Single-Step Genomic Analysis Increases the Accuracy of Within-Family Selection in a Clonally Replicated Population of Pinus taeda L.

The use of genomic markers in forest tree breeding is expected to improve the response to selection, especially within family. To evaluate the potential improvements from genotyping, we analyzed a large Pinus taeda L. clonal population (1,831 cloned individuals) tested in multiple environments. Of the total, 723 clones from five full-sib families were genotyped using 10,337 single-nucleotide polymorphism markers. Single-step models with genomic and pedigree-based relationships produced similar heritability estimates. Breeding value predictions were greatly improved with inclusion of genomic relationships, even when clonal replication was abundant. The improvement was limited to genotyped individuals and attributable to accounting for the Mendelian sampling effect. Reducing clonal replication by omitting data indicated that genotyping improved breeding values similar to clonal replication. Genomic selection predictive ability (masking phenotypes) was greater for stem straightness (0.68) than for growth traits (0.41 to 0.44). Predictive ability for a new full-sibling family was poorer than when full-sibling relationships were present between model training and validation sets. Species that are difficult to propagate clonally can use genotyping to improve within-family selection. Clonal testing combined with genotyping can produce breeding value accuracies adequate to graft selections directly into deployment orchards without progeny testing. Study Implications Genomic markers can improve the reliability of breeding values, resulting in a more confident ranking of individuals within families. For genotyped individuals, the improvements were comparable to clonal testing. Breeding programs for species that are difficult to propagate clonally should consider genotyping to replace or supplement clonal testing as a means to improve within-family selection. For genomic prediction of breeding values without phenotypes (genomic selection), a robust genetic relationship between model training and validation sets is required. The single-step model allows genotyping a subset of the population and is a straightforward extension of well-established methods.

Genotype-environment interaction and stability of fiber properties and growth traits in triploid hybrid clones of Populus tomentosa

Background Clones provide a sensitive method for evaluating genotypic stability and detecting genotype-environment (G × E) interactions because of non-additive genetic effects among clones and there being no genetic effect among ramets of an ortet. With this study, we aimed to confirm and expand earlier findings, estimate stability parameters, and provide accurate estimates of clonal repeatabilities and genetic gains for a triploid breeding program of P. tomentosa Carr. Results Six 5-year-old clonal trials established in Northern China were used to determine the clonal variation, clone × site interactions, and the stability parameters of fiber properties of wood and growth traits. 360 trees from ten hybrid clones were collected from six sites. The clonal and site effects had a highly significant effect (P < 0.001) for all studied traits. While the clone × site interactions had a highly significant effect (P < 0.001) on fiber length (FL), coarseness (C), and tree growth (tree height [H], diameter at breast height [DBH] and stem volume [SV]), and a moderate effect (P < 0.05) on fiber width (FW) and fiber length/width (FL/W). For FL and SV, most of the triploid hybrid clones had higher reaction norms to the improvement in growth conditions and higher phenotypic plasticity. The estimated clonal repeatability of FW (0.93) was slightly higher than for FL (0.89), FL/W (0.83), C (0.91), DBH (0.76), H (0.85), and SV (0.80). Three clonal testing sites were sufficient to estimate quantitative parameters of fiber properties, however, more clonal testing sites would help improve the accuracy of quantitative parameters of the growth traits. Conclusions Our results highlight that accurate estimation of quantitative parameters for growth traits in triploid hybrid clones of P. tomentosa requires more clonal testing sites than the fiber properties.

Genotype-Environment Interaction and Stability of Fiber Properties and Growth Traits in Triploid Hybrid Clones of Populus Tomentosa

Background: Clones provide a sensitive method for evaluating genotypic stability and detecting genotype-environment (G × E) interactions because of non-additive genetic effects among clones and no genetic effect among ramets of an ortet. The experiments aimed at confirming and expanding the earlier findings, estimating stability parameters, and providing accurate estimates of clonal repeatabilities and genetic gains for an triploid breeding programme of Populus tomentosa Carr. Results: Six 5-year-old clonal trials established in Northern China were used to determine the clonal variation, clone × site interactions and the stability parameters of fiber properties of wood and growth traits. Three hundred sixty trees from ten hybrid clones were collected in the six sites. The clonal and site effects had a highly significant effect (P < 0.001) for all studied traits. The clone × site interactions had a highly significant effect (P < 0.001) on fiber length (FL), coarseness (C), and tree growth (tree height [H], diameter at breast height [DBH] and stem volume [SV]), and a moderate effect (P < 0.05) on fiber width (FW) and fiber length/width (FL/W). For FL and SV, most of the triploid hybrid clones had higher reaction norms to the improvement in growth conditions and higher phenotypic plasticity. The estimated clonal repeatability of FW (0.93) was slightly higher than for FL (0.89), FL/W (0.83), C (0.91), DBH (0.76), H (0.85), and SV (0.80). Three clonal testing sites were sufficient to estimate quantitative parameters of fiber properties. However, more than three clonal testing sites will help improve the accuracy of quantitative parameters of growth traits.Conclusions: Our results unraveled that accurate estimation of quantitative parameters for growth traits in triploid hybrid clones of Populus tomentosa required more clonal testing sites than fiber properties.

Micropropagation of Elite Genotypes of Castanea Sativa (MILL.)

