Clonal Differences Research Articles

Immature growth performance of three important rubber tree (Hevae brasiliensis) clones in a drought-prone area

Adaptation of rubber tree clones to water-limited areas and maintenance of trunk radial growth are important keys for performance of genetic material. The rubber farmers need to shorten the interim phases to produce latex, which is considered “immature” phase, i.e. the time without income. The objective of this study was to compare the performance of three important rubber tree clones: GT1, the elder clone as control, which is still widely used in Cambodia and West Africa; RRIM600, the “all-round” clone, the most planted clone in Thailand, the first world producer; and RRIT251, the expanding clone, recommended by the Rubber Authority of Thailand, all in the field condition. The investigation was conducted in a drought-prone area of Northeast Thailand, where the dry season lasts 5 to 6 months. The cumulated growth and the annual growth were analyzed 4.5 years after planting. The trunk girth and height were measured monthly. Main climatic variables were hourly recorded. The year was separated in three periods: the leaves-shed season from January to April, the wet season from May to September, and the dry season with canopy maintenance from October to December. The results showed significant clonal effect on both trunk girth and height; however, with relatively low differences. The trunk girth of clone RRIT251 was about 29 cm and 10% higher than GT1. The difference was not significant in RRIM600. The annual girth increment was mainly located in wet season (63%) without clonal effect. The clonal difference was occurred in the dry season, where RRIT251 was better performed particularly in the leave-shed period preceding wet season. On a monthly basis, the relative trunk girth increment rate was highly negatively related to the vapor pressure deficit. We hypothesized that rubber clones shared a common strategy of dehydration avoidance, while RRIT251 expressed a little less degree of avoidance.

Treatment of upper urinary tract urothelial carcinoma

Upper tract urothelial (transitional cell) carcinoma (UTUC) is a rare malignant disease occurring in roughly two people per 100 000 population. UTUCs comprise 5–10% of urothelial carcinomas overall. 1 Roupret M Babjuk M Comperat E et al. European Association of Urology Guidelines on upper urinary tract urothelial carcinoma: 2017 update. Eur Urol. 2018; 73: 111-122 Summary Full Text Full Text PDF PubMed Scopus (448) Google Scholar A paucity of dedicated high-level evidence has led to extrapolation from studies of urothelial bladder cancer to establish treatment recommendations. Although UTUC biology and clinical features overlap with those of urothelial bladder cancer, differences exist in gene alteration patterns (eg, FGFR3 and HRAS are more frequently altered in UTUC whereas TP53, RB1, and ERBB2 are less frequently mutated), clinical stage at presentation (higher stage at presentation, on average, for patients with UTUC), gender differences (a higher percentage of women get UTUC, although in terms of total numbers they are still in a minority compared with men), and stage-for-stage outcomes (prognosis is poorer for patients with UTUC). 2 Audenet F Isharwal S Cha EK et al. Clonal relatedness and mutational differences between upper tract and bladder urothelial carcinoma. Clin Cancer Res. 2019; 25: 967-976 Crossref PubMed Scopus (67) Google Scholar , 3 Winters BR De Sarkar N Arora S et al. Genomic distinctions between metastatic lower and upper tract urothelial carcinoma revealed through rapid autopsy. JCI Insight. 2019; 4e128728 Crossref Scopus (12) Google Scholar As with many rare disease settings, patients with UTUC are disenfranchised because dedicated research is challenging. Adjuvant chemotherapy in upper tract urothelial carcinoma (the POUT trial): a phase 3, open-label, randomised controlled trialGemcitabine–platinum combination chemotherapy initiated within 90 days after nephroureterectomy significantly improved disease-free survival in patients with locally advanced UTUC. Adjuvant platinum-based chemotherapy should be considered a new standard of care after nephroureterectomy for this patient population. Full-Text PDF Open Access

Variation in canopy structure, leaf area, light interception and light use efficiency among Eucalyptus clones

