Estimating number of resistance genes to root-legion nematodes from synthetic hexaploids wheat lines

Two root-lesion nematode species (Pratylenchus thornei and P. neglectus) reduce the value of Australian wheat production by AUD$123 million per year. Five synthetic hexaploid wheats (SHW) with resistance to both P. thornei and P. neglectus have been identified. To further investigate inheritance of resistance to P. thornei and P. neglectus, doubled haploid (DH) populations between these SHW and the susceptible Australian bread wheat cultivar Janz (90-120 individuals) were tested as 6 replicates in separate glasshouse experiments for each DH population and nematode species. Plants were grown singly in pots of 330 g of pasteurised vertosol containing 3,300 nematodes at constant soil temperature (22oC) and water tension (-2 cm). Analysis of variance (ANOVA) was conducted on nematode populations at 16 weeks of plant growth for each experiment with data transformed by ln(Pratylenchus sp./kg soil + c). Genetic variance (σ2g), heritability (h2) on a line mean basis and minimum number of effective resistance genes were calculated from the ANOVA. Heritabilities for the five DH populations ranged 0.88–0.92 for P. thornei and 0.59–0.88 for P. neglectus populations. The minimum number of resistance genes segregating in the populations was 4, 6, 3, 4 and 4 for P. thornei and 3, 4, 6, 4 and 4 for P. neglectus for the respective five SH parents (Yallaroi/AUS24152), (TAMD870167/AUS18913), CPI13842, CPI133859 and CPI133872. There was no correlation between P. thornei population density and P. neglectus for four of the DH populations and a low correlation for one (TAMD870167/AUS18913 x Janz DHs, r = 0.28, P < 0.01, n = 106). A small number of individual DHs with moderate resistance to both P. thornei and P. neglectus could be recovered from all populations, which will be valuable in pre-breeding for dual resistance. These results indicate that the genes conditioning resistance are mainly additive in action for each nematode species independently

Resistance to root-lesion nematode Pratylenchus neglectus identified in a new collection of two wild chickpea species (Cicer reticulatum and C. echinospermum) from Turkey

Abstract Chickpea (Cicer arietinum) is a major legume crop, with Australia being the second largest producer worldwide. Pratylenchus neglectus is a root-lesion nematode that invades, feeds and reproduces in roots of pulse and cereal crops. In Australia, chickpea and wheat (Triticum aestivum) are commonly grown in rotation and annual damage by P. neglectus accounts for large economic losses to both crops. Cultivated chickpea has narrow genetic diversity that limits the potential for improvement in resistance breeding. New collections of wild chickpea species, C. reticulatum and C. echinospermum, have substantially increased the previously limited world collection of wild Cicer germplasm and offer potential to widen the genetic diversity of cultivated chickpea through the identification of accessions with good resistance. This research assessed 243 C. reticulatum and 86 C. echinospermum accessions for response to P. neglectus in replicated experiments under controlled glasshouse conditions from 2013 and 2014 collection missions that were received, tested and analysed in two experimental sets. Multi-experiment analyses showed lower P. neglectus population densities in both sets of wild Cicer accessions tested than Australia's elite breeding cultivar PBA HatTrick at the significance level p < 0.05. Provisional resistance ratings were given to all genotypes tested in both experimental sets, with C. reticulatum accessions CudiB_008B and Kayat_066 rated as resistant in both Set 1 and Set 2. New sources of resistance to P. neglectus observed in this study can be introgressed into commercial chickpea cultivars to improve their resistance to this nematode

Constitutive and Induced Expression of Total Phenol and Phenol Oxidases in Wheat Genotypes Ranging in Resistance/Susceptibility to the Root-Lesion Nematode Pratylenchus thornei

Plant-derived phenolic compounds contribute to the defense against various pathogens, including root-lesion nematodes (Pratylenchus spp.). However, there are no reports on the role of phenolic compounds in wheat (Triticum aestivum) against Pratylenchus thornei. In this study, wheat genotypes ranging from resistant to very susceptible to P. thornei were used to investigate the level of total phenols and phenol oxidases, polyphenol oxidase (PPO), and peroxidase (POD) expressed in root tissues when grown in the presence and absence of P. thornei over time (2–8 weeks). Higher constitutive levels of total phenols were found in resistant synthetic hexaploid wheats CPI133872 (576 µg gallic acid equivalent (GAE)/g root) and CPI133859 (518 µg GAE/g root) at 8 weeks after sowing, compared with moderately resistant and susceptible genotypes (192 to 390 µg GAE/g root). The activity of PPO was induced in resistant (CPI133872) and moderately resistant (GS50a and its derivate QT8343) genotypes, becoming maximal at 4 weeks after P. thornei inoculation. The activity of POD was induced in CPI133872 at 6 weeks after P. thornei inoculation. Different genetic sources of resistance to P. thornei showed diverse defense mechanisms and differences in timing responses. The combined effects of total phenols and oxidative enzymes could be important for defense against P. thornei in some resistant wheat genotypes

A systematic review of the effects of arbuscular mycorrhizal fungi on root-lesion nematodes Pratylenchus spp.

