High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa.

Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.

Creation and Genomic Analysis of Irradiation Hybrids in Populus.

Establishing efficient functional genomic systems for creating and characterizing genetic variation in forest trees is challenging. Here we describe protocols for creating novel gene-dosage variation in Populus through gamma-irradiation of pollen, followed by genomic analysis to identify chromosomal regions that have been deleted or inserted in each F1 individual. Irradiated pollen is used in a controlled, interspecific cross to create F1 progeny that carry deletions and insertions of chromosomal regions. These insertions and deletions result in novel changes in gene dosage that in turn affect both qualitative and quantitative phenotypic traits. The protocols described here outline the processes involved in optimizing irradiation levels and performing controlled crosses, sowing seed and propagating seedlings, and genome-wide sequence-based analysis of deletions and insertions in the F1 progeny. The same approach could be applied to other vegetatively propagated species. © 2016 by John Wiley & Sons, Inc.

Cryopreservation of Populus trichocarpa and Salix dormant buds with recovery by grafting or direct rooting.

BACKGROUND: Methods are needed for the conservation of clonally maintained trees of Populus and Salix. In this work, Populus trichocarpa and Salix genetic resources were cryopreserved using dormant scions as the source explant. OBJECTIVE: We quantified the recovery of cryopreserved materials that originated from diverse field environments by using either direct sprouting or grafting. MATERIALS AND METHODS: Scions (either at their original moisture content of 48 to 60% or dried to 30%) were slowly cooled to -35 degree C, transferred to the vapor phase of liquid nitrogen (LNV, -160 degree C), and warmed before determining survival. RESULTS: Dormant buds from P. trichocarpa clones from Westport and Boardman, OR had regrowth levels between 42 and 100%. Direct rooting of cryopreserved P. trichocarpa was also possible. Ten of 11 cryopreserved Salix accessions, representing 10 different species, exhibited at least 40% bud growth and rooting after 6 weeks when a bottom-heated rooting system was implemented. CONCLUSION: We demonstrate that dormant buds of P. trichocarpa and Salix accessions can be cryopreserved and successfully regenerated without the use of tissue culture.