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Welcome to PopIndels: The database of insertion and deletion mutations in Populus




What?
Via a DOE-funded project, we (the Comai and Groover laboratories, in Davis, CA), are studying the effect of genomic copy number variation on poplar hybrid performance. To do so, we have produced a population of interspecific hybrids carrying deletions and insertions and characterized these mutations using next generation sequencing.

How?
In short, we are using γ−irradiation of pollen to introduce large-scale insertions and deletions mutations (indel mutations) throughout the genome. The pollen is then used to produce a population of interspecific hybrid progeny, each with a slightly different chromosomal constitution. A detailed description of the approach and type of results obtained is summarized in a recent publication in Plant Cell (Henry, Zinkgraf, Groover and Comai, 2015).

We are crossing γ−irradiated (100 Gy dose) P. nigra pollen to P. deltoides to produce DN hybrids. A genomic sequencing library is produced from each interspecific hybrid. 100 samples are pooled into a lane of 50 SE Illumina sequencing and the reads are analyzed for dosage variation. Sequencing reads are mapped to the poplar genomic reference sequence and binned into consecutive non-overlapping 100 kb bins. The relative number of reads in each bin is plotted to detect indel mutations.

What do we see?
The karyotype of an individual is illustrated below (colored bars = chromosomes). A terminal insertion and a terminal deletion are visible.

We found at least one indel in approximately 50% of the progeny, with about 3/4 deletions and 1/4 insertions. We also found approximately 7% triploidy in our population, probably from 2N gamete formation independent of the γ−irradiation. Triploids overall carry more indel mutations than their diploid siblings and add an interesting additional level of dosage variation to our population. Overall, we have ~700 trees characterized. Collectively, they carry indel mutations that cover the entire populus genome several times.

What is the significance?
Perennial, clonally propagated plants provide a challenge to crop improvement as conventional breeding is 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. Dosage variation is a type of variation that can be obtained rapidly, result in wide phenotypic variation and can be maintained in clonally-propagated crops. Dosage variation is particularly well suited for poplar because ploidy variants (tripoids) and even aneuploids are regularly found in breeding populations and in natural populations. Moreover, poplar breeding is based on interspecific hybridization and dosage variation is expected to play an important role in the observed heterotic response. Dosage and ploidy changes are also believed to play fundamental roles in the evolution of poplar species and populations, and may be a fundamental influence on adaptive traits.
This resource constitutes a functional genomic tool for the poplar community but might also result in the discovery of clones with superior performance that can be integrated rapidly into breeding programs.

What now?
Information about our indel mutations is available here, in the form of a database that lets you browse for indel mutations that cover a specific gene or locus, and visualize the lesions in the form of dosage plots. Most of the trees are now growing in a field trial and in the process of being phenotypes for a variety of vegetative traits relevant to yield and wood formation.

Contact info:
Please contact us if you have questions about this resource or if you are interested in a particular set of trees. We can provide cuttings or collaborative opportunities to screen the trees in our field trial. These trees are not transgenic.

E-mails: Luca Coma (lcomai@ucdavis.edu), Andrew Groover (agroover@fs.fed.us)

Ackowledgments
This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0007183

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