among those cured with DAA with and without IFN, respectively. In patients with previous HCC treated with curative therapies, HCC recurrence occurred in two (25%) out of eight patients treated with IFN-based regimens and four (21%) out of 19 treated with DAA-IFN-free regimens (P = 1.0). CONCLUSION: The frequency of HCC emergence after SVR has not increased after widespread use of DAA in HIV/HCV-coinfected patients. DAA do not seem to impact on HCC recurrence in the short-term among those with previously treated HCC.

Changes in Liver Steatosis After Switching From Efavirenz to Raltegravir Among Human Immunodeficiency Virus-Infected Patients With Nonalcoholic Fatty Liver Disease.

BACKGROUND: Antiretroviral drugs with a lower potential to induce hepatic steatosis in human immunodeficiency virus (HIV) infection need to be identified. We compared the effect of switching efavirenz (EFV) to raltegravir (RAL) on hepatic steatosis among HIV-infected patients with nonalcoholic fatty liver disease (NAFLD) receiving EFV plus 2 nucleoside analogues. METHODS: HIV-infected patients on EFV plus tenofovir/emtricitabine or abacavir/lamivudine with NAFLD were randomized 1:1 to switch from EFV to RAL (400 mg twice daily), maintaining nucleoside analogues unchanged, or to continue with EFV plus 2 nucleoside analogues. At baseline, eligible patients should show controlled attenuation parameter (CAP) values ≥238 dB/m. Changes in hepatic steatosis at 48 weeks of follow-up over baseline levels were measured by CAP. RESULTS: Overall, 39 patients were included, and 19 of them were randomized to switch to RAL. At week 48, median CAP for the RAL group was 250 (Q1-Q3, 221-277) dB/m and 286 (Q1-Q3, 269-314) dB/m for the EFV group (P = .035). The median decrease in CAP values was -20 (Q1-Q3, -67 to 15) dB/m for the RAL arm and 30 (Q1-Q3, -17 to 49) dB/m for the EFV group (P = .011). CAP values <238 dB/m at week 48 were observed in 9 (47%) patients on RAL and 3 (15%) individuals on EFV (P = .029). CONCLUSIONS: After 48 weeks, HIV-infected individuals switching EFV to RAL showed decreases in the degree of hepatic steatosis, as measured by CAP, compared with those continuing with EFV. In addition, the proportion of patients without significant hepatic steatosis after 48 weeks was greater for those who switched to RAL. CLINICAL TRIALS REGISTRATION: NCT01900015.

Correction: Abacavir/Lamivudine plus Rilpivirine Is an Effective and Safe Strategy for HIV-1 Suppressed Patients: 48 Week Results of the SIMRIKI Retrospective Study.

[This corrects the article DOI: 10.1371/journal.pone.0164455.].

Liver stiffness predicts variceal bleeding in HIV/HCV-coinfected patients with compensated cirrhosis.

BACKGROUND: A liver stiffness below 21 kPa has a high negative predictive value to exclude the presence of esophageal varices at risk of bleeding in HIV/hepatitis C virus (HCV)-coinfected patients. Consequently, upper gastrointestinal endoscopy (UGE) for the screening of esophageal varices could be avoided in these patients. However, this strategy has not been widely accepted due to concerns about its safety. OBJECTIVE: To assess the ability of liver stiffness to predict the risk of portal hypertensive gastrointestinal bleeding (PHGB) in HIV/HCV-coinfected patients with compensated cirrhosis. METHODS: Prospective study of 446 HIV/HCV-coinfected patients with a new diagnosis of cirrhosis and no previous decompensation. All patients underwent a UGE for the screening of esophageal varices at entry in the cohort before November 2009. From this date, UGE was not recommended in patients with liver stiffness below 21 kPa. The time from diagnosis of cirrhosis to the emergence of PHGB was evaluated. RESULTS: After a median (quartile1-quartile3) follow-up of 49 (25-68) months, 15 (3.4%, 95% confidence interval 1.7-5%) patients developed a first PHGB episode. In all cases, baseline liver stiffness was at least 21 kPa. Thus, the negative predictive value of a liver stiffness below 21 kPa to predict PHGB during follow-up was 100%. At the time of the bleeding episode, liver stiffness was above this threshold in all patients. CONCLUSIONS: Liver stiffness identifies HIV/HCV-coinfected patients with compensated cirrhosis with a very low risk of PHGB. In fact, no individual with liver stiffness below 21 kPa developed this outcome. Our results confirm that UGE can be safely spared in patients with liver stiffness below 21 kPa.

Abacavir/Lamivudine plus Rilpivirine Is an Effective and Safe Strategy for HIV-1 Suppressed Patients: 48 Week Results of the SIMRIKI Retrospective Study.

