Delhomme, Nicolas
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences
Research article2024Peer reviewedOpen access
Robinson, Kathryn M.; Schiffthaler, Bastian; Liu, Hui; Rydman, Sara M.; Rendon-Anaya, Martha; Kalman, Teitur Ahlgren; Kumar, Vikash; Canovi, Camilla; Bernhardsson, Carolina; Delhomme, Nicolas; Jenkins, Jerry; Wang, Jing; Mahler, Niklas; Richau, Kerstin H.; Stokes, Victoria; A'Hara, Stuart; Cottrell, Joan; Coeck, Kizi; Diels, Tim; Vandepoele, Klaas; Mannapperuma, Chanaka; Park, Eung-Jun; Plaisance, Stephane; Jansson, Stefan; Ingvarsson, Par K.; Street, Nathaniel R.
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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 Umea 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 similar to 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.
genome assembly; natural selection; co-expression; population genetics; Populus; aspen; GWAS; leaf physiognomy; leaf shape; leaf size; genetic architecture; ATAC-Seq; lncRNA
Physiologia Plantarum
2024, Volume: 176, number: 5, article number: e14511Publisher: WILEY
Botany
Forest Science
DOI: https://doi.org/10.1111/ppl.14511
https://res.slu.se/id/publ/132724