Genetic characterisation of a Eucalyptus nitens base breeding population in South Africa

The measurement and statistical analysis of data from eight Eucalyptus nitens trials, established in the summer rainfall forestry region of South Africa during the 1980s and 1990s, have enabled the characterisation of the Institute for Commercial Forestry Research’s breeding population. Provenance testing showed that the more northerly New South Wales (Australia) Eucalyptus nitens provenances of Barren Mountain and Barrington Tops are distinctly better suited to the summer rainfall areas of South Africa than the southern New South Wales provenances and the Victorian provenance, Penny Saddle. Generally, the species was not badly affected by Coniothyrium canker. High type B genetic correlations for all site pairs, except one comparison, ranged from 0.75 to 0.99 for diameter at breast height (dbh), indicating very little or no genotype environment interaction for dbh for the genotypes tested in this study. Narrow-sense heritability coefficients ranged from 0.01 to 0.34, indicating that the species generally exhibited sufficient breeding opportunity for improvement of diameter growth. High genetic correlations of greater than 0.90 between diameter measurements at 52 to 62 months after establishment and diameter measurements at 94 or 113 months were found, indicating that selections can be reliably made at five or six years. Predicted genetic gains were highest in the trials at Goedehoop and Arthur’s Seat, with increases in dbh of 3.07 cm (17.1%) and 3.17 cm (20.7%), respectively, at full rotation.http://www.tandfonline.com/loi/tsfs20hj201

A comparison of the effect of genetic improvement, seed source and seedling seed orchard variables on progeny growth in Eucalyptus nitens in South Africa

Eucalyptus nitens is an important forestry species grown for pulp and paper production in the temperate, summer-rainfall regions of South Africa. A tree improvement programme has been ongoing at the Institute for Commercial Forestry Research for two decades, but genetic improvement in the species has been slow due to delayed and infrequent flowering and seed production. Three trials were established, firstly, to quantify the gains that have been made in the first generation of improvement in the breeding programme and, secondly, to establish whether a number of seed source and orchard variables influence the performance of the progeny. These variables were the amount of flowering trees in the seed orchard, year of seed collection, seed orchard origin and composition of seed orchard bulks. Diameter at breast height and tree heights were measured in the trials at between 87 and 97 months after establishment, and timber volumes and survival were calculated. Improved seed orchard bulks performed significantly better (p<0.01) than unimproved controls in the field trials. Genetic gains ranging from 23.2 to 164.8 m3ha−1 were observed over the unimproved commercial seed. There were significant differences (p<0.01) in progeny growth between the levels of seed orchard flowering, with higher levels of flowering (≥40 %) producing substantially greater progeny growth than lower flowering levels (≤20 %). The seed orchard had no effect on progeny growth in this trial series. This suggests that seed collected from any of the four seed orchards tested will produce trees with significant improvement in growth.http://link.springer.com/journal/11295hj201

Genetic parameters and genotype by environment interaction of Eucalyptus grandis populations used in intraspecific hybrid production in South Africa

In South Africa, Eucalyptus grandis is an important species due to its fast growth and general suitability of its timber for a range of products. However, E. grandis is susceptible to fungal diseases such as Crysoporthe austroafricana and Coniothyrium sp. cankers in the subtropical region of Zululand and is therefore mainly planted as a parental species in a hybrid combination with E. urophylla in this region. The current strategy is to maintain large breeding populations of both parental species in order to provide improved elite selections for hybrid crosses. In order to develop the best interspecific hybrid breeding strategy for E. grandis, it is important to first determine estimates of genetic parametersof the pure species parents. Estimating the genotype by environment interaction (G×E) is also necessary in proposing the basis for setting up breeding populations and selecting environmentally stable genotypes. With this in mind, two E. grandis full-sib progeny trials were planted in Zululand and one in the KwaZulu-Natal Midlands region. The aims of this study were firstly to determine the magnitude of G×E of E. grandis across the three sites; secondly, to estimate the genetic parameters for growth of the E. grandis parents selected for intraspecific crosses; and lastly, to identify the best parents to use for intra- and interspecific crosses in future hybrid breeding programmes. Results of our study indicated that G×E would be practically negligible for growth in Zululand and one group of elite parents can be used for hybrid crosses in this region. In general, growth traits were under low to moderate genetic control, and the variation in additive geneticsenabled us to identify E. grandis parents that could be utilised for intraspecific crosses and deliver progeny with genetic gains of 28.4%. Our study also highlighted that a relatively large portion of the genetic variation was explained by dominance geneticvariation and a strategy to capture this non-additive variation needs investigation. Although our study achieved the stated aims, it must be kept in mind that E. grandis is mainly used as a hybrid parent with E. urophylla in Zululand. A study to investigate whether the parents with good general combining ability values from our study are also good general combiners in interspecific hybrid combinations with E. urophylla needs to be conducted.Mondi training departmenthttp://www.tandfonline.com/loi/tsfs202017-11-28fb2017Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant Patholog

