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Soybean rust, caused by the fungal pathogen Phakopsora pachyrhizi, is an economically significant disease for soybean (Glycine max (L.) Merr.) production throughout the world. Genes for resistance ...

Kidney fibrosis is the hallmark of chronic kidney disease progression; however, at present no antifibrotic therapies exist1–3. The origin, functional heterogeneity and regulation of scar-forming cells that occur during human kidney fibrosis remain poorly understood1,2,4. Here, using single-cell RNA sequencing, we profiled the transcriptomes of cells from the proximal and non-proximal tubules of healthy and fibrotic human kidneys to map the entire human kidney. This analysis enabled us to map all matrix-producing cells at high resolution, and to identify distinct subpopulations of pericytes and fibroblasts as the main cellular sources of scar-forming myofibroblasts during human kidney fibrosis. We used genetic fate-tracing, time-course single-cell RNA sequencing and ATAC–seq (assay for transposase-accessible chromatin using sequencing) experiments in mice, and spatial transcriptomics in human kidney fibrosis, to shed light on the cellular origins and differentiation of human kidney myofibroblasts and their precursors at high resolution. Finally, we used this strategy to detect potential therapeutic targets, and identified NKD2 as a myofibroblast-specific target in human kidney fibrosis.

QTL analysis identified 16 QTLs, grouped in eight loci on seven soybean chromosomes that were associated with carbon isotope ratio (δ13C) in a biparental recombinant inbred population. Drought is a major limitation to soybean yield, and the frequency of drought stress is likely to increase under future climatic scenarios. Water use efficiency (WUE) is associated with drought tolerance, and carbon isotope ratio (δ13C) is positively correlated with WUE. In this study, 196 F6-derived recombinant inbred lines from a cross of PI 416997 (high WUE) × PI 567201D (low WUE) were evaluated in four environments to identify genomic regions associated with δ13C. There were positive correlations of δ13C values between different environments (0.67 ≤ r ≤ 0.78). Genotype, environment, and genotype × environment interactions had significant effects on δ13C. Narrow sense heritability of δ13C was 90% when estimated across environments. There was a total of 16 QTLs on seven chromosomes with individual QTLs explaining between 2.5 and 29.9% of the phenotypic variation and with additive effects ranging from 0.07 to 0.22‰. These 16 QTLs likely identified eight loci based on their overlapping confidence intervals. Of these eight loci, two loci on chromosome 20 (Gm20) were detected in at least three environments and were considered as stable QTLs. Additive QTLs on Gm20 showed epistatic interactions with 10 QTLs present across nine chromosomes. Five QTLs were identified across environments and showed significant QTL × environment interactions. These findings demonstrate that additive QTLs and QTL × QTL interactions play significant roles in genetic control of the δ13C trait. Markers flanking identified QTLs may facilitate marker-assisted selection to accumulate desirable QTLs to improve WUE and drought tolerance in soybean.

Nitrogen (N) plays a key role in plants because it is a major component of RuBisCO and chlorophyll. Hence, N is central to both the dark and light reactions of photosynthesis. Genotypic variation in canopy greenness provides insights into the variation of N and chlorophyll concentration, photosynthesis rates, and N2 fixation in legumes. The objective of this study was to identify significant loci associated with the intensity of greenness of the soybean [Glycine max (L.) Merr.] canopy as determined by the Dark Green Color Index (DGCI). A panel of 200 maturity group IV accessions was phenotyped for canopy greenness using DGCI in three environments. Association mapping identified 45 SNPs that were significantly (P ≤ 0.0003) associated with DGCI in three environments, and 16 significant SNPs associated with DGCI averaged across all environments. These SNPs likely tagged 43 putative loci. Out of these 45 SNPs, eight were present in more than one environment. Among the identified loci, 21 were located in regions previously reported for N traits and ureide concentration. Putative loci that were coincident with previously reported genomic regions may be important resources for pyramiding favorable alleles for improved N and chlorophyll concentrations, photosynthesis rates, and N2 fixation in soybean.

Soybean [Glycine max (L.) Merr.] is an important source of protein and vegetable oil. Genetic improvement of soybean seed yield and composition are ultimate breeding goals. During the past 80 yr, breeders have selected for high yield and other desired traits to make genetic improvements. To quantify the genetic changes to seed yield, yield stability, and other important agronomic and end-use quality traits, we evaluated 93 soybean cultivars in Maturity Groups (MG) V, VI, and VII that were released from 1928 to 2008. Replicated yield trials specific for each MG set of cultivars were conducted during 2010 to 2011 in a total of 27 southeastern US year-location environments. A mixed linear model was used to calculate best linear unbiased predictors (BLUPs) for each cultivar for each measured trait within each MG. Regressed cultivar effect BLUPs of each trait by year of cultivar release revealed positive linear trends for annualized genetic yield gains of 17.6, 13.5, and 10.3 kg ha⁻¹ yr⁻¹ for MG V, VI, and VII, respectively. Averaged across MGs, the annualized rate of genetic gain was estimated to be 13.7 kg ha⁻¹ yr⁻¹. Yield stability analyses revealed significant differences in regression coefficients (b), which were >1.0 for newer cultivars but

Charcoal rot is a major disease of soybean (Glycine max) caused by Macrophomina phaseolina and results in significant loss in yield and seed quality. The effects of charcoal rot on seed composition (seed protein, oil, and fatty acids), a component of seed quality, is not well understood. Therefore, the objective of this research was to investigate the impact of charcoal rot on seed protein, oil, and fatty acids in different soybean genotypes differing in their charcoal rot susceptibility under irrigated and non-irrigated conditions. Two field experiments were conducted in 2012 and 2013 in Jackson, TN, USA. Thirteen genotypes differing in charcoal rot resistance (moderately resistant and susceptible) were evaluated. Under non-irrigated conditions, moderately resistant genotypes showed either no change or increased protein and oleic acid but had lower linolenic acid. Under non-irrigated conditions, most of the susceptible genotypes showed lower protein and linolenic acid but higher oleic acid. Most of the moderately resistant genotypes had higher protein than susceptible genotypes under irrigated and non-irrigated conditions but lower oil than susceptible genotypes. The different responses among genotypes for protein, oil, oleic acid, and linolenic acid observed in each year may be due to both genotype tolerance to drought and environmental conditions, especially heat differences in each year (2012 was warmer than 2013). This research showed that the increases in protein and oleic acid and the decrease in linolenic acid may be a possible physiological mechanism underlying the plant’s responses to the charcoal rot infection. This research further helps scientists understand the impact of irrigated and non-irrigated conditions on seed nutrition changes, using resistant and susceptible genotypes.

