Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a century. Genomic selection (GS) is a useful tool in plant breeding, particularly with perennial trees, contributing to an increased rate of genetic gain and reducing the length of the breeding cycle. We investigated the potential of using GS methods to increase genetic gain and accelerate selection efficiency in the Australian macadamia breeding program with comparison to traditional breeding methods. This study evaluated the prediction accuracy of GS in a macadamia breeding population of 295 full-sib progeny from 32 families (29 parents, reciprocals combined), along with a subset of parents. Historical yield data for tree ages 5 to 8 years were used in the study, along with a set of 4113 SNP markers. The traits of focus were average nut yield from tree ages 5 to 8 years and yield stability, measured as the standard deviation of yield over these 4 years. GBLUP GS models were used to obtain genomic estimated breeding values for each genotype, with a five-fold cross-validation method and two techniques: prediction across related populations and prediction across unrelated populations

Genetic parameters of husk spot resistance in macadamia breeding families

Husk spot caused by the Pseudocercospora macadamiae fungus induces premature abscission of fruit in many industry standard macadamia cultivars. Fungicides and other management strategies add to farm costs, thus breeding for varietal resistance is important. Genetic parameters of husk spot symptom expression had not previously been estimated. To guide selection methods for field resistance, over 300 open-pollinated seedlings of 32 families and 24 parent genotypes were inoculated, and seven symptom expression traits were evaluated. Narrow-sense and broad-sense heritabilities were estimated, breeding values were predicted, and correlations between breeding values of trait pairs were tested for significance. The traits with the highest heritabilities were necrotic lesion number per fruit (H2 = 0.41–0.59; h2 = 0.21–0.30) and necrotic incidence (H2 = 0.19–0.27; h2 = 0.17–0.24). Breeding values of the two traits were highly correlated (r = 0.98; p < 0.001), suggesting that either trait could be used to indirectly select for the other. All genotypes expressed symptoms to some degree, however, breeding values for necrotic traits and symptom-induced premature abscission were low for clones and progeny of cultivar ‘HAES791’. Necrotic trait breeding values were also promising for progeny of cultivar ‘HAES246’ and clones of Australian Macadamia Breeding Program elite selection, ‘BAM263’. Having been identified as potentially partially resistant, these selections can now be further evaluated and used as parents of new progeny populations

Global Macadamia Science: Overview of the Special Section

Macadamia is a rapidly developing global crop; however, limited cultivation history and size of the industry means many challenges remain to support sustained productivity and profitability of this industry. This paper summarizes oral and poster presentations, and subsequent papers included in this volume, delivered at the 2017 International Macadamia Research Symposium, held in Hilo, HI, in September of that year. This was the first international meeting of macadamia researchers since 1992. The 28 oral and seven poster presentations covered propagation technology, tree physiology, soils and nutrition, pollination, pest and disease, orchard management, genetics and breeding, product development, and new production regions. Notable messages were that micrografting of macadamias is commercially viable; planting density and girdling could increase early yield per hectare; resource availability may limit cross-pollination yield; and yield production of individual branches is not independent. Integrated pest management was described to develop pest-resilient farming systems and manage felted coccid; an international collaborative approach was proposed for effective disease management and early detection; and the concept of integrated orchard management was used to translate research outputs into a common language for grower adoption. In the areas of breeding and genetic resources, research demonstrated that modern macadamia cultivars are two to four generations from wild but do not capture all wild diversity; progress was reported on the Macadamia Genome Project to produce the first macadamia reference genome; and advances in phenotypic selection and cultivar development were described

Cost and accuracy of advanced breeding trial designs in apple

Trialing advanced candidates in tree fruit crops is expensive due to the long-term nature of the planting and labor-intensive evaluations required to make selection decisions. How closely the trait evaluations approximate the true trait value needs balancing with the cost of the program. Designs of field trials of advanced apple candidates in which reduced number of locations, the number of years and the number of harvests per year were modeled to investigate the effect on the cost and accuracy in an operational breeding program. The aim was to find designs that would allow evaluation of the most additional candidates while sacrificing the least accuracy. Critical percentage difference, response to selection, and correlated response were used to examine changes in accuracy of trait evaluations. For the quality traits evaluated, accuracy and response to selection were not substantially reduced for most trial designs. Risk management influences the decision to change trial design, and some designs had greater risk associated with them. Balancing cost and accuracy with risk yields valuable insight into advanced breeding trial design. The methods outlined in this analysis would be well suited to other horticultural crop breeding programs