Genetic parameters of interspecific hybrids of Eucalyptus grandis and E.urophylla seedings and cuttings

The current E. grandis x E. urophylla hybrid breeding strategy of South Africa’s Forestry Industry is to maintain large breeding populations of both parental species in which parents are selected based on their general combining ability (GCA) estimates or predicted individual tree breeding values and are used for interspecific hybrid crosses. The hybrid material is first screened in seedling progeny trials after which superior individuals are selected and tested as clones. Although this strategy has delivered superior clones for commercial production in South Africa, it is a time consuming strategy to follow and more cost effective strategies are being investigated. In order to review the current hybrid breeding strategy, information on the genetic control of the traits of interest is needed for E. grandis x E. urophylla seedling and clonal populations. The main objectives of this study were therefore to firstly estimate genetic parameters for E. grandis x E. urophylla hybrid seedling and clonal populations; secondly to investigate the correlation between E. grandis and E. urophylla parental (GCA) or individual breeding values and their general hybridising ability (GHA); and lastly to determine the correlation between E. grandis x E. urophylla hybrid seedling ortets and their ramets. Results of our study indicated that non-additive genetic variation explained the majority of the total genetic variation in E. grandis x E. urophylla seedling and clonal populations. Due to the pre-eminence of non-additive variance, the pure-hybrid correlations were weak, especially for clonal populations. It would therefore seem that GCA or predicted individual breeding values are not good predictors of GHA for growth performance in the observed populations. Our study also indicated a weak coefficient of correlation between the growth performance of seedling ortets and their ramets. These results suggest that: firstly a hybrid breeding strategy to capture non-additive genetic variation should be adopted; and secondly that the first phase of screening E. grandis x E. urophylla hybrid material as seedlings should be revisited. Genetic Parameters of Interspecific Hybrids of Eucalyptus grandis and E. urophylla Seedlings and Cuttings.Mondi training departmenthttp://www.sauerlaender-verlag.com/zeitschriften/silvae-geneticaPlant Production and Soil Scienc

Estimates of genetic parameters and genetic gains for growth traits of two Eucalyptus urophylla populations in Zululand, South Africa

In South Africa, Eucalyptus urophylla is an important species due to its disease tolerance to fungal diseases like Crysoporthe austroafricana and the Coniothyrium sp. cankers. It is mainly planted as a parental species in a hybrid combination with E. grandis. Generally, the E. grandis x E. urophylla hybrid has better disease tolerance and higher wood density than pure E. grandis. The current strategy is to maintain large breeding populations of both parental species in order to provide improved elite selections for hybrid crosses on a regular basis. With this in mind, two E. urophylla populations, consisting of five provenance/progeny trials, were established in the subtropical region of Zululand. The aims of this study were firstly to determine the magnitude of genotype by environment interaction of E. urophylla in Zululand; secondly to estimate genetic parameter and correlations for DBH, height and volume; and lastly to identify selections to advance the current breeding population as well as to hybridise with E. grandis. Results indicated that genotype by environment interaction effects would be practically negligible for growth in Zululand and a single breeding population will therefore be appropriate. In general, all growth traits were under low to moderate genetic control, with narrow sense heritabilities ranging between 0.14 and 0.48 for volume. The genetic correlations between growth traits were high (0.98 and 0.99 for DBH-volume). This is an indication that DBH is a sufficient growth measure to use in E. urophylla breeding programmes. BLUP estimates indicated that a selection scenario of 200 individuals will generate genetic gains of 44.7% over the population mean. The estimated gains for the top 50 individuals that could potentially be used as hybrid parents to cross with E. grandis was 59.8% over the population mean.Funding was provided by Mondi training department.http://www.tandfonline.com/loi/tsfs202017-08-31hb2016Plant Production and Soil Scienc

Comparison of the tolerance of Pinus patula seedlings and established trees to infection by Fusarium circinatum

Since the first appearance of Fusarium circinatum in South Africa in 1990, foresters have been challenged with poor field survival of seedlings at establishment. One of the best long-term solutions is to improve the genetic tolerance of Pinus patula to infection by the pathogen. Currently, large numbers of families are routinely screened for their tolerance to F. circinatum by infecting open-pollinated seedlings from orchard clones in a greenhouse and assess-ing lesion development. In this study, nine-year-old P. patula trees from 96 families were inoculated with F. circina-tum in the field. Their levels of tolerance were assessed and compared to those observed in seedlings originating from seed harvested from the same trees. The field results were also compared with those from previous greenhouse screening trials where seedlings from a number of the same families had been inoculated with F. circinatum. The results showed that there was a strong phenotypic (r = 0.71) and genetic (rg = 0.94) correlation in the performance of the families common in both the greenhouse studies. A comparison of the tolerance of the families, screened as both seedlings and as trees, was also meaningful (r = 0.40). Furthermore, the seedlings raised from seeds collected from the infected P. patula trees, that ranked more tolerant than the mean of the P. elliottii trees, were similar in tolerance to P. elliottii seedlings in the greenhouse trial. Our results indicate that utilising seedlings from clones known to be tolerant should improve the tolerance of mature trees to infection by F. circinatum.Tree Protection Co-operative Programme (TPCP)http://www.tandfonline.com/loi/tsfs202015-06-30hb201

