Development of a SNaPshot assay for the genotyping of organellar SNPs in four closely related pines

Dendrobiology, Journal Year: 2023, Volume and Issue: 90, P. 76 - 85

Published: Oct. 27, 2023

Mitochondrial (mtDNA) and chloroplast (cpDNA) polymorphisms are valuable resources to study past demographic changes, phylogenetics evolution, especially in forest tree species, where these genomes haploid uniparentally transferred. The organellar markers were usually scored separately using direct sequencing or PCR-based approaches, which can be time-consuming expensive, large-scale population genetics research. In this study, we developed an efficient cost-effective SNaPshot assay for genotyping preselected ­mtDNA cpDNA polymorphism four closely related pine species including Scots (Pinus sylvestris L.) three taxa from the Pinus mugo complex. We validated method by samples derived 12 populations of their wide geographical distribution range Europe. results proved high accuracy with a success rate 99.7%. set assayed shows significant genetic variation. By multiplex assay, provided sensitive molecular tool intra- interspecific analyses. presented protocol is useful fast relatively cheap SNP organelle genome species. SNPs allow studying discrimination detailed investigations history structure. Given its numerous benefits rate, appears practical resource makeup Particularly, it proves advantageous genetics.

Language: Английский

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Uncovering epigenetic and transcriptional regulation of growth in Douglas‐fir: identification of differential methylation regions in mega‐sized introns

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 22(4), P. 863 - 875

Published: Nov. 20, 2023

Summary Tree growth performance can be partly explained by genetics, while a large proportion of variation is thought to controlled environmental factors. However, what extent DNA methylation, stable epigenetic modification, contributes phenotypic plasticity in the long‐lived trees remains unclear. In this study, comparative analysis targeted genotyping, methylation and mRNAseq profiling for needles 44‐year‐old Douglas‐fir ( Pseudotsuga menziesii (Mirb.) Franco) having contrasting characteristics was performed. total, we identified 195 differentially expressed genes (DEGs) 115 methylated loci (DML) that are associated with involved fitness‐related processes such as growth, stress management, plant development energy resources. Interestingly, all four intronic DML were mega‐sized (between 100 180 kbp length) highly genes, suggesting specialized regulation mechanisms these long intron gymnosperms. repetitive sequences mainly comprising long‐terminal repeats retroelements growth‐associated (both hyper‐ hypomethylation) 99 (86.1% total DML). Furthermore, nearly 14% not tagged single nucleotide polymorphisms, unique contribution tree growth.

Language: Английский

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Regulations of multiplex genome-edited crops and CRISPR/Cas gene drives

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 397 - 445

Published: Jan. 1, 2024

Language: Английский

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Gene-Editing for Production Traits in Forest Trees: Challenges to Integration and Gene Target Identification

Forests, Journal Year: 2022, Volume and Issue: 13(11), P. 1887 - 1887

Published: Nov. 10, 2022

Gene-editing methods, particularly CRISPR, provide extraordinary opportunities for scientific insights and applications in the life sciences. However, prospects near-term to commercial forestry appear limited. Loss-of-function phenotypes that can be imparted by mutation of one or a few conserved genes offer best near term. For traits with complex inheritance, there is insufficient science guide gene-editing efforts, Genome-Wide Association Studies (GWASs), without strong validation, typically cannot high-confidence gene identification. Other obstacles include difficulty transformation many important genotypes, difficulties transient editing complete editor removal, complexity use breeding programs. Gene edits cause loss-of-function will generally recessive, thus not expressed among outbred progeny, so vegetative propagules (clones) required most cases. There are also societal constraints, such as strict regulations field trials countries, market certification systems do allow any kinds recombinant DNA-modified trees, including those produced gene-editing, certified production forests. We conclude extremely limited foreseeable future (i.e., at least 10 years). Nevertheless, very powerful tool widely used molecular forest scientists lead longer term, if research advances made on key fronts regulatory greatly attenuated.

Language: Английский

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CRISPR genome editing of woody trees: Current status and future prospects

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 401 - 418

Published: Jan. 1, 2024

Language: Английский

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