Unequal deployment of clones to seed orchards by considering genetic gain, relatedness and gene diversity

Related clones in seed orchards lead to inbreeding depressionand reduced genetic value of the seeds. This study aims to developthe methodology for deployment of related clones to seed orchardswhen the breeding value and the pedigree are available for eachcandidate. The following goals were considered: high geneticgain, high genetic gain adjusted for predicted inbreeding depression(net gain), high gene diversity, and high effective clone number.The selection strategies included truncation selection withor without relatedness restrictions, maximizing genetic gain(linear deployment) with or without restrictions on relatednessand maximizing net gain. The selection strategies were appliedto Norway spruce seed orchard candidates evaluated in clonaltests. The material comprised full-sib and half-sib relationships.Comparisons were made both at the same gene diversity and atthe effective clone number. Maximizing net gain by unequal rametnumber deployment resulted in considerable higher net gain anda considerable reduction of related ramets in many comparisons.Linear deployment restricted against related clones comparedat the same status number resulted in almost as high net gain.Reduction in gene diversity may be a more important reason toavoid relatives in seed orchards than the subsequent inbreedingfor achieving a high net gain.     

Background pollination in Pinus sylvestris seed orchards

The proportion of background pollen grains in the seed crops of two Pinus sylvestris seed orchards in Central Finland was estimated with the aid of multilocus allozyme markers. The orchards studied were more than 30 years old and in full pollen production. For the bulked seed crops of the seed orchard with southern clones the estimated average of background pollination over four years was 26%. There were statistically significant differences between years. No significant heterogeneity in the degree of background pollination between clones was found. Among single ramets there was significant heterogeneity in the estimated contamination rates, but the variation was not related to position in the orchard. For the seed orchard with northern clones the bulked seed crop was studied only for one year and the level of background pollination was found to be 33 %. These estimates are fairly high, but lower than for many other orchards. Background pollination at this level will cause losses in expected genetic gains. Part of the seeds from northern orchards will not be adapted to the intended area of use.     

Clonal variations in nutritional components of <Emphasis Type="Italic">Pinus koreansis</Emphasis> seeds collected from seed orchards in Northeastern China

From four Korean pine (Pinus koraiensis) orchards, 60 clones were selected and analyzed for the fatty acid and amino acid components of the seeds to reveal the variations and correlations of the seed characteristics among the clonal source orchards and clones. The nutritional components of the seeds of the P. koraiensis trees exhibited rich genetic variation; the variation coefficient of the fatty acids was 2.24–66.83 %, while the variation coefficient of the amino acids was 14.70–38.88 %. Relatively high genetic-improvement potential exists for the nutritional components of the seeds. The phenotypic differentiation of the fatty acid and amino acid components reveals that variation within the population (85.18 %) was the primary source for the variation of the fatty acid components; variation among the orchards (63.08 %) was the primary source of the variation of the amino acid components. Data drawn from various clonal source orchards all showed that the seed characteristics were highly controlled by heritability (h² > 80 %), and the seed characteristics of the P. koraiensis trees exhibited a similar genetic gain trend. The principal components were analyzed to obtain the comprehensive principal component value for each clonal seed orchard. Twelve clones were selected based on a clonal selection rate of 20 %. Correlation and multiple stepwise-regression analyses were conducted, considering different location conditions, to reveal the stable correlations between the seed characteristics to facilitate improvements of the seed yield of P. koraiensis trees and the clonal selection. Species of real characteristics in P. koraiensis were controlled by higher heritability. Genetic gain was obtained by selecting of superior clones.     

