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Gene copy number variations in adaptive evolution: The genomic distribution of gene copy number variations revealed by genetic mapping and their adaptive role in an undomesticated species, white spruce ( Picea glauca )
Author(s) -
Prunier Julien,
Caron Sébastien,
Lamothe Manuel,
Blais Sylvie,
Bousquet Jean,
Isabel Nathalie,
MacKay John
Publication year - 2017
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.14337
Subject(s) - biology , copy number variation , genetics , loss of heterozygosity , gene , adaptation (eye) , phenotype , genome , comparative genomic hybridization , gene dosage , evolutionary biology , allele , gene expression , neuroscience
Gene copy number variation ( CNV ) has been associated with phenotypic variability in animals and plants, but a genomewide understanding of their impacts on phenotypes is largely restricted to human and agricultural systems. As such, CNV s have rarely been considered in investigations of the genomic architecture of adaptation in wild species. Here, we report on the genetic mapping of gene CNV s in white spruce, which lacks a contiguous assembly of its large genome (~20 Gb), and their relationships with adaptive phenotypic variation. We detected 3,911 gene CNV s including de novo structural variations using comparative genome hybridization on arrays ( aCGH ) in a large progeny set. We inferred the heterozygosity at CNV loci within parents by comparing haploid and diploid tissues and genetically mapped 82 gene CNV s. Our analysis showed that CNV s were distributed over 10 linkage groups and identified four CNV hotspots that we predict to occur in other species of the Pinaceae. Significant relationships were found between 29 of the gene CNV s and adaptive traits based on regression analyses with timings of bud set and bud flush, and height growth, suggesting a role for CNVs in climate adaptation. The importance of CNV s in adaptive evolution of white spruce was also indicated by functional gene annotations and the clustering of 31% of the mapped adaptive gene CNV s in CNV hotspots. Taken together, these results illustrate the feasibility of studying CNV s in undomesticated species and represent a major step towards a better understanding of the roles of CNVs in adaptive evolution.