Optimization of genetic gain and diversity in seed orchard crops considering variation in seed germination

Abstract

Balancing genetic gain and diversity in seed orchard crops is of a major regeneration importance. Here we extend our earlier work on the development of an optimization protocol that maximizes crops' genetic gain at any predefined diversity level, considering parental reproductive output, co-ancestry, and inbreeding, by incorporating variation in seed germination as an input. Variation in seed germination capacity substantially affected seedlots' genetic diversity by either under- or overestimating their effective population size; however, genetic gains were robust and their differences were negligible. The contrasting results of gain and diversity support the inclusion of the germination capacity, when available, in the optimization protocol.     

Variability in seed traits and genetic divergence in a clonal seed orchard of Dalbergia sissoo Roxb.

The variations in seed and pod traits, genetic superiority and genetic divergence were evaluated for a Clonal Seed Orchard (CSO) of Dalbergia sissoo Roxb. at Bithmera, India consisting of 20 clones from different agro-climatic conditions of four northern states (Uttar Pradesh, Uttarakhand, Haryana and Rajasthan). The seeds and pods of various clones in the orchard exhibited significant variability in size, weight and other characters. Significant positive correlations were observed between seed length and seed width (p<0.05), seed length and seed thickness (p<0.01), seed length and seed weight (p<0.01), seed thickness and seed weight (p<0.01), seed length and germination value (p<0.05). The genetic parameters for seed and pod traits also showed a wide range of variations in the orchard. Heritability values were found to be over 50 percent for most of the seed and pod traits. Seed weight, seed length and seed thickness showed high heritability values coupled with maximum genetic gain for these characters. Ward’s minimum variance dendrogram of clones of D. sissoo showed three distinct clusters; cluster 1 was the largest with 12 better clones whereas cluster 2 and 3 consisting of seven moderate clones and one poor clone, respectively. Mean cluster values showed sufficient variation among the clusters for seed weight, germination value and seed length. The possible hybridization between best clones of cluster 1 to the disease resistant clone of cluster 2 (resistant against deadly Gandoderma lucidum root rot disease of D. sissoo) is also suggested for further breeding programmes of the species. The deployment of clone 194 (better performed and disease resistant) is also recommended in future plantation programmes of D. sissoo in northern India.     

Genetic variation, mating patterns and gene flow in a Pinus pinaster Aiton clonal seed orchard

? Relatedness among parents, variation in clonal fertility and background pollination deviate the realized genetic gain and the gene diversity of open pollinated seed orchard from expectation, in particular in wind pollinated species such as Pinus pinaster Aiton.

? This work investigates the genetic variation, the mating system and the pollen contamination in a P. pinaster clonal seed orchard (CSO), by screening the 60 clones from the CSO and the seeds collected from 21 mother-trees with three nuclear microsatellites.

? The expected diversity was similar, but the observed heterozygosity decreased 20% in the progenies compared with the parental trees. The outcrossing rate was 90.1%, the biparental inbreeding 21.7% computed through a multilocus approach, and the observed selfing 3.9%. The observed gene flow from outside the CSO was 52.4%.

? From the results we concluded that the observed gene flow and the biparental inbreeding were high, and care should be taken in the implementation and management of future CSO, in particular clones should be checked for relatedness and the ramet number could be directly proportional to their breeding value.

     

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。     

抗松材线虫病马尾松无性系种子园营建技术

松材线虫病是危害松属树种的毁灭性病害,危害严重、防治困难。安徽省从2001年开始从疫区和非疫区的马尾松林分中选择324株抗病优树以及部分广东、广西种源,通过嫁接繁殖和人工接种松材线虫的方法进行无性系抗病性测定。2011年利用筛选出的68个家系的89个高抗无性系营建了1.6 hm2抗松材线虫病马尾松无性系种子园。各家系成活率90.9%～100%,平均成活率93.6%。     