Differences in growth rates between Eucalyptus clones depend on differences in the acquisition of resources, and the efficiency of using resources to produce carbohydrates and grow wood. We examined differences in canopy structure, light interception, and light use efficiency for the 18 TECHS clones in a common garden experiment in Brazil. The degree of clumping within canopies varied substantially among clones, leading to large differences in both leaf area and light interception per unit of leaf area. Two methods of determining plot-level leaf area index (LP-80 and LAI-2000) were moderately well correlated (R2 = 0.4), but both methods underestimated actual leaf area index (determined by destructive sampling) by about one-third. Completely overcast sky conditions increased accuracy of leaf area estimates, reducing variation among measurements within plots and lowering the number of samples needed to obtain a given level of precision. Genotypes with high leaf area clumping also had higher leaf angle inclinations than genotypes with lower clumping. The apparent light interception coefficient (k) averaged 0.56 for the LP-80, and 0.47 for the LAI-2000. The range of k estimates differed by up to 2-fold among clones, underscoring the limited generality of light extinction coefficients. Light interception ranged from about 70 to 95% of incoming light, and leaf area index accounted for only 30% of the pattern in light interception among clones. Differences in stemwood production were influenced more strongly by clonal differences in efficiency of light use (stemwood production per unit of light intercepted) than by differences in leaf area or light interception. The efficiency of producing wood per unit of light intercepted spanned a two-fold range, with higher efficiencies for more productive clones. We suggest that production ecology studies focus more on measurements of light interception than on leaf area, avoiding issues about difficult-to-measure features of crown and canopy structures. The additional step of characterizing light use efficiency would also be very important.

Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Knowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec isolates from ECB episodes with different epidemiological characteristics. A random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG. ST73 was most prevalent among the 212 non-ESBL-Ec (N = 26, 12.3%) and ST131 among the 69 ESBL-Ec (N = 30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N = 22, P value < .001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1-6) and 7 (IQR 4-9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < .001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1-8). Median VG scores were 13 (IQR 9-20) and 12 (IQR 8-14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = .002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11-21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 5-13) or hepatic-biliary focus (median 11, IQR 5-18) (P values = .007 and .04, respectively). VG content varied between different E. coli STs. Non-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.

Matching site-suitable poplars to rotation length for optimized productivity

Diversity of applications, productivity potential, broad suitability and genetic variations make Populus a valuable fast-growing genus. Our goal was to assess if clonal site-suitability varies with rotation-length. We examined survival, growth (height, diameter at breast height) and estimated stem and total-wood (stem and branches) biomass of 89 clones near Fountain, North Carolina (35°42′7.52″ N, 77°34′35.04″ W) in the coastal southeastern USA at four- and eight-year rotations. The unsuitability of some clones was evident at early age while other clones became less suitable with stand age. Specifically, most mortality occurred by year-four, yet 25% clones experienced 17 to 50% mortality at older ages. Clone ‘379’ was the most site-suitable with 100% survival and 141.3 kg total-wood per tree (approximately 47.5 Mg ha−1 yr−1). Moreover, several clones with low survival produced high per-hectare biomass. Biomass (stem and total-wood) rankings changed between four- and eight-year rotations with only three top-ten clones in year-four (‘379’, ‘402’, ‘449’) in the top-ten of year-eight and two top-ten clones in year-eight (‘379’, ‘402’) also in the top-ten of year-four. Clonal productivity differences increased by 25 to 836% with age. Clones of TD (Populus trichocarpa Torr and Gray × P. deltoids Barts Ex Marsh) and DD (P. deltoides × P. deltoides) genotypes were affected by wood infection (Septoria musiva) indicating that selection based on disease resistance should be performed at clonal level. Hence, for productivity-focused stands, site-suitable clones should be selected by productivity first, then narrowed by survival and rotation length. Changes in the most ‘site-suitable’ clones can be expected between longer and shorter rotations.

Re: Clonal Relatedness and Mutational Differences between Upper Tract and Bladder Urothelial Carcinoma.

Re: Clonal Relatedness and Mutational Differences between Upper Tract and Bladder Urothelial Carcinoma.

