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

Area of Science:

• Forest tree genomics
• Plant genetics
• Evolutionary biology

Background:

• Aspen (Populus tremula L.) is a keystone species and a model organism for forest tree genomics.
• Understanding the genetic basis of natural variation in complex traits like leaf morphology is crucial for tree breeding and ecological studies.

Purpose of the Study:

• To provide an updated, chromosome-scale genome assembly and comprehensive genomics data for aspen.
• To explore the genetic architecture underlying natural variation in leaf size and shape using genome-wide association studies (GWAS).
• To integrate new and existing genomics data into a user-friendly web resource for the scientific community.

Main Methods:

• Chromosome-scale genome assembly using long-read sequencing, optical, and genetic maps.
• Whole-genome resequencing of multiple aspen collections (UmAsp, SwAsp, ScotAsp).
• Genome-wide association studies (GWAS) for 26 leaf phenotypes, incorporating Assay of Transposase Accessible Chromatin sequencing (ATAC-Seq) data and exploring long non-coding RNAs.

Main Results:

• A high-quality, chromosome-scale genome assembly for aspen was generated.
• GWAS identified significant Single Nucleotide Polymorphism (SNP) associations for seven leaf physiognomy traits, with candidate genes involved in developmental functions.
• A specific ~177-kbp region showed strong associations with multiple leaf phenotypes in the Scottish Aspen (ScotAsp) collection.

Conclusions:

• The updated aspen genome resource facilitates the exploration of the genetic basis of complex traits.
• Identified genetic variants and candidate genes provide a foundation for understanding leaf trait evolution and for future tree improvement.
• The integrated data in the PlantGenIE.org web resource enhances accessibility and promotes further research in forest tree genomics.