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 to quantitative traits and heterosis.
authors: Department of Plant Biology and Genome Center, University of California, Davis, California 95616.
authors: Isabelle M
authors: http://orcid.org/0000-0002-6796-1119
authors: IM
authors: Henry
authors: Pacific Southwest Research Station, U.S. Forest Service, Davis, California 95618.
authors: Matthew S
authors: http://orcid.org/0000-0002-7229-8016
authors: MS
authors: Zinkgraf
authors: Pacific Southwest Research Station, U.S. Forest Service, Davis, California 95618 Department of Plant Biology, University of California, Davis, California 95616.
authors: Andrew T
authors: http://orcid.org/0000-0002-6686-5774
authors: AT
authors: Groover
authors: Department of Plant Biology and Genome Center, University of California, Davis, California 95616 lcomai@ucdavis.edu.
authors: Luca
authors: http://orcid.org/0000-0003-2642-6619
authors: L
authors: Comai
mesh_terms: D005720:Gamma Rays; D018628:Gene Dosage; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D006824:Hybridization, Genetic; D009154:Mutation; D000069600:Plant Breeding / Q000379:methods*; D011058:Pollen / Q000235:genetics / Q000528:radiation effects; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics*; D057885:Triploidy