Abstract 1348: Characterization of SLFN11 protein expression in circulating tumor cells (CTCs) of patients with metastatic castration resistant prostate cancer (mCRPC) prior to platinum based chemotherapy

Abstract Background: Clinical benefit in response to chemotherapeutic agents that induce replication stress such as PARP inhibitors and cisplatin has been associated with mutations in DNA damage repair (DDR) genes. However, prediction of benefit is not solely explained by DDR mutations; therefore, additional biomarkers for prediction of clinical benefit of these agents are needed. SLFN11 is recruited to stalled replication forks where it sensitizes cells to DNA damage induced replication stress . Presence of SLFN11 protein expression in tumor cells is related to pre-clinical and clinical benefit of PARPi in small cell lung cancer. Previously, we reported high cellular heterogeneity in progressive mCRPC, and as such, we sought to examine whether SLFN11 protein expression was expressed in patients offered platinum chemotherapy to understand the subclonal heterogeneity of CTCs with and without SLFN11 protein expression. Material and methods: 30 blood samples from mCRPC patients prior to treatment with a platinum chemotherapy from MSKCC were sent to Epic Sciences for CTC enumeration and SLFN11 protein expression characterization. Nuclear localization of SLFN11 was reviewed by a trained technician. 70 CTCs from patients with and without SLFN11 CTCs were single cell sequenced and analyzed for copy number alterations (CNA) and clonality. Results: 83% (25/30) of patient samples had detectable CTCs, and 53% (16/30) samples had at least one SLFN11+ CTC. For patients with SLFN11(+) CTCs, 81% (13/16) had only nuclear localized SLFN11 expression; 6% (1/16) had a mix of CTCs with nuclear and non-nuclear localized SLFN11 expression; 13% (2/16) had no nuclear localized SLFN11 expression. In 13 patients with exclusively nuclear localized SLFN11 expression, the % of SLFN11(+) CTCs ranged from 2-100% with median of 11%. Single CTC NGS analysis of patients demonstrated genomic heterogeneity between CTCs. In patients with both SLFN11+ and SLFN11- CTCs, no discernable clonal or CNA difference was observed between SLFN11+ and SLFN11- CTCs. Conclusions: SLFN11 protein expression was observed subclonally in a majority fraction of patients with progressive mCRPC prior to platinum chemotherapy. SLFN11 expression heterogeneity was not consistent with a genetic mechanism. Studies examining whether SLFN11+ CTCs as a sensitivity marker to PARPi &amp; cisplatin, but not ARSi or taxanes in mCRPC are ongoing. Citation Format: Luisa Fernandez, John Poirier, Angel Rodriguez, Melanie Hulling, Robin Richardson, Ramsay Sutton, Rhett Jiles, Joseph Schonhoft, Jerry Lee, Nadia Ebrahim, Emily Carbone, Ethan Barnett, Mark Landers, Yipeng Wang, Ryan Dittamore, Charles Rudin, Howard Scher. Characterization of SLFN11 protein expression in circulating tumor cells (CTCs) of patients with metastatic castration resistant prostate cancer (mCRPC) prior to platinum based chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1348.

Local Coastal Configuration Rather Than Latitudinal Gradient Shape Clonal Diversity and Genetic Structure of Phymatolithon calcareum Maerl Beds in North European Atlantic

Maerl beds are one of the world’s key coastal ecosystems and are threatened by human activities and global change. In this study, the genetic diversity and structure of one of the major European maerl-forming species, Phymatolithon calcareum, was studied using eight microsatellite markers. Two sampling scales (global: North East Atlantic and regional: Galicia) were investigated and fifteen maerl beds from Atlantic Europe were sampled. At the regional-scale the location of sites outside and within four estuaries allowed to test for the influence of coastal configuration on population connectivity and genetic diversity. Results suggested that clonal reproduction plays an important role in the population dynamics of P. calcareum maerl beds. Clonality was variable among populations, even within the same region. At the European scale, these differences in clonality cannot be explained by the geographic or latitudinal distribution of the populations studied. A significant genetic differentiation was found among almost all population pairs and a positive correlation between geographic and genetic distances showed the limited dispersal capacity of P. calcareum. Moreover, a very clear pattern of genetic structure was revealed at the regional scale between populations located within and at the mouth of the estuaries. Genetic differentiation among estuaries was less marked for the sites located in outer-zones compared to those located in the inner-zones. In addition, variation in level of clonality linked to seascape was also observed: populations situated in the outer-zones of the estuaries were less clonal than those in the inner-zones. Finally, populations from the same estuary generally shared one or several mutilocus genotypes.

