Poplar Indels


Perennial, clonally propagated plants provide a challenge and an opportunity for functional gene discovery. Meiotic recombination-based genetic analysis and breeding are hampered by the long generation cycle. On the other hand, clonal propagation enables the production of many individuals with identical genotypes and economic exploitation of plants without the need for sexual reproduction. In collaboration with Andrew Groover at US Forest Service, Davis we are studying the effect of genomic copy number variation on poplar hybrid performance. We are studying both variation induced by hybridization and by ionizing radiation, the latter applied to pollen during interspecific hybridization.

Approach and example of results

Next generation sequencing-based genotyping and karyotyping is being used to characterize ploidy changes, deletions and possible rearrangements in Populus hybrids, including both F1 pedigrees and unrelated F1 individuals.

Variation in crosses between different species is being characterized genotypically and karyotypically

To enhance variation and test the contribution of smaller chromosomal regions to phenotype, γ−irradiation of pollen is used to induce deletions of varying size. The method produces germplasm enriched with genotypic and chromosomal dosage variation compared to traditional Populus hybrids. This germplasm will serve as a testbed for exploring correlations between chromosomal segments, their dosage and phenotypes, and to identify commercially-relevant genomic combinations.

RESCAN libraries from 96 γ-irradiated hybrid poplar individuals were sequenced in a single lane of Hiseq. Reads were binned and the relative abundance of each chromosomal segment was calculated relative to 2 copies in a diploid. The copy number was plotted for each bin. The karyotype of an individual is illustrated (colored bars = chromosomes). An insertion and deletion are visible. See our paper in the Plant Cell for details.

We are using an ~800 plant population to identify dosage QTL, i.e. genomic sites that affect traits when their dosage changes. We have been successful in identifying such sites for just about any trait we have considered (Bastiaanse et al. 2017. in preparation).


This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant no DE-SCSC0007183 entitled “Creation of High-Precision Characterization of Novel Poplar Biomass Germplasm” and “A novel poplar biomass germplasm resource for functional genomics and breeding”

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