尾叶桉与赤桉正反交杂种F1代生长、材性及其化学组分与抗风性能的分析

以广东江门尾叶桉(Eucalyptus urophylla)与赤桉(Eucalyptus camaldulensis)正反析因交配杂种F_1代9年生测定林为材料,用Excel计算各杂交组合抗风指数、生长性状、材质形状以及木素、综纤素的均值;用R软件对这些性状进行单因素方差分析、相关性分析以及多性状指数综合评价。单因素方差分析表明正交与反交组合杂种的生长性状如树高、胸径、材积和冠幅等差异都不显著;而材质形状如基本密度和纤维宽度差异则较为显著,但纤维长度和纤维长宽比差异不显著;另外,正反交组合杂种的木素和综纤素含量的差异也较为显著。相关性分析表明,抗风指数与木材基本密度及纤维长呈正显著相关性,而与纤维长宽比呈负显著相关性;但抗风指数与树高、胸径、材积、冠幅、纤维宽、木素含量及综纤素含量之间的相关性都不显著;木材基本密度及纤维长与抗风指数的显著相关性为抗风优质的桉树选择提供参考。综合评价结果表明,当各变量权重相同时,正交组合中综合得分前3名的是杂交组合77、81和82;反交组合中综合得分前3名的是杂交组合50、51和29;同时还选出5株优良单株29-3、51-4、77-1、77-3及50-2,为今后大规模人工制种提供优质亲本材料。     

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.     

Estimation of genetic gain and diversity under various genetic thinning scenarios in a breeding seed orchard of Quercus acutissima

Genetic gain and diversity were estimated based on three simulated thinning scenarios at various thinning intensities in a breeding seed orchard of Quercus acutissima. The seed orchard was composed of 32 families with 744 individual trees with volume at age 15. The three thinning scenarios were individual thinning (IT) which thinning was based on the individual performance, family thinning (FT) with the removal of inferior families regardless of individual performance, and family + within family thinning (FWF) with family first and then individual from inferior families. The genetic gain was estimated based on stem volume. Expected genetic gain (volume at age 15) under IT was higher than FT and FWF at all thinning intensities. The FWF provided higher genetic gain than FT but lower than IT. The FT gave the lowest genetic gain compared to the other thinning scenarios at all thinning intensities. The loss of gene diversity (GD), estimated by coancestry and family size, was higher under FWF and lower under FT at moderate thinning intensities. The study showed that genetic gain estimation and GD loss were inversely coupled. The IT gave highest genetic gain but lowest GD at the highest thinning intensity.     

疏枝对华北落叶松种子园结实的影响

对进入结实盛期的华北落叶松种子园,采取不同的疏枝方式,比较其对华北落叶松大小年现象及种子品质的影响。在同一个无性系中选择5个单株,分别对5个单株采取不同的疏枝措施,强度由小到大,分别去掉母树主枝的1/4、1/3、1/2、2/3,以不疏枝为对照,结果发现:随着疏枝强度的加大,第2年和第3年(小年)的结实量与疏枝强度呈正相关,种子品质也相应提高,说明通过人工疏枝措施,可降低明显的大小年现象,提升种子品质。     

Selection strategy for a seedling seed orchard design based on trait selection index and genomic analysis by molecular markers: a case study for Eucalyptus dunnii

Molecular genetic analysis was applied to 162 individuals of 37 half-sib selected families belonging to six provenances of Eucalyptus dunnii Maiden in a provenance/family trial. The individuals were selected by a trait selection index and genetic diversity criteria were later applied for designing seedling seed orchards. Genetic diversity and its distribution, as well as relationships among individuals, were assessed on the basis of nine microsatellite loci and 243 amplified fragment length polymorphism markers. High diversity was found with both kinds of markers. Clear-cut genomic patterns of identification (fingerprinting) were obtained for each individual. Genetic differentiation estimates consistently showed low differentiation among provenances (R(ST1) = 0.069, theta(P) = 0.026 and F(CT) = 0.035) and great differentiation among families (R(ST2) = 0.223, theta(S) = 0.174 and F(SC) = 0.164). A high proportion of the total variation was observed within families (around 80% by both marker analyses), suggesting that orchard design should be based on individual or family selection rather than on provenance selection, and that individual ranking by both trait selection index and molecular genetic diversity criteria should be considered. A selection procedure for a seedling seed orchard design is proposed.     