Drought causes significant soybean [Glycine max (L.) Merr.] yield losses each year in rain-fed production systems of many regions. Genetic improvement of soybean for drought tolerance is a cost-effective approach to stabilize yield under rain-fed management. The objectives of this study were to confirm previously reported soybean loci and to identify novel loci associated with canopy wilting (CW) using a panel of 200 diverse maturity group (MG) IV accessions. These 200 accessions along with six checks were planted at six site-years using an augmented incomplete block design with three replications under irrigated and rain-fed treatments. Association mapping, using 34,680 single nucleotide polymorphisms (SNPs), identified 188 significant SNPs associated with CW that likely tagged 152 loci. This includes 87 SNPs coincident with previous studies that likely tagged 68 loci and 101 novel SNPs that likely tagged 84 loci. We also determined the ability of genomic estimated breeding values (GEBVs) from previous research studies to predict CW in different genotypes and environments. A positive relationship (P ≤ 0.05;0.37 ≤ r ≤ 0.5) was found between observed CW and GEBVs. In the vicinity of 188 significant SNPs, 183 candidate genes were identified for both coincident SNPs and novel SNPs. Among these 183 candidate genes, 57 SNPs were present within genes coding for proteins with biological functions involved in plant stress responses. These genes may be directly or indirectly associated with transpiration or water conservation. The confirmed genomic regions may be an important resource for pyramiding favorable alleles and, as candidates for genomic selection, enhancing soybean drought tolerance.

Background Associations between mitochondrial genetic abnormalities (variations and copy number, i.e. mtDNAcn, change) and elevated ROS have been reported in cancer compared to normal cells. Since excessive levels of ROS can trigger apoptosis, treating cancer cells with ROS-stimulating agents may enhance their death. This study aimed to investigate the link between baseline ROS levels and mitochondrial genetic abnormalities, and how mtDNA abnormalities might be used to predict cancer cells’ response to ROS-stimulating therapy. Methods Intracellular and mitochondrial specific-ROS levels were measured using the DCFDA and MitoSOX probes, respectively, in four cancer and one non-cancerous cell lines. Cells were treated with ROS-stimulating agents (cisplatin and dequalinium) and the IC50s were determined using the MTS assay. Sanger sequencing and qPCR were conducted to screen the complete mitochondrial genome for variations and to relatively quantify mtDNAcn, respectively. Non-synonymous variations were subjected to 3-dimensional (3D) protein structural mapping and analysis. Results Our data revealed novel significant associations between the total number of variations in the mitochondrial respiratory chain (MRC) complex I and III genes, mtDNAcn, ROS levels, and ROS-associated drug response. Furthermore, functional variations in complexes I/III correlated significantly and positively with mtDNAcn, ROS levels and drug resistance, indicating they might mechanistically influence these parameters in cancer cells. Conclusions Our findings suggest that mtDNAcn and complexes I/III functional variations have the potential to be efficient biomarkers to predict ROS-stimulating therapy efficacy in the future.

Soybean (Glycine max (L.) Merr.) meets a large portion of its nitrogen (N) need via biological N2 fixation, which is highly sensitive to drought stress. Nitrogen isotope ratios between 15N and 14N (δ15N) can be used as a metric for relative differences among soybean genotypes for N2 fixation, as δ15N is negatively associated with N2 fixation. This study aimed to dissect the genetic basis of δ15N using a mapping population of 196 F6-derived recombinant inbred lines developed from a cross between PI 416997 and PI 567201D that was evaluated in multiple environments. There was a wide range of δ15N in all environments and narrow-sense heritability for δ15N was 35% when estimated across environments. Analysis of variance of δ15N showed significant effects of genotype and environment, whereas the genotype × environment interaction was not significant (P

The endometrium is a dynamic tissue that exhibits remarkable resilience to repeated episodes of differentiation, breakdown, regeneration, and remodeling. Endometrial physiology relies on a complex interplay between the stromal and epithelial compartments with the former containing a mixture of fibroblasts, vascular, and immune cells. There is evidence for rare populations of putative mesenchymal progenitor cells located in the perivascular niche of human endometrium, but the existence of an equivalent cell population in mouse is unclear. We used the Pdgfrb-BAC-eGFP transgenic reporter mouse in combination with bulk and single-cell RNA sequencing to redefine the endometrial mesenchyme. In contrast to previous reports we show that CD146 is expressed in both PDGFRβ + perivascular cells and CD31 + endothelial cells. Bulk RNAseq revealed cells in the perivascular niche which express the high levels of Pdgfrb as well as genes previously identified in pericytes and/or vascular smooth muscle cells (Acta2, Myh11, Olfr78, Cspg4, Rgs4, Rgs5, Kcnj8, and Abcc9). scRNA-seq identified five subpopulations of cells including closely related pericytes/vascular smooth muscle cells and three subpopulations of fibroblasts. All three fibroblast populations were PDGFRα+/CD34 + but were distinct in their expression of Ngfr/Spon2/Angptl7 (F1), Cxcl14/Smoc2/Rgs2 (F2), and Clec3b/Col14a1/Mmp3 (F3), with potential functions in the regulation of immune responses, response to wounding, and organization of extracellular matrix, respectively. Immunohistochemistry was used to investigate the spatial distribution of these populations revealing F1/NGFR + cells in most abundance beside epithelial cells. We provide the first definitive analysis of mesenchymal cells in the adult mouse endometrium identifying five subpopulations providing a platform for comparisons between mesenchymal cells in endometrium and other adult tissues which are prone to fibrosis.

The endometrium is a dynamic tissue that exhibits remarkable resilience to repeated episodes of differentiation, breakdown, regeneration and remodelling. Endometrial physiology relies on a complex interplay between the stromal and epithelial compartments with the former containing a mixture of fibroblasts, vascular and immune cells. There is evidence for rare populations of putative mesenchymal progenitor cells located in the perivascular niche of human endometrium, but the existence of an equivalent cell population in mouse is unclear.In the current study we used the Pdgfrb-BAC-eGFP transgenic reporter mouse in combination with bulk and single cell RNA sequencing (scRNAseq) to redefine the endometrial mesenchyme. Contrary to previous reports we show that CD146 is expressed in both PDGFRβ+ perivascular cells as well as CD31+ endothelial cells. Bulk RNAseq revealed cells in the perivascular niche which express high levels of Pdgfrb as well as genes previously identified in pericytes and/or vascular smooth muscle cells (Acta2, Myh11, Olfr78, Cspg4, Rgs4, Rgs5, Kcnj8, Abcc9). scRNAseq identified five subpopulations of cells including closely related pericytes/vascular smooth muscle cells and three subpopulations of fibroblasts. All three fibroblast populations were PDGFRα+/CD34+ but were distinct in their expression of Spon2/Angptl7 (fibroblast 1), Smoc2/Rgs2 (fibroblast 2) and Clec3b/Col14a1/Mmp3 (fibroblast 3), with potential functions in regulation of immune responses, response to wounding and organisation of extracellular matrix respectively.In conclusion, these data are the first to provide a single cell atlas of the mesenchymal cell landscape in mouse endometrium. By identifying novel markers for subpopulations of mesenchymal cells we can use mouse models investigate their contribution to endometrial function, compare with other tissues and apply these findings to further our understanding of human endometrium.HighlightsGFP expression in the mouse endometrium, under the control of the Pdgfrb promoter, is restricted to two cell populations based on the intensity of GFP with GFPbright cells close to the vasculatureSingle cell RNAseq identified five subpopulations of GFP+ mesenchymal cells: pericytes, vascular smooth muscle cells (vSMC) and three closely related but distinct populations of fibroblastsBioinformatics revealed that pericytes and vSMC share functions associated with the circulatory system, actin-filament process and cell adhesion, and an apparent role for pericytes in smooth muscle cell migration and response to interferonsComparisons between the fibroblast subpopulations suggest distinct roles in regulation of immune response, response to wound healing and collagen organisation.Graphical Abstract