Sprouted buds of eight mature plus-trees of Castanea sativa were collected from two natural populations (Mt. Paiko and Mt. Hortiatis, Greece). Explants were cultured on Murashige and Skoog (MS) medium (three concentrations of macro and micro-elements) combined with three concentrations of BAP (6-Benzylaminopurine). Results were evaluated based on three multiplication traits: (a) number of shoots produced, (b) length of the longest shoot segments and (c) percentage of responsive explants. A high genotype-dependant variation for the number of shoots produced per explant was detected. MS medium at full salt strength and 0.2 mg l-1 BAP provided the best results based on the multiplication traits measured. Elite mature tree P-2 proved to be highly favourable for multiplication. Rooting was attempted on ½ MS medium at five different NAA concentrations. Successful rooting (56%) was obtained by using 0.50 mg l-1 NAA in vermiculite medium after eight weeks. These results indicate that the P-2 genotype can be micropropagated from the protocol developed for ornamental purposes, clonal testing and tree improvement applications.Â

A Clonal Testing Program for Loblolly Pine Plantation Forests

Forest products companies would like to grow clonal plantations of superior loblolly pine (Pinus taeda L.) to improve fiber yields. Feasibility depends on developing efficient propagation techniques and finding superior clones. Horticultural stem-cutting propagation methods and micropropagation techniques are being coupled to test, preserve, multiply, and ultimately deploy clones. Outstanding clones are being found through a series of field tests; each beginning with a superior full-sibling cross from a 40-year-old breeding program. Clones are first screened for rooting ability, and the top 25% to 35% of clones are then established on four sites. Since maintenance of juvenile phase tissue is critical to perpetuating high rooting rates and fast subsequent growth, each clone is preserved as a set of serially propagated hedges and as cold-stored microshoots. As field tests age, better-performing clones are multiplied gradually. Large-production stock blocks of juvenile hedges consequently may be established from both rooted cuttings and microshoots as soon as field tests end. Clones producing large numbers of long branches have been noted for their potential value as fast-growing ornamentals. Since such characters are opposite those desirable for forestry, these clones would need to be preserved, multiplied, and marketed separately from clones for plantation forests.

Predicted and Realized Response of Strawberry Production Traits to Selection in Differing Environments and Propagation Systems

Strawberry (Fragaria ×ananassa Duch.) seedlings from a factorial mating design were tested in each of two locations using two propagule types (seedlings and runners). Genotypic correlations were used to indicate G × E interaction across these locations and propagation systems and to predict correlated responses between selection under specific conditions and commercial propagation. A combined index on relatives was constructed and used to select four groups of individuals—one for each location-propagule combination—for each of two production traits. Comparison was then made with realized responses from subsequent clonal testing at a single site representing the commercial environment. Although selection in the commercial environment (Watsonville) was predicted to give the greatest selection response, realized responses were greatest for the Wolfskill site. Additionally, the present system of selecting seedlings at Wolfskill and testing clones at Watsonville offers considerable logistical advantages that may outweight genetic considerations. The concept of effective index heritability was introduced to enable the calculation of predicted response based on index selection. Neither the use of clonally tested parents nor a comparative seedling set selected for another trait was ideal for estimating realized response.

Marker-aided selection and propagation systems in trees: advantages of cloning for studying quantitative inheritance

Genetic maps with a high density of markers have been used to locate discrete Mendelian components of quantitatively inherited traits in a few crop plants. In principle, a similar approach can be used to map economically important quantitative trait loci in trees; however, tree pedigrees and propagation systems are quite different from those used in crops. Recent theoretical work suggests that clonal propagation of advanced generation offspring from pedigrees segregating for molecular marker genotype, and with substantial segregating variation in the phenotype(s) of interest, is an effective strategy for linkage analysis of polygenic traits. The successful application of marker-aided selection to tree improvement depends upon precise estimation of phenotypic variation attributable to marker genotype even when heritability is low, and clonal testing is the best experimental design to achieve this goal. For many practical reasons (including replication of plantations in time and space, destructive sampling, or sharing known genotypes with other researchers), clonal propagation maximizes the benefits from genome mapping efforts.

Genetics and breeding of Sitka spruce

SynopsisSitka spruce is a monoecious, wind-pollinated, cross-fertilising species showing wide genetic variation which suggests heterozygosity for many alleles and natural selection against self-fertilisation. Phenotypic selection for the important trait of vigour is ineffective, so testing progenies of selected individuals and clonal testing is an essential and time-consuming part of any improvement programme. Old trees can be vegetatively propagated by grafting and very young trees by rooted cuttings.The British tree improvement programme is based, in the short term, on the use of seed collected from superior plantation trees of desirable origins; in the mid term on seed derived from clonal orchards based on mixtures of clones previously tested for superiority in family tests; and in the longer term on highly superior seed or clones derived from a system of recurrent mating with family selection. Three populations are being developed. There is a small interspecific hybridisation programme.

Clonal testing efficiency: the trade-offs between clones tested and ramets per clone

Three contrasting simulation models were developed to investigate testing efficiencies in a clonal selection program. The variables investigated were number of total plants tested, number of candidate clones tested, number of ramets per clone, number of clones selected, selection intensity, and broad-sense heritability. The model deemed appropriate to most clonal forestry situations selected a fixed number of clones in an experiment with the total number of plants in the test held constant. In this model, as the number of ramets per clone was varied, the number of candidate clones tested and the selection intensity necessarily also varied. This model indicates that cloning individuals for testing is useful when selection is based on a characteristic or index with broad-sense heritability less than about 0.6. At the lower heritabilities, two to six ramets per clone per site usually produces the optimum level of cloning, the exact number depending upon the selection intensity and heritability. Predictions generated by this fixed number of selected clones model were compared with average phenotypic values of selections using different subsamples of data for 8-year height and for 8-year diameter in a radiata pine (Pinusradiata D. Don) clonal experiment. Agreement between predictions and average phenotypic values in both these two comparisons was close.