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

Identifieur interne : 001642 ( Main/Corpus ); précédent : 001641; suivant : 001643

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

Auteurs : Annette M. Fahrenkrog ; Leandro G. Neves ; Márcio F R. Resende ; Ana I. Vazquez ; Gustavo De Los Campos ; Christopher Dervinis ; Robert Sykes ; Mark Davis ; Ruth Davenport ; William B. Barbazuk ; Matias Kirst

Source :

RBID : pubmed:27596807

English descriptors

Abstract

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.

DOI: 10.1111/nph.14154
PubMed: 27596807

Links to Exploration step

pubmed:27596807

Le document en format XML

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<term>Genetic Loci (MeSH)</term>
<term>Genetic Markers (MeSH)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Polymorphism, Single Nucleotide (genetics)</term>
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<div type="abstract" xml:lang="en">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.</div>
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<AbstractText>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.</AbstractText>
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<DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
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</MeshHeadingList>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">Populus deltoides </Keyword>
<Keyword MajorTopicYN="N">eastern cottonwood</Keyword>
<Keyword MajorTopicYN="N">exome resequencing</Keyword>
<Keyword MajorTopicYN="N">genome-wide association studies (GWAS)</Keyword>
<Keyword MajorTopicYN="N">low-frequency single-nucleotide polymorphisms (SNPs)</Keyword>
<Keyword MajorTopicYN="N">poplar</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="received">
<Year>2016</Year>
<Month>05</Month>
<Day>17</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2016</Year>
<Month>07</Month>
<Day>13</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2016</Year>
<Month>9</Month>
<Day>7</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2018</Year>
<Month>2</Month>
<Day>10</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>2016</Year>
<Month>9</Month>
<Day>7</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">27596807</ArticleId>
<ArticleId IdType="doi">10.1111/nph.14154</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
</record>

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{{Explor lien
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   |flux=    Main
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   |texte=   Genome-wide association study reveals putative regulators of bioenergy traits in Populus deltoides.
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