Heat-induced changes in lipidome and their influence on stress adaptation are not well-defined in plants. We investigated if lipid metabolic changes contribute to differences in heat stress responses in a heat-tolerant soybean genotype DS25-1 and a heat-susceptible soybean genotype DT97-4290. Both genotypes were grown at optimal temperatures (OT, 30/20 &deg, C) for 15 days. Subsequently, half of the plants were exposed to heat stress (38/28 &deg, C) for 11 days, and the rest were kept at OT. Leaf samples were collected for lipid and RNA extractions on the 9th and 11th days of stress, respectively. We observed a decline in the lipid unsaturation level due to a decrease in the polyunsaturated linolenic acid (18:3) content in DS25-1. When examined under OT conditions, DS25-1 and DT97-4290 showed no significant differences in the expression pattern of the Fatty Acid Desaturase (FAD) 2-1A, FAD2-2B, FAD2-2C, FAD3A genes. Under heat stress conditions, substantial reductions in the expression levels of the FAD3A and FAD3B genes, which convert 18:2 lipids to 18:3, were observed in DS25-1. Our results suggest that decrease in levels of lipids containing 18:3 acyl chains under heat stress in DS25-1 is a likely consequence of reduced FAD3A and FAD3B expression, and the decrease in 18:3 contributes to DS25-1&prime, s maintenance of membrane functionality and heat tolerance.

Charcoal rot, caused by the fungus Macrophomina phaseolina (Tassi) Goid., is a disease of soybean (Glycine max (L.) Merr.) that causes yield loss worldwide. The purpose of this research was to dete...

Charcoal rot (CR), caused by the fungus Macrophomina phaseolina (Tassi) Goid. is a pervasive disease of economic significance on soybeans (Glycine max (L.) Merr.). Similarly, drought is the leading cause of yield loss in soybean worldwide. In this study, CR severity and seed yield were determined in irrigated and non-irrigated environments in 2011, 2012, and 2013 for thirteen soybean genotypes, nine of which were previously determined to be drought tolerant (DT). The objectives were to determine the severity of CR in the putative DT genotypes and to determine the over-all effect of CR on yield in irrigated and non-irrigated environments. Colony Forming Units (CFUs) at reproductive stage R7 were used to assess disease severity and classify each genotype's response to CR. A stress tolerance index (STI) was used to determine the relative impact of soil moisture stress (i.e. no irrigation) on the 13 genotypes. Over all three years in both irrigated and non-irrigated environments, five genotypes were consistently rated as moderately resistant to CR (MRCR) and three genotypes were consistently rated as susceptible to CR (SCR), whereas the responses of the remaining five genotypes varied between MRCR and SCR. Averaged over the three years, there was a wide range (0.36–1.09) of STI values among genotypes. Even though there was a consistent trend, there was a very weak relationship between STI and CFU's at the R7 growth stage. Regression analysis indicated that as CFUs at R7 increased, seed yield decreased, although the relationship was not significant in every year and irrigation environment. Nonetheless, across all years and irrigation environments, a pooled (global) slope indicated a yield loss of 11.5 kg ha−1 for every 1000 CFUs at R7. These data indicated that as CFUs at R7 increased, seed yield decreased in both irrigated and non-irrigated environments. However, as the relationship between CR disease severity and DT was minimal, it may be necessary to select for resistance to both traits using environments where both soil moisture stress and CR are high.

The objective of this study was to enquire how the chemistry experience of pharmacy students can be enhanced and how the virtual learning environment (VLE) for chemistry-related pharmacy modules might be improved. All MPharm students at the University of Portsmouth UK were asked to complete a project-designed online questionnaire. Data from University course module feedback questionnaires were also analysed. Qualitative and quantitative analyses were performed, using appropriate statistical evaluation. Pre-university chemistry was not correlated with current perceived relevance, difficulty or workload (p > 0.05). The latter two were positively correlated (p = 0.003). Students realised their study of chemistry was important (89%). Chemistry- and biology-related areas were rated equally enjoyable (p > 0.05), but less than pharmacy practice areas (p < 0.0001). Students' preferred choices for VLE development were video lectures > VLE quizzes > audio content. Keeping chemistry content relevant on pharmacy programmes is important. Strategies for improving learning through extended use of the VLE have been identified.

Background Mitochondria are considered a primary intracellular site of reactive oxygen species (ROS) generation. Generally, cancer cells with mitochondrial genetic abnormalities (copy number change and mutations) have escalated ROS levels compared to normal cells. Since high levels of ROS can trigger apoptosis, treating cancer cells with low doses of mitochondria-targeting / ROS-stimulating agents may offer cancer-specific therapy. This study aimed to investigate how baseline ROS levels might influence cancer cells’ response to ROS-stimulating therapy. Methods Four cancer and one normal cell lines were treated with a conventional drug (cisplatin) and a mitochondria-targeting agent (dequalinium chloride hydrate) separately and jointly. Cell viability was assessed and drug combination synergisms were indicated by the combination index (CI). Mitochondrial DNA copy number (mtDNAcn), ROS and mitochondrial membrane potential (MMP) were measured, and the relative expression levels of the genes and proteins involved in ROS-mediated apoptosis pathways were also investigated. Results Our data showed a correlation between the baseline ROS level, mtDNAcn and drug sensitivity in the tested cells. Synergistic effect of both drugs was also observed with ROS being the key contributor in cell death. Conclusions Our findings suggest that mitochondria-targeting therapy could be more effective compared to conventional treatments. In addition, cancer cells with low levels of ROS may be more sensitive to the treatment, while cells with high levels of ROS may be more resistant. Doubtlessly, further studies employing a wider range of cell lines and in vivo experiments are needed to validate our results. However, this study provides an insight into understanding the influence of intracellular ROS on drug sensitivity, and may lead to the development of new therapeutic strategies to improve efficacy of anticancer therapy.