Production of hybrid seed in a seed orchard of two larch species,Larix sibirica and Larix decidua

The larch seed orchard studied is intended to produce interspecific hybrid seed between Larix sibirica and Larix decidua. Only the L. sibirica clone (half of the grafts) in the orchard was intended to act as the seed parent, and the six L. decidua clones are pollinators. The proportion of hybrid seed produced was determined using Mdh3 locus as a genetic marker. The mean percentage of hybrid seed produced by the grafts of L. decidua was 93, but that of the hybrid seed produced by L. sibirica was only 18. The results can be explained by differences in flowering abundance. The grafts of L. sibirica produced several times more pollen than those of L. decidua. Contrary to the original plans, L. decidua should be used as the seed parent and L. sibirica only as the pollen parent in the studied seed orchard.     

Evaluation of Irrigation Practices for Growth,Biomass Production,and Nutrient Partitioning in Eucalyptus camaldulensis Plants in Indian Dry Zone

Supplemental irrigation is essential to increase tree productivity in dry areas to fulfill the local needs. One-year-old Eucalyptus camaldulensis Dehnh plants were planted in July 1998 and supplemental irrigation was provided at 36.2 mm (I₁), 26.5 mm (I₂), 20.2 mm (I₃), 18.1 mm (I₄), and live saving (I₅). Frequency and quantity of irrigation increased with an increase in irrigation level enhancing plant height, collar diameter, and biomass. These variables were highest at I₁, but water use efficiency (WUE) was highest at I₂. Dry biomass production increased from 1.18 kg plant^?1 at I₅ to 13.75 kg plant^?1 at I₁ at 24-month age. Biomass allocation to root increased from I₁ to I₅ but it was at the expense of leaf and branches. Height, collar diameter, dry biomass, and nutrient uptake indicated a non-linear increase with total quantity of water. Partitioning of N, Mg, Fe, Mn, Cu, and Zn was greater to stem; and those of P, K, and Ca was greater to leaf than to the other parts. Conclusively, I₃ and I₄ levels supported establishment whereas I₂ level was best for growth and productivity of E. camaldulensis plants in dry areas. The I₁ level could be tried to increase water use and reduce salinity buildup.     

Final results from a trial to test the effect of plot size on Eucalyptus hybrid clonal ranking in coastal Zululand,South Africa

Hybrid clones with Eucalyptus grandis as one parent and, generally, E. urophylla as the other parent, are deployed commercially as monoclonal blocks by Sappi in the subtropical region of coastal Zululand, South Africa. In monoclonal blocks genotypes are grown in self-competition. Performance under this scenario may not necessarily correlate well with performance where genotypes are competing for resources with a number of genetically dissimilar genotypes. There is an uncertainty whether plot configuration or size influences clonal ranking and therefore selection of clones for commercialisation. Final results at age eight years of a trial testing eight selected Eucalyptus hybrid clones in single-tree, eight-tree line, and eight x eight tree square plots are reported in this paper. Ranking of the eight clones between the half rotation (44 months) and full rotation (94 months) measurement have remained stable in the single-tree and line plots, but there have been some changes in the square plots. At 94 months, clonal ranking between the single-tree and line plots was consistent (r_p = 0.98) with only two clones changing ranks. When comparing the clonal ranking of the single-tree plots to the large square plots rank changes have been significant (r_p = 0.65). The overall means for the three different plot types are very similar. The range of the clonal means for tree volume in the single-tree plots (0.4042 m³) is more than five times the range for the square plots (0.0709 m³). Gain predictions using data from the single-tree plots overestimated the realised gains measured in the square plots. The top-performing clone in the single-tree plots had a predicted gain of 74% over the trial mean, but only yielded 7% more in the square plots. Similarly, the worst-ranked clone in the single-tree plots did not perform as poorly as what was predicted (?59%) and produced only 13% less than the trial mean on the square plots.     

