An Improved Chromosome‐scale Genome Assembly and Population Genetics resource for <i>Populus tremula</i>.

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a ~177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

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Publication Details

Journal
Physiologia Plantarum
Published
2024-09-01
DOI
https://doi.org/10.1111/ppl.14511
Citations
8
Primary Topic
Bioenergy crop production and management
Type
article
Field-Weighted Citation Impact
3.97

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article

An Improved Chromosome‐scale Genome Assembly and Population Genetics resource for Populus tremula.

Stefan Jansson, Camilla Canovi, Pär K. Ingvarsson, Chanaka Mannapperuma et al.
8 citations
Physiologia Plantarum
Bioenergy crop production and management
3.97
article

An Improved Chromosome‐scale Genome Assembly and Population Genetics resource for Populus tremula.

Stefan Jansson, Camilla Canovi, Pär K. Ingvarsson, Chanaka Mannapperuma, Kathryn M. Robinson, Bastian Schiffthaler, Niklas Mähler, Jerry Jenkins, Nicolas Delhomme, Stuart A’Hara, Martha Rendón‐Anaya, Klaas Vandepoele, Tim Diels, Eung‐Jun Park, Carolina Bernhardsson, Stéphane Plaisance, Joan Cottrell, Jing Wang, Victoria Stokes, Nathaniel R. Street, Hui Liu, Kizi Coeck, Vikash Kumar, Sara M. Rydman, Kerstin H. Richau, Teitur Ahlgren Kalman
article en
8 citations

Abstract

Aspen (Populus tremula L.) is a keystone species and a model system for forest tree genomics. We present an updated resource comprising a chromosome-scale assembly, population genetics and genomics data. Using the resource, we explore the genetic basis of natural variation in leaf size and shape, traits with complex genetic architecture. We generated the genome assembly using long-read sequencing, optical and high-density genetic maps. We conducted whole-genome resequencing of the Umeå Aspen (UmAsp) collection. Using the assembly and re-sequencing data from the UmAsp, Swedish Aspen (SwAsp) and Scottish Aspen (ScotAsp) collections we performed genome-wide association analyses (GWAS) using Single Nucleotide Polymorphisms (SNPs) for 26 leaf physiognomy phenotypes. We conducted Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq), identified genomic regions of accessible chromatin, and subset SNPs to these regions, improving the GWAS detection rate. We identified candidate long non-coding RNAs in leaf samples, quantified their expression in an updated co-expression network, and used this to explore the functions of candidate genes identified from the GWAS. A GWAS found SNP associations for seven traits. The associated SNPs were in or near genes annotated with developmental functions, which represent candidates for further study. Of particular interest was a ~177-kbp region harbouring associations with several leaf phenotypes in ScotAsp. We have incorporated the assembly, population genetics, genomics, and GWAS data into the PlantGenIE.org web resource, including updating existing genomics data to the new genome version, to enable easy exploration and visualisation. We provide all raw and processed data to facilitate reuse in future studies.

Physiologia PlantarumVol. 176(5)
Uppsala University (SE), Sichuan University (CN), Science for Life Laboratory (SE), Korea Forest Service (KR), Vlaams Instituut voor Biotechnologie (BE), Swedish University of Agricultural Sciences (SE), Beijing Forestry University (CN), Ghent University (BE), Umeå Plant Science Centre (SE), Forest Research (GB), HudsonAlpha Institute for Biotechnology (US), Umeå University (SE)
VINNOVA, Svenska Forskningsrådet Formas, Vetenskapsrådet, China Scholarship Council
Life in Land
Openalex Percentile: Top 7%
Bioenergy crop production and management
3.97
DOIOpen Access PDFOpenAlex
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