Objective Soybean seed development is negatively impacted by elevated temperatures during seed fill, which can decrease seed quality and economic value. Prior germplasm screens identified an exotic landrace able to maintain ~ 95% seed germination under stress conditions that reduce germination dramatically (> 50%) for typical soybean seeds. Seed transcriptomic analysis was performed for two soybean lines (a heat-tolerant landrace and a typical high-yielding adapted line) for dry, mature seed, 6-h imbibed seed and germinated seed. Seeds were produced in two environments: a typical Midwestern field and a heat stressed field located in the Midsouth soybean production region. Results Transcriptomic analysis revealed 23–30K expressed genes in each seed tissue sample, and differentially expressed genes (DEGs) with ≥ twofold gene expression differences (at q-value

The protozoan parasite Leishmania possesses a single flagellum, which is remodelled during the parasite’s life cycle from a long motile flagellum in promastigote forms in the sand fly to a short immotile flagellum in amastigotes residing in mammalian phagocytes. This study examined the protein composition and in vivo function of the promastigote flagellum. Protein mass spectrometry and label free protein enrichment testing of isolated flagella and deflagellated cell bodies defined a flagellar proteome for L. mexicana promastigote forms (available via ProteomeXchange with identifier PXD011057). This information was used to generate a CRISPR-Cas9 knockout library of 100 mutants to screen for flagellar defects. This first large-scale knockout screen in a Leishmania sp. identified 56 mutants with altered swimming speed (52 reduced and 4 increased) and defined distinct mutant categories (faster swimmers, slower swimmers, slow uncoordinated swimmers and paralysed cells, including aflagellate promastigotes and cells with curled flagella and disruptions of the paraflagellar rod). Each mutant was tagged with a unique 17-nt barcode, providing a simple barcode sequencing (bar-seq) method for measuring the relative fitness of L. mexicana mutants in vivo. In mixed infections of the permissive sand fly vector Lutzomyia longipalpis, paralysed promastigotes and uncoordinated swimmers were severely diminished in the fly after defecation of the bloodmeal. Subsequent examination of flies infected with a single paralysed mutant lacking the central pair protein PF16 or an uncoordinated swimmer lacking the axonemal protein MBO2 showed that these promastigotes did not reach anterior regions of the fly alimentary tract. These data show that L. mexicana need directional motility for successful colonisation of sand flies., Author summary Leishmania are protozoan parasites, transmitted between mammals by the bite of phlebotomine sand flies. Promastigote forms in the sand fly have a long flagellum, which is motile and used for anchoring the parasites to prevent clearance with the digested blood meal remnants. To dissect flagellar functions and their importance in life cycle progression, we generated here a comprehensive list of >300 flagellar proteins and produced a CRISPR-Cas9 gene knockout library of 100 mutant Leishmania. We studied their behaviour in vitro before examining their fate in the sand fly Lutzomyia longipalpis. Measuring mutant swimming speeds showed that about half behaved differently compared to the wild type: a few swam faster, many slower and some were completely paralysed. We also found a group of uncoordinated swimmers. To test whether flagellar motility is required for parasite migration from the fly midgut to the foregut from where they reach the next host, we infected sand flies with a mixed mutant population. Each mutant carried a unique tag and tracking these tags up to nine days after infection showed that paralysed and uncoordinated Leishmania were rapidly lost from flies. These data indicate that directional swimming is important for successful colonisation of sand flies.

Soybean (Glycine max (L.) Merr.) winter nurseries have been planted in Puerto Rico at the USDA's Isabela farm for 25 consecutive years. The field has had one soybean crop each year, with a summer fallow period between winter nursery seasons. In February 1998, during an inspection of root nodulation, cysts were discovered on roots of an F2 population (Benning × Pureunkong). Microscopic examination of roots confirmed the presence of female nematodes of Heterodera glycines Ichinohe in various stages of development. No cysts were found when soil and roots were randomly sampled at various growth stages (R1 to R7) from other soybean fields in Puerto Rico (Isabela, Salinas, Lajas, and Juana Diaz). Also, no cysts were observed on roots of common bean (Phaseolus vulgaris) at growth stages R7 to R8 in a neighboring research field. However, cysts were observed on 35-day-old roots of soybean cv. Lee, common bean, and pigeon pea (Cajanas cajun) grown in the above infested soil. A race assay, slightly modified from standard protocols (3), determined that the infested soil contained race 2 of H. glycines. The infested field was rotated to sorghum during the summer of 1998 and then soybeans were planted in the 1998-1999 winter nursery. H. glycines occurs in at least 26 states of the U.S., and in Canada, Asia, and South America (1,2). References: (1) M. L. Mendes and D. W. Dickson. Plant Dis. 77:499, 1993. (2) R. D. Riggs and D. P. Schmitt. 1989. Soybean Cyst Nematode. Page 65 in: Compendium of Soybean Diseases. 3rd ed. J. B. Sinclair and P. A. Backman, eds. American Phytopathological Society, St. Paul, MN. (3) D. P. Schmitt and G. Shannon. Crop Sci. 32:275, 1992.