Field survival and growth of clonal,micropropagated Eucalyptus marginata selected for resistance to Phytophthora cinnamomi

Clones of jarrah (Eucalyptus marginata), micropropagated from glasshouse-grown seedlings selected for resistance or susceptibility to Phytophthora cinnamomi, were planted in a former bauxite mine-site in the jarrah forest and inoculated with P. cinnamomi. Mortality after 13 years in resistant clones was 0–30%, while that of susceptible clones was 40–100%. Mean heights of resistant clones after 13 years were 7.8–13.6 m, while heights of surviving susceptible clones were 0.9–6.7 m. The resistance character of the seedling ortets was transmitted consistently to the clones. The field mortality of clones of some rare, apparently resistant seedlings selected from susceptible half-sib families was low after 1 year, but approached that of the susceptible clones after 2 years. The results show that Phytophthora-resistant jarrah ortets can be selected using stem-inoculation of glasshouse-grown seedlings; the resistance of the resulting clones has been validated in the field in an inoculation trial.     

Effect of flowering phenology,date of cone collection,cone-storage treatment and seed pretreatment on yield and germination of seeds from a Douglas-Fir seed orchard

The effects of reproductive phenology, date of cone harvest, cone storage and seed pretreatment on yield and germination of seeds from a Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco] seed orchard were studied. Flowering phenology (early, intermediate or late) had no discernible effect on seed maturation. Higher germination and yields of filled seeds were obtained from cones collected in mid-August, approximately 2 weeks prior to cone opening, than from cones collected just as they began to open. Seeds extracted immediately following harvest germinated better than those from cones stored for 2 months. Seeds from all treatments were dormant and responded to prechilling by exhibiting increased germination rates. The implications of these findings for cone-crop management are discussed.     

Growth and heritability estimates among clones of <Emphasis Type="Italic">Dalbergia sissoo</Emphasis> Roxb. in a clonal seed orchard

The study of genetic variability is a prerequisite for any tree improvement program. Screening of clones showing the effect of dominance in growth and tree form is essential to identify productive clones, matched to sites. Our study performed in a clonal seed orchard at Lacchiwala of India, represented by 31 clones of Dalbergia sissoo (Shisham) Roxb. from diverse locations revealed significant variability at the 0.1% level of significance in various morphological traits. At the age of 13 years, clone 196 (Gonda) revealed maximum height of 20.2 m and a girth at breast height of 74.2 cm. The five identified clones viz. 196, 198, 192, 123 and 235 were well adapted to the climatic conditions of this zone, hence survived well and showed good performance compared to other clones. Heritability estimates of 87%, 83% and 80% for height, crown width and crown length respectively coupled with high genetic gains indicated strong genetic control of these variables. A correlation matrix of various growth attributes revealed positive correlation among these attributes. On the basis of the entire set of growth variables, the clones were grouped into two major clusters with three subgroups.     

Genetic variation and relationships to growth traits for microfibril angle,wood density and modulus of elasticity in a Picea abies clonal trial in southern Sweden

Abstract

Genetic variation in wood density, microfibril angle (MFA), wood stiffness (MOE), height, diameter and volume was investigated in a 26-year-old Norway spruce [(Picea abies (L.) Karst.] clonal trial in southern Sweden. Wood quality measurements were performed on 10 mm increment cores using SilviScan. For MFA, mean values of annual rings showed the highest value (30°) at ring 2 counting from the pith, followed by a steep decrease and a gradual stabilization around ring 12 at approximately 14°. MOE showed a monotonic increase from 5 GPa to 14 GPa when moving from pith to bark. High broad-sense heritability values were found for wood density (0.48), MFA (0.41) and MOE (0.50). All growth traits displayed heritability values of similar magnitudes as reported in earlier studies. The generally high age–age correlations between different sections of the wood cores suggested that early selection for wood quality traits would be successful. Owing to unfavorable genetic correlations between volume and MOE, the correlated response indicated that selection for volume only at age 10 would result in a 0.27% decrease in weighted MOE at age 26 for every 1% increase in volume.     