Adaptability of Populus to Physiography and Growing Conditions in the Southeastern USA

Populus species have a high productivity potential as short-rotation woody crops, provided that site-suitable varieties are planted. The Coastal Plain, the Piedmont, and the Blue Ridge Mountains make up a significant part of the eastern and southeastern USA, and an insight into poplar productivity and adaptability will be valuable for the successful implementation of large-scale poplar stands in these regions. The objectives of this study were to examine the green wood biomass (hereafter biomass), biomass allocation, and wood properties of poplars in relation to growing conditions, physiography, and topography. The biomass of 4-year-old poplars was estimated using an equation derived through destructive sampling. Biomass-based clonal rankings were compared across the various site conditions (fertility, irrigation, land marginality, soil preparation, and topography) and the three physiographic provinces. Although not all clonal differences in biomass were significant, growing conditions, physiography, and soil preparation affected the clonal rankings and the significance of the clonal differences. Biomass changes due to physiography and land conditions were more structured at the genomic-group level. A higher-altitude physiography led to greater biomass increases in Populus trichocarpa × Populus deltoids (TD) clones than in P. deltoids × P. deltoids (DD) clones and vice versa. Favorable soil quality or management generally led to greater biomass of DD clones than of TD and P. deltoids × Populus maximowiczii (DM) clones. Weather-related variables were not clearly correlated with biomass, while land aspect was a significant influence on the biomass of genomic groups and clones. The site significantly affected wood density, moisture content, and carbon and nitrogen concentrations, while the clonal effects on wood composition and the clonal and site effects on biomass allocation were insignificant. Although clones showing greater biomass responses to growing conditions generally belonged to the same genomic group, clone-level selection could produce greater biomass gains than selection at the genomic-group level.

Clonal Relatedness and Mutational Differences between Upper Tract and Bladder Urothelial Carcinoma.

To investigate genomic differences between urothelial carcinomas of the upper tract (UTUC) and bladder (UCB), with a focus on defining the clonal relatedness of temporally distinct tumors. We prospectively sequenced tumors and matched germline DNA using targeted next-generation sequencing methods. The cohort included 195 UTUC patients and 454 UCB patients. For a subgroup of 29 patients with UTUC and a history of a subsequent UCB, both tumors were analyzed to assess their clonal relatedness. With the progression to higher UTUC clinical state, there were fewer alterations in the RTK/RAS pathway but more alterations in TP53/MDM2. Compared with UCB, TP53, RB1, and ERBB2 were less frequently altered in UTUC (26% vs. 46%, 3% vs. 20%, 8% vs. 19%, respectively; Q < 0.001), whereas FGFR3 and HRAS were more frequently altered (40% vs. 26%, 12% vs. 4%, respectively; Q < 0.001). On the basis of an integrated analysis of tumor mutational burden, MSIsensor score and mutational signature, 7.2% of UTUC tumors were classified as MSI-high/MMR-deficient (MSI-H/dMMR). The risk of bladder recurrence after UTUC was significantly associated with mutations in FGFR3, KDM6A, CCND1, and TP53. Comparison of UCB with corresponding UTUC tumors from the same patient supports their clonal relatedness. UTUC and UCB exhibit significant differences in the prevalence of common genomic alterations. In individual patients with a history of both tumors, UCB and UTUC were always clonally related. Genomic characterization of UTUC provides information regarding the risk of bladder recurrence and can identify tumors associated with Lynch syndrome.

