Tree Clones Research Articles

Micropropagation and in vitro rejuvenation of Eucalyptus cloeziana F. Muell.

Micropropagation is an important tool for the propagation for recalcitrant species, like Eucalyptus cloeziana. This is a first reported about a complete study of the E. cloeziana, it includes the vegetative rescue protocol of mature trees, its micropropagation up to the implementation of a mini-garden and clonal micro-garden and evaluation of adventitious rooting of their propagules. The in vitro rejuvenation of E. cloeziana genotypes (03, 05, 06, 13 and 15), over 21 successive subcultures, was evaluated by comparing minicutting and microcutting techniques and the efficiency of this biotechnological tool for cloning of the mature trees. The results provide evidence of the in vitro rejuvenation occurring in the mature E. cloeziana trees during micropropagation, leading to increases in the multiplication ratios of the microstumps of three genotypes (03, 05 and 15). The survival and callogenesis percentages of the mini and microcuttings of E. cloeziana were higher than 80% upon exiting of the greenhouse (30-days old) in the three cutting times. The results suggesting that factors beyond tissue maturity influence the adventitious rooting of the E. cloeziana because minicuttings and microcuttings of the 05 and 13 elite genotypes exhibited rooting percentages lower than 20%. These findings provided a theoretical basis for realizing the micropropagation of the epicormic shoots of the mature trees and, subsequently, its in vitro rejuvenation by axillary bud proliferation.

Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback.

Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for T. cacao L. and provide insights into the genetics underlying resistance and susceptibility to VSD.

Physical and Mechanical Properties of 20-Year-Old Clonal Teak Trees in Ngawi, East Java, Indonesia

Physical and Mechanical Properties of 20-Year-Old Clonal Teak Trees in Ngawi, East Java, Indonesia

Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data

Single-cell RNA sequencing (scRNA-seq) enables comprehensive characterization of the micro-evolutionary processes of B cells during an adaptive immune response, capturing features of somatic hypermutation (SHM) and class switch recombination (CSR). Existing phylogenetic approaches for reconstructing B cell evolution have primarily focused on the SHM process alone. Here, we present tree inference of B cell clonal lineages (TRIBAL), an algorithm designed to optimally reconstruct the evolutionary history of B cell clonal lineages undergoing both SHM and CSR from scRNA-seq data. Through simulations, we demonstrate that TRIBAL produces more comprehensive and accurate B cell lineage trees compared to existing methods. Using real-world datasets, TRIBAL successfully recapitulates expected biological trends in a model affinity maturation system while reconstructing evolutionary histories with more parsimonious class switching than state-of-the-art methods. Thus, TRIBAL significantly improves B cell lineage tracing, useful for modeling vaccine responses, disease progression, and the identification of therapeutic antibodies.

Фенотипическая оценка клонов плюсовых деревьев сосны обыкновенной (Pinus sylvestris L.) в лесостепной зоне Башкирского Предуралья

An assessment of the main morphometric features of the ramets of clones of Scots pine plus trees in a comparative aspect has been carried out. The vegetative progeny of plus trees of the species are represented as part of a clonal plantation created in 2005 in the Dyurtyulinskiy forestry of the forest-steppe zone of the Republic of Bashkortostan in an area with the С2 type of forest growing conditions. Compliance with the breeding and genetic principle of phenotypic assessment of intraand intergroup differences in Scots pine clones and ramets, as well as methodical and methodological requirements for conducting the field stage of the study, has been ensured. Taxation indicators (the height and diameter of the stem, the diameter and length of the crown, the increment of the central shoot in height) have been taken into account for 100 clones at a continuous count. A varying nature of the distribution of the average values of the analyzed stem indicators in the vegetative progeny of plus trees has been revealed. The best growth in stem diameter (25.5±0.73 cm) and height (11.2±0.16 m), as well as central shoot increment (0.45±0.02 m), are typical for the progeny of clones of the plus tree 29/17. Clones 263/40, 264/41, 262/39 with taxation indicators above the average for the entire set of trees in the clone archive are of high breeding value, which indicates the specificity of the genotypes of these specimens. The levels of significance of the differences and the intensity of selection of the best clones of plus trees based on morphometric features have been determined, which indicates the different nature of the individual non-identity of each of the plus trees relative to the rest of the trees studied. The valuable genotypes of the progeny of Scots pine plus trees identified in the clone archive can be recommended for further use in forest seed breeding when creating highly productive and sustainable artificial plantations of this valuable tree species in the region.

