A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees

Bastiaanse, Héloïse; Zinkgraf, Matthew; Canning, Courtney; Tsai, Helen; Lieberman, Meric; Comai, Luca; Henry, Isabelle; Groover, Andrew

doi:10.1073/pnas.1903229116

Title: A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees

Journal Article · Tue Jun 18 00:00:00 EDT 2019 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1903229116· OSTI ID:1558427

Bastiaanse, Héloïse ^[1]; Zinkgraf, Matthew ^[2]; Canning, Courtney ^[3]; Tsai, Helen ^[4]; Lieberman, Meric ^[4];

^[4]; Henry, Isabelle ^[4]; Groover, Andrew ^[1]

U.S. Dept. of Agriculture Forest Service, Davis, CA (United States); Univ. of California, Davis, CA (United States)
U.S. Dept. of Agriculture Forest Service, Davis, CA (United States); Western Washington Univ., Bellingham, WA (United States)
U.S. Dept. of Agriculture Forest Service, Davis, CA (United States)
Univ. of California, Davis, CA (United States)

Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Furthermore our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.

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Research Organization:: Univ. of California, Davis, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0007183

OSTI ID:: 1558427

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 116, Issue 27; ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 19 works

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