Dormancy is an elusive and deadly component of cancers. Rare, therapy resistant cells lay dormant for decades and when reactivated cause disease progression and relapse. Eradicating dormant cancer cells is key to curing cancers yet is an unrealized goal. The skeleton remains a common location for dissemination and dormancy, yet our understanding of the cellular and molecular pathways that control dormant cancer cells in the the skeleton is limited. We hypothesized that dormant cancer cells occupy a common niche in the skeleton and this supports long-term dormancy. To test this we developed technology to identify and analyse dormant cancers cells from different cancer types and the compartment in the skeleton in which they reside. Membrane label retention was able to distinguish dormant cancer cells from reactivated cancer cells. Intravital imaging showed that dormant cancer cells were found associated with endosteal bone surface suggesting that different cancers may occupy a common niche. Single cell RNA sequencing of dormant cancer cells showed they expressed a distinct gene signature that was enriched for myeloid genes. Single cell RNA sequencing of >130,000 cells isolated from the endosteal bone compartment and the bone marrow identified 32 distinct cell clusters. Detailed transcriptional analysis facilitated construction of a map of all of the cell types/states present in the endosteal bone compartment. In silico ligand/receptor interaction mapping enabled identification of the cell types and the molecular pathways that may mediate dormant cell niche formation in vivo. Non-haemopoietic cells, particularly cells of the osteoblast lineage and endothelia cells were the most enriched for dormant cell binding partners. This was common across three different dormant tumor types. Detailed analysis of cells of the osteoblast lineage showed greatest enrichment for binding partners in LeprHigh/Cxcl12High mesenchymal cells. Further analysis of the molecular pathways that can interact with binding partners identified a number of potential molecular regulators of dormancy. For example, Gas6, which is expressed by LeprHigh/Cxcl12High mesenchymal cells, has the binding partners Axl expressed by dormant myeloma cells, Mertk in dormant breast cancer cells and Mertk and Tyro3 in dormant prostate cancer. Treatment of mice bearing myeloma cells with small molecule inhibitors of Axl reduced dormant cells and increased tumor burden suggesting the Axl/Gas6 interaction is functional important in controlling dormancy. Together these data show that single cell sequencing can be used to define the cells and molecular pathways that facilitate dormant cancer cell niche formation in the skeleton. This approach suggests that that cancer cell specific molecules interact with common molecules in the endosteal niche, including LeprHigh/Cxcl12High mesenchymal cells, to switch on common molecular pathways to control dormancy. Citation Format: Peter Croucher, Weng Hua Khoo, Ryan Chai, Alex Corr, James Smith, Qihao Ren, Paul Baldock, Michelle McDonald, Sheila Stewart, Tri G. Phan. Niche-dependent control of tumor cell dormancy [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr IA015.

The "liana dominance hypothesis" posits that lianas are increasing in abundance in tropical forests, thereby potentially reducing tree biomass due to competitive interactions between trees and lianas. This scenario has implications not only for forest ecosystem function and species composition, but also climate change given the mass of carbon stored in tropical trees. In 2003 and 2013, all Myristicaceae trees in the 50-ha Yasuni Forest Dynamics Plot, Ecuador, were surveyed for liana presence and load in their crowns. We tested the hypothesis that the proportion of trees with lianas increased between 2003 and 2013 in line with the liana dominance hypothesis. Contrary to expectations, the total proportion of trees with lianas decreased from 35% to 32%, and when only trees ≥10 cm diameter at breast height were considered liana incidence increased 44-48%. Liana load was dynamic with a large proportion of trees losing or gaining lianas over the 10-yr period; large trees with intermediate liana loads increased in proportion at the expense of those with low and high loads. Lianas also impacted performance: trees with 26-75% crown cover by lianas in 2003 had reduced growth rates of 80% compared to of liana-free trees, and trees with >75% crown cover had 33% the growth rate and a log odds of mortality eight times that of liana-free trees. We suggest that the lack of strong support found for the liana dominance hypothesis is likely due to the aseasonal climate of Yasuni, which limits the competitive advantage lianas maintain over trees during dry seasons due to their efficient capture and use of water. We propose further research of long-term liana dynamics from aseasonal forests is required to determine the generality of the increasing liana dominance hypothesis in Neotropical forests.

We have applied three techniques to the study of subunit assembly of the Type IC Restriction–Modification enzyme EcoR124I. This fully functional enzyme EcoR124I consists of a complex of the three subunits HsdR, HsdM and HsdS in a R2M2S1 stoichiometry, but is known to dissociate readily, releasing free HsdR and producing first an R1-complex and then the core, DNA-binding methyltransferase (M2S1) complex. Analysis of the assembly pathway of this enzyme has previously employed gel retardation and Surface Plasmon Resonance (SPR), but the studies to date have not included the cofactors required for full enzyme activity. In this paper, we have also used atomic force microscopy (AFM)-based molecular volume measurements, and have analysed the effect of the cofactors ATP and AdoMet on enzyme stability and subunit assembly. We compare the data obtained from all three techniques and we show that they all give consistent results, but inherent differences in the methodologies provide additional information useful for the study of subunit assembly.

Mengistu, A., Smith, J. R., Ray, J. D., and Bellaloui, N. 2011. Seasonal progress of charcoal rot and its impact on soybean productivity. Plant Dis. 95:1159-1166. The seasonal progress of charcoal rot (caused by Macrophomina phaseolina) was measured over two growing seasons in four separate experiments: irrigated infested, irrigated non-infested, non-irrigated infested, and non-irrigated noninfested. Disease was assessed at V5, R1, R3, R5, R6, and R7 growth stages based on colony forming units (CFU) of M. phaseolina recovered from the lower stem and root tissues and the area under the disease progress curve (AUDPC). The population density of M. phaseolina increased slowly from the V5 to R6 growth stages and then rapidly from the R6 to R7 growth stages for all genotypes in all four experiments. Yield loss due to charcoal rot ranged from 6 to 33% in irrigated environments. The extent of yield loss was affected by severity of charcoal rot, which in turn was affected by year. Yield loss due to charcoal rot was consistently measured in all paired comparisons in irrigated environments, suggesting that charcoal rot can be an important disease in irrigated environments. Disease severity based on CFU accounted for more yield loss variation (42%) than did the AUDPC (36%) when used to assess disease. Growth stage R7 was found to be the optimum stage for assessing disease using CFU. In addition, screening soybean genotypes under irrigation environment may have utility in breeding programs where there is a need for evaluating soybean genotypes for both disease resistance and yield. Charcoal rot of soybean (Glycine max (L.) Merr.), caused by Macrophomina phaseolina (Tassi) Goid., is a disease of economic

The mineral composition of crop shoot tissues is important for yield formation and nutrient remobilization to seeds. The natural diversity that exists within crop species can be used to investigate mechanisms that define plant mineral composition and to identify important genomic loci for these processes. The objective of this study was to determine shoot mineral nutrient concentrations in genetically diverse soybean [ (L.) Merr.] genotypes and to identify genomic regions associated with concentrations of different nutrients in shoot tissue. The genotypes were grown at two locations in 2 yr and characterized for macronutrient (Ca, Mg, P, K, and S) and micronutrient (B, Cu, Fe, Mn, and Zn) concentrations in shoot tissues. Genome-wide association studies were conducted with 31,748 single nucleotide polymorphisms (SNPs) via a unified mixed model to identify SNPs associated with macro- and micronutrient concentrations. The number of putative loci identified for the macronutrients ranged from 11 for Ca to 20 for K. For the micronutrients, the number ranged from 10 for Mn to 24 for Fe. In addition to colocated loci for multiple nutrients, 22 individual SNPs were associated with more than one nutrient such that 11 different nutrient combinations were encompassed by these SNPs. Ultimately, the putative loci identified in this study will need to be confirmed and are expected to aid in the identification of new sources of variation for use in soybean breeding programs as well as for mechanistic studies aimed at understanding the regulation of mineral nutrient uptake, translocation, and shoot tissue concentrations.