Response of rubber tree clones to black crust

AbstractThe occurrence of black crust, a disease previously considered secondary, has become a cause for concern due to early leaf fall in rubber trees (Hevea brasiliensis). This study aimed to identify sources of resistance to black crust in 21 clones of rubber trees in a clonal garden. To achieve this, the disease severity was evaluated through eight assessments conducted over a 2‐year period. In each evaluation, 15 leaflets from three different parts of the plant (bottom, middle third and crown) were randomly collected, resulting in a total of 45 leaflets per plant. These leaflets were then taken to the laboratory, and the software Leaf Doctor was used to measure the percentage of leaf area exhibiting symptoms of black crust. The results were analysed using the Scott‐Knott test at a 5% probability level. The clones with the highest infected leaf area observed during the evaluations were IAC300, IAC418, IAC503, PB311 and RRIM600. Clone IAC511 did not show any symptoms of the disease in any of the evaluations. Clones IAC301, IAC411, IAC501, IAC507 and IRCA111 exhibited low percentages of affected leaf areas. Additionally, this study revealed the progression of the disease over the evaluation period. The infection initially starts on the youngest leaves (crown) in March and subsequently intensifies in the middle third of the plant, corresponding to the youngest leaf previously infected in the crown. Furthermore, environmental data collected in the experimental area over the 2‐year evaluation period indicated that the disease manifests with greater severity when the average temperatures fall below 25°C after periods of heavy rainfall, followed by dry periods with low relative humidity. The data presented in this study significantly contribute to the management of this disease in the field by identifying clones where the disease manifests with lower severity.

Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data.

Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing cells, by means of a relatively error-prone process resulting in somatic mutations in their genome. Because of the higher mutation rate compared to the nuclear genome, mitochondrial mutations have been used to track cellular lineage, particularly using single-cell sequencing that measures mitochondrial mutations in individual cells. However, existing methods to infer the cell lineage tree from mitochondrial mutations do not model "heteroplasmy," which is the presence of multiple mitochondrial clones with distinct sets of mutations in an individual cell. Single-cell sequencing data thus provide a mixture of the mitochondrial clones in individual cells, with the ancestral relationships between these clones described by a mitochondrial clone tree. While deconvolution of somatic mutations from a mixture of evolutionarily related genomes has been extensively studied in the context of bulk sequencing of cancer tumor samples, the problem of mitochondrial deconvolution has the additional constraint that the mitochondrial clone tree must be concordant with the cell lineage tree. We formalize the problem of inferring a concordant pair of a mitochondrial clone tree and a cell lineage tree from single-cell sequencing data as the Nested Perfect Phylogeny Mixture (NPPM) problem. We derive a combinatorial characterization of the solutions to the NPPM problem, and formulate an algorithm, MERLIN, to solve this problem exactly using a mixed integer linear program. We show on simulated data that MERLIN outperforms existing methods that do not model mitochondrial heteroplasmy nor the concordance between the mitochondrial clone tree and the cell lineage tree. We use MERLIN to analyze single-cell whole-genome sequencing data of 5220 cells of a gastric cancer cell line and show that MERLIN infers a more biologically plausible cell lineage tree and mitochondrial clone tree compared to existing methods. https://github.com/raphael-group/MERLIN.

