BackgroundGenome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.Methodology/Principal Findings Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA.Conclusions/SignificanceMost of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.

Open-pollinated loblolly pine seedlings derived from seven maternal parents were inoculated in a greenhouse with 10 different bulked inocula of the fusiform rust fungus and assessed for disease incidence. The maternal parents are heterozygous (Rr) for one or two of nine known pathotype-specific Fr genes (fusiform rust resistance genes). Progeny were genotyped to identify carriers of known R and r alleles inherited from the maternal parents. The R alleles condition resistance to specific genotypes of the fungal pathogen, while r alleles do not condition for resistance. Interactions were tested among different host genotypes and different bulked inocula. Significant differences in virulence against R genotypes were observed in the bulked inocula. Likewise, the inocula were significantly different with regard to their ability to incite disease at the family level and in r genotypes. Across the inocula, disease levels differed significantly among families. Within each family, r genotype seedlings typically exhibited higher disease rates than did R genotype seedlings. The magnitude of difference (odds ratio) between the R versus r genotypes for disease incidence within each family varied from 1 to 32 times.Significant interactions between host and pathogen genotypes were observed in four of the seven families. These greenhouse assessments using bulked inocula sources revealed wide ranges of pathogen virulence levels against the different R alleles. Barring virulence masking by unknown resistance genes, similar virulence assessments should be effective guides for the field deployment of seedlings carrying specific R alleles to regions where inocula samples show low or no corresponding virulence.

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Nearly two decades of research on the host-pathogen interaction in fusiform rust of loblolly pine is detailed. Results clearly indicate that pathotype-specific genes in the host interacting with pathogen avirulence cause resistance as defined by the non-gall phenotype under favorable environmental conditions for disease development. In particular, nine fusiform rust resistance genes (Fr genes) are described here including the specific methods to determine each and their localization on the reference genetic map of loblolly pine. Understanding how these and other apparent Fr genes in loblolly pine and other rust-susceptible pines impact resistance screening, parental and progeny selection, and family and clonal deployment is an important area in forest genetics research and OPEN ACCESSForests 2015, 6 2740 operational tree breeding. The documentation of these Fr genes is a key piece of information towards gaining that understanding and ultimately improving breeding and deployment strategies.

Controlled inoculations with 10 bulk inocula of Cronartium quercuum (Berk) Miyabe ex Shirai f.sp. fusiforme were carried out on open-pollinated progeny of 25 fast-growing Pinus taeda L. parents. The parents had a range of breeding values for resistance to fusiform rust in progeny field trials. There were highly significant differences among the half-sib families in response to inoculations, and these differences were very reproducible; the half-sib family-mean heritability of resistance to controlled inoculation was 0.97. All of the families that were susceptible in the field were susceptible in controlled inoculations, and most (12 of 17) of the field-resistant families were resistant in response to controlled inoculations. Significant pathogenic variability was observed among the different bulk inocula, although this accounted for only 1.9% of the total variation. Genetic differences among families within field-resistant or field-susceptible groups accounted for 13.7% of the total variation. The family by inocula interaction was highly significant, but a single field-resistant family contributed 44% of the total family by inocula interaction variance, and two other field-resistant families also showed significant interactions.