Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

Fahrenkrog, Annette M.; Neves, Leandro G.; Resende, Jr., Marcio F. R.; Vazquez, Ana I.; de los Campos, Gustavo; Dervinis, Christopher; Sykes, Robert; Davis, Mark; Davenport, Ruth; Barbazuk, William B.; Kirst, Matias

doi:10.1111/nph.14154

Title: Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

Journal Article · Tue Sep 06 00:00:00 EDT 2016 · New Phytologist

DOI:https://doi.org/10.1111/nph.14154· OSTI ID:1337536

Fahrenkrog, Annette M. ^[1]; Neves, Leandro G. ^[1]; Resende, Jr., Marcio F. R. ^[1]; Vazquez, Ana I. ^[2]; de los Campos, Gustavo ^[2]; Dervinis, Christopher ^[1]; Sykes, Robert ^[3]; Davis, Mark ^[3]; Davenport, Ruth ^[1]; Barbazuk, William B. ^[1]; Kirst, Matias ^[1]

Univ. of Florida, Gainesville, FL (United States)
Michigan State Univ., East Lansing, MI (United States)
National Renewable Energy Lab. (NREL), Golden, CO (United States)

Summary Genome‐wide association studies (GWAS) have been used extensively to dissect the genetic regulation of complex traits in plants. These studies have focused largely on the analysis of common genetic variants despite the abundance of rare polymorphisms in several species, and their potential role in trait variation. Here, we conducted the first GWAS in Populus deltoides , a genetically diverse keystone forest species in North America and an important short rotation woody crop for the bioenergy industry. We searched for associations between eight growth and wood composition traits, and common and low‐frequency single‐nucleotide polymorphisms detected by targeted resequencing of 18 153 genes in a population of 391 unrelated individuals. To increase power to detect associations with low‐frequency variants, multiple‐marker association tests were used in combination with single‐marker association tests. Significant associations were discovered for all phenotypes and are indicative that low‐frequency polymorphisms contribute to phenotypic variance of several bioenergy traits. Our results suggest that both common and low‐frequency variants need to be considered for a comprehensive understanding of the genetic regulation of complex traits, particularly in species that carry large numbers of rare polymorphisms. These polymorphisms may be critical for the development of specialized plant feedstocks for bioenergy.

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Research Organization:: National Renewable Energy Laboratory (NREL), Golden, CO (United States)

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

Grant/Contract Number:: AC36-08GO28308; FG02-05ER64114; SC0003893; IOS-1444543

OSTI ID:: 1337536

Alternate ID(s):: OSTI ID: 1401014

Report Number(s):: NREL/JA-5100-67133

Journal Information:: New Phytologist, Vol. 213, Issue 2; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 65 works

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Title: Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides

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