Crop improvement studies based on molecular approaches in interspecific Oil palm hybrids

162 p.Oil Palm (OP) is the crop with the highest oil yield per hectare and as a result, its use has spread rapidly in tropical regions of Asia, Africa and America. The main OP plantations consist of Elaeis guineensis (Eg) species, known to produce high amounts of oil. However, in American regions this species is being affected by the ¿Pudrición de Cogollo¿ disease leading to dead palms. Therefore, OP companies started crossing this species with E. oleifera (Eo) palms which is resistant to this disease. The obtained interspecific hybrids show interesting characteristic inherited from both parents; resistance to different diseases, interesting oil quality characteristics, competitive oil production and decreased height which prolongs its useful life. However, little work has been done in the improvement of these hybrids. This thesis tries to address this gap applying different molecular approaches. First, an extensive study of an amplicon of the ¿Shell-thickness¿ (Sh) gene has been conducted on 568 Eg, Eo and hybrid genotypes. Then, with the aim to discover promising new Candidate Genes (CG) that could be exploited in further molecular assisted selection systems (MAS) a large phenotypic study of 25 production and quality traits have been performed within 198 hybrid genotypes fllowed by two Association Mapping (AM) assays. These latter have been based on targeted CG and random Restriction site associated RNA sequencing(RARSeq) approaches.Neiker teknalia Lafabril Energy & Palma Sampoerna Agr

Crop improvement studies based on molecular approaches in interspecific Oil palm hybrids

162 p.Oil Palm (OP) is the crop with the highest oil yield per hectare and as a result, its use has spread rapidly in tropical regions of Asia, Africa and America. The main OP plantations consist of Elaeis guineensis (Eg) species, known to produce high amounts of oil. However, in American regions this species is being affected by the ¿Pudrición de Cogollo¿ disease leading to dead palms. Therefore, OP companies started crossing this species with E. oleifera (Eo) palms which is resistant to this disease. The obtained interspecific hybrids show interesting characteristic inherited from both parents; resistance to different diseases, interesting oil quality characteristics, competitive oil production and decreased height which prolongs its useful life. However, little work has been done in the improvement of these hybrids. This thesis tries to address this gap applying different molecular approaches. First, an extensive study of an amplicon of the ¿Shell-thickness¿ (Sh) gene has been conducted on 568 Eg, Eo and hybrid genotypes. Then, with the aim to discover promising new Candidate Genes (CG) that could be exploited in further molecular assisted selection systems (MAS) a large phenotypic study of 25 production and quality traits have been performed within 198 hybrid genotypes fllowed by two Association Mapping (AM) assays. These latter have been based on targeted CG and random Restriction site associated RNA sequencing(RARSeq) approaches.Neiker teknalia Lafabril Energy & Palma Sampoerna Agr

Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis of CHD8 heterozygous cerebral organoids

More than 100 genes have been associated with significantly increased risks of autism spectrum disorders (ASD) with an estimate of ∼1000 genes that may contribute. The new challenge is to investigate the molecular and cellular functions of these genes during neural and brain development, and then even more challenging, to link the altered molecular and cellular phenotypes to the ASD clinical manifestations. In this study, we used single-cell RNA-seq analysis to study one of the top risk genes, CHD8, in cerebral organoids, which models early neural development. We identified 21 cell clusters in the organoid samples, representing non-neuronal cells, neural progenitors, and early differentiating neurons at the start of neural cell fate commitment. Comparisons of the cells with one copy of a CHD8 knockout allele, generated by CRISPR/Cas9 editing, and their isogenic controls uncovered thousands of differentially expressed genes, which were enriched with functions related to neural and brain development, cilium organization, and extracellular matrix organization. The affected genes were also enriched with genes and pathways previously implicated in ASD, but surprisingly not for schizophrenia and intellectual disability risk genes. The comparisons also uncovered cell composition changes, indicating potentially altered neural differential trajectories upon CHD8 reduction. Moreover, we found that cell-cell communications were affected in the CHD8 knockout organoids, including the interactions between neural and glial cells. Taken together, our results provide new data and information for understanding CHD8 functions in the early stages of neural lineage development and interaction

Polycomb repressive complex 2 in adult hair follicle stem cells is dispensable for hair regeneration.

