Genotype by environment interaction for grain yield in spring barley using additive main effects and multiplicative interaction model

Monoculture and use of disease resistant varieties on large scale usually leads to selection of new pathogen races able to overcome the resistance. The use of variety mixtures can significantly improve the control of the disease and provides stable yield among different environments. The objective of this study was to assess genotype by environment interaction for grain yield in spring barley genotypes grown in two places different in terms of soil and meteorological conditions by the additive main effects and multiplicative interaction model. The study comprised 25 spring barley genotypes (five cultivars: Basza, Blask, Skarb, Rubinek and Antek, and 20, two- and three-component mixtures), analyzed in eight environments (compilations of two locations and four years) through field trials arranged in a randomized complete block design, with three replicates. Grain yield of the tested genotypes varied from 32.88 to 74.31 dt/ha throughout the eight environments, with an average of 54.69 dt/ha. In the variance analysis, 68.80% of the total grain yield variation was explained by environment, 6.20% by differences between genotypes, and 7.76% by genotype by environment interaction. Grain yield is highly influenced by environmental factors

MarrowQuant Across Aging and Aplasia: A Digital Pathology Workflow for Quantification of Bone Marrow Compartments in Histological Sections.

The bone marrow (BM) exists heterogeneously as hematopoietic/red or adipocytic/yellow marrow depending on skeletal location, age, and physiological condition. Mouse models and patients undergoing radio/chemotherapy or suffering acute BM failure endure rapid adipocytic conversion of the marrow microenvironment, the so-called "red-to-yellow" transition. Following hematopoietic recovery, such as upon BM transplantation, a "yellow-to-red" transition occurs and functional hematopoiesis is restored. Gold Standards to estimate BM cellular composition are pathologists' assessment of hematopoietic cellularity in hematoxylin and eosin (H&E) stained histological sections as well as volumetric measurements of marrow adiposity with contrast-enhanced micro-computerized tomography (CE-μCT) upon osmium-tetroxide lipid staining. Due to user-dependent variables, reproducibility in longitudinal studies is a challenge for both methods. Here we report the development of a semi-automated image analysis plug-in, MarrowQuant, which employs the open-source software QuPath, to systematically quantify multiple bone components in H&E sections in an unbiased manner. MarrowQuant discerns and quantifies the areas occupied by bone, adipocyte ghosts, hematopoietic cells, and the interstitial/microvascular compartment. A separate feature, AdipoQuant, fragments adipocyte ghosts in H&E-stained sections of extramedullary adipose tissue to render adipocyte area and size distribution. Quantification of BM hematopoietic cellularity with MarrowQuant lies within the range of scoring by four independent pathologists, while quantification of the total adipocyte area in whole bone sections compares with volumetric measurements. Employing our tool, we were able to develop a standardized map of BM hematopoietic cellularity and adiposity in mid-sections of murine C57BL/6 bones in homeostatic conditions, including quantification of the highly predictable red-to-yellow transitions in the proximal section of the caudal tail and in the proximal-to-distal tibia. Additionally, we present a comparative skeletal map induced by lethal irradiation, with longitudinal quantification of the "red-to-yellow-to-red" transition over 2 months in C57BL/6 femurs and tibiae. We find that, following BM transplantation, BM adiposity inversely correlates with kinetics of hematopoietic recovery and that a proximal to distal gradient is conserved. Analysis of in vivo recovery through magnetic resonance imaging (MRI) reveals comparable kinetics. On human trephine biopsies MarrowQuant successfully recognizes the BM compartments, opening avenues for its application in experimental, or clinical contexts that require standardized human BM evaluation

Raman microspectroscopy reveals unsaturation heterogeneity at the lipid droplet level and validates an in vitro model of bone marrow adipocyte subtypes

