Genetic management of northern red oak (Quercus rubra L.) seed orchards

The studies detailed herein provide the first description of the influence of northern red oak flowering patterns and seed orchard design on reproductive success and estimates of genetic parameters, and describe novel management tools including a method for rating floral synchrony and a fully sequenced chloroplast genome with characterized polymorphisms. A male and female floral phenology rating system was developed and used to rate phenological overlap (PO) in a northern red oak clonal seed orchard in Indiana, USA in 2008, 2009, and 2010. The mean PO value for each seed orchard pair (n = 146 genotypes) was 0.30 (range 0–0.98). In each year, phenologically early clones had significantly lower mean PO values than intermediate or late clones. Most clones were dichogamous, with female flowers reaching receptivity an average of 1.4–3 days after male flowers of the same tree. Year explained a significant amount of the variation in clonal dichogamy; genotype was not significant. Yearly variation in spring temperatures strongly affected the placement of clones into phenological classes and the degree of dichogamy and phenological overlap in the seed orchard. Ten clones were chosen from the Indiana, USA northern red oak seed orchard that represented the early, intermediate, and late phenology groups and had offspring in established multi-year progeny tests throughout Indiana. Surviving offspring of the selected 10 clones were sampled in July 2009 and genotyped using 11 microsatellite markers previously tested in northern red oak. A total of 432 offspring were analyzed for paternity. Paternity was assigned to 61% and 93% of progeny at the 80% and 95% confidence levels, respectively, while 7% of offspring could not be assigned paternity within the orchard. Phenologically early clones had the highest pollen contamination rate (13%), followed by intermediate (5%) and late (\u3c1%) clones. Early and intermediate clones experienced more gene flow from distant orchard blocks compared to late clones. Half of the clones contributed as males each year with 68% of males contributing to two consecutive cohorts. Males sired between 1 and 31 offspring each year and differed significantly in the number of offspring sired. Male parents in the early phenology group sired more offspring per male (5.31±1.44) than male parents in the intermediate phenological group (n = 38) or the late phenological group (n = 19; mean number off offspring per male 3.71±0.55 and 3.37±1.28, respectively). For each mother tree, variance in number of offspring per male was best described by a model containing physical distance and male phenology (R 2 = 0.207; F = 7.44, p \u3c 0.0001). The average number of offspring from mother trees by within-subline males was 2.75±0.24, significantly higher than any other distance category. Males in distance categories 2, 3, and 4 sired an average of 1.49, 1.24, and 1.37 offspring, and mean number of offspring sired by males in more distant sublines was not significantly different. The average genetic correlation among OP progeny ranged between 0.253 and 0.353, with a mean of 0.281. These data reinforce the importance of near-neighbor gene flow in seed orchard design and support the use of OP progeny tests for estimating genetic parameters. High-resolution chloroplast DNA markers are needed for northern red oak management goals such as monitoring reintroduced populations, tracking wood products, and certifying seed lots and forests. We report the sequencing, assembly, and annotation of the chloroplast genome of northern red oak via pyrosequencing and reference guided assembly. The 161301 bp chloroplast genome contained 137 genes and one pseudogene. The genome sequence was compared to that of Quercus robur and Q. nigra with 951 and 186 polymorphisms detected, respectively. A total of 51 intraspecific polymorphisms were detected among four northern red oak individuals. These and other advancements in northern red oak seed orchard genetic management will improve conservation success of this species, inform population and evolutionary genetic studies of natural populations, and improve the genetic base for long-term support of land owners and wood products industries