Hair follicle stem cells (HFSCs) are multipotent cells that cycle through quiescence and activation to continuously fuel the production of hair follicles. Prior genome mapping studies had shown that tri-methylation of histone H3 at lysine 27 (H3K27me3), the chromatin mark mediated by Polycomb Repressive Complex 2 (PRC2), is dynamic between quiescent and activated HFSCs, suggesting that transcriptional changes associated with H3K27me3 might be critical for proper HFSC function. However, functional in vivo studies elucidating the role of PRC2 in adult HFSCs are lacking. In this study, by using in vivo loss-of-function studies we show that, surprisingly, PRC2 plays a non-instructive role in adult HFSCs and loss of PRC2 in HFSCs does not lead to loss of HFSC quiescence or changes in cell identity. Interestingly, RNA-seq and immunofluorescence analyses of PRC2-null quiescent HFSCs revealed upregulation of genes associated with activated state of HFSCs. Altogether, our findings show that transcriptional program under PRC2 regulation is dispensable for maintaining HFSC quiescence and hair regeneration

Detection of significant SNP associated with production and oil quality traits in interspecific oil palm hybrids using RARSeq

International audienceA RARSeq based Association mapping study was performed in a population of 104 Elaeis oleifera x E. guineensis hybrids of five origins with the aim of finding functional markers associated to six productive and 19 oil quality traits. For this purpose mRNA of each genotype was isolated and double stranded cDNA was synthesized. Following digestion with two restriction enzymes and adapter ligation, a size selected pool of barcoded amplicons was produced and sequenced using Illumina MiSeq. The obtained sequences were processed with a "snakemake" pipeline, filtered and missing values were imputed. For all traits except two significant effects of the origin was observed. Genetic diversity analyses revealed high variability within origins and an excess of heterozygosity in the population. Two GLM models with Q matrix or PCA matrix as covariates and two MLM models incorporating in addition a Kinship matrix were tested for genotype-phenotype associations using GAPIT software. Using unadjusted p values ( < 0.01) 78 potential associations were detected involving 25 SNP and 20 traits. When applying FDR multiple testing with p < 0.05, 25 significant associations remained involving eight SNP and six quality traits. Four SNP were located in genes with a potential relevant biological meaning

Association Mapping between Candidate Gene SNP and Production and Oil Quality Traits in Interspecific Oil Palm Hybrids

Oil palm production is gaining importance in Central and South America. However, the main species Elaeis guineensis (Eg) is suffering severely from bud rod disease, restricting the potential cultivation areas. Therefore, breeding companies have started to work with interspecific Elaeis oleifera x Eg (Eo x Eg) hybrids which are tolerant to this disease. We performed association studies between candidate gene (CG) single nucleotide polymorphisms (SNP) and six production and 19 oil quality traits in 198 accessions of interspecific oil palm hybrids from five different origins. For this purpose, barcoded amplicons of initially 167 CG were produced from each genotype and sequenced with Ion Torrent. After sequence cleaning 115 SNP remained targeting 62 CG. The influence of the origins on the different traits was analyzed and a genetic diversity study was performed. Two generalized linear models (GLM) with principle component analysis (PCA) or structure (Q) matrixes as covariates and two mixed linear models (MLM) which included in addition a Kinship (K) matrix were applied for association mapping using GAPIT. False discovery rate (FDR) multiple testing corrections were applied in order to avoid Type I errors. However, with FDR adjusted p values no significant associations between SNP and traits were detected. If using unadjusted p values below 0.05, seven of the studied CG showed potential associations with production traits, while 23 CG may influence different quality traits. Under these conditions the current approach and the detected candidate genes could be exploited for selecting genotypes with superior CG alleles in Marker Assisted Selection systems

COVID-19 immune signatures in Uganda persist in HIV co-infection and diverge by pandemic phase

Abstract Little is known about the pathobiology of SARS-CoV-2 infection in sub-Saharan Africa, where severe COVID-19 fatality rates are among the highest in the world and the immunological landscape is unique. In a prospective cohort study of 306 adults encompassing the entire clinical spectrum of SARS-CoV-2 infection in Uganda, we profile the peripheral blood proteome and transcriptome to characterize the immunopathology of COVID-19 across multiple phases of the pandemic. Beyond the prognostic importance of myeloid cell-driven immune activation and lymphopenia, we show that multifaceted impairment of host protein synthesis and redox imbalance define core biological signatures of severe COVID-19, with central roles for IL-7, IL-15, and lymphotoxin-α in COVID-19 respiratory failure. While prognostic signatures are generally consistent in SARS-CoV-2/HIV-coinfection, type I interferon responses uniquely scale with COVID-19 severity in persons living with HIV. Throughout the pandemic, COVID-19 severity peaked during phases dominated by A.23/A.23.1 and Delta B.1.617.2/AY variants. Independent of clinical severity, Delta phase COVID-19 is distinguished by exaggerated pro-inflammatory myeloid cell and inflammasome activation, NK and CD8+ T cell depletion, and impaired host protein synthesis. Combining these analyses with a contemporary Ugandan cohort of adults hospitalized with influenza and other severe acute respiratory infections, we show that activation of epidermal and platelet-derived growth factor pathways are distinct features of COVID-19, deepening translational understanding of mechanisms potentially underlying SARS-CoV-2-associated pulmonary fibrosis. Collectively, our findings provide biological rationale for use of broad and targeted immunotherapies for severe COVID-19 in sub-Saharan Africa, illustrate the relevance of local viral and host factors to SARS-CoV-2 immunopathology, and highlight underemphasized yet therapeutically exploitable immune pathways driving COVID-19 severity