Bone marrow adipocytes (BMAds) constitute the most abundant stromal component of adult human BM. Two subtypes of BMAds havebeen described, the more labile regulated adipocytes (rBMAds) and the more stable constitutive adipocytes (cBMAds), which develop earlier and are more resilient to environmental and metabolic disruptions. In vivo, rBMAds are enriched in saturated fatty acids, contain smaller lipid droplets (LDs) and more readily provide hematopoietic support than their cBMAd counterparts. Mouse models have been used for BMAds research, but isolation of primary BMAds presents many challenges, and thus in vitro models remain the current standard to study nuances of adipocyte differentiation. No in vitro model has been described for the study of rBMAds/cBMAds.Here, we present an in vitro model of BM adipogenesis with differential rBMAd and cBMAd-like characteristics. We used OP9 BM stromal cells derived from a (C57BL/6xC3H)F2-op/op mouse, which have been extensively characterized as feeder layer in hematopoiesis research. We observed similar canonical adipogenesis transcriptional signatures for spontaneously-differentiated (sOP9) and induced (iOP9) cultures, while fatty acid composition and desaturase expression differed at the population level. To resolve differences at the single adipocyte level we show that Raman microspectroscopy presents a high-resolution method for studying adipogenesis in vitro in a label-free manner, with resolution to individual LDs in this model. We find sOP9 adipocytes have lower unsaturation ratios, smaller LDs and higher hematopoietic support than iOP9 adipocytes, thus functionally resembling rBMAds and cBMAds, respectively. Validation in human samples confirms a higher unsaturation ratio for lipids extracted from stable cBMAds (femoral head upon hip-replacement surgery) versus labile rBMAds (iliac crest after chemotherapy). Moreover, the 16:1/16:0 fatty acid unsaturation ratio, already shown to discriminate cBMAds from rBMAd in rabbit and rat marrow, was validated in both the OP9 model in vitro system and in human samples. We expect our model will be useful for cBMAd and rBMAd studies, particularly where isolation of primary BMAds is a limiting step.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Blumeria graminis f. sp. hordei virulence frequency and the powdery mildew incidence on spring barley in the Wielkopolska province

Powdery mildew caused by fungi Blumeria graminis f. sp. hordei is one of the most common barley diseases in Polish meteorological conditions. The powdery mildew fungus is made up of different races and forms that are highly specialized. Barley cultivars might be resistant to a certain race of the mildew fungus, but susceptible to another race. Development of the disease is rapid in temperatures from 12 to 20°C, and in humid weather. The aim of the two-year experiment was to assess B. graminis f. sp. hordei virulence frequency and powdery mildew occurrence on five spring barley cultivars. Virulence frequency of the pathogen depended on place and term of exposition. The occurrence of powdery mildew on spring barley cultivars depended on virulence frequency of the pathogen and weather conditions

A mildew infection resistance study of winter barley varieties and their mixtures by the logistic model

Biological diversity within a mixture field allows for better use of habitat and agro-tech- nical conditions by the mixtures, which can be seen by higher and more stable yields than varieties sown separately. Our studies were conducted in the growing seasons 2011/2012–2014/2015 as field experiments with four winter barley varieties (Bombaj, Gil, Gregor, Bażant) and three, two- and three-component mixtures (Bombaj/Gil, Bombaj/Gre- gor, Gil/Gregor/Bażant). Seven different chemical treatments with fungicides were applied. The aim of this study was to compare the different varieties of winter barley with their mix- tures for resistance to powdery mildew infection. To achieve this aim the logistic model for the analysis of data was used. Of the varieties under consideration, the best and the most re- sistant variety was Gregor, while the weakest and the most susceptible to diseases (powdery mildew) was Gil. This variety was also significantly weaker than any of the other mixtures taken into account. Moreover, it was so weak that when it was included in mixtures with other varieties, it weakened these mixtures as well

Bone marrow adiposity and the hematopoietic niche: A historical perspective of reciprocity, heterogeneity, and lineage commitment.

