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Title: A System for Dosage-Based Functional Genomics in Poplar

Abstract

Altering gene dosage through variation in gene copy number is a powerful approach to addressing questions regarding gene regulation, quantitative trait loci, and heterosis, but one that is not easily applied to sexually transmitted species. Elite poplar (Populus spp) varieties are created through interspecific hybridization, followed by clonal propagation. Altered gene dosage relationships are believed to contribute to hybrid performance. Clonal propagation allows for replication and maintenance of meiotically unstable ploidy or structural variants and provides an alternative approach to investigating gene dosage effects not possible in sexually propagated species. Here, we built a genome-wide structural variation system for dosage-based functional genomics and breeding of poplar. We pollinated Populus deltoides with gamma-irradiated Populus nigra pollen to produce >500 F1 seedlings containing dosage lesions in the form of deletions and insertions of chromosomal segments (indel mutations). Using high-precision dosage analysis, we detected indel mutations in ~55% of the progeny. These indels varied in length, position, and number per individual, cumulatively tiling >99% of the genome, with an average of 10 indels per gene. Combined with future phenotype and transcriptome data, this population will provide an excellent resource for creating and characterizing dosage-based variation in poplar, including the contribution of dosage tomore » quantitative traits and heterosis.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]
  1. Univ. of California, Davis, CA (United States)
  2. U.S. Forest Service, Davis, CA (United States).Pacific Southwest Research Station
  3. Univ. of California, Davis, CA (United States); U.S. Forest Service, Davis, CA (United States).Pacific Southwest Research Station
Publication Date:
Research Org.:
Univ. of California, Davis, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1454685
Grant/Contract Number:  
sc0007183
Resource Type:
Accepted Manuscript
Journal Name:
Plant Cell
Additional Journal Information:
Journal Volume: 27; Journal Issue: 9; Journal ID: ISSN 1040-4651
Publisher:
American Society of Plant Biologists
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Henry, Isabelle M., Zinkgraf, Matthew S., Groover, Andrew T., and Comai, Luca. A System for Dosage-Based Functional Genomics in Poplar. United States: N. p., 2015. Web. doi:10.1105/tpc.15.00349.
Henry, Isabelle M., Zinkgraf, Matthew S., Groover, Andrew T., & Comai, Luca. A System for Dosage-Based Functional Genomics in Poplar. United States. doi:10.1105/tpc.15.00349.
Henry, Isabelle M., Zinkgraf, Matthew S., Groover, Andrew T., and Comai, Luca. Fri . "A System for Dosage-Based Functional Genomics in Poplar". United States. doi:10.1105/tpc.15.00349. https://www.osti.gov/servlets/purl/1454685.
@article{osti_1454685,
title = {A System for Dosage-Based Functional Genomics in Poplar},
author = {Henry, Isabelle M. and Zinkgraf, Matthew S. and Groover, Andrew T. and Comai, Luca},
abstractNote = {Altering gene dosage through variation in gene copy number is a powerful approach to addressing questions regarding gene regulation, quantitative trait loci, and heterosis, but one that is not easily applied to sexually transmitted species. Elite poplar (Populus spp) varieties are created through interspecific hybridization, followed by clonal propagation. Altered gene dosage relationships are believed to contribute to hybrid performance. Clonal propagation allows for replication and maintenance of meiotically unstable ploidy or structural variants and provides an alternative approach to investigating gene dosage effects not possible in sexually propagated species. Here, we built a genome-wide structural variation system for dosage-based functional genomics and breeding of poplar. We pollinated Populus deltoides with gamma-irradiated Populus nigra pollen to produce >500 F1 seedlings containing dosage lesions in the form of deletions and insertions of chromosomal segments (indel mutations). Using high-precision dosage analysis, we detected indel mutations in ~55% of the progeny. These indels varied in length, position, and number per individual, cumulatively tiling >99% of the genome, with an average of 10 indels per gene. Combined with future phenotype and transcriptome data, this population will provide an excellent resource for creating and characterizing dosage-based variation in poplar, including the contribution of dosage to quantitative traits and heterosis.},
doi = {10.1105/tpc.15.00349},
journal = {Plant Cell},
number = 9,
volume = 27,
place = {United States},
year = {2015},
month = {8}
}

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Cited by: 11 works
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