Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

Sorghum Crop Modeling and Its Utility in Agronomy and Breeding

Crop models are simplified mathematical representations of the interacting biological and environmental components of the dynamic soil–plant–environment system. Sorghum crop modeling has evolved in parallel with crop modeling capability in general, since its origins in the 1960s and 1970s. Here we briefly review the trajectory in sorghum crop modeling leading to the development of advanced models. We then (i) overview the structure and function of the sorghum model in the Agricultural Production System sIMulator (APSIM) to exemplify advanced modeling concepts that suit both agronomic and breeding applications, (ii) review an example of use of sorghum modeling in supporting agronomic management decisions, (iii) review an example of the use of sorghum modeling in plant breeding, and (iv) consider implications for future roles of sorghum crop modeling. Modeling and simulation provide an avenue to explore consequences of crop management decision options in situations confronted with risks associated with seasonal climate uncertainties. Here we consider the possibility of manipulating planting configuration and density in sorghum as a means to manipulate the productivity–risk trade-off. A simulation analysis of decision options is presented and avenues for its use with decision-makers discussed. Modeling and simulation also provide opportunities to improve breeding efficiency by either dissecting complex traits to more amenable targets for genetics and breeding, or by trait evaluation via phenotypic prediction in target production regions to help prioritize effort and assess breeding strategies. Here we consider studies on the stay-green trait in sorghum, which confers yield advantage in water-limited situations, to exemplify both aspects. The possible future roles of sorghum modeling in agronomy and breeding are discussed as are opportunities related to their synergistic interaction. The potential to add significant value to the revolution in plant breeding associated with genomic technologies is identified as the new modeling frontier.

In vitro Induction of Banana Autotetraploids by Colchicine Treatment of Micropropagated Diploids

Alternative breeding strategies, based on colchicine-induced autotetraploids, have been proposed as a means of introducing disease resistance into banana breeding programs. This paper describes techniques for the in vitro induction of banana autotetraploids by the use of colchicine on cultured explants. The technique can be readily applied and large numbers of autotetraploids produced. The optimum treatment involved immersing shoot tips in a 0.5% w/v colchicine solution for 2 h under aseptic conditions. Dimethyl sulfoxide (DMSO) was applied with the colchicine treatments to increase cell permeability and so absorption of colchicine, resulting in the optimum treatment unchanged at 0.5% colchicine, but including the addition of 2% v/v DMSO. Of the shoot tips treated over 30% were induced to the autotetraploid level. Methods for in vitro selection of induced tetraploids from treated diploid plantlets were also developed. Tetraploid plants were more robust with thicker pseudostems, roots and broader leaves than diploids and they could be selected on these morphological characteristics. Mean stornatal lengths of diploid banana plants growing in vitro were significantly smaller (16.0 pm) than the tetraploids (26.9pm) and were used as a more reliable indicator of ploidy than morphological criteria alone. A root tip squash technique using carbol fuchsin was developed for positive confirmation of ploidy change by chromosome counts. Although chimerism and reversion to the diploid form occurred, it was not considered a problem because of the large number of autotetraploids induced. Stable autotetraploids were recovered and established in the field and were characterised by their large, drooping leaves and thick pseudostems. They have retained these characteristics for more than 3 years in the field.

Location of major effect genes in sorghum (Sorghum bicolor (L.) Moench).

Major effect genes are often used for germplasm identification, for diversity analyses and as selection targets in breeding. To date, only a few morphological characters have been mapped as major effect genes across a range of genetic linkage maps based on different types of molecular markers in sorghum (Sorghum bicolor (L.) Moench). This study aims to integrate all available previously mapped major effect genes onto a complete genome map, linked to the whole genome sequence, allowing sorghum breeders and researchers to link this information to QTL studies and to be aware of the consequences of selection for major genes. This provides new opportunities for breeders to take advantage of readily scorable morphological traits and to develop more effective breeding strategies. We also provide examples of the impact of selection for major effect genes on quantitative traits in sorghum. The concepts described in this paper have particular application to breeding programmes in developing countries where molecular markers are expensive or impossible to access.

Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Review of genetic improvement of pineapple.