Root-lesion nematodes (Pratylenchus spp.) and arbuscular mycorrhizal fungi (AMF) occupy the same ecological niche in the phytobiome of many agriculturally important crops. Arbuscular mycorrhizal fungi can enhance the resistance or tolerance of a plant to Pratylenchus and previous studies have been undertaken to investigate the relationship between these organisms. A restructuring of the AMF phylum Glomeromycota has reallocated the species into genera according to molecular analysis. A systematic review of the literature was synthesized to assess the interaction between Pratylenchus spp. and AMF using the revised classification. Plants inoculated with AMF generally exhibited greater tolerance as demonstrated by increased biomass under Pratylenchus pressure. Species of AMF fromthe order Diversisporales tended to increase Pratylenchus population densities compared to those from the order Glomerales. Species from the genera Funneliformis and Glomus had a reductive effect on Pratylenchus population densities. The interaction between AMF and Pratylenchus spp. showed variation in responses as a result of cultivar, crop species, and AMF species. Putative mechanisms involved in these interactions are discussed

Resistance to plant-parasitic nematodes in chickpea: current status and future perspectives

Plant-parasitic nematodes constrain chickpea (Cicer arietinum) production, with annual yield losses estimated to be 14% of total global production. Nematode species causing significant economic damage in chickpea include root-knot nematodes (Meloidogyne artiella, M. incognita, M. javanica), cyst nematode (Heterodera ciceri), and root-lesion nematode (Pratylenchus thornei). Reduced functionality of roots from nematode infestation leads to water stress and nutrient deficiency, which in turn lead to poor plant growth and reduced yield. Integration of resistant crops with appropriate agronomic practices is recognized as the safest and most practical, economic and effective control strategy for plant-parasitic nematodes. However, breeding for resistance to plant-parasitic nematodes has numerous challenges that originate from the narrow genetic diversity of the C. arietinum cultigen. While levels of resistance to M. artiella, H. ciceri and P. thornei have been identified in wild Cicer species that are superior to resistance levels in the C. arietinum cultigen, barriers to interspecific hybridization restrict the use of these crop wild relatives, as sources of nematode resistance. Wild Cicer species of the primary genepool, C. reticulatum and C. echinospermum, are the only species that have been used to introgress resistance genes into the C. arietinum cultigen. The availability of genomic resources, including genome sequence and re-sequence information, the chickpea reference set and mini-core collections, and new wild Cicer collections, provide unprecedented opportunities for chickpea improvement. This review surveys progress in the identification of novel genetic sources of nematode resistance in international germplasm collections and recommends genome-assisted breeding strategies to accelerate introgression of nematode resistance into elite chickpea cultivars

Transcriptome analysis reveals key genes associated with root‑lesion nematode Pratylenchus thornei resistance in chickpea

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (resistant advanced breeding line), PBA HatTrick (moderately resistant cultivar), and Kyabra (susceptible cultivar) were studied at 20 and 50 days post inoculation using the RNA-seq approach. On analyzing the 633.3 million reads generated, 962 differentially expressed genes (DEGs) were identified. Comparative analysis revealed that the majority of DEGs upregulated in the resistant genotype were downregulated in the moderately resistant and susceptible genotypes. Transcription factor families WRKY and bZIP were uniquely expressed in the resistant genotype. The genes Cysteine-rich receptor-like protein kinase 10, Protein lifeguard-like, Protein detoxification, Bidirectional sugar transporter Sugars Will Eventually be Exported Transporters1 (SWEET1), and Subtilisin-like protease were found to play cross-functional roles in the resistant chickpea genotype against P. thornei. The identified candidate genes for resistance to P. thornei in chickpea can be explored further to develop markers and accelerate the introgression of P. thornei resistance into elite chickpea cultivars

Co-Inhibition of BCL-W and BCL2 Restores Antiestrogen Sensitivity through BECN1 and Promotes an Autophagy-Associated Necrosis

BCL2 family members affect cell fate decisions in breast cancer but the role of BCL-W (BCL2L2) is unknown. We now show the integrated roles of the antiapoptotic BCL-W and BCL2 in affecting responsiveness to the antiestrogen ICI 182,780 (ICI; Fulvestrant Faslodex), using both molecular (siRNA; shRNA) and pharmacologic (YC137) approaches in three breast cancer variants; MCF-7/LCC1 (ICI sensitive), MCF-7/LCC9 (ICI resistant), and LY2 (ICI resistant). YC137 inhibits BCL-W and BCL2 and restores ICI sensitivity in resistant cells. Co-inhibition of BCL-W and BCL2 is both necessary and sufficient to restore sensitivity to ICI, and explains mechanistically the action of YC137. These data implicate functional cooperation and/or redundancy in signaling between BCL-W and BCL2, and suggest that broad BCL2 family member inhibitors will have greater therapeutic value than targeting only individual proteins. Whereas ICI sensitive MCF-7/LCC1 cells undergo increased apoptosis in response to ICI following BCL-W±BCL2 co-inhibition, the consequent resensitization of resistant MCF-7/LCC9 and LY2 cells reflects increases in autophagy (LC3 cleavage; p62/SQSTM1 expression) and necrosis but not apoptosis or cell cycle arrest. Thus, de novo sensitive cells and resensitized resistant cells die through different mechanisms. Following BCL-W+BCL2 co-inhibition, suppression of functional autophagy by 3-methyladenine or BECN1 shRNA reduces ICI-induced necrosis but restores the ability of resistant cells to die through apoptosis. These data demonstrate the plasticity of cell fate mechanisms in breast cancer cells in the context of antiestrogen responsiveness. Restoration of ICI sensitivity in resistant cells appears to occur through an increase in autophagy-associated necrosis. BCL-W, BCL2, and BECN1 integrate important functions in determining antiestrogen responsiveness, and the presence of functional autophagy may influence the balance between apoptosis and necrosis

Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.

Bone Mineral Density (BMD) is a highly heritable trait, but genome-wide association studies have identified few genetic risk factors. Epidemiological studies suggest associations between BMD and several traits and diseases, but the nature of the suggestive comorbidity is still unknown. We used a novel genetic pleiotropy-informed conditional False Discovery Rate (FDR) method to identify single nucleotide polymorphisms (SNPs) associated with BMD by leveraging cardiovascular disease (CVD) associated disorders and metabolic traits. By conditioning on SNPs associated with the CVD-related phenotypes, type 1 diabetes, type 2 diabetes, systolic blood pressure, diastolic blood pressure, high density lipoprotein, low density lipoprotein, triglycerides and waist hip ratio, we identified 65 novel independent BMD loci (26 with femoral neck BMD and 47 with lumbar spine BMD) at conditional FDR < 0.01. Many of the loci were confirmed in genetic expression studies. Genes validated at the mRNA levels were characteristic for the osteoblast/osteocyte lineage, Wnt signaling pathway and bone metabolism. The results provide new insight into genetic mechanisms of variability in BMD, and a better understanding of the genetic underpinnings of clinical comorbidity

Cerebral small vessel disease genomics and its implications across the lifespan

White matter hyperintensities (WMH) are the most common brain-imaging feature of cerebral small vessel disease (SVD), hypertension being the main known risk factor. Here, we identify 27 genome-wide loci for WMH-volume in a cohort of 50,970 older individuals, accounting for modification/confounding by hypertension. Aggregated WMH risk variants were associated with altered white matter integrity (p = 2.5×10-7) in brain images from 1,738 young healthy adults, providing insight into the lifetime impact of SVD genetic risk. Mendelian randomization suggested causal association of increasing WMH-volume with stroke, Alzheimer-type dementia, and of increasing blood pressure (BP) with larger WMH-volume, notably also in persons without clinical hypertension. Transcriptome-wide colocalization analyses showed association of WMH-volume with expression of 39 genes, of which four encode known drug targets. Finally, we provide insight into BP-independent biological pathways underlying SVD and suggest potential for genetic stratification of high-risk individuals and for genetically-informed prioritization of drug targets for prevention trials.Peer reviewe

SUGAR-DIP trial: Oral medication strategy versus insulin for diabetes in pregnancy, study protocol for a multicentre, open-label, non-inferiority, randomised controlled trial

Introduction In women with gestational diabetes mellitus (GDM) requiring pharmacotherapy, insulin was the established first-line treatment. More recently, oral glucose lowering drugs (OGLDs) have gained popularity as a patient-friendly, less expensive and safe alternative. Monotherapy with metformin or glibenclamide (glyburide) is incorporated in several international guidelines. In women who do not reach sufficient glucose control with OGLD monotherapy, usually insulin is added, either with or without continuation of OGLDs. No reliable data from clinical trials, however, are available on the effectiveness of a treatment strategy using all three agents, metformin, glibenclamide and insulin, in a stepwise approach, compared with insulin-only therapy for improving pregnancy outcomes. In this trial, we aim to assess the clinical effectiveness, cost-effectiveness and patient experience of a stepwise combined OGLD treatment protocol, compared with conventional insulin-based therapy for GDM. Methods The SUGAR-DIP trial is an open-label, multicentre randomised controlled non-inferiority trial. Participants are women with GDM who do not reach target glycaemic control with modification of diet, between 16 and 34 weeks of gestation. Participants will be randomised to either treatment with OGLDs, starting with metformin and supplemented as needed with glibenclamide, or randomised to treatment with insulin. In women who do not reach target glycaemic control with combined metformin and glibenclamide, glibenclamide will be substituted with insulin, while continuing metformin. The primary outcome will be the incidence of large-for-gestational-age infants (birth weight >90th percentile). Secondary outcome measures are maternal diabetes-related endpoints, obstetric complications, neonatal complications and cost-effectiveness analysis. Outcomes will be analysed according to the intention-to-treat principle. Ethics and dissemination The study protocol was approved by the Ethics Committee of the Utrecht University Medical Centre. Approval by the boards of management for all participating hospitals will be obtained. Trial results will be submitted for publication in peer-reviewed journals