Ibrutinib Increases the Clonality of TCR Repertoire in Patients with Chronic Lymphocytic Leukemia

The T-cell receptor (TCR) repertoire in patients with chronic lymphocytic leukemia (CLL) is more clonal than in healthy individuals. Shared TCR clonotypes among patients may reflect the expansion of T-cell clones that recognize common antigens. It is unknown whether these antigens are tumor-derived to which T cells react, or microbial or auto-antigens that promote expansion of both T cells and the leukemic clone. Ibrutinib inhibits Bruton tyrosine kinase and interleukin-2-inducible kinase and has been shown to modulate the T-cell compartment of patients with CLL.We performed deep sequencing of the TCRβ repertoire (Adaptive Biotechnologies) in 26 patients with CLL prior to treatment with ibrutinib, at the time of response, and either at disease progression or during sustained remission. TCR clonality was calculated as the inverse of Shannon entropy normalized to the number of productive clones in a sample and it accounts for both the number of unique clonotypes and the extent to which one or a few clonotypes dominate the sample repertoire. Clonality values may range between 0 and 1 with values closer to 1 indicating a more oligoclonal repertoire. Nonparametric tests were applied for statistical analyses, and paired analyses were performed to compare metrics across different time points.The median productive clonality in CLL patients before treatment was .1795, more than double the clonality reported for healthy donors (.0750, provided by Adaptive Biotechnologies). Differences in clonality were studied between subgroups of patients defined by clinical and biologic features. Overall, the TCR repertoire in treatment naïve patients (clonality = .1454, n = 15) was less clonal than in patients with relapsed/refractory CLL (clonality = .2468, n = 11, P = .002). β2-microglobulin ≥ 3.5 mg/L and CD8+ T-cell counts above the normal reference range were also associated with higher clonality (P = .030 and .003, respectively). Further, CD8+ T-cell counts (median 1134 /uL, IQR 670 - 2474) when assessed as a continuous variable, were correlated with clonality (ρ = .620, P = .001).Next, we evaluated the TCR repertoire at partial (n = 23) or complete (n = 2) response after a median duration of 12 months (range 6-36) on ibrutinib. Clonality increased at the time of response compared to baseline (median increase 33.2%, P = .048) despite a concomitant decrease in CD4+ and CD8+ T-cell counts. In 12 patients who subsequently developed progressive disease, analysis of the TCR repertoire revealed a decrease in clonality (median decrease 5.7%, P = .026) from the time of response to relapse (median 13 months, range 4-32) while CD4+ and CD8+ T-cell counts increased. In contrast, clonality did not significantly change among patients with sustained response to ibrutinib measured 12 months after the first response time point.Overrepresented clonotypes comprising more than .05% of the TCR repertoire at baseline or at the time of response were selected for further analyses (median of 95 clonotypes per patient). Eighteen out of 25 patients shared at least one clonotype. In total, 20 shared clonotypes were identified and interestingly, their frequencies decreased with ibrutinib treatment (P = .003).Interrogation of overrepresented clonotypes in public databases identified 46 clonotypes previously reported in viral infections (77%) followed by those associated with autoimmune conditions (13%) and cancer (10%). The most commonly implicated viruses were Epstein Barr virus, cytomegalovirus and influenza. We observed the convergence of multiple clonotypes recognizing the same viral epitopes and 8 clonotypes were shared between at least 2 patients. However, they behaved differently on treatment with an increase in frequency in some patients and decrease in others.In summary, we show that ibrutinib induces a more clonal TCR repertoire and that it is lost at relapse. Overrepresented clonotypes were generally patient-specific and correlated with CD8+ T cells. These findings suggest that CD8+ T-cell clonotypes recognizing private antigens expand and mediate anti-tumor activity during treatment with ibrutinib.This research was in part supported by the Intramural Research Program of the NIH, NHLBI. DisclosuresWiestner:Pharmacyclics LLC, an AbbVie Company: Research Funding.

