Locating QTL conferring resistance against net blotch, leaf rust, and stripe rust in the wild barley nested association mapping (NAM) population HEB-25

Net blotch, caused by the fungus Pyrenophora teres f. teres, Puccinia hordei, causing leaf rust, and Puccinia striiformis f. sp. hordei, the causal agent of stripe rust, are important fungal diseases of barley with the potential to cause severe yield losses and a reduction in feed and malting quality. The identification of QTL conferring resistance is the basis for targeted breeding approaches aiming to improve resistance of modern barley cultivars against these fungi. Initial domestication from its wild progenitor Hordeum vulgare subsp. spontaneum and extensive breeding resulted in a loss of genetic diversity in modern elite barley varieties. Many modern barley varieties are similar in their genotype resulting in an increased risk of occurrence of severe epidemics. There is an urgent need to broaden the genetic basis of resistance of modern barley cultivars to ensure a stable production. Wild barley accessions possessing high allelic richness have shown to be a valuable source of resistance alleles no longer present in the current breeding pool. In the framework of this thesis, the NAM population HEB-25 was utilized to detect QTL conferring resistance against net blotch, leaf rust, and stripe rust. Screening of HEB-25 in two-year field trials revealed the presence of a high genetic diversity within HEB-25 and allowed for the identification of HEB-lines with a high degree of resistance to one or more of the evaluated fungi. NAM applying the 9k iSelect barley chip performed independently for all three fungi resulted in the identification of a high number of QTL conferring resistance on all chromosomes with predominantly small effect. In case of net blotch six QTL, eight QTL for stripe rust and two QTL for leaf rust, are considered novel showing no overlap with previously reported resistance QTL. Estimation of parent-specific QTL effects indicates the presence of alleles with increasing or decreasing effect on genotype resistance, respectively. Leucine-rich repeat, NB-ARC, and serine/threonine-protein kinase-like genes were found at high frequency in the QTL intervals and due to their important role in plant defense response represent putative candidate genes causing the QTL effect. HEB-25 showed to be well suited for the detection of QTL conferring resistance to net blotch, leaf rust, or stripe rust and represents a valuable source for improving genetic diversity and resistance of modern barley cultivars against these fungi.Net blotch, caused by the fungus Pyrenophora teres f. teres, Puccinia hordei, causing leaf rust, and Puccinia striiformis f. sp. hordei, the causal agent of stripe rust, are important fungal diseases of barley with the potential to cause severe yield losses and a reduction in feed and malting quality. The identification of QTL conferring resistance is the basis for targeted breeding approaches aiming to improve resistance of modern barley cultivars against these fungi. Initial domestication from its wild progenitor Hordeum vulgare subsp. spontaneum and extensive breeding resulted in a loss of genetic diversity in modern elite barley varieties. Many modern barley varieties are similar in their genotype resulting in an increased risk of occurrence of severe epidemics. There is an urgent need to broaden the genetic basis of resistance of modern barley cultivars to ensure a stable production. Wild barley accessions possessing high allelic richness have shown to be a valuable source of resistance alleles no longer present in the current breeding pool. In the framework of this thesis, the NAM population HEB-25 was utilized to detect QTL conferring resistance against net blotch, leaf rust, and stripe rust. Screening of HEB-25 in two-year field trials revealed the presence of a high genetic diversity within HEB-25 and allowed for the identification of HEB-lines with a high degree of resistance to one or more of the evaluated fungi. NAM applying the 9k iSelect barley chip performed independently for all three fungi resulted in the identification of a high number of QTL conferring resistance on all chromosomes with predominantly small effect. In case of net blotch six QTL, eight QTL for stripe rust and two QTL for leaf rust, are considered novel showing no overlap with previously reported resistance QTL. Estimation of parent-specific QTL effects indicates the presence of alleles with increasing or decreasing effect on genotype resistance, respectively. Leucine-rich repeat, NB-ARC, and serine/threonine-protein kinase-like genes were found at high frequency in the QTL intervals and due to their important role in plant defense response represent putative candidate genes causing the QTL effect. HEB-25 showed to be well suited for the detection of QTL conferring resistance to net blotch, leaf rust, or stripe rust and represents a valuable source for improving genetic diversity and resistance of modern barley cultivars against these fungi

Metabolome Profiling Supports the Key Role of the Spike in Wheat Yield Performance

Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction.This work was supported by the Spanish Ministry of Economy and Competitiveness (MEC) [grant number AGL2016-76527- R]. We also acknowledge EIG CONCERT-Japan (EC) / PCIN-2017-063 (MINECO, Spain) project

Metabolome profiling supports the key role of the spike in wheat yield performance