Strategies for breeding macadamias in Australia

Macadamia (Macadamia integrifolia Maiden & Betche and M. tetraphylla L.A.S. Johnson) is an Australian native, evergreen nut tree adapted to the subtropics. Large tree size and slow maturity of the crop pose particular problems for breeding and selection. Funding for an industry breeding program commenced in 1996 and 20 elite seedlings were selected. A second generation of hybrid seedlings is planned for production using the elite selections identified from previous breeding as parents. Four breeding strategies were compared in terms of the time to commercial deployment of elite selections, cost of breeding and expected rates of genetic gain determined by stochastic modelling. A tandem selection strategy, which selected for kernel recovery in a seedling trial and nut-in-shell yield in a clonal trial, produced the highest gain to cost ratio but was limited in the number of genotypes assessed in the clonal trial. The full assessment and progeny cull strategies, which selected for nut-in-shell yield and kernel recovery in both a seedling and clonal trial were similar in terms of gain per unit cost and a cloned seedling strategy was intermediate in value

Population demography and fecundity do not decline with habitat fragmentation in the rainforest tree 'Macadamia integrifolia' (Proteaceae)

Habitat fragmentation is often associated with reduced levels of fitness and local extinction of plant species, and consequently poses a major threat to the persistence of species worldwide. The majority of demography-based fragmentation studies to date have focussed primarily on fragmentation impacts on individual plant fecundity. Here we investigate the impact of habitat fragmentation on the demography (plant height classes and density) and key population dynamic processes for the rainforest tree species 'Macadamia integrifolia' (Proteaceae). Raceme and fruit production and seedling emergence across fragmented sites exceeded that in more intact sites with no apparent difference in short-term mortality rates. Fecundity of flowering trees did not appear to be affected by fragmentation. Instead, overall reproductive output in fragmented sites was enhanced relative to undisturbed sites due to a higher proportion of reproductively active individuals. The probability of flowering and fruiting was negatively correlated with the projected foliage cover (PFC) surrounding individual trees, and average PFC was significantly lower in small and medium fragments, suggesting light availability as a potential contributor to the trends observed here. This study demonstrates that the short-term effects of habitat fragmentation on population viability may not necessarily be detrimental for some species, and highlights the importance of assessing not only the fecundity of flowering individuals but also the proportion of individuals reproducing within fragments

Prediction of breeding values for average fruit weight in mango using a multivariate individual mixed model

Mango is an important horticultural fruit crop and breeding is a key strategy to improve ongoing sustainability. Knowledge of breeding values of potential parents is important for maximising progress from breeding. This study successfully employed a mixed linear model methods incorporating a pedigree to predict breeding values for average fruit weight from highly unbalanced data for genotypes planted over three field trials and assessed over several harvest seasons. Average fruit weight was found to be under strong additive genetic control. There was high correlation between hybrids propagated as seedlings and hybrids propagated as scions grafted onto rootstocks. Estimates of additive genetic correlation among trials ranged from 0.69 to 0.88 with correlations among harvest seasons within trials greater than 0.96. These results suggest that progress from selection for broad adaptation can be achieved, particularly as no repeatable environmental factor that could be used to predict G x E could be identified. Predicted breeding values for 35 known cultivars are presented for use in ongoing breeding programs

Relationships between early growth and Quambalaria shoot blight tolerance in Corymbia citriodora progeny trials established in Queensland, Australia

The fungal pathogen Quambalaria pitereka can cause significant damage to spotted gum (Corymbia sp.) plantations in Australia. A series of seven progeny trials, involving seed from a range-wide collection from 527 individuals within 25 native populations of Corymbia citriodora sub-species variegata, were assessed for height growth and damage from Quambalaria around 1 year after planting. Infection at this young age has been found to detrimentally impact growth, form, and wood quality for many years. Genetic variance was found to be significant at both the provenance and family level. However, selection of families within provenances should lead to greater levels of genetic gain than what can be realized from selecting among provenances as estimates of additive genetic variance were consistently greater than estimates of variance among populations. Strong relationships between height and Quambalaria shoot blight (QSB) damage assessments in these trials were evidenced by very high genetic correlations between the traits; therefore, selection for any of these traits could be used to identify more productive and QSB-tolerant populations. While both provenances and families were found to interact with the trial environments at a similar level across traits, genetic correlations indicated that rankings for growth were be less stable than rankings for QSB tolerance across environments. Genetic parameter estimates derived from general and generalized linear models were very similar and either analytical method could be used to evaluate fungal damage