Biomass yield and metal phytoextraction efficiency of Salix and Populus clones harvested at different rotation lengths in the field experiment

BackgroundPhytoextraction belongs to environmentally well-accepted remediation technologies to remove metals from contaminated soils. Due to long-time requirement, sufficient data for proper phytoextraction evaluation are missing. Four clones of fast-growing trees: two willow species (S1), Salix viminalis L. (Salix schwerinii E.L.Wolf × S. viminalis) × S. viminalis) and (S2)—Salix smithiana (Salix × smithiana Willd.), and two poplar clones (P1), Populus Max-4 (Populus nigra L. × Populus maximowiczii A. Henry) and (P2) Wolterson (P. nigra L.) were cultivated under field conditions at medium-to-high Cd and Pb, and low Zn soil contamination to assess trees’ long-term ability of biomass production and removal of potentially toxic elements (PTEs). The biomass yield and PTE uptake were measured during 8 years of regular growth under three rotation lengths: four harvests following 2-year periods (4 × 2y), two harvests in 4-year periods (2 × 4y), and one harvest representing 8 years of growth (1 × 8y).ResultsIn most cases, the highest annual dry biomass yield was achieved with a 2 × 4y rotation (P1 = 20.9 t ha−1 y−1, S2 = 18.4 t ha−1y−1), and the yield decreased in order 2 × 4y > 1 × 8y > 4 × 2y of harvesting periods. Only clone S1 showed a different pattern. The differences in biomass yield substantially affected the PTE phytoextraction. The greatest amount of Cd and Zn was removed by willow S2, with the highest biomass yield, and the strongest ability to accumulate PTEs. With 2 × 4y rotation, S2 removed a substantial amount of Cd (9.07%) and Zn (3.43%) from the topsoil horizon (0–20 cm) and 5.62% Cd and 2.04% Zn from horizon 20–40 cm; phytoextraction rate was slightly lower for 1 × 8y rotation. The poplar P1 removed the most Pb in the 1 × 8y rotation, but the overall Pb phytoextraction was negligible. The results indicated that lignin and cellulose contents increased, and hemicellulose content decreased with increased concentrations of Cd, Pb and Zn in poplars wood.ConclusionsThe data confirmed that phytoextraction over longer harvest periods offered promising results for removing Cd from medium- to high-level contaminated soils; however, the ability of Pb removal was extremely low. The longer harvest period should be more economically feasible.Graphical

Why are triploid quaking aspen (Populus tremuloides) common?

Quaking aspen is a clonal tree species that has mixed ploidy, often with high relative abundance of both diploids and triploids but no haploids or tetraploids. Triploids typically have low fertility, leaving their occurrence apparently unlikely from an evolutionary perspective, unless they provide a "triploid bridge" to generating higher-fitness tetraploids-which are not observed in this species. This study focused on how triploidy can be maintained in quaking aspen. A computational model was used to simulate gamete production, sexual reproduction, asexual reproduction, parent survival, and offspring survival in a population. All parameters were assumed to be cytotype-dependent and environment-independent. Sampling methods were used to identify parameter combinations consistent with observed cytotype frequencies. Many processes and parameter values were sufficient to yield a moderate frequency of triploids, and very few were necessary. The most plausible route involved higher triploid survival at the parent or offspring stage and limited unreduced gamete production by either diploid or triploid parents. Triploid fertility was helpful but not necessary. The coexistence of diploids and triploids in quaking aspen is statistically likely and promoted by the existenceof commonly observed, long-lived triploid clones. However, other mechanisms not captured by the model related to environmental variation could also occur. Further empirical data or more complex but difficult-to-parameterize models are needed to gain further insight.

Comparing the antibody repertoire of XBB1.5 booster immunization with mRNA or protein-based platforms