Clonal and atypical Toxoplasma strain differences in virulence vary with mouse sub-species

The severe virulence of Toxoplasma gondii in classical laboratory inbred mouse strains contradicts the hypothesis that house mice (Mus musculus) are the most important intermediate hosts for its transmission and evolution because death of the mouse before parasite transmission equals death of the parasite. However, the classical laboratory inbred mouse strains (Mus musculus domesticus), commonly used to test Toxoplasma strain differences in virulence, do not capture the genetic diversity within Mus musculus. Thus, it is possible that Toxoplasma strains that are severely virulent in laboratory inbred mice are avirulent in some other mouse sub-species. Here, we present insight into the responses of individual mouse strains, representing strains of the genetically divergent Mus musculus musculus, Mus musculus castaneus and Mus musculus domesticus, to infection with individual clonal and atypical Toxoplasma strains. We observed that, unlike M. m. domesticus, M. m. musculus and M. m. castaneus are resistant to the clonal Toxoplasma strains. For M. m. musculus, we show that this is due to a locus on chromosome 11 that includes the genes that encode the interferon gamma (IFNG)-inducible immunity-related GTPases (Irgs) that can kill the parasite by localising and subsequently vesiculating the parasitophorous vacuole membrane. However, despite the localization of known effector Irgs to the Toxoplasma parasitophorous vacuole membrane, we observed that some atypical Toxoplasma strains are virulent in all the mouse strains tested. The virulence of these atypical strains in M. m. musculus could not be attributed to individual rhoptry protein 5 (ROP5) alleles, a secreted parasite pseudokinase that antagonises the canonical effector Irgs and is indispensable for parasite virulence in laboratory inbred mice (M. m. domesticus). We conclude that murine resistance to Toxoplasma is modulated by complex interactions between host and parasite genotypes and may be independent of known effector Irgs on murine chromosome 11.

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay.

Chardonnay is the basis of some of the world’s most iconic wines and its success is underpinned by a historic program of clonal selection. There are numerous clones of Chardonnay available that exhibit differences in key viticultural and oenological traits that have arisen from the accumulation of somatic mutations during centuries of asexual propagation. However, the genetic variation that underlies these differences remains largely unknown. To address this knowledge gap, a high-quality, diploid-phased Chardonnay genome assembly was produced from single-molecule real time sequencing, and combined with re-sequencing data from 15 different Chardonnay clones. There were 1620 markers identified that distinguish the 15 clones. These markers were reliably used for clonal identification of independently sourced genomic material, as well as in identifying a potential genetic basis for some clonal phenotypic differences. The predicted parentage of the Chardonnay haplomes was elucidated by mapping sequence data from the predicted parents of Chardonnay (Gouais blanc and Pinot noir) against the Chardonnay reference genome. This enabled the detection of instances of heterosis, with differentially-expanded gene families being inherited from the parents of Chardonnay. Most surprisingly however, the patterns of nucleotide variation present in the Chardonnay genome indicate that Pinot noir and Gouais blanc share an extremely high degree of kinship that has resulted in the Chardonnay genome displaying characteristics that are indicative of inbreeding.

Screening of 19 Salix clones in effective phytofiltration potentials of manganese, zinc and copper in pilot-scale wetlands

Willows (Salix spp.) have been regarded as one of interesting plants for phytofiltration of water contaminated with trace metals. In this paper, the clonal differences in tolerance and phytofiltration capacity of mixed metals (Mn, Zn, and Cu) were evaluated in greenhouse pilot-scale wetlands with a floating-support culture system. The results showed that broad clonal variations of biomass accumulation in response to mixed metals ranging from growth inhibition to stimulation. Clones differed in tolerance to multi-metals by tolerance index (TI) based on shoot and root biomass. We also found that wide variations in uptake and accumulation of three metals, which was related to species/clones and metal species. The willows showed high Mn and Zn translocation capacity from roots to leaves suitable for phytoextraction. In contrast, all clones had poor Cu translocation capacity, and Cu mainly retained in roots suitable for rhizofiltration. Among all Salix clones, clones SM30 and J903 had large phytofiltration potential for three metals with their high tolerance.

