Abstract Detail

Population Genetics/Genomics

Wu, Yihan [1], Adams, Keith [2].

Copy number variation in wild poplar.

Genomic structural variation, including copy number variations, gene presence/absence, and genomic rearrangements, have been relatively understudied compared to single nucleotide polymorphisms despite affecting a higher proportion of the genome. Copy number variations (CNVs), duplication and deletions of the genome ranging from 50bp to 1Mb, are therefore an important contributor to genetic variation in the genome, and may influence phenotypic variation and adaptation. Using whole genome sequencing data and RNA-sequencing data, we studied the natural diversity of CNVs across the range of Populus trichocarpa and the effects of CNVs on gene expression. Populus trichocarpa, also known as black cottonwood, is a dioecious tree with a geographic range along the west coast of North America from Alaska to Mexico. Field and common garden experiments have found phenotypic variation along the coast in multiple phenotypic traits between northern and southern populations. Signatures of local adaptation and population structure have been detected through studies of single nucleotide polymorphisms. However, the diversity of CNVs and the impacts the CNVs may have on expression are unknown in this model tree species. We analyzed whole genome sequencing data of 778 P. trichocarpa individuals to quantify the diversity and location of CNVs in the genome and quantified gene expression through RNA-sequencing data of leaf and xylem tissue for 390 individuals. We found delections and duplications covering a significant percentage of the genome. Genes overlapping with CNVs were enriched in important biological processes such as reproduction, cellulose production, and defense. Strong correlations between copy number and expression were found for a significant minority of genes overlapping with CNVs. Our identified CNVs help provide insights into the diversity of CNVs in wild populations of P. trichocarpa, and the effects of CNVs on gene expression on a genomic scale.

1 - University of British Columbia, Botany, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
2 - University Of British Columbia, Botany Department, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada

Keywords:
genomics
RNA-seq
Whole genome re-sequencing
copy number variation
structural variation
Poplar.

Presentation Type: Oral Paper
Session: PGG3, Population Genetics and Genomics III
Location: /
Date: Wednesday, July 21st, 2021
Time: 2:00 PM(EDT)
Number: PGG3007
Abstract ID:542
Candidate for Awards:Margaret Menzel Award