Abstract The SARS-CoV-2 spike (S) protein is an essential target for neutralizing antibodies, accumulating mutations, and generating variants of concern (VOC). The Omicron variant is a VOC that continues to evolve into antibody-resistant subvariants, such as XBB1.5. This led to the approval of an updated mRNA vaccine and a protein-based vaccine to target the XBB1.5 strain. However, whether these vaccines can elicit functional monoclonal antibodies specifically against this strain and how the different vaccine platforms (mRNA vs protein) shape the antibody repertoire is unknown. Here, we analyzed the antibody repertoire of five humans who either received the updated mRNA or the protein-based vaccine. We used the Immcantation framework to analyze the VDJ sequences. We assigned V, D, and J genes using IgBlast according to the Change-O pipeline. Clonal groups were defined using the SCOPer package v.1.3.0, and then we calculated somatic hypermutation (SHM) for the BCR sequences. Firstly, we reconstructed germline V and J sequences. The total number of mutations was found for the V gene using SHazaM v.1.2.0, and clonal lineage trees were built using the dowser package v.2.0. We are currently expressing human monoclonal antibodies from the participants and will assess binding, neutralization, and affinity. Our results will compare the antibody activity elicited by vaccination between protein-based (Novavax) and mRNA (Pfizer/Moderna) in humans receiving the XBB1.5 booster.

Promising conilon coffee trees clones for agroforestry and intercropping systems

Promising conilon coffee trees clones for agroforestry and intercropping systems

Abstract 2326: Integrating single nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs) into single-cell clonal lineage inference

Abstract Background: We extend algorithms for clonal lineage inference (``tumor phylogenetics'') from single-cell DNA sequence (scDNA-seq) data to accommodate broader classes of genetic variants, including single nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). Methods: We develop a computational method based on constrained optimization, posing a problem of inferring cellular lineage trees consistent with a given scDNA-seq data set constrained to follow a Dollo parsimony model for SNVs and SVs. We then seek an optimal tree consistent with these constraints so as to optimize for a CNA minimum evolution model balanced against measure of consistency of the different data types with one another relative to the reconstructed set of clones. We pose this problem as an integer linear program (ILP) that we solve heuristically via a coordinate descent algorithm. We tested the resulting method on a combination of synthetic scDNA-seq data and publicly available real data. Results: Results on synthetic data show the method to be effective at constructing lineage trees under a variety of parameter domains, including variations in noise levels, clone numbers, single cells, and mutation rates. We further show it to yield improved accuracy over widely used prior models that operate on only subsets of these variant types. Application to previously published scDNA-seq data demonstrate the method to be effective at inferring clonal lineage trees incorporating all three variant types. The results further show how the different kinds of variants can contribute in tandem to progression along single cell lineages or to the emergence of clones exhibiting hallmarks of distinct mechanisms of progression. Conclusion: The results support the effectiveness of our method in resolving accurate trees from scDNA-seq data including diverse variant types, as well as the value of considering these mutation types collectively in developing a comprehensive understanding of how various forms of somatic mutability together shape clonal evolution in cancers. Citation Format: Nishat Bristy, Xuecong Fu, Russell Schwartz. Integrating single nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs) into single-cell clonal lineage inference [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2326.

Лесная селекция и генетическое разнообразие древесных пород

In scientific literature there are different views on the connection between forest tree breeding and genetic variability of wood species. This article has aimed to review the current Russian and foreign literary sources on the impact of breeding measures on the level of genetic diversity of forest wood species. Maintaining adequate genetic variability is necessary for adaptation to the environmental changes, as well as for long-term breeding. As soon as seed plantations are the source of improved seeds for forest regeneration, the influence of such factors as the number of clones and background pollination on the level of genetic variability of the progeny has been considered in detail. The data on the minimal clone number in seed plantations in different countries has been presented and the variability of the clones based on their fertility has been discussed. The importance of background pollination in seed plantations has been highlighted as soon as, on the one hand, it reduces the effect of breeding, but on the other hand, it increases the level of genetic variability of the progeny. A decline in genetic diversity of wood species can be caused by clone selection (which is the basis for clonal forestry). However the analysis of literary sources has shown that the reduction in genetic diversity is minimal if scientific recommendations are fulfilled. The use of the seeds from controlled cross-breeding of plus trees selected as a result of genetic evaluation (the so-called family forestry with vegetative propagation) in the somatic embryogenesis of the common spruce increases the level of genetic variability of the progeny. It has been shown that the multiple population breeding system allows to combine intensive long-term breeding and genetic conservation of wood species. The conclusion has been drawn that the implementation of optimally planned wood species breeding programs does not lead to significant narrowing of genetic diversity. On the contrary, forest tree breeding contributes to the preservation of a better gene pool, transmitting it in the process of forest regeneration through improved seeds and clones into homogeneous stands. Moreover, the objects of forest seed growing such as the archives of plus tree clones and forest seed plantations, as well as test cultures contain valuable genetic material ex situ.

Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar

BackgroundDespite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome.ResultsWe present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring’s phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment.ConclusionsGenome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as biomarkers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.

Inheritance of growth ring components and the possibility of early selection for higher wood density in Japanese cedar (Cryptomeria japonica D. Don)

Key messageWe elucidated the age trends of narrow-sense heritability and phenotypic/genetic correlations and the age–age genetic correlation of growth ring components of Cryptomeria japonica D. Don by investigating progenies of controlled crossings by soft X-ray densitometry analysis. Wood density in the C. japonica breeding program can be efficiently improved by selecting trees with a higher earlywood density and latewood percentage as early as forest stand ages of 5–9 years.ContextWood density within the trunk is affected by the intra-ring wood density profile and its age trend from pith to bark. Wood density can be efficiently improved by clarifying whether wood density and highly correlated intra-ring components are under additive genetic control.AimsThe aim of this study was to elucidate the age trends of narrow-sense heritability and phenotypic/genetic correlations of growth ring components and investigate the possibility of early selection for improving wood density in Cryptomeria japonica.MethodsWe quantified seven growth ring components (width, density, earlywood/latewood width, average earlywood/latewood density, and latewood percentage) for 5112 annual rings of 342 18-year-old trees derived from 24 controlled pollinated full-sib families of C. japonica plus tree clones by soft X-ray densitometry analysis. Genetic parameters and correlations among the seven growth ring components were analyzed using a linear mixed model and the breedR package.ResultsEarlywood density and latewood percentage exhibited a higher phenotypic and genetic correlation with ring density than the other ring components at almost all ages. Earlywood density and latewood percentage exhibited a lower correlation with ring width than the other ring components after a stand age of 5 years. The age–age genetic correlation of earlywood density and latewood percentage was 0.70 for a stand age of 17 years and was strong at stand ages of 5 and 9 years.ConclusionEfforts focusing on improving earlywood density and latewood percentage may contribute to improving wood density efficiently in tree breeding programs for C. japonica. Traits related to the ring density of C. japonica trees can possibly be selected as early as stand ages of 5–9 years, and the required period for progeny selection may be substantially shortened when selecting trees with high wood density.

Genome-wide identification of rubber tree pathogenesis-related 10 (PR-10) proteins with biological relevance to plant defense

Pathogenesis-related 10 (PR-10) is a group of small intracellular proteins that is one of 17 subclasses of pathogenesis-related proteins in plants. The PR-10 proteins have been studied extensively and are well-recognized for their contribution to host defense against phytopathogens in several plant species. Interestingly, the accumulation of PR-10 proteins in the rubber tree, one of the most economically important crops worldwide, after being infected by pathogenic organisms has only recently been reported. In this study, the homologous proteins of the PR-10 family were systemically identified from the recently available rubber tree genomes in the NCBI database. The sequence compositions, structural characteristics, protein physical properties, and phylogenetic relationships of identified PR-10 proteins in rubber trees support their classification into subgroups, which mainly consist of Pru ar 1-like major allergens and major latex-like (MLP) proteins. The rubber tree PR10-encoding genes were majorly clustered on chromosome 15. The potential roles of rubber tree PR-10 proteins are discussed based on previous reports. The homologous proteins in the PR-10 family were identified in the recent genomes of rubber trees and were shown to be crucial in host responses to biotic challenges. The genome-wide identification conducted here will accelerate the future study of rubber tree PR-10 proteins. A better understanding of these defense-related proteins may contribute to alternative ways of developing rubber tree clones with desirable traits in the future.

