A Combined Analysis in Complementary Progeny Tests: Effects on breeding value accuracies

Complementary progeny tests allow for simultaneously ranking parents for their general combining ability (GCA) and within-family forward selection. To do this, progeny tests are established with different types of genetic entries (i.e., half-sib and full-sib seedlings, respectively), and different experimental designs. This study proposes a combined analysis of the GCA and full-sib (FS) tests using the mixed model approach to predict simultaneously the breeding values of grandparents, parents, full-sib families and offspring on the same scale. Moreover, a first order autoregressive spatial mixed model for the GCA tests was also implemented in the combined analysis. Our empirical study in coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) shows that additional information provided from relatives and the overlap genetic entry among GCA and FS tests via the proposed combined analysis, improves the accuracies of breeding values compared to the non-combined analysis. The improvements in the accuracies of breeding values for backward and forward selections were generally modest. Spatial and combined analyses gave slightly better results than the non-spatial combined model.

Realized Genetic Gains in Coastal Douglas-fir in British Columbia: Implications for Growth and Yield Projections

Realized genetic gain trials for coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) at five different sites with four different spacings were assessed at age 12 to compare early gain predictions in growth from small plot progeny test designs to those obtained from large block designs. Seedlings from three genetic levels, i.e., local wild-stand controls (WS), a mid-gain seedlot (MG), and a top-cross seedlot (TC) were planted in 12 × 12 tree plots with two replications at spacings of 1.6 m, 2.3 m, 2.9 m and 4.0 m. Two replications of a “single-tree plot” design at 2.9 m spacing for the three genetic levels (30 trees per genetic level) were also established, to allow for more detailed comparisons between single-tree and multiple-tree plot means. Although these trials are still relatively young, trees in the closest spacing had the highest levels of mortality with the TC trees having the highest rate of survival. Height gains in the block trials ranged from 10.4% to 16.1% for MG and TC trees, respectively, and were relatively close to the predicted values; however, volume (individual tree and volume/ha) gains exceeded expectations. Effects of genetic entry on height at age 12 were highly significant, while spacing, genetic entry by spacing, and genetic entry by test site interactions were not significant. We also compared height growth over the first 12 years to growth estimated from the “Bruce height growth model” for Douglas-fir and found that on four of the five test sites our MG and TC seedlings follow the expected height growth trajectories.

Genetics of P-Element Transposition Into Drosophila melanogaster Centric Heterochromatin

Heterochromatin is a major component of higher eukaryotic genomes, but progress in understanding the molecular structure and composition of heterochromatin has lagged behind the production of relatively complete euchromatic genome sequences. The introduction of single-copy molecular-genetic entry points can greatly facilitate structure and sequence analysis of heterochromatic regions that are rich in repeated DNA. In this study, we report the isolation of 502 new P-element insertions into Drosophila melanogaster centric heterochromatin, generated in nine different genetic screens that relied on mosaic silencing (position-effect variegation, or PEV) of the yellow gene present in the transposon. The highest frequencies of recovery of variegating insertions were observed when centric insertions were used as the source for mobilization. We propose that the increased recovery of variegating insertions from heterochromatic starting sites may result from the physical proximity of different heterochromatic regions in germline nuclei or from the association of mobilizing elements with heterochromatin proteins. High frequencies of variegating insertions were also recovered when a potent suppressor of PEV (an extra Y chromosome) was present in both the mobilization and selection generations, presumably due to the effects of chromatin structure on P-element mobilization, insertion, and phenotypic selection. Finally, fewer variegating insertions were recovered after mobilization in females, in comparison to males, which may reflect differences in heterochromatin structure in the female and male germlines. FISH localization of a subset of the insertions confirmed that 98% of the variegating lines contain heterochromatic insertions and that these schemes produce a broader distribution of insertion sites. The results of these schemes have identified the most efficient methods for generating centric heterochromatin P insertions. In addition, the large collection of insertions produced by these screens provides molecular-genetic entry points for mapping, sequencing, and functional analysis of Drosophila heterochromatin.