The study of the hydrothermal pretreatment of bagasse for the effective production of bioethanol

75 σ.Η παρούσα διπλωματική εργασία πραγματοποιήθηκε στο Εργαστήριο Βιοτεχνολογίας της Σχολής Χημικών Μηχανικών του Εθνικού Μετσόβιου Πολυτεχνείου.Ο σκοπός της παρούσας διπλωματικής είναι η μελέτη και η βελτιστοποίηση των συνθηκών υδροθερμικής προκατεργασίας βαγάσσης σόργου και η ενζυμική υδρόλυση του προκατεργασμένου υλικού. Το γλυκό σόργο θεωρείται εξαιρετική πρώτη ύλη για την παραγωγή βιοαιθανόλης, λόγω των υψηλών αποδόσεών του σε βιομάζα και του υψηλού ποσοστού άμεσα ζυμώσιμων σακχάρων του χυμού του.Αρχικά, η βαγάσση σόργου κατεργάστηκε υδροθερμικά σε ένα πλήθος από διαφορετικές συνθήκες λειτουργίας, όπου ο χρόνος κατεργασίας κυμάνθηκε μεταξύ 9 και 51 λεπτών και η θερμοκρασία ρυθμίστηκε σε τιμές μεταξύ 170 και 240 oC. Οι συνθήκες της προκατεργασίας προσδιορίστηκαν βάση της μεθοδολογίας επιφάνειας απόκρισης (RSM) όπου διερευνήθηκε η σχέση μεταξύ θερμοκρασίας και χρόνου προκατεργασίας. Ακολούθησε υδρόλυση της προκατεργασμένης βαγάσσης με χρήση των εμπορικών ενζυμικών σκευασμάτων Cellic® CTec2 και το μείγμα Celluclast® 1.5L και Novozym 188 σε αναλογίες 5:1 v/v (ενεργότητα ολικής κυτταρινάσης 10 FPU/g βαγάσσης σόργου) και για συγκέντρωση στερεών 3% w/v. Από το μοντέλο που προέκυψε βρέθηκε ότι οι βέλτιστες συνθήκες προκατεργασίας για να επιτευχθεί η μέγιστη % υδρόλυση της κυτταρίνης ήταν 229 οC και 33,8 λεπτά με μέγιστη προβλεπόμενη υδρόλυση ίση με 26,3%. Αυτό το ζεύγος τιμών ήταν πολύ κοντά στην δοκιμή 8 (230 οC και 30 min) με το ποσοστό αποπολυμερισμού της κυτταρίνης να ανέρχεται στο 30,4%. Μεταξύ των δυο ενζυμικών σκευασμάτων που χρησιμοποιήθηκαν καλύτερα αποτελέσματα προέκυψαν κατά τη χρήση του Cellic® CTec2.Τέλος, μελετήθηκε η ικανότητα παραγωγής αιθανόλης από την υδροθερμικά κατεργασμένη βαγάσση εφαρμόζοντας διεργασίες ξεχωριστής σακχαροποίισης και ζύμωσης, SHF (Separate Hydrolysis and Fermentation) και ταυτόχρονης σακχαροποίησης και ζύμωσης, SSF (Simultaneous Saccharification and Fermentation). Πιο συγκεκριμένα, στη διεργασία SHF πραγματοποιήθηκε διερεύνηση της επίδρασης του χρόνου σακχαροποίησης (12 και 24 ώρες) καθώς και η προσθήκη επιπλέον ενζύμων κατά την έναρξη της ζύμωσης στην παραγωγή αιθανόλης. Παρατηρήθηκε ότι η SHF διεργασία είχε καλύτερα αποτελέσματα σε σύγκριση με την SSF διεργασία ως προς την παραγωγή αιθανόλης, καθώς η αιθανόλη έφτασε στα 41,4 g/L στις 22 ώρες σε αντίθεση με τη διεργασία SSF που έφτασε τα 41,4g/L στις 96 ώρες. Επίσης παρατηρήθηκε ότι η αύξηση του χρόνου σακχαροποίησης από 12 σε 24 ώρες δεν είχε πολύ σημαντική επίδραση στην αύξηση της συγκέντρωσης σακχάρων και της παραγόμενης αιθανόλης. Τέλος, βρέθηκε ότι η προσθήκη επιπλέον ενζύμων συντέλεσε στην αύξηση της συγκέντρωσης αιθανόλης, καθώς η παραγόμενη αιθανόλη αυξήθηκε από 41,4 g/L σε 47,9 g/L.The present thesis was carried out in the Laboratory of Biotechnology, in the School of Chemical Engineering of the National Technical University of Athens. The subject of the present thesis was the study and the optimization of the conditions of hydrothermal pretreatment of bagasse and the enzyming hydrolysis of the pretreated material. The Sorghum bicolor is considered to be an excellent raw material for the production of bioethanol because of the high production of biomass and the high percentage of the directly fermentable sugars that are include in sorghum. Firstly, the bagasse was treated hydrothermally in various operational conditions, where the time of treatment ranged from 9 to 51 minutes and the temperature was adjusted between 170 and 240 oC. The conditions of treatment were determined based on the RSM where the relationship between the temperature and the time of treatment was investigated. Afterwards, the hydrolysis of the pretreated bagasse with the use of the commercial enzyme products Cellic® CTec2 and the mixture of Celluclast® 1.5L and Novozym 188 at ratios 5:1 v/v (total cellulase activity 10 FPU/g bagasse) and for solids’ concentration equal to 3% w/v, was performed. The model, which was derived from the experiments, showed that the optimal conditions of pretreatment that lead to the maximum % hydrolysis of the cellulose is 229 οC and 33,8 minutes with the maximum predicted hydrolysis equal to 26,3%. This pair of values was close to those of run 8 (230 οC and 30 min) where the percentage of depolymerization of cellulose is 30,4%. The best results, between the two enzyme products which were used, were noticed for Cellic® CTec2. Finally, the ability of the hydrothermally treated bagasse to produce ethanol by implementing processes of (1) SHF (Separate Hydrolysis and Fermentation) and (2) SSF (Simultaneous Saccharification and Fermentation) was investigated. More specifically, (a) the impact of the time of Saccharification (12 and 24 hours) and (b) the addition of further enzymes in the beginning of fermentation on the production of ethanol in the process of the SHF was studied. It was noticed that the process of SHF process gives better results compared to the SSF process regarding the production of ethanol; ethanol was equal to 41,4 g/L at 22 hours while in the SSF was equal to 41,4 g/L at 96 hours. Morever, results showed that the increase of the time of Saccharification from 12 to 24 hours does not have a significant impact on the increase of the concentration sugars and the produced ethanol. Moreover, the addition of further enzymes contributed to the rise of the ethanol concentration since the produced ethanol was increased from 41,4 g/L to 47,9 g/L.Αρετή Κ. Μήτσ