Glioblastoma multiforme (GBM) is a highly invasive (WHO grade IV) brain tumour that has a very poor prognosis for patients with the condition (median survival 14.2 months). Quantitative Imaging (QI)® mode atomic force microscopy (AFM) was used to measure the heights of the leading-edge cell peripheries, the lamellipodia, of two such cell lines (SNB-19 and UP-007), together with those from non-neoplastic astrocyte control cells (CC-2565 and SC-1800) and from a low-grade (WHO grade I) glioma cell line (SEBTA-048). The lamellipodia heights of the glioma cells SNB-19 and UP-007 were 2.45 ± 0.59 and 1.57 ± 0.42 μm, respectively, which were higher than those of the CC-2565 and SC-1800 cells (1.03 ± 0.58 and 0.85 ± 0.40 μm, respectively; p p p p > 0.05) but lower than those of the high-grade gliomas (p p

CD44, a transmembrane glycoprotein receptor for extracellular matrix molecules such as hyaluronic acid and osteopontin, is involved in glioma cellular signalling, adhesion and invasion. Although a great deal is known concerning the molecular players in adhesion, migration and invasion, little is known relating to how these invasive and migratory-promoting proteins influence biomechanical properties of glioma cells. Herein, we extend previous CD44 blocking experiments to examine effects of CD44 knock-down on expression of cytoskeletal proteins and cellular stiffness. An atomic force microscope (AFM) nanoindentation method was used to measure deformation or cellular stiffness (Young’s modulus, E) in real time, at the single-cell level over nuclear and cytoplasmic regions. A glioblastoma cell line (SNB-19) was transfected with either CD44 small interfering RNA (siRNA), scrambled siRNA or a non-related gene siRNA. In SNB-19 CD44 knock-down cells, levels of microtubule, vimentin and glial fibrillary acidic protein (GFAP) proteins were lower compared to cells transfected with scrambled siRNA. Functionally, CD44 knock-down cells were less migratory compared to controls. AFM nanoindentation results show that the areas over the nuclei of both knock-down and parental control cells examined were significantly more compliant than their cytoplasmic regions (p E = 0.56 ± 0.50 kPa) were less stiff than parental cells (E = 1.93 ± 2.86 kPa; p

Ureides are the N-rich products of N-fixation that are transported from soybean nodules to the shoot. Ureides are known to accumulate in leaves in response to water-deficit stress, and this has been used to identify genotypes with reduced N-fixation sensitivity to drought. Our objectives in this research were to determine shoot ureide concentrations in 374 Maturity Group IV soybean accessions and to identify genomic regions associated with shoot ureide concentration. The accessions were grown at two locations (Columbia, MO, and Stuttgart, AR) in 2 yr (2009 and 2010) and characterized for ureide concentration at beginning flowering to full bloom. Average shoot ureide concentrations across all four environments (two locations and two years) and 374 accessions ranged from 12.4 to 33.1 µmol g−1 and were comparable to previously reported values. SNP–ureide associations within and across the four environments were assessed using 33,957 SNPs with a MAF ≥0.03. In total, 53 putative loci on 18 chromosomes were identified as associated with ureide concentration. Two of the putative loci were located near previously reported QTL associated with ureide concentration and 30 loci were located near genes associated with ureide metabolism. The remaining putative loci were not near chromosomal regions previously associated with shoot ureide concentration and may mark new genes involved in ureide metabolism. Ultimately, confirmation of these putative loci will provide new sources of variation for use in soybean breeding programs.

Background CD15, which is overexpressed on various cancers, has been reported as a cell adhesion molecule that plays a key role in non-CNS metastasis. However, the role of CD15 in brain metastasis is largely unexplored. This study provides a better understanding of CD15/CD62E interaction, enhanced by tumor necrosis factor-α (TNF-α), and its correlation with brain metastasis in non–small cell lung cancer (NSCLC). Methods CD15 and E-selectin (CD62E) expression was demonstrated in both human primary and metastatic NSCLC cells using flow cytometry, immunofluorescence, and Western blotting. The role of CD15 was investigated using an adhesion assay under static and physiological flow live-cell conditions. Human tissue sections were examined using immunohistochemistry. Results CD15, which was weakly expressed on hCMEC/D3 human brain endothelial cells, was expressed at high levels on metastatic NSCLC cells (NCI-H1299, SEBTA-001, and SEBTA-005) and at lower levels on primary NSCLC (COR-L105 and A549) cells (P < .001). The highest expression of CD62E was observed on hCMEC/D3 cells activated with TNF-α, with lower levels on metastatic NSCLC cells followed by primary NSCLC cells. Metastatic NSCLC cells adhered most strongly to hCMEC/D3 compared with primary NSCLC cells. CD15 immunoblocking decreased cancer cell adhesion to brain endothelium under static and shear stress conditions (P < .0001), confirming a correlation between CD15 and cerebral metastasis. Both CD15 and CD62E expression were detected in lung metastatic brain biopsies. Conclusion This study enhances the understanding of cancer cell-brain endothelial adhesion and confirms that CD15 plays a crucial role in adhesion in concert with TNF-α activation of its binding partner, CD62E.

Soybean rust, caused by Phakopsora pachyrhizi Sydow, results in significant soybean (Glycine max (L.) Merr.) yield losses worldwide. The purpose of this research was to confirm the inheritance, gene action, and genomic location of resistance to P. pachyrhizi in soybean accession PI 587905. Two independent populations (F2-derived F3 lines and F2 plants) were inoculated with P. pachyrhizi in a greenhouse and assayed in a field, respectively, in southeastern Paraguay. Both the field F2 and the greenhouse F2-inferred segregation ratios fit the 1:2:1 ratio expected for segregation of a single gene (P > 0.05). Unlike previous studies, gene action differed according to ontogeny. Among seedlings in the greenhouse, gene action was dominant, but in the field assay among adult plants, the gene exhibited incomplete dominance. Molecular markers were used to map the resistance gene in PI 587905 to the Rpp1 locus. This information should be useful to plant breeders for developing and selecting resistant cultivars.