An evaluation of the conical approximation as a generic model for estimating stem volume, biomass and nutrient content in young Eucalyptus plantations

Accurately and non-destructively quantifying the volume, mass or nutrient content of tree components is fundamental for assessing the impact of site, treatment, and climate on biomass, carbon sequestration, and nutrient uptake of a growing plantation. Typically, this has involved the application of allometric equations utilising diameter and height, but for accurate results, these equations are often specific to species, site, and silvicultural treatment. In this study, we assessed the value of incorporating a third piece of information: the height of diameter measurement. We derived a more general volume equation, based on the conical approximation, using a diameter projected to the base of the tree. Common equations were developed which allowed an accurate estimate of stem volume, dry weight and nutrient content across two key plantation grown eucalypt species, Eucalyptus grandis W. Hill ex Maiden and Eucalyptus globulus (Labill.). The conical model was developed with plantation-grown E. grandis trees ranging from 0.28 to 15.85 m in height (1.05 g to 80.3 kg stem wood dry weight), and E. globulus trees ranging from 0.10 to 34.4 m in height (stem wood dry weight from 0.48 g to 652 kg), grown under a range of contrasting cultural treatments, including spacing (E. grandis), site (E. globulus) and fertilization (nitrogen and phosphorus) for both species. With log transformed data the conical function (V_con) was closely related to stem sectional volume over bark and stem weight (R² = 0.996 and 0.990, respectively) for both E. grandis and E. globulus, and the same regressions can be applied to both species. Back transformed data compared with the original data yielded modelling efficiencies of 0.99 and 0.97, respectively. Relationships between V_con and bark dry weight differed for the two species, reflecting differing bark characteristics. Young trees with juvenile foliage had a different form of relationship to older trees with intermediate or adult foliage, the change of slope corresponding to heights about 1.5 m for E. grandis and age 1 year for E. globulus. The V_con model proved to be robust, and unlike conventional models, does not need additional parameters for estimating biomass under different cultural treatments. More than 99% of the statistical variance of the logarithm of biomass was accounted for in the model. V_con captures most of the change in stem taper associated with cultural treatments and some of the change in stem form that occurs after the crown base has lifted appreciably. Fertilization increased N and P concentrations in stem wood and bark, and regressions to estimate N and P contents (the products of biomass and concentration) were dependent on treatment. For instance, there was a large growth response to N fertilization in E. globulus corresponding with a change (P < 0.05) in the intercept of the regression to estimate N content.     

Development and evaluation of a real‐time PCR seed lot screening method for Fusarium circinatum,causal agent of pitch canker disease

Fusarium circinatum is a serious pathogen of Pinus spp. worldwide, causing pitch canker disease. F. circinatum can contaminate seeds both internally and externally and is readily disseminated via contaminated seed. Many countries require screening of pine seeds for F. circinatum before they can be imported. The currently accepted screening method is based on culturing the pathogen on a semi‐selective medium and identifying it using morphological traits. This method is time‐consuming and does not allow for accurate identification of the pathogen to the species level. A bulk DNA extraction and real‐time PCR procedure to screen seeds for the presence of F. circinatum were developed in this study. The real‐time PCR method resulted in the detection of F. circinatum in 5 of 6 commercial seed lots tested and has a lower detection limit of 1 × 10^?5 ng of F. circinatum DNA per PCR. The culture‐based method detected Fusarium spp. in four of six of the same seed lots. The real‐time PCR method can be used to screen multiple seed lots in 2 days, whereas the culture‐based method requires a minimum of 1–2 weeks. This new real‐time PCR seed screening method allows for fast, sensitive and accurate screening and can be adapted to handle larger volumes of seeds.