World consumption of fresh pineapple has quadrupled in less than 15 years (Loeillet and Pacqui, 2009). This phenomenal event started around 1996 when the first dedicated fresh market pineapple, '73-114', was released by Del Monte Inc. This was the culmination of somewhere in the vicinity of 34 years of breeding and selection and comprised 24 individual parent combinations (Anon., PRI breeding records). This demonstrates the difficulty of breeding new pineapple cultivars but also the value of a successful program. The success of '73-114' and the competitive nature of world pineapple markets have provided impetus for pineapple breeding programs. However, the highly heterozygous nature and self-incompatibility of pineapple limit breeding strategy options. This review looks at the collective experience in pineapple genetic improvement both conventional and using biotechnology tools, with an emphasis on fresh market pineapple. It focus on relevant pineapple reproductive biology, breeding strategies, parent cultivars and the relevance of biotechnology.

Induced Variations in Brassinosteroid Genes Define Barley Height and Sturdiness, and Expand the Green Revolution Genetic Toolkit

Reduced plant height and culm robustness are quantitative characteristics important for assuring cereal crop yield and quality under adverse weather conditions. A very limited number of short-culm mutant alleles were introduced into commercial crop cultivars during the Green Revolution. We identified phenotypic traits, including sturdy culm, specific for deficiencies in brassinosteroid biosynthesis and signaling in semidwarf mutants of barley (Hordeum vulgare). This set of characteristic traits was explored to perform a phenotypic screen of near-isogenic short-culm mutant lines from the brachytic, breviaristatum, dense spike, erectoides, semibrachytic, semidwarf, and slender dwarf mutant groups. In silico mapping of brassinosteroid-related genes in the barley genome in combination with sequencing of barley mutant lines assigned more than 20 historic mutants to three brassinosteroid-biosynthesis genes (BRASSINOSTEROID-6-OXIDASE, CONSTITUTIVE PHOTOMORPHOGENIC DWARF, and DIMINUTO) and one brassinosteroid-signaling gene (BRASSINOSTEROID-INSENSITIVE1 [HvBRI1]). Analyses of F2 and M2 populations, allelic crosses, and modeling of nonsynonymous amino acid exchanges in protein crystal structures gave a further understanding of the control of barley plant architecture and sturdiness by brassinosteroid-related genes. Alternatives to the widely used but highly temperature-sensitive uzu1.a allele of HvBRI1 represent potential genetic building blocks for breeding strategies with sturdy and climate-tolerant barley cultivars.

Comparison of three pollination methods for Eucalyptus argophloia, a small-flowered eucalypt

Context Most studies assess pollination success at capsule maturity, and studies of pre-zygotic processes are often lacking. Aims This study investigates the suitability of controlled pollination for a potential forestry plantation species, Eucalyptus argophloia, by examining pre- and post-zygotic pollination success. Methods Pollen tube development, capsule set and seed set are compared following three-stop pollination, artificially induced protogyny (AIP), AIP unpollinated and open pollination. The fecundity of stored pollen was compared with that of fresh pollen. Results Three-stop pollination, AIP and open pollination had similar numbers of pollen tubes, but AIP unpollinated had none. Open pollination produced significantly more capsules and total number of seeds than the other treatments. There were significantly more seeds per retained capsule for the open pollination and three-stop pollination treatments than for the AIP and AIP unpollinated pollination treatments. There were no significant differences relative to the age of pollen. Conclusions Pre-zygotic success in terms of pollen tubes was similar for open-pollinated, three stop and AIP, but was not reflected in post-zygotic success when the open pollination and three-stop method produced significantly more seeds per retained capsule than the AIP treatments and open pollination yielded more seeds. Capsule set and total seed set for open pollination, and fewer capsules in controlled pollinations, may reflect physical damage to buds because of the small E. argophloia flowers. Suitable alternative breeding strategies other than controlled pollinations are discussed for this species.

Global trade in ornamental fish from an Australian perspective: The case for revised import risk analysis and management strategies