The timing of harvest is a major factor affecting seed quality in soybean, particularly in Midsouthern USA, when rain during harvest period is not uncommon. The objective of this research was to evaluate the effects of time of harvest on soybean seed quality (seed composition, germination, seed coat boron, and lignin) in high germinability (HG) breeding lines (50% exotic) developed under high heat. The hypothesis was that seeds of HG lines possess physiological and genetic traits for a better seed quality at harvest maturity and delayed harvest. A 2-year field experiment was conducted under irrigated conditions. Results showed that, at harvest maturity, the exotic HG lines had higher seed protein, oleic acid, sugars, seed coat boron, and seed coat lignin, but lower seed oil compared with the non-exotic checks (Control), confirming our hypothesis. At 28 days after harvest maturity (delayed harvest), the content of seed protein, oleic acid, sugars, seed coat boron, and seed coat lignin were higher in some of the HG lines compared with the checks, indicating a possible involvement of these seed constituents, especially seed coat boron and seed coat lignin, in maintaining seed coat integrity and protecting seed coat against physical damage. Highly significant positive correlations were found between germination and seed protein, oleic acid, sugars, and seed coat boron and seed coat lignin. Highly significant negative correlation was found between germination and oil, linoleic acid, seed coat wrinkling, shattering, and hard seed. Yields of some HG lines were competitive with checks. This research demonstrated that time of harvesting is an important factor influencing seed protein and oil production. Also, since high oleic acid is desirable for oxidative stability, shelf-life and biodiesel properties, using HG lines could positively influence these important traits. This result should suggest to breeders of some of the advantages of selecting for high seed coat boron and lignin, and inform growers of the importance of timely harvest for maintaining high seed quality.

Using genome-wide association studies, 39 SNP markers likely tagging 21 different loci for carbon isotope ratio (δ (13) C) were identified in soybean. Water deficit stress is a major factor limiting soybean [Glycine max (L.) Merr.] yield. Soybean genotypes with improved water use efficiency (WUE) may be used to develop cultivars with increased yield under drought. A collection of 373 diverse soybean genotypes was grown in four environments (2 years and two locations) and characterized for carbon isotope ratio (δ(13)C) as a surrogate measure of WUE. Population structure was assessed based on 12,347 single nucleotide polymorphisms (SNPs), and genome-wide association studies (GWAS) were conducted to identify SNPs associated with δ(13)C. Across all four environments, δ(13)C ranged from a minimum of -30.55‰ to a maximum of -27.74‰. Although δ(13)C values were significantly different between the two locations in both years, results were consistent among genotypes across years and locations. Diversity analysis indicated that eight subpopulations could contain all individuals and revealed that within-subpopulation diversity, rather than among-subpopulation diversity, explained most (80%) of the diversity among the 373 genotypes. A total of 39 SNPs that showed a significant association with δ(13)C in at least two environments or for the average across all environments were identified by GWAS. Fifteen of these SNPs were located within a gene. The 39 SNPs likely tagged 21 different loci and demonstrated that markers for δ(13)C can be identified in soybean using GWAS. Further research is necessary to confirm the marker associations identified and to evaluate their usefulness for selecting genotypes with increased WUE.

Phomopsis seed decay (PSD) caused by Diaporthe longicolla has been documented as part of a soybean (Glycine max) fungal disease complex that affects the quality of soybean seed. Soybean-producing countries that have not yet documented the presence of PSD impose soybean seed import restrictions to protect their soybean production. The purpose of this study was to determine the frequency of occurrence of Diaporthe spp. in Paraguay. In 2006, 16 isolates of Diaporthe were recovered for the first time from soybean seed in San Alberto, Paraguay in the south-eastern section of the country. The 16 isolates were used to inoculate mature pods harvested from greenhouse grown PSD-susceptible soybean cultivar ‘Maverick’. Among the16 isolates, six isolates (TN 214, TN 218, TN 224, TN 226, TN 227 and TN 229) caused infection on both pods and seeds within pods. Two groups of isolates were identified based on conidial types: isolates that produced only α conidia and isolates that produced both α and β conidia. The...

Charcoal rot disease, caused by the fungus Macrophomina phaseolina, results in major economic losses in soybean production in southern USA. M. phaseolina has been proposed to use the toxin (-)-botryodiplodin in its root infection mechanism to create a necrotic zone in root tissue through which fungal hyphae can readily enter the plant. The majority (51.4%) of M. phaseolina isolates from plants with charcoal rot disease produced a wide range of (-)-botryodiplodin concentrations in a culture medium (0.14&ndash, 6.11 &micro, g/mL), 37.8% produced traces below the limit of quantification (0.01 &micro, g/mL), and 10.8% produced no detectable (-)-botryodiplodin. Some culture media with traces or no (-)-botryodiplodin were nevertheless strongly phytotoxic in soybean leaf disc cultures, consistent with the production of another unidentified toxin(s). Widely ranging (-)-botryodiplodin levels (traces to 3.14 &micro, g/g) were also observed in the roots, but not in the aerial parts, of soybean plants naturally infected with charcoal rot disease. This is the first report of (-)-botryodiplodin in plant tissues naturally infected with charcoal rot disease. No phaseolinone was detected in M. phaseolina culture media or naturally infected soybean tissues. These results are consistent with (-)-botryodiplodin playing a role in the pathology of some, but not all, M. phaseolina isolates from soybeans with charcoal rot disease in southern USA.

Alternative methods are needed to assess the severity of charcoal rot disease [Macrophomina phaseolina (Tassi) Goid] in soybean [Glycine max (L.)] plant tissue. The objective of this study was to define the relationship between light reflectance properties and microsclerotia content of soybean stem and root tissue. Understanding that relationship could lead to using spectral reflectance data as a tool to assess the severity of charcoal rot disease in soybean plants, thus reducing human bias associated with qualitative analysis of soybean plant tissue and cost and time issues connected with quantitative analysis. Hyperspectral reflectance measurements (400-2490 nm) were obtained with a non-imaging spectroradiometer of non-diseased and charcoal rot diseased ground stem and root tissue samples of six soybean genotypes (“Clark”, “LD00-3309”, “LG03- 4561-14”, “LG03-4561-19”, “Saline”, and “Y227-1”). Relationships between the reflectance measurements and tissue microsclerotia content were evaluated with Spearman correlation (rs) analysis (p < 0.05). Moderate (rs = ±0.40 to ±0.59), strong (rs = ±0.60 to ±0.79), and very strong (rs = ±0.80 to ±1.00) negative and positive statistically significant (p < 0.05) monotonic relationships were observed between tissue spectral reflectance values and tissue microsclerotia content. Near-infrared and shortwave-infrared wavelengths had the best relationships with microsclerotia content in the ground tissue samples, with consistent results obtained with near-infrared wavelengths in that decreases in near-infrared spectral reflectance values were associated with increases in microsclerotia content in the stem and root tissue of the soybean plants. The findings of this study provided evidence that relationships exist between tissue spectral reflectance and tissue microsclerotia content of soybean plants, supporting spectral reflectance data as a means for assessing variation of microsclerotia content in soybean plants. Future research should focus on the modelling capabilities of the selected wavelengths and on the feasibility of using these wavelengths in machine learning algorithms to differentiate non-diseased from charcoal rot diseased tissue.