Evaluation of in-field inoculation methods for characterisation of macadamia germplasm to husk spot incidence and severity

Husk spot, a fungal (Pseudocercospora macadamiae) disease of macadamia pericarps, induces premature abscission in several major commercial cultivars. Breeding for resistance to husk spot is a priority of the Australian macadamia industry. Due to the large tree size of macadamia and high numbers of progeny in breeding populations, inoculating for resistance screening is laborious and time consuming. Previously utilised methods included direct applications of P. macadamiae suspensions and hanging of bags of diseased husks above developing fruit in tree canopies. In this study, both methods were modified to allow for efficient application in large-scale breeding populations and their efficacy was evaluated. Two quantities of diseased husk per bag: 'large' (75 g) and 'small' (30 g) and two concentrations of sprayed P. macadamiae suspensions: 5 x 105 propagules/mL 'stock' and 'dilute' 2.5 x 105 propagules/mL were tested across two fruiting seasons. Treatments were compared against a control (sterile water) in commercial cultivars 'A38' and 'A4'. Husk spot incidence and severity produced by small bags were significantly affected by season. A significant season effect was less common for other treatments. All four treatments infected over 50% of target fruit in each season, but the highest husk spot incidence across both seasons (≥85%) was produced from large bags. Overall, the large bags were the most reliable method for infection of target fruit. Results also demonstrate the importance of considering the effect of season when selecting husk spot inoculation methods