巨桉种子园种子与普通种子造林对比试验初报

在福建永安国有林场开展了巨桉种子园种子与普通种子造林对比试验,结果表明:4年生时,巨桉种子园种子的林分生长量明显优于普通种子的林分生长量,其中以二代种子园种子的林分生长最快,一代种子园种子的林分次之;桉树种子园的种子造林增益明显,遗传改良成效显著;柳桉与巨桉普通种子造林的林分生长量相似。试验林遭遇-3.9℃寒流袭击仅受到轻微冻害,说明柳桉和巨桉具有较好的耐寒能力,在永安周边地区具有造林推广潜力。     

Female fertility variation in mature Pinus sylvestris clonal seed orchards

Abstract

Female fertility is the basis for the output of seeds from clonal orchards and its variation is of major interest for the economics and biology of seed orchards, especially for the efficiency and diversity of seed orchard crops. Assessments of female fertility variation in 10 mature (>15 years old) seed orchards of Scots pine (Pinus sylvestris L.) were evaluated and compared. Depending on the individual orchard, fertility variation for each clone was assessed in slightly different ways, e.g. number of strobili, cones, seeds or litre of cones per ramet. Assessments in five of the orchards were made over consecutive years. The main result was that the clonal variation in mean female fertility per surviving ramet was lower than expected from the literature; the Kang–Lindgren sibling coefficient (Ψ) within individual years averaged 1.35. The variation between ramets within clones and years was of similar magnitude as that between clones. Clone by year interactions were noticeable, but were slightly lower than the variation between as well as that within clones in individual years. There was considerable variation in the variance components between years. The limited variation in female fertility indicated that it should not be a selection criterion when selecting clones for a seed orchard. Furthermore, it will not result in large differences between clones in seed set or large reductions in gene diversity in productive Scots pine seed orchards.     

A tool for identifying potential Eucalyptus nitens seed orchard sites based on climate and topography

Shy seed production in orchards of Eucalyptus nitens is a major barrier to the deployment of genetic gain in South African plantations. A machine learning method was used to identify optimal sites for the establishment of E. nitens seed orchards within the plantation forestry landscape of the summer rainfall region of South Africa. The ensemble classifier random forests (RF) was used to identify the environmental factors conducive to E. nitens floral bud production, and, based on these, build a predictive model deployable to the plantation forestry landscape for identifying suitable areas for E. nitens seed orchards. The RF model predicted site suitability likelihood for floral bud production with a high level of accuracy (area under the receiver operating characteristic curve = 0.83). Within the climatically optimal range for growing E. nitens, flower bud production was more abundant and consistent on cold slopes, i.e. sites experiencing lower minimum air temperatures during spring and autumn. The model was applied to the commercial plantation forestry landscape for the purpose of indicating sites climatically optimal for floral bud production in E. nitens and the establishment of breeding and seed production orchards of the same species.     

Advanced generation seed orchards’ turnover as affected by breeding advance,time to sexual maturity and costs,with special reference to Pinus sylvestris in Sweden

Abstract

The effect of various biological, genetic, economic and management factors relevant to advanced generation seed orchard establishment was investigated using numerical estimates for Scots pine (Pinus sylvestris L.) in Sweden. Factors considered were planting density, rate of genetic advance in the breeding population, timing of first seed collection, seed value, seed production cost (stratified to establishment, annual management, cone harvest and seed extraction), orchard rotation age and contamination level. The developed model demonstrated its utility in studying and evaluating various economic and biological options associated with advanced generation seed orchard establishment/turnover. Sensitivity analyses demonstrated the robustness of the developed model through various arbitrarily changes in genetic gain advances, establishment, management and seed production, particularly those associated with cone harvests from upper crown and costs. The Swedish Scots pine case study produced results supporting faster turnover of seed orchard generations (30 vs 40 years) with shorter orchard lifespan (early start of seed cone after 8 years vs 15 years) delivering higher gain through minimizing the genetic gain differential between the breeding and production populations and allowing the capture of this gain for inclusion in the seed orchards. Orchard planting densities of 400 and 600 grafts per hectare produced similar results with marginal differences, and the latter was recommended for future orchard establishment.     