Although the relevance of spike bracts in stress acclimation and contribution to wheat yield was recently revealed, the metabolome of this organ and its response to water stress is still unknown. The metabolite profiles of flag leaves, glumes and lemmas were characterized under contrasting field water regimes in five durum wheat cultivars. Water conditions during growth were characterized through spectral vegetation indices, canopy temperature and isotope composition. Spike bracts exhibited better coordination of carbon and nitrogen metabolisms than the flag leaves in terms of photorespiration, nitrogen assimilation and respiration paths. This coordination facilitated an accumulation of organic and amino acids in spike bracts, especially under water stress. The metabolomic response to water stress also involved an accumulation of antioxidant and drought tolerance related sugars, particularly in the spikes. Furthermore, certain cell wall, respiratory and protective metabolites were associated with genotypic outperformance and yield stability. In addition, grain yield was strongly predicted by leaf and spike bracts metabolomes independently. This study supports the role of the spike as a key organ during wheat grain filling, particularly under stress conditions and provides relevant information to explore new ways to improve wheat productivity including potential biomarkers for yield prediction

Psychological outcomes in advanced cancer patients after receiving genomic tumor profiling results

Background: Comprehensive tumor genomic profiling (CGP) offers hope for personalized treatment for cancer patients when other treatment options have been exhausted. However, receipt of nonactionable or ambiguous results could be an ongoing source of distress. We investigated patterns of hope, anxiety, depression, and CGP-specific anxiety in advanced cancer patients after receiving CGP results and 2–3months later. Method: Participants were enrolled in a longitudinal psychosocial substudy, embedded in the Molecular Screening and Therapeutics Program, and had advanced solid cancers of any histological type with sufficient and accessible tissue for CGP. At T0 (before receiving CGP results), 1,431 participants completed sociodemographic, disease and psychosocial measures. At T1 (1–4 weeks after receiving CGP results) and T2 (2–3 months post-T1), 374 participants completed psychological outcome measures. Predictors of outcomes at T2 were identified using multinomial logistic regression. Results: Approximately 75% of participants did not experience significant hopelessness or distress at T1 and T2.Hope decreased by T2, yet general anxiety and CGP-specific anxiety also decreased. Receiving actionable results did not impact psychological outcomes at T2. At T2, lower hope, and higher anxiety, depression and CGP-specific anxiety were associated with lower self-efficacy. Psychological and demo-graphic factors (age, socioeconomic status, language, medical occupation, urban living, family history of cancer) independently predicted one or more psychological trajectories. Worse health status and perceived susceptibility to cancer progression predicted hope and anxiety trajectories. Conclusion: Further research on interventions to best support patients undergoing CGP with high anxiety, hopelessness, fear of cancer progression, and poorer health is urgently needed

Defining durum wheat ideotypes adapted to Mediterranean environments through remote sensing traits

An acceleration of the genetic advances of durum wheat, as a major crop for the Mediterranean region, is required, but phenotyping still represents a bottleneck for breeding. This study aims to define durum wheat ideotypes under Mediterranean conditions by selecting the most suitable phenotypic remote sensing traits among different ones informing on characteristics related with leaf pigments/photosynthetic status, crop water status, and crop growth/green biomass. A set of 24 post–green revolution durum wheat cultivars were assessed in a wide set of 19 environments, accounted as the specific combinations of a range of latitudes in Spain, under different management conditions (water regimes and planting dates), through 3 consecutive years. Thus, red–green–blue and multispectral derived vegetation indices and canopy temperature were evaluated at anthesis and grain filling. The potential of the assessed remote sensing parameters alone and all combined as grain yield (GY) predictors was evaluated through random forest regression models performed for each environment and phenological stage. Biomass and plot greenness indicators consistently proved to be reliable GY predictors in all of the environments tested for both phenological stages. For the lowest-yielding environment, the contribution of water status measurements was higher during anthesis, whereas, for the highest-yielding environments, better predictions were reported during grain filling. Remote sensing traits measured during the grain filling and informing on pigment content and photosynthetic capacity were highlighted under the environments with warmer conditions, as the late-planting treatments. Overall, canopy greenness indicators were reported as the highest correlated traits for most of the environments and regardless of the phenological moment assessed. The addition of carbon isotope composition of mature kernels was attempted to increase the accuracies, but only a few were slightly benefited, as differences in water status among cultivars were already accounted by the measurement of canopy temperature

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus

Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs. Cis-acting SNPs of hippocampal meQTLs and eQTLs significantly overlap schizophrenia-associated SNPs. Correlations of CpG methylation and RNA expression are found for 34 genes. Our comprehensive maps of cis-acting hippocampal meQTLs and eQTLs provide a link between disease-associated SNPs and the regulatory genome that will improve the functional interpretation of non-coding genetic variants in the molecular genetic dissection of brain disorders