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

Anatomical structure associated with vegetative growth variation in macadamia

Aims Low-vigour scion cultivars and dwarfing rootstocks are a significant contributing factor to the success of modern temperate orchard systems. Planting density and canopy efficiency are currently limited in macadamia by a lack of low-vigour cultivars and rootstocks. The relationships between xylem vessel diameter, hydraulic conductivity and vigour are implicated in dwarf cultivars and low-vigour rootstocks of peach and apple. This study aims to determine relationships between vessel anatomy and tree-scale vigour in subtropical macadamia, to stimulate the development of low vigour cultivars and dwarfing rootstocks. Methods Stem sections from the most recent mature flush were collected from five replicates of three macadamia cultivars: ‘D4’ (high vigour), ‘B25’ (intermediate vigour) and ‘B63’ (low vigour). Sections were imaged under a fluorescence microscope in order to measure the number and size of all xylem vessels in the stem. Results The three cultivars showed distinct differences in height over 5 years of measurement (P

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

Breeding strategies for atemoya and cherimoya

Current production of annonas in Australia is mainly based on atemoya (Annona squamosa x Annona cherimola) hybrids. Very little cherimoya (Annona cherimola) is grown. Fruit quality and/or yield of atemoyas and cherimoyas are highly variable. Consumer acceptance for the fruit could be markedly increased by improving both internal (seed number, flavour) and external (shape, blemish, symmetry) fruit quality characteristics. A major breeding programme, funded by the Australian Custard Apple Growers Association, has been initiated. The objective of this breeding programme is to select new varieties of atemoya with smooth skin, symmetrical shape, low seed number (less than 10 seeds per 100 g of pulp), low susceptibility to blemish and high level of self-pollination, eliminating the need for labour intensive and expensive hand-pollination. The breeding programme is using a multi-pronged approach in achieving its breeding objectives. A conventional breeding programme using polycrosses of 11 of the best, advanced selections/cultivars (‘Hillary White’, ‘Martin’, ‘Paxton’, ‘MHRS Gold’, ‘MHRS Red’, ‘Palethorpe’, ‘R11-T3’; ‘R11-T4’; ‘R11-T6’; ‘Ruby Queen’, ‘Bullock's Heart’) has been initiated. The breeding programme will also attempt to develop seedless cultivars by first producing tetraploids either through gamma irradiation or colchicine and then crossing to diploids to produce seedless triploids. Other approaches such as embryo rescue of crosses of reported seedless selections of A. cherimola and currently available seedless A. squamosa may also be feasible. The programme has introduced red and pink skin-coloured germplasm (A. reticulata, A. reticulata x A. cherimola hybrids) from Florida and crosses to transfer skin colour genes into the best of the Australian selections and varieties are currently being developed

Phenotypic association of multi-scale architectural traits with canopy volume and yield: moving toward high-density systems for macadamia

The vigorous growth and large canopy size of commercial macadamia (Macadamia integrifolia, M. tetraphylla, and hybrids) cultivars generally restricts macadamia orchards to low-density planting. Little is known of the detailed interactions between plant architecture and yield components specific to macadamia. This chapter examines how dependent traits such as canopy size and yield might be determined by direct and indirect interactions between traits at different scales within the canopy. Fifteen genotypes (n = 3) were phenotyped in two growing seasons for architectural and reproductive traits, around the age of their transition from juvenility to maturity. Genotypes varied in canopy volume, cumulative yield, and canopy efficiency, and particular genotypes with low canopy volume and high yield were considered potentially useful for future high-density orchard systems. There was high variability in architectural, floral, and yield traits at multiple scales. Direct and indirect effects of architectural traits on the variability of yield and tree size were quantified using path coefficient analysis. Canopy volume was subject to positive direct effects from trunk cross-sectional area (TCA; 0.72), lateral branching (0.24), and branch unit (BU) length (0.24). Other traits showed significant indirect effects with canopy volume via TCA, such as branch cross-sectional area (BCA; 0.43), BU length (0.40), lateral branching (0.35), and internode length (0.32). Branch angle had a significant indirect negative effect on canopy volume via BU length (−0.11). Nut number had the strongest direct effect on yield (0.97), and this relationship was significantly indirectly influenced by raceme number (0.47), raceme length (0.50), nut number per raceme (0.33), canopy volume (0.37), and branch angle (0.35). In these relatively young trees, early yield was directly and positively influenced by canopy volume (0.12), presumably due to increased early light interception, which suggests that early canopy vigor contributes to early yield. This study suggests that yield and canopy size are determined by complex phenotypic interactions between architectural traits at different scales. Therefore, preplanting (i.e., scion and rootstock selections) and postplanting (i.e., pruning and training) manipulations that specifically manage architectural traits such as shoot length, branching, branch angle, raceme length, and nuts per raceme may result in the creation of efficient macadamia canopies

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

Computational data from: Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Computational files associated with the publication Langdon et al. 2020 Maximising recombination across macadamia populations to generate linkage maps for genome anchoring. Scientific Reports

Predicting the effect of rotation design on N, P, K balances on organic farms using the NDICEA model

The dynamic model Nitrogen Dynamics in Crop rotations in Ecological Agriculture (NDICEA) was used to assess the nitrogen (N), phosphorus (P) and potassium (K) balance of long-term organic cropping trials and typical organic crop rotations on a range of soil types and rainfall zones in the UK. The measurements of soil N taken at each of the organic trial sites were also used to assess the performance of NDICEA. The modeled outputs compared well to recorded soil N levels, with relatively small error margins. NDICEA therefore seems to be a useful tool for UK organic farmers. The modeling of typical organic rotations has shown that positive N balances can be achieved, although negative N balances can occur under high rainfall conditions and on lighter soil types as a result of leaching. The analysis and modeling also showed that some organic cropping systems rely on imported sources of P and K to maintain an adequate balance and large deficits of both nutrients are apparent in stockless systems. Although the K deficits could be addressed through the buffering capacity of minerals, the amount available for crop uptake will depend on the type and amount of minerals present, current cropping and fertilization practices and the climatic environment. A P deficit represents a more fundamental problem for the maintenance of crop yields and the organic sector currently relies on mined sources of P which represents a fundamental conflict with the International Federation of Organic Agriculture Movements organic principles

Predicting the effect of rotation design on N, P, K balances on organic farms using the NDICEA model - CORRIGENDUM

The dynamic model Nitrogen Dynamics in Crop rotations in Ecological Agriculture (NDICEA) was used to assess the nitrogen (N), phosphorus (P) and potassium (K) balance of long-term organic cropping trials and typical organic crop rotations on a range of soil types and rainfall zones in the UK. The measurements of soil N taken at each of the organic trial sites were also used to assess the performance of NDICEA. The modeled outputs compared well to recorded soil N levels, with relatively small error margins. NDICEA therefore seems to be a useful tool for UK organic farmers. The modeling of typical organic rotations has shown that positive N balances can be achieved, although negative N balances can occur under high rainfall conditions and on lighter soil types as a result of leaching. The analysis and modeling also showed that some organic cropping systems rely on imported sources of P and K to maintain an adequate balance and large deficits of both nutrients are apparent in stockless systems. Although the K deficits could be addressed through the buffering capacity of minerals, the amount available for crop uptake will depend on the type and amount of minerals present, current cropping and fertilization practices and the climatic environment. A P deficit represents a more fundamental problem for the maintenance of crop yields and the organic sector currently relies on mined sources of P which represents a fundamental conflict with the International Federation of Organic Agriculture Movements organic principles