The Environmental and Genetic Controls of Increment Suggest a Limited Adaptability of Native Populations of Norway Spruce to Weather Extremes

In the Baltics, warming is expected to burden the growth of Norway spruce Picea abies, with weather anomalies/extremes having strong triggering effects, which can be mitigated by tree breeding. Within the region, breeding programmes have been aiming for productivity, yet being conservative, their sustainability depends on the adaptability of native genotypes, which is unclear. The adaptability of genotypes can be assessed through local adaptations and phenotypic plasticity, with the sensitivity of increment depicting the conformity of genotypes and environments. To assess the adaptability of native populations to anticipated climates, local genetic adaptation and phenotypic plasticity of the weather sensitivity of the radial increment were assessed by the methods of time series analysis and quantitative genetics based on three clonal trials (low-density single-tree plot plantations of grafted clones of native plus trees) representing the local climatic gradient in Latvia. The growth of trees was sensitive to the moisture availability in summer and the thermal regime in winter, yet coinciding anomalies in both were associated with abrupt changes in tree ring width. These environmental effects differed among the clones, indicating genetic controls over the sensitivity of increment, which, however, decreased under a warmer climate, suggesting a limited adaptability of local populations to warming. Still, the weather-growth relationships showed moderate phenotypic plasticity, suggesting some mid-term adaptability. Accordingly, supplementation of breeding populations via assisted gene transfer with the genotypes that are adapted to warmer and drier climates appears crucial.

Genome Sequencing to Discover Drivers of Clonal Expansion in Smoldering Multiple Myeloma

Background Better prediction models are required to identify patients with high-risk smoldering multiple myeloma (SMM) who can benefit from early intervention therapy before progression. Several studies have reported heterogeneity of genetic abnormalities found at the SMM stage, but whether any mutations are sufficient to cause, or instead prevent progression, remains an important open question. We leveraged whole-genome sequencing (WGS) in a large cohort of precursor patients, including repeated assessment over time, to discover drivers of disease growth and monitor malignant transformation to multiple myeloma (MM). Methods WGS was performed on tumor and normal cells from 141 untreated patients with SMM or Monoclonal Gammopathy of Undetermined Significance (MGUS) from the PCROWD study. Moreover, this dataset was combined with genomic data from the literature totaling 1,034 patients with WGS and/or exomes sampled across MM stages for comparative analysis and biomarker discovery. MutSig2CV, GISTIC2, and a novel method for structural variants were used to establish the list of candidate drivers across disease stages, with statistical power to detect myeloma drivers from points mutations found in ≥2% of patients. Longitudinal WGS data were analyzed with the PhylogicNDT suite of tools to characterize clonal competition in treated and untreated patients. Results Patients were followed for a median time of 20 months from the sample date (range: 3 to 78 months), during which 11 progressed. Patients evenly distributed across 20/2/20 stages: 44 Low-Risk (37%), 29 Intermediate-Risk (24%), 47 High-Risk (39%) SMM were combined with 20 MGUS, showing our method is reliable to perform WGS in lower disease burden settings. A validation cohort comprising 61 SMM with a median follow-up time of 36 months (range: 5 to 121), with 22 progressions was used to corroborate our findings. As significant drivers could be specifically enriched among indolent disease (i.e., protective alleles), we ran de novo driver mutation discovery across MM stages. In addition to well-characterized MM drivers ( KRAS, NRAS, etc.), 16 new candidate genes were found significantly mutated, including IKFZ3 (Aiolos), a transcription factor and direct target of degradation with lenalidomide therapy, harboring frameshift and stop-gain mutations in the protein dimerization domain which could affect complete differentiation of plasma cells. Mutants in KRAS found primarily at codons Q61, G12, G13, and A146, were found in all disease risk groups and associated with progression to overt myeloma (Odds Ratio: 6.1, CI95%: [1.4, 27], p=0.01, q<0.1). Next, we investigated genes targeted by copy-number abnormalities and found candidates in four regions with focal gains, including on chr(1q21), chr(8q24)( MYC), chr(3q26), and chr(16p13) encompassing BCMA. These genes have higher expression in patients with broad gain (e.g. BCMA: P=8.8E-3) or focal amplification (e.g. BCMA: P=6.2E-5), and therefore are likely to be underlying targets of the rearrangements driving cancer growth. Of note, BCMA antigen point mutations remained undetected in SMM, therefore patients with gain(16p) represent an attractive population for targeted therapy with anti-BCMA agents, in particular when the gain is clonal (n=3/8, 38%). In 15 patients, serial sampling of tumor cells allowed longitudinal WGS analyses and reconstruction of phylogenetic trees of disease clones (2 to 3 timepoints, 4 progressors, median 14 months). Maintenance of the major clone with subclonal structure evolving over time was confirmed in all patients, and we observed a steady increase in the cancer cell fraction of known MM mutations (del(13q), KRAS, DIS3 loss of function) in untreated patients. In one patient receiving early interventional treatment, a 70% reduction of M-spike concentration was achieved after four cycles of therapy; however, partial response was found in tandem with the selection of a high-risk del(1p) and of a KRAS activating G12S mutation, before increase and clinical progression to MM. Conclusion These results highlight the power of genomic profiling in MM for early detection, discovery of novel drivers, monitoring of clonal selection and transformation to malignant disease. We show SMM is not a simple genomically-mature disorder, but rather a dynamic state with competing subclones, which could be leveraged for therapeutic interventions.