Variation in cone and seed characters in clonal seed orchards of <Emphasis Type="Italic">Pinus sylvestris</Emphasis>

Cone and seed characters were observed on top, middle and bottom portions of tree crown in 3 ramets/clone in three Turkish Pinus sylvestris seed orchards. Broad sense heritability (clonal repeatability), and correlations among characters were estimated. Around one quarter of the seed production occurred in the top portion, half in the middle and one quarter in the bottom portion of the crown for all orchards. The percentage of filled seeds varied little with the crown position, indicating more or less similar levels of selfing in the bottom of the crown as in the top. The seed weight was typically 11 mg. Differences were found for studied cone and seed characters among orchards and crown positions. Variation among grafts within clone was higher than among clones for most characters. The heritability was on average below 0.5 (e.g., cone diameter, number of filled seed per cone) and rarely rose above that (e.g., cone form, length/diameter; percentage of filled seed) for any individual characters. The coefficient of variation within clones was often higher than among clones. Thus, non-genetic factors seem often more important for the variation in performance of grafts than their genetic constitution. Cone form (length/diameter) was the character where the clone influence was the strongest. Cone number and cone dry weight showed significant correlations with seed characters (numbers of total and filled seed, percentage and weight of filled seeds). Significant correlation was found between seed characters.     

Balancing seed yield and breeding value in clonal seed orchards

Seed orchards should produce seeds that are both abundant and of high genetic value. This study suggests methods to achieve such a compromise and study their efficiency. The methods were applied on data obtained from 41 seed orchard clones of Scots pine from mid-Sweden. The value of the seed orchard crop was set as a function of its breeding value, the amount of seeds produced and their gene diversity, measured as the effective number of clones. The proportion of ramets of different clones that maximized this value was regarded as the optimum for deployment of the clones in a seed orchard. The results were compared with truncation selection for breeding value, truncation selection for clone benefit (the product of seed production and breeding value) and linear deployment (where ramets are deployed linearly in relation to breeding value). The influence of two parameters was studied: the relative importance of breeding value for seed value and the size of the penalty for reducing the value of the seed crop with respect to lost gene diversity. The conventional wisdom is to select the clones with the highest breeding values, but that turned out to be the most inferior alternative studied. Clone benefit truncation provided a good approximation to optimal benefit for cases, where the effective number was low and dependence of breeding value limited.     

黄山地区杉木优良家系区域选择及效果研究*

60年代以来,国内叶培忠、陈岳武等林木遗传育种专家系统地开展了杉木产地间、产地内、个体间的遗传变异规律和遗传改良研究。中国林科院于1976年和1979年先后两次组织了杉木全分布区的大规模试验研究,摸清了不同地理种源的遗传变异规律,选出了一批杉木优良种源。通过“六五”国家攻关,全国杉木种子园攻关协作组提出了杉木多层次利用的育种策略和程序。把优树经子代测定后筛选出的优良家系,在杉木分布区内进行区域化试验,进一步筛选出适应各种生境的优良家系,同时在这些家系中选择表现突出的优良单株进行多种途径     

Magnitude and efficiency of genetic diversity captured from seed stands of <Emphasis Type="Italic">Pinus nigra</Emphasis> (Arnold) subsp. <Emphasis Type="Italic">pallasiana</Emphasis> in established seed orchards and plantations

To test how efficiently plantations and seed orchards captured genetic diversity from natural Anatolian black pine (Pinus nigra Arnold subspecies pallasiana Holmboe) seed stands, seed sources were chosen from 3 different categories (seed stands (SS), seed orchards (SO) and plantations (P)) comprising 4 different breeding zones of the species in Turkey. Twenty-five trees (mother trees) were selected from each SS, SO and P seed sources and were screened with 11 Random Amplified Polymorphic DNA (RAPD) markers. Estimated genetic diversity parameters were found to be generally high in all Anatolian black pine seed sources and the majority of genetic diversity is contained within seed sources (94%). No significant difference in genetic diversity parameters (numbers of effective alleles, % of polymorphic loci and heterozygosity) among seed source categories was found, except for a slight increase in observed heterozygosities in seed orchards. For all seed source categories, observed heterozygosity values were higher (H_o = 0.49 for SS, 0.55 for SO and 0.49 for P) than expected ones (H_e = 0.40 for SS, 0.39 for SO and 0.38 for P) indicating the excess of heterozygotes. In general, genetic diversity in seed stands has been transferred successfully into seed orchards and plantations. However, the use of seeds from seed orchards can increase the amount of genetic diversity in plantations further. The study also demonstrated that number of plus-tree clones (25–38) used in the establishment of seed orchards was adequate to capture the high level of diversity from natural stands.     

