Dataset Information

RNAseq based variant dataset in a black poplar association panel.

ABSTRACT:

Objective

Black poplar (Populus nigra L.) is a species native to Eurasia with a wide distribution area. It is an ecologically important species from riparian ecosystems, that is used as a parent of interspecific (P. deltoides x P. nigra) cultivated poplar hybrids. Variant detection from transcriptomics sequences of 241 P. nigra individuals, sampled in natural populations from 11 river catchments (in four European countries) is described here. These data provide new valuable resources for population structure analysis, population genomics and genome-wide association studies.

Data description

We generated transcriptomics data from a mixture of young differentiating xylem and cambium tissues of 480 Populus nigra trees sampled in a common garden experiment located at Orléans (France), corresponding to 241 genotypes (2 clonal replicates per genotype, at maximum) by using RNAseq technology. We launched on the resulting sequences an in-silico pipeline that allowed us to obtain 878,957 biallelic polymorphisms without missing data. More than 99% of these positions are annotated and 98.8% are located on the 19 chromosomes of the P. trichocarpa reference genome. The raw RNAseq sequences are available at the NCBI Sequence Read Archive SPR188754 and the variant dataset at the Recherche Data Gouv repository under https://doi.org/10.15454/8DQXK5 .

SUBMITTER: Rogier O

PROVIDER: S-EPMC10546633 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Publications

RNAseq based variant dataset in a black poplar association panel.

Rogier Odile O Chateigner Aurélien A Lesage-Descauses Marie-Claude MC Mandin Claire C Brunaud Véronique V Caius José J Soubigou-Taconnat Ludivine L Almeida-Falcon José J Bastien Catherine C Benoit Vanina V Bodineau Guillaume G Boizot Nathalie N Buret Corinne C Charpentier Jean-Paul JP Déjardin Annabelle A Delaunay Alain A Fichot Régis R Laine Prade Véronique V Laurans Françoise F Le Jan Isabelle I Legac Anne-Laure AL Maury Stéphane S Gebreselassie Mesfin Nigussie MN Poursat Patrick P Ridel Céline C Sanchez Léopoldo L Jorge Véronique V Segura Vincent V

BMC research notes 20231002 1

<h4>Objective</h4>Black poplar (Populus nigra L.) is a species native to Eurasia with a wide distribution area. It is an ecologically important species from riparian ecosystems, that is used as a parent of interspecific (P. deltoides x P. nigra) cultivated poplar hybrids. Variant detection from transcriptomics sequences of 241 P. nigra individuals, sampled in natural populations from 11 river catchments (in four European countries) is described here. These data provide new valuable resources for ...[more]

PMID: 37784104

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Project description:BackgroundGenomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation by breeders. Low density panels imputed to higher densities offer a cheaper alternative during the first stages of genomic resources development. Our study is the first to explore the imputation in a tree species: black poplar. About 1000 pure-breed Populus nigra trees from a breeding population were selected and genotyped with a 12K custom Infinium Bead-Chip. Forty-three of those individuals corresponding to nodal trees in the pedigree were fully sequenced (reference), while the remaining majority (target) was imputed from 8K to 1.4 million SNPs using FImpute. Each SNP and individual was evaluated for imputation errors by leave-one-out cross validation in the training sample of 43 sequenced trees. Some summary statistics such as Hardy-Weinberg Equilibrium exact test p-value, quality of sequencing, depth of sequencing per site and per individual, minor allele frequency, marker density ratio or SNP information redundancy were calculated. Principal component and Boruta analyses were used on all these parameters to rank the factors affecting the quality of imputation. Additionally, we characterize the impact of the relatedness between reference population and target population.ResultsDuring the imputation process, we used 7540 SNPs from the chip to impute 1,438,827 SNPs from sequences. At the individual level, imputation accuracy was high with a proportion of SNPs correctly imputed between 0.84 and 0.99. The variation in accuracies was mostly due to differences in relatedness between individuals. At a SNP level, the imputation quality depended on genotyped SNP density and on the original minor allele frequency. The imputation did not appear to result in an increase of linkage disequilibrium. The genotype densification not only brought a better distribution of markers all along the genome, but also we did not detect any substantial bias in annotation categories.ConclusionsThis study shows that it is possible to impute low-density marker panels to whole genome sequence with good accuracy under certain conditions that could be common to many breeding populations.