EVALUATION OF THE BEHAVIOR OF RUBBER TEAS IN THE MARGINAL ZONE OF COTE DIVOIRE: CASE OF THE LOCALITIES OF MAN, TOUMODI AND PRIKRO

For a better orientation of Ivorian rubber cultivation in new areas of occupation, a study with the main objective of evaluating the behavior of rubber trees, with a view to better orientation of the extension of this culture was undertaken in the localities of Man, Toumodi and Prikro. The plant material used was rubber tree clones. During this study, the methodology consisted of evaluatingthe evolution of trees at 1.7m from the ground for mature plants and 1m from the ground for immature plants by measuring the circumference of the trees planted with a tape measure on different biotopes and soil textures previously defined. Production, dry notch rate and dry notch length of mature trees was also measured on the same parameters of the previous crop and texture. The results revealed thatthe previous cultivation of the rubber plots influences the mortality rate of the plants with a low rate observed in Man (17.30%) on the previous forest, also the trees had good growth on this previous one in Man (8.5cm.year-1) and Prikro (9cm.year-1). At ground level, the plants had a better level of radial growth in the localities of Man (8.30 and 9.06 cm.year-1) and Prikro (8.01 cm.year-1) with a more texture clayey (25% < clay < 50%). The average rubber production was also better in Man on the previous forest crop (63.85 ± 15.1 g.a-1s-1) similarly for the more clayey texture (25% < clay < 50%) with 63.27 ± 6 .1 g.a-1s-1. Rubber production from these new localities was generally good. So, through the results of this investigation, it should be noted that new rubber growing areas could be an asset for rubber production in Côte dIvoire. As a result, this culture can be encouraged in these areas, but with monitoring and supervision of producers on good agricultural practices.

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.

Emerging ultra-low coverage single-cell DNA sequencing (scDNA-seq) technologies have enabled high resolution evolutionary studies of copy number aberrations (CNAs) within tumors. While these sequencing technologies are well suited for identifying CNAs due to the uniformity of sequencing coverage, the sparsity of coverage poses challenges for the study of single-nucleotide variants (SNVs). In order to maximize the utility of increasingly available ultra-low coverage scDNA-seq data and obtain a comprehensive understanding of tumor evolution, it is important to also analyze the evolution of SNVs from the same set of tumor cells. We present Phertilizer, a method to infer a clonal tree from ultra-low coverage scDNA-seq data of a tumor. Based on a probabilistic model, our method recursively partitions the data by identifying key evolutionary events in the history of the tumor. We demonstrate the performance of Phertilizer on simulated data as well as on two real datasets, finding that Phertilizer effectively utilizes the copy-number signal inherent in the data to more accurately uncover clonal structure and genotypes compared to previous methods.