OBJECTIVES: Based on data from clinical practice, we evaluated the effectiveness and safety of switching to abacavir/lamivudine plus rilpivirine (ABC/3TC+RPV) treatment in virologically suppressed HIV-1-infected patients. METHODS: We performed a multicenter, non-controlled, retrospective study of HIV-1-infected patients who switched treatment to ABC/3TC+RPV. Patients had an HIV-RNA <50 copies/mL for at least 24 weeks prior to changing treatments. The primary objective was HIV-1 RNA <50 copies/mL at week 48. Effectiveness was analyzed by intention-to-treat (ITT), missing = failure and on-treatment (OT) analyses. The secondary objectives analyzed were adverse effects changes in renal, hepatic or lipid profiles, changes in CD4+ cell count and treatment discontinuations. RESULTS: Of the 205 patients included, 75.6% were men and the median age was 49. At baseline, before switching to ABC/3TC+RPV, median time since HIV diagnosis was 13.1 years, median time with undetectable HIV-1 RNA was 6.2 years and median time of previous antiretroviral regimen was 3.1 years (48.3% patients were taking efavirenz and ABC/3TC was the most frequent backbone coformulation in 69.7% of patients). The main reasons for switching were drug toxicity/poor tolerability (60.5%) and simplification (20%). At week 48, the primary objective was achieved by 187 out of 205 (91.2%) patients by ITT analysis, and 187 out of 192 (97.4%) patients by OT analysis. The CD4+ lymphocyte count and CD4+ percentage increased significantly from baseline to week 48 by a median of 48 cells/µL (-50 to 189) and 1.2% (-1.3% to 4.1%), respectively, P<0.001. Thirty-eight adverse events (AE) were detected in 32 patients. Of these, 25 had no clear association with treatment. Three patients interrupted therapy due to AE. We observed a decrease in all lipid parameters, P<0.001, and a slight improvement in the glomerular filtration rate, P<0.01. Therapy was considered to have failed in 18 patients owing to virological failure (5 [2.4%]), toxicity/poor tolerability (4 [2%]), clinical decision (3 [1.5%]), loss to follow-up (3 [1.5%]), death (1 [0.5%]), and no clinical data (2 [1%]). CONCLUSIONS: The results of this study confirms that ABC/3TC+RPV is an effective, safe, and cost-effective option for the treatment of patients with virologically stable HIV-1 infection.

Low risk of liver decompensation among human immunodeficiency virus/hepatitis C virus-coinfected patients with mild fibrosis in the short term.

UNLABELLED: Liver fibrosis is used to make decisions about the timing of therapy against hepatitis C virus (HCV) in routine clinical practice, which should be based on the short-term likelihood of liver decompensations. Thus, we aimed at evaluating the risk of decompensations and death among human immunodeficiency virus (HIV)/HCV-coinfected individuals according to their baseline fibrosis classified by either liver biopsy or liver stiffness measurement (LSM). Patients coinfected with HIV/HCV, naive or without sustained virological response to HCV therapy, were included in this cohort. Fibrosis was classified by biopsy in 683 patients and by LSM in 1046 individuals. Reference categories were fibrosis stage 0 and LSM <6 kPa. For patients with biopsy, the adjusted subhazard ratio for decompensations and 95% confidence interval (95% CI) by fibrosis stage were as follows: stage 1, 2.3 (0.27-20.3), P = 0.443; stage 2, 2.8 (0.33-24), P = 0.345; stage 3, 4.91 (0.60-41), P = 0.137; stage 4, 9.89 (1.25-79.5), P = 0.030. For patients with LSM, the adjusted subhazard ratio and 95% CI by LSM category were as follows: 6-9.4 kPa, 1.89 (0.18-20.3), P = 0.599; 9.5-14.5 kPa, 6.59 (0.73-59.2), P = 0.092; ≥14.6 kPa, 59.5 (8.3-427), P < 0.0001. Regarding the risk of death, the adjusted hazard ratio and 95% CI for death by fibrosis stage were as follows: stage 1, 1.3 (0.4-4.11), P = 0.677; stage 2, 2.68 (0.86-8.36), P = 0.090; stage 3, 2.58 (0.82-8.15), P = 0.106; stage 4, 4.35 (1.43-13.3), P = 0.010. For patients with LSM, the adjusted hazard ratio and 95% CI for death by LSM were as follows: 6-9.4 kPa, 1.7 (0.63-4.79), P = 0.288; 9.5-14.5 kPa, 3.38 (1.2-9.5), P = 0.021; ≥14.6 kPa, 12.7 (4.9-33.6), P < 0.0001. CONCLUSION: Patients coinfected with HIV/HCV without advanced fibrosis are at very low risk of decompensations in the short term; deferral of HCV therapy for a few years and monitoring fibrosis progression is a safe option until cheaper, more effective, and more convenient HCV treatment becomes widely available.