Nutritional Value of the Duckweed Species of the Genus Wolffia (Lemnaceae) as Human Food.

Species of the genus Wolffia are traditionally used as human food in some of the Asian countries. Therefore, all 11 species of this genus, identified by molecular barcoding, were investigated for ingredients relevant to human nutrition. The total protein content varied between 20 and 30% of the freeze-dry weight, the starch content between 10 and 20%, the fat content between 1 and 5%, and the fiber content was ~25%. The essential amino acid content was higher or close to the requirements of preschool-aged children according to standards of the World Health Organization. The fat content was low, but the fraction of polyunsaturated fatty acids was above 60% of total fat and the content of n-3 polyunsaturated fatty acids was higher than that of n-6 polyunsaturated fatty acids in most species. The content of macro- and microelements (minerals) not only depended on the cultivation conditions but also on the genetic background of the species. This holds true also for the content of tocopherols, several carotenoids and phytosterols in different species and even intraspecific, clonal differences were detected in Wolffia globosa and Wolffia arrhiza. Thus, the selection of suitable clones for further applications is important. Due to the very fast growth and the highest yield in most of the nutrients, Wolffia microscopica has a high potential for practical applications in human nutrition.

Transcriptomic analysis dissects the mechanistic insight into the Daphnia clonal variation in tolerance to toxic Microcystis

AbstractCyanobacteria have become more prevalent than other phytoplankton in freshwater assemblages during summer. In such conditions, cyanobacterial traits may reduce zooplankton fitness and the energy flow efficiency from primary producers to aquatic herbivores. Cladocerans, as the dominant zooplankton grazers in freshwater ecosystems, exhibit clonal variation in their tolerance to cyanobacteria with an increasing gradient in eutrophication history. Hitherto, research on the full modes of action (MoAs) of Daphnia clonal differences in tolerance to toxic Microcystis still remains in its infancy. We conducted fitness and transcriptome analyses on two Daphnia clones, clone TH09 and TH14. A significant decline in body growth rate was detected in the sensitive clone TH09 compared with the tolerant clone TH14 at the presence of toxic Microcystis. Furthermore, transcriptional analysis indicated that major MoAs such as glutathione metabolism, protein processing in endoplasmic reticulum, amino sugar/nucleotide sugar metabolism, and arachidonic acid metabolism were linked to the tolerance fitness in Daphnia similoides. These results provided mechanistic insights into the pathways of genetic and biological processes involved in cyanobacteria tolerance in the Daphnia clonal variation, and propose that the genetic architecture of this fitness‐related trait would be helpful to clarify how zooplankton clones adapt to harmful algal blooms.

The Sugar and Polyol Composition of Hevea Brasiliensis Latex Depends on the Clonal Origin of the Tree

The variability of natural rubber (NR) properties has been partly ascribed to the 3 to 5% non-isoprene components (lipids, proteins, carbohydrates and minerals) present in NR. Of all the factors that might be held responsible for this variability, clonal origin has appeared to be prominent. The sugars and polyols of latex from five Hevea brasiliensis clones (RRIM600, GT1, PB235, PB260 and PB217) were extracted with ethanol after specific NR sample pretreatment in a cyclohexane/ethanol solution. Latex carbohydrates were characterised by high performance anion-exchange chromatography equipped with a pulsed amperometric detector (HPAE-PAD). Total extractable carbohydrates, single sugars and polyols were analysed for each clone to evaluate how clonal origin affected the variability of latex carbohydrate compositions. Significant clonal differences were identified, both in the total sugar and polyol contents of the latex, and in the quantity of each element. The differences between the latex extracts of clones GT1, PB217, PB260, PB235 and RRIM600 did not come solely from the presence of major carbohydrates, such as quebrachitol or sucrose, but also effectively from minor carbohydrates, such as sorbitol or galactose. Some minor carbohydrates could even be used as biochemical clone indicators.