Genomic consequences of artificial selection during early domestication of a wood fibre crop

DATA AVAILABILITY : The genomic data generated and analysed in this study are available online via the Dryad archives under accession https://doi. org/10.5061/dryad.h18931zj6.SUPPLEMENTARY MATERIAL : FIG. S1. Population structure in relation to wild Eucalyptus grandis and other species in section Latoangulatae based on principal component analysis, discriminant analysis of principal components and sparse nonnegative matrix factorization. FIG. S2. Breeding Eucalyptus grandis population structure for all breeding samples, those excluding introgressed, and those excluding infused individuals in relation to the wild progenitor populations based on principal component analysis, sparse nonnegative matrix factorization and discriminant analysis of principal components analyses. FIG. S3. Population differentiation FST estimates among breeding Eucalyptus grandis, wild E. grandis and other species in section Latoangulatae. FIG. S4. Chloroplast (cp) haplotype network based on 24 cp single nucleotide polymorphisms. FIG. S5. Marker-specific Hardy–Weinberg equilibrium signed R values of wild vs breeding populations. FIG. S6. Genomic outliers and linkage disequilibrium plots per chromosome. FIG. S7. Breeding population linkage disequilibrium decay over genomic distance in kb. FIG. S8 Outlier detection by pcadapt scan.TABLE S1. Ancestry assignment of chromosomal segments.TABLE S2. Cluster assignment of samples using discriminant analysis of principal components to identify genetically infused breeding individuals. TABLE S3. Summary statistics of genetic diversity using hierfstat v.0.04-22. TABLE S4. Wilcoxon signed rank test P-values supporting the alternative hypothesis that the mean of the outliers was greater than the mean of the rest of the single nucleotide polymorphisms. TABLE S5. Gene Ontology enrichment analysis for genes in linkage disequilibrium with outlier single nucleotide polymorphisms (SNPs) before excluding organellar-targeting SNPs.TABLE S6. Blastn against the organellar genomes.TABLE S7. Marker statistics of single nucleotide polymorphisms with multigenome targets. Please note: Wiley Blackwell are not responsible for the content or functionality of any Supporting Information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office.From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.The Department of Science and Innovation and Technology Innovation Agency (DSI/TIA, Strategic Grant-Eucalyptus Genomics Platform), the Forestry Sector Innovation Fund (FSIF Eucalyptus Genome Diversity Atlas grant), National Research Foundation (NRF) of South Africa, the Technology and Human Resources for Industry Programme and by the Forest Molecular Genetics (FMG) Industry Consortium at the University of Pretoria.www.newphytologist.comam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Realised genetic gains and estimated genetic parameters of two Eucalyptus grandis × E. urophylla hybrid breeding strategies

Conventionally, Eucalyptus grandis x E. urophylla (GU) hybrid material has first been tested as seedlings in progeny trials for at least four years before ortets were selected and ramets of the selected ortets were propagated to test in clonal trials. The primary constraint with this “conventional hybrid breeding strategy” (CHBS) is the time required to first test the hybrid material as seedlings. In order to address this, an “accelerated hybrid breeding strategy” (AHBS) was investigated to reduce the time spend on testing GU hybrid material as seedlings. However, it is of utmost importance to quantify the impact the AHBS might have on genetic gains and genetic information. With this in mind, two clonal populations have been established with genetic material that derived from the CHBS and the AHBS. The main purpose of this study is therefore to do a comparative study between the CHBS and AHBS to firstly quantify the genetic gains per unit time for GU hybrid clonal populations that have been derived from the CHBS and AHBS respectively; and secondly to obtain genetic parameters such as heritabilities, the ratio of dominance, clonal within family variance and the proportion of additive and non-additive genetic variance. The results of our study indicated that the percentage realised volume gains per year was higher for the AHBS (3.7%) than for the CHBS (1.9%) when compared to the GU commercial clone. Thus, shortening the testing time of GU seedlings had a positive impact on volume gains per year. With regards to genetic parameters, both the AHBS and CHBS clonal populations indicated that non-additive genetic variation explained majority (88% and 71% respectively) of the genetic variation. Due to the pre-eminence of non-additive genetic variation, the narrow sense heritabilties for the female and male effects were negligible for both clonal populations. Overall, the majority of the non-additive genetic variation was explained by the proportion of dominance variance, and less by the clone within family effect. These results suggest that: firstly the time spend on testing GU hybrid material as seedlings should be minimised; and secondly a hybrid breeding strategy to capture non-additive genetic variation should be adopted.Funding was provided by Mondi training department.http://www.tandfonline.com/loi/tsfs202018-01-31hb2017Microbiology and Plant Patholog