Soybean [Glycine max (L.) Merr.] shoot nitrogen (N) traits are important for seed production and may hold potential for improving seed yield and quality. Field experiments were established to survey shoot N traits in i) plant introductions, ii) a recombinant inbred line (RIL) population, and iii) modern cultivars. A wide range of N concentrations was observed at beginning seed fill for leaves, petioles, and stems and at maturity for stems. Significant genotypic variations in stem N traits were found in modern cultivars and the RIL population. Molecular marker analysis identified multiple loci associated with stem N concentration. Significant relationships between various tissue N traits and seed yield and quality were also observed. These results illustrate the importance of N dynamics in vegetative tissues for soybean yield and seed composition. The observed variation in N traits indicates that selecting for vegetative N traits could potentially increase yield and improve seed quality.

Although the Early Soybean Production System (ESPS) in the Midsouthern USA increased seed yield under irrigated and non-irrigated conditions, heat stress and drought still lead to poor seed quality in heat sensitive soybean cultivars. Our breeding goal was to identify breeding lines that possess high germination, nutritional quality, and yield potential under high heat and dryland production conditions. Our hypothesis was that breeding lines derived from exotic germplasm might possess physiological and genetic traits allowing for higher seed germinability under high heat conditions. In a two-year field experiment, breeding lines derived from exotic soybean accessions, previously selected for adaptability to the ESPS in maturity groups (MG) III and IV, were grown under non-irrigated conditions. Results showed that three exotic breeding lines had consistently superior germination across two years. These lines had a mean germination percentage of greater than 80%. Two (25-1-1-4-1-1 and 34-3-1-2-4-1) out of the three lines with ≥80% germination in both years maintained high seed protein, oleic acid, N, P, K, B, Cu, and Mo in both years. Significant (P < 0.05) positive correlations were found between germination and oleic acid and with K and Cu in both years. Significant negative correlations were found between germination and linoleic acid, Ca, and hard seed in both years. There were positive correlations between germination and N, P, B, Mo, and palmitic acids only in 2013. A negative correlation was found between germination and green seed damage and linolenic acid in 2013 only. Seed wrinkling was significantly negatively correlated with germination in 2012 only. A lower content of Ca in the seed of high germinability genotypes may explain the lower rates of hard seed in those lines, which could lead to higher germination. Many of the differences in yield, germination, diseases, and seed composition between years are likely due to heat and rainfall differences between years. The results also showed the potential roles of seed minerals, especially K, Ca, B, Cu, and Mo, in maintaining high seed quality. The knowledge gained from this research will help breeders to select for soybean with high seed nutritional qualities and high germinability.

Background Chlorophyll is a major component of chloroplasts and a better understanding of the genetic basis of chlorophyll in soybean [Glycine max (L.) Merr.] might contribute to improving photosynthetic capacity and yield in regions with adverse environmental conditions. A collection of 332 diverse soybean genotypes were grown in 2 years (2009 and 2010) and chlorophyll a (eChl_A), chlorophyll b (eChl_B), and total chlorophyll (eChl_T) content as well as chlorophyll a/b ratio (eChl_R) in leaf tissues were determined by extraction and spectrometric determination. Total chlorophyll was also derived from canopy spectral reflectance measurements using a model of wavelet transformed spectra (tChl_T) as well as with a spectral reflectance index (iChl_T). Results A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify loci associated with the extract based eChl_A, eChl_B, eChl_R and eChl_T measurements and the two canopy spectral reflectance-based methods (tChl_T and iChl_T). A total of 23 (14 loci), 15 (7 loci) and 14 SNPs (10 loci) showed significant association with eChl_A, eChl_B and eChl_R respectively. A total of 52 unique SNPs were significantly associated with total chlorophyll content based on at least one of the three approaches (eChl_T, tChl_T and iChl_T) and likely tagged 27 putative loci for total chlorophyll content, four of which were indicated by all three approaches. Conclusions Results presented here show that markers for chlorophyll traits can be identified in soybean using both extract-based and canopy spectral reflectance-based phenotypes, and confirm that high-throughput phenotyping-amenable canopy spectral reflectance measurements can be used for association mapping. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0861-x) contains supplementary material, which is available to authorized users.

International audience; We report here the cloning and characterization of a novel KRAB zinc finger gene, ZFQR, which has eight tandemly repeated zinc fingers, a complete KRAB box at the N-terminal region, and a unique C-terminal sequence. It is expressed in a variety of human tissues, and mRNA levels are upregulated in nondividing senescent and quiescent human fibroblasts. Overexpression of the protein in quiescent cells stimulated with serum growth factors results in inhibition of entry into the cell cycle. The latter activity is lost when the N-terminal KRAB domain is deleted. The KRAB domain is also required for the transcriptional repression activity of ZFQR and in maintaining association of the protein with the nuclear matrix. The gene has been mapped to human chromosome 19q13.4. The association of ZFQR with the nuclear matrix, transcriptional repression activity, increased expression in senescent and quiescent cells, and the ability to inhibit quiescent cells stimulated with growth factors from entering the cell cycle suggests a role for ZFQR in the maintenance of the nondividing state of normal human cells.

Seed coat wrinkling is a major factor affecting the germinability of soybean [Glycine max (L.) Merr.] seed produced in high-temperature environments, such as in the Early Soybean Production System of the midsouthern United States. Exposure of seed to high temperatures, coupled with alternating periods of wet and dry conditions, promotes seed coat wrinkling. This can predispose the seed to mechanical damage at harvest, further reducing germinability, and reducing the usability of the grain for seed beans. Previous studies identified a single recessive gene (shr) in a mutant line (T-311), located on chromosome 13 (linkage group F), which causes seed shriveling and seed coat wrinkling. The current study was undertaken to identify and genetically map new gene(s) that affect seed coat wrinkling. Crosses were made between a smooth-seeded accession (PI 567743) and a wrinkled-seeded accession (PI 87623). The parents, F1, F2, and BC1 generations were phenotyped for seed coat wrinkling in a greenhouse in Stoneville, MS during the summer of 2006. Genetic analysis indicated that the wrinkled seed coat trait in PI 87623 was inherited as a single recessive gene. A test for allelism, conducted in the greenhouse with a segregating F2 population derived from T-311 × PI 87623, showed that the gene from PI 87623 is different from the shr gene in T-311. A field study of a larger population, derived from a reciprocal cross of the same parents, confirmed these results, but also suggested epistatic interactions between the genes. A linkage map was developed using 195 SSR and SNP markers on 168 F2 individuals of the cross PI 567743 × PI 87623. Linkage analysis identified only one significant locus which was located on chromosome 5 (linkage group A1), confirming identification of a new gene that controls seed coat wrinkling in soybean. This study demonstrates genetic control of seed coat wrinkling, which offers the potential for selecting cultivars with less seed coat wrinkling for heat-stressed production environments.