马尾松种子园优良无性系的选择与评价

通过对马尾松种子园132个无性系种子产量性状调查与木材比重测定及种子园自由授粉子代8年生生长性状调查,在统计分析、相关分析基础上采用综合评分法进行优良无性系的选择,入选率为20%。结果表明:对马尾松种子园无性系再选择,以营建改良代种子园是可行的。8年生子代材积可获得改良增益10.6%,木材比重可获得4.6%的增益,种子园单株产种量可获得增益37.5%,选择效果明显,达到提高种子园产量、增加改良增益的目的。     

Production of a new generation of seeds through the use of somatic clones in controlled crosses of black spruce (Picea mariana)

To assess the potential to integrate somatic clones (SC) of desired characteristics in production of high genetic quality seed, controlled crosses between different SCs of black spruce (Picea mariana (Mill) B.S.P.) were used to assess their suitability for the production of viable pollen, cones, seeds and seedlings. These SC produced male and female strobili at an early stage. Pollen, cones and seeds produced were characterized (mass, size, germination); their characteristics were similar to those produced by trees in natural forests or seed orchards. A maternal effect was demonstrated for the cone size and seed mass. Although seeds had excellent germination rates, the somatic biparental crosses were divided into three distinct groups with different germination curves using the Weibull function. Seeds from controlled crosses between different SC enabled the production of high morpho-physiological quality seedlings in a forest nursery. Using black spruce as a model, we showed, for the first time, that SC can be used as seed producers. These encouraging results open new perspectives on the tangible integration of somatic embryogenesis (SE) in the chain of seed, vegetative propagation (cuttings and SE) and production of plants for high productivity plantations. Controlled crosses can be made between SC with the desired characteristics (fewer large branches, fewer nodes, good growth, high wood density, performance, improved yield, etc.), vegetative propagules produced and deployed to clonal tests. After elimination of the worst performing SC, clonal tests can be converted into seed orchards that produce a new generation of seeds of high genetic quality. This will allow the rapid introduction of new materials in elite breeding programs of forest species.     

林木种子园研究现状与发展趋势

林木种子园是重要的良种生产基地。近年来, 林木种子园发展迅速。文中概括了种子园建园和经营过程中保障产量和品质的技术措施, 阐述了种子园增益的表现规律, 提出了未来种子园发展趋势, 以期为我国种子园经营实践提供参考, 促进林木良种化进程。     

Petroleum flotation technique upgrades the germinability of <Emphasis Type="Italic">Casuarina equisetifolia</Emphasis> seed lots

The germination of Casuarina equisetifolia Forst seed lots is low (40–50%) even when freshly collected. This study aimed at upgrading the germination performance by removing non-germinable seeds using petroleum flotation technique. Seeds collected from 19 individual trees in seedling seed orchards in India were assessed using X-ray to determine the proportion of different seed lot fractions. The feasibility of petroleum ether as a separation medium was tested. Morphological characters of floating and sunken seeds were further studied using image analysis technique to examine their effects on the separation efficiency. The X-ray analysis revealed a large quantity of shrivelled, empty and insect-damaged seeds, altogether accounting 50%, which were the causes of low percentage germination of un-graded seed lots (48%). Petroleum flotation resulted in 90% germination in the sunken fraction and 4% in the floating fraction. The separation was distinct for most seed lots, except few seed lots that had relatively low germination in the sunken fractions and more than 10% germination in the floating fractions. As a whole, petroleum flotation appears to be a feasible technique to upgrade the germination of C. equisetifolia seed lots, and its efficacy is influenced by wing surface area, seed density and wing quotient of filled and empty seeds.     

Genetic thinning of clonal seed orchards using linear deployment may improve both gain and diversity

The linear deployment algorithm defines a straight line relationship between the number of ramets and the breeding value of a given clone. However, when used to determine thinning in clonal seed orchards, there is an upper limit, determined by the number of ramets in the seed orchard prior to thinning. Linear deployment thinning maximises genetic gain and effective clone number whilst minimising thinning intensity, thus both production and genetic diversity are optimised. Here two applications of linear deployment to Swedish Norway spruce seed orchards are described.     