Here we review the current knowledge on bone marrow adipocytes (BMAds) as active contributors to the regulation of the hematopoietic niche, and as potentially pivotal players in the progression of hematological malignancies. We highlight the hierarchical and functional heterogeneity of the adipocyte lineage within the bone marrow, and how potentially different contexts dictate their interactions with hematopoietic populations. Growing evidence associates the adipocyte lineage with important functions in hematopoietic regulation within the BM niche. Initially proposed to serve as negative regulators of the hematopoietic microenvironment, studies have also demonstrated that BMAds positively influence the survival and maintenance of hematopoietic stem cells (HSCs). These seemingly incongruous findings may at least be partially explained by stage-specificity across the adipocytic differentiation axis and by BMAds subtypes, suggesting that the heterogeneity of these populations allows for differential context-based interactions. One such distinction relies on the location of adipocytes. Constitutive bone marrow adipose tissue (cBMAT) historically associates to the "yellow" marrow containing so-called "stable" BMAs larger in size, less responsive to stimuli, and linked to HSC quiescence. On the other hand, regulated bone marrow adipose tissue (rBMAT)-associated adipocytes, also referred to as "labile" are smaller, more responsive to hematopoietic demand and strategically situated in hematopoietically active regions of the skeleton. Here we propose a model where the effect of distinct BM stromal cell populations (BMSC) in hematopoiesis is structured along the BMSC-BMAd differentiation axis, and where the effects on HSC maintenance versus hematopoietic proliferation are segregated. In doing so, it is possible to explain how recently identified, adipocyte-primed leptin receptor-expressing, CXCL12-high adventitial reticular cells (AdipoCARs) and marrow adipose lineage precursor cells (MALPs) best support active hematopoietic cell proliferation, while adipose progenitor cells (APCs) and maturing BMAd gradually lose the capacity to support active hematopoiesis, favoring HSC quiescence. Implicated soluble mediators include MCP-1, PAI-1, NRP1, possibly DPP4 and limiting availability of CXCL12 and SCF. How remodeling occurs within the BMSC-BMAd differentiation axis is yet to be elucidated and will likely unravel a three-way regulation of the hematopoietic, bone, and adipocytic compartments orchestrated by vascular elements. The interaction of malignant hematopoietic cells with BMAds is precisely contributing to unravel specific mechanisms of remodeling. BMAds are important operative components of the hematopoietic microenvironment. Their heterogeneity directs their ability to exert a range of regulatory capacities in a manner dependent on their hierarchical, spatial, and biological context. This complexity highlights the importance of (i) developing experimental tools and nomenclature adapted to address stage-specificity and heterogeneity across the BMSC-BMAd differentiation axis when reporting effects in hematopoiesis, (ii) interpreting gene reporter studies within this framework, and (iii) quantifying changes in all three compartments (hematopoiesis, adiposity and bone) when addressing interdependency

Cryogel-based Injectable 3D Microcarrier Co-culture for Support of Hematopoietic Progenitor Niches.

Although hematopoietic stem cell (HSC) transplantation can restore functional hematopoiesis upon immune or chemotherapy-induced bone marrow failure, complications often arise during recovery, leading to up to 25% transplant-related mortality in treated patients. In hematopoietic homeostasis and regeneration, HSCs in the bone marrow give rise to the entirety of cellular blood components. One of the challenges in studying hematopoiesis is the ability to successfully mimic the relationship between the stroma and hematopoietic stem and progenitor cells (HSPCs). This study and the described protocols propose an advantageous method for culturing and assessing stromal hematopoietic support in three dimensions, representing a simplified in vitro model of the bone marrow niche that can be transplanted in vivo by injection. By co-culturing OP9 bone marrow-derived stromal cells (BMSCs) and cKit <sup>+</sup> Sca-1 <sup>+</sup> Lin <sup>-</sup> (KLS <sup>+</sup> ) HSPCs on collagen-coated carboxymethylcellulose scaffolds for 2 weeks in the absence of cytokines, we established a methodology for in vivo subcutaneous transplantation. With this model we were able to detect early signs of extramedullary hematopoiesis. This work can be useful for studying various stromal cell populations in co-culture, as well as simple transfer by injection of these scaffolds in vivo for heterotopic regeneration of the marrow microenvironment. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Isolation of HSPCs from mice Basic Protocol 2: Co-seeding of HSPCs and BMSCs on collagen-coated CCMs Basic Protocol 3: Maintenance, real-time imaging, and analysis of co-seeded scaffolds Basic Protocol 4: End-point analysis of co-seeded scaffolds using flow cytometry and CFU assays Basic Protocol 5: Transplantation of scaffolds by subcutaneous injection Support Protocol: Preparation of custom scaffold drying device