Project description:Poplars are fast-growing, high-yielding forest tree species, whose cultivation as second-generation biofuel crops is of increasing interest and can efficiently meet emission reduction goals. Yet, breeding elite poplar trees for drought resistance remains a major challenge. Worldwide breeding programs are largely focused on intra/interspecific hybridization, whereby Populus nigra L. is a fundamental parental pool. While high-throughput genotyping has resulted in unprecedented capabilities to rapidly decode complex genetic architecture of plant stress resistance, linking genomics to phenomics is hindered by technically challenging phenotyping. Relying on unmanned aerial vehicle (UAV)-based remote sensing and imaging techniques, high-throughput field phenotyping (HTFP) aims at enabling highly precise and efficient, non-destructive screening of genotype performance in large populations. To efficiently support forest-tree breeding programs, ground-truthing observations should be complemented with standardized HTFP. In this study, we develop a high-resolution (leaf level) HTFP approach to investigate the response to drought of a full-sib F2 partially inbred population (termed here 'POP6'), whose F1 was obtained from an intraspecific P. nigra controlled cross between genotypes with highly divergent phenotypes. We assessed the effects of two water treatments (well-watered and moderate drought) on a population of 4603 trees (503 genotypes) hosted in two adjacent experimental plots (1.67 ha) by conducting low-elevation (25 m) flights with an aerial drone and capturing 7836 thermal infrared (TIR) images. TIR images were undistorted, georeferenced, and orthorectified to obtain radiometric mosaics. Canopy temperature (Tc) was extracted using two independent semi-automated segmentation techniques, eCognition- and Matlab-based, to avoid the mixed-pixel problem. Overall, results showed that the UAV platform-based thermal imaging enables to effectively assess genotype variability under drought stress conditions. Tc derived from aerial thermal imagery presented a good correlation with ground-truth stomatal conductance (gs) in both segmentation techniques. Interestingly, the HTFP approach was instrumental to detect drought-tolerant response in 25% of the population. This study shows the potential of UAV-based thermal imaging for field phenomics of poplar and other tree species. This is anticipated to have tremendous implications for accelerating forest tree genetic improvement against abiotic stress.

Project description:ImportanceA genetic variant in the TTR gene (rs76992529; Val122Ile), present more commonly in individuals with African ancestry (population frequency: 3%-4%), causes misfolding of the tetrameric transthyretin protein complex that accumulates as extracellular amyloid fibrils and results in hereditary transthyretin amyloidosis.ObjectiveTo estimate the association of the amyloidogenic Val122Ile TTR variant with the risk of heart failure and mortality in a large, geographically diverse cohort of Black individuals.Design, setting, and participantsRetrospective population-based cohort study of 7514 self-identified Black individuals living in the US participating in the REGARDS (Reasons for Geographic and Racial Differences in Stroke) study with genetic data available and without heart failure at baseline. The participants were enrolled at the baseline visit (2003-2007). The end of follow-up for the majority of outcomes was on December 31, 2018. All-cause mortality data were available through December 31, 2020.ExposuresTTR Val122Ile (rs76992529) genotype.Main outcome and measuresThe primary outcome was incident heart failure (first hospitalization for heart failure or death due to heart failure). The secondary outcomes were heart failure mortality, cardiovascular mortality, and all-cause mortality. The multivariable Cox proportional hazards regression analyses were adjusted for genetic ancestry and demographic, clinical, and social factors.ResultsAmong 7514 Black participants (median age, 64 years [IQR, 57-70 years]; 61% women), the population frequency of the TTR Val122Ile variant was 3.1% (232 variant carriers and 7282 noncarriers). During a median follow-up of 11.1 years (IQR, 5.9-13.5 years), incident heart failure occurred in 535 individuals (34 variant carriers and 501 noncarriers) and the incidence of heart failure was 15.64 per 1000 person-years among variant carriers vs 7.16 per 1000 person-years among noncarriers (adjusted hazard ratio [HR], 2.43 [95% CI, 1.71-3.46]; P < .001). Deaths due to heart failure occurred in 141 individuals (13 variant carriers and 128 noncarriers) and the incidence of heart failure mortality was 6.11 per 1000 person-years among variant carriers vs 1.85 per 1000 person-years among noncarriers (adjusted HR, 4.19 [95% CI, 2.33-7.54]; P < .001). Deaths due to cardiovascular causes occurred in 793 individuals (34 variant carriers and 759 noncarriers) and the incidence of cardiovascular death was 15.18 per 1000 person-years among variant carriers vs 10.61 per 1000 person-years among noncarriers (adjusted HR, 1.69 [95% CI, 1.19-2.39]; P = .003). Deaths due to any cause occurred in 2715 individuals (100 variant carriers and 2615 noncarriers) and the incidence of all-cause mortality was 41.46 per 1000 person-years among variant carriers vs 33.94 per 1000 person-years among noncarriers (adjusted HR, 1.46 [95% CI, 1.19-1.78]; P < .001). There was no significant interaction between TTR variant carrier status and sex on incident heart failure and the secondary outcomes.Conclusions and relevanceAmong a cohort of Black individuals living in the US, being a carrier of the TTR Val122Ile variant was significantly associated with an increased risk of heart failure.

Dataset Information

RNAseq based variant dataset in a black poplar association panel.

Objective

Data description

Publications

RNAseq based variant dataset in a black poplar association panel.

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