Mating patterns in an indoor miniature <Emphasis Type="Italic">Cryptomeria japonica</Emphasis> seed orchard as revealed by microsatellite markers

To evaluate the practical application of an indoor seed orchard, we compared the seed production, final germination rates and mating patterns of potted Cryptomeria japonica D. Don clones in two miniature seed orchards: one in a glasshouse and the other outdoors. There was no statistically significant difference in total seed production between the orchards (P = 0.275, ANOVA). However, the final germination rate of seeds produced in the indoor orchard was significantly lower than that of seeds produced in the outdoor orchard (P < 0.01, Wilcoxon test). The average self-fertilization rate was higher in the indoor orchard (27.2%) than in the outdoor orchard (5.6%), and this parameter was strongly associated with the reduced final germination rates of the seeds harvested in the glasshouse. Pollen contamination was considerably lower in the indoor seed orchard (48.9% in the outdoor seed orchard and 4.4% in the indoor seed orchard). χ² tests indicated that the paternal contributions of each constituent clone differed significantly in both orchards (P < 0.001 in both cases). The strong variations in paternal contributions among indoor orchard clones was significantly correlated with their respective pollen production capacities (Spearman ρ = 0.693, P < 0.001). To reduce the high self-fertilization rates, we recommend the use of orchard clones with similar pollen production capacity in indoor seed orchards.     

Jackknife resampling for precision measurement of direct gene flow estimates

Gene flow from outside pollen sources reduces the expected genetic gain of seed orchards, and has been quantified by genotyping seed samples from crop years to determine the proportion of seed sired by outside sources. Random bulk seed sampling and microsatellite genotyping allows for fast, unbiased identification of orchard contamination rates. Bulk seed sampling has been employed in multiple studies of seed orchard gene flow, but a method of determining precision of gene flow estimates from this sampling method has yet to be described. In this study, we used jackknife resampling to generate random samples of migrant and within-population genotypes obtained from an empirical sample of Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) genotypes of five microsatellite loci. We generated samples of 50, 100, 150, 200, and 250 genotyped individuals from a sample of 400 seeds, with genotypes corresponding to low (6%), moderate (14%), or high (56%) pollen contamination levels. The mean gene flow estimate and confidence interval were calculated for each sample size and gene flow scenario to determine the precision of gene flow estimates obtained from each sample size in each contaminant gene flow scenario. Genotyping 150 individuals was sufficient to produce gene flow estimates with calculated confidence interval values below ± 1%, indicating that 150 genotyped individuals were sufficient for precise gene flow estimation in this population. This resampling method will enable precise and unbiased estimation of gene flow into seed orchards for future monitoring of gene flow, to allow better management of seed orchard genetic resources.     

Optimum age for selection based on a time trend of genetic parameters related to diameter growth in seedling seed orchards of Eucalyptus pellita in Indonesia

The time trend of genetic parameters related to diameter growth was investigated using data at ages from 1 to 6 years to determine the optimum age for selection in four seedling seed orchards of Eucalyptus pellita in South Kalimantan and Riau (Sumatra), Indonesia. The seed orchards at each location were from three geographically distinct provenances from Papua New Guinea. The pooled sum of squares and sum of cross products derived from an analysis of variance of growth of the three provenance populations were used to estimate genetic parameters at each location. Because the genetic parameters at rotation age, 8 years in this study, were not available, they were estimated using functions derived from their time trends. Phenotypic variances and genetic variances calculated at each age were converted to the corresponding square roots, and then analyzed by the linear regression using means as independent variables. The trend of juvenile–mature correlation was fitted by a modified Richards function with the ratio of the older diameter mean to the juvenile diameter as an independent variable. Early selection always resulted in more genetic gain per year than selection at rotation age, and the optimum age for selection, where genetic gain per year was maximized, was found to be 4 and 5 years in the two locations.