Population‐level responses to temperature, density and clonal differences in Daphnia magna as revealed by integral projection modelling

Abstract Raising global temperatures are predicted to have strong consequences for ectotherms, as metabolic rates depend directly on external temperatures. To understand consequences for population fitness, a full life cycle approach is important because (a) temperature can have opposite effects on different vital rates (growth, survival, reproduction) and (b) sensitivities of population growth rate to changes in vital rates can vary in magnitude. As vital rates are concurrently influenced by other factors, adequately predicting temperature effects requires factors such as body size, population density and genetics to be taken into account. The aim of this study was to quantify the role of temperature on all vital rates of Daphnia magna individuals and their integrated effects on population dynamics. In addition, we evaluated how clonal lineages differed in their temperature response, both on the vital rate and population level. We performed a laboratory experiment, in which we followed 40 populations (five clonal lineages × eight temperatures) during 80 days. Due to our novel set‐up, we were able to quantify vital rates of individuals within those populations. We identified relations between vital rates and body size, lineage, temperature and population density and used a size‐structured integral projection model to integrate the experimental effects over all vital rates. We found negative density dependence in growth and reproduction, resulting in lineage‐specific carrying capacities. Population fitness showed a thermal optimum that differed among genotypes. It is interesting that we found that clones had different life‐history strategies, optimizing population fitness via different routes. As no lineage outperformed the others in all vital rates, we identified trade‐offs between vital rates, which had strong effects on the dynamics of the population. Moreover, simulations suggest that the genetic composition of mixed populations is temperature‐dependent. Our results underscore the importance of studying individuals within their population when predicting responses to environmental change. The observed density effects, which were as strong as temperature effects but explained considerably more variation in population growth, would have been overlooked in life table experiments. Furthermore, differential temperature responses emphasize the importance of genetic variation in the ability of ectotherm species such as Daphnia magna to respond to climate change. A plain language summary is available for this article.

Establishment strategies for poplars, including mulch and plant types, on agricultural land in Sweden

Biomass from forestry is one of the largest components of Sweden’s renewable resources. Poplars are currently the highest producing tree species available and are therefore natural choices for biomass-oriented production. Growing poplars has been of most interest on agricultural land, but the knowledge and experience about their cultivation is still limited. Factors that have a large impact on the regeneration results are plant material, competing vegetation, browsing and damage caused by voles or climatic factors. Due to large establishment costs, there is a need to find methods to secure the establishment both biologically and economically. In this study the effect of plastic mulch in combination with three different plant types (short cuttings, long cuttings and rooted plants) were tested at three different sites. Five years after planting, the overall effect of mulch was an improved plant survival and growth. In most cases, long cuttings outperformed short cuttings and rooted plants. Clonal differences were present, indicating the importance of using plant material adapted to site conditions. All sites were heavily affected by browsing and during the experimental period 100% of the plants were damaged at some point. Planting poplars without fencing is therefore doubtful. Results from this study conclude that poplars can be established with success on agricultural land if proper measures are used depending on the site to be planted.

The timing of latewood formation determines the genetic variation of wood density in Larix kaempferi

The seasonal change of the wood formation stage, especially the timing of the cessation of cell division, are key to understanding the genetic difference of wood density. Wood density is important in terms of various wood properties and forest carbon sequestration properties. Wood density is genetically variable, although the mechanism that causes this variability is not well clarified. We hypothesized that wood formation dynamics differ genetically and that this affects wood density. We analyzed the dynamics of wood formation, including the timing of earlywood-latewood transition and the cessation of cell division, and their relationship to clonal differences in wood density using nine clones of Larix kaempferi, through microscopy observations and X-ray densitometry. Wood density showed a strong correlation with the proportion of latewood. The clonal variation of the timing of the earlywood-latewood transition was small. The timing of the cessation of cell division differed clonally by a maximum of 42.7 days and was correlated with the duration of latewood formation. The duration of latewood formation showed a correlation coefficient of 0.925 with the proportion of latewood. We described a hierarchical relationship that explained the genetic difference in wood density in mature L. kaempferi wood in the following sequence; the timing of cessation of latewood formation, the duration of latewood formation, the proportion of latewood, and wood density.