Over 1 billion ornamental fish comprising more than 4000 freshwater and 1400 marine species are traded internationally each year, with 8-10 million imported into Australia alone. Compared to other commodities, the pathogens and disease translocation risks associated with this pattern of trade have been poorly documented. The aim of this study was to conduct an appraisal of the effectiveness of risk analysis and quarantine controls as they are applied according to the Sanitary and Phytosanitary (SPS) agreement in Australia. Ornamental fish originate from about 100 countries and hazards are mostly unknown; since 2000 there have been 16-fold fewer scientific publications on ornamental fish disease compared to farmed fish disease, and 470 fewer compared to disease in terrestrial species (cattle). The import quarantine policies of a range of countries were reviewed and classified as stringent or non-stringent based on the levels of pre-border and border controls. Australia has a stringent policy which includes pre-border health certification and a mandatory quarantine period at border of 1-3 weeks in registered quarantine premises supervised by government quarantine staff. Despite these measures there have been many disease incursions as well as establishment of significant exotic viral, bacterial, fungal, protozoal and metazoan pathogens from ornamental fish in farmed native Australian fish and free-living introduced species. Recent examples include Megalocytivirus and Aeromonas salmonicida atypical strain. In 2006, there were 22 species of alien ornamental fish with established breeding populations in waterways in Australia and freshwater plants and molluscs have also been introduced, proving a direct transmission pathway for establishment of pathogens in native fish species. Australia's stringent quarantine policies for imported ornamental fish are based on import risk analysis under the SPS agreement but have not provided an acceptable level of protection (ALOP) consistent with government objectives to prevent introduction of pests and diseases, promote development of future aquaculture industries or maintain biodiversity. It is concluded that the risk analysis process described by the Office International des Epizooties under the SPS agreement cannot be used in a meaningful way for current patterns of ornamental fish trade. Transboundary disease incursions will continue and exotic pathogens will become established in new regions as a result of the ornamental fish trade, and this will be an international phenomenon. Ornamental fish represent a special case in live animal trade where OIE guidelines for risk analysis need to be revised. Alternatively, for countries such as Australia with implied very high ALOP, the number of species traded and the number of sources permitted need to be dramatically reduced to facilitate hazard identification, risk assessment and import quarantine controls. Lead papers of the eleventh symposium of the International Society for Veterinary Epidemiology and Economics (ISVEE), Cairns, Australia

Trends in therapeutic and prevention strategies for management of Bovine Mastitis: An overview

Mastitis is one of the most economically significant diseases for the dairy industry for backyard farmers in developing countries and high producing herds worldwide. Two of the major factors impeding reduction in the incidence of this disease is [a] the lack of availability of an effective vaccine capable of protecting against multiple etiological agents and [b] propensity of some of the etiological agents to develop persistent antibiotic resistance in biofilms. This is further complicated by the continuing revolving shift in the predominant etiological agents of mastitis, depending upon a multitude of factors such as variability in hygienic practices on farms, easy access leading to overuse of appropriate or inappropriate antibiotics at suboptimal concentrations, particularly in developing countries, and lack of compliance with the recommended treatment schedules. Regardless, Staphylococcus aureus and Streptococcus uberis followed by Escherichia coli, Streptococcus agalactiae has become the predominant etiological agents of bovine mastitis followed Streptococcus agalactiae, Streptococcus dysagalactiae, Klebsiella pneumonia and the newly emerging Mycoplasma bovis. Current approaches being pursued to reduce the negative economic impact of this disease are through early diagnosis of infection, immediate treatment with an antibiotic found to either inhibit or kill the pathogen(s) in vitro using planktonic cultures and the use of the currently marketed vaccines regardless of their demonstrated effectiveness. Given the limitations of breeding programs, including genetic selection to improve resistance against infectious diseases including mastitis, it is imperative to have the availability of an effective broad-spectrum, preferably cross-protective, vaccine capable of protecting against bovine mastitis for reduction in the incidence of bovine mastitis, as well as interrupting the potential cross-species transmission to humans. This overview highlights the major etiological agents, factors affecting susceptibility to mastitis, and the current status of antibiotic-based therapies and prototype vaccine candidates or commercially available vaccines against bovine mastitis as potential preventative strategies. © 2013 Tiwari JG, et al.

Resistance to Fusarium oxysporum f. sp fragariae and Predicted Breeding Values in Strawberry

Fusarium wilt of strawberry, incited by Fusarium oxysporum f. sp. fragariae (Fof), is a major disease of the cultivated strawberry (Fragaria xananassa) worldwide. An increase in disease outbreaks of the pathogen in Western Australia and Queensland plus the search for alternative disease management strategies place emphasis on the development of resistant cultivars. In response, a partial incomplete diallel cross involving four parents was performed for use in glasshouse resistance screenings. The resulting progeny were evaluated for their susceptibility to Fof. Best-performing progeny and suitability of progenies as parents were determined using data from disease severity ratings and analyzed using a linear mixed model incorporating a pedigree to produce best linear unbiased predictions of breeding values. Variation in disease response, ranging from highly susceptible to resistant, indicates a quantitative effect. The estimate of the narrow-sense heritability was 0.49 +/- 0.04 (SE), suggesting the population should be responsive to phenotypic recurrent selection. Several progeny genotypes have predicted breeding values higher than any of the parents. Knowledge of Fof resistance derived from this study can help select best parents for future crosses for the development of new strawberry cultivars with Fof resistance.

Implementing technologies and strategies to maintain resistance to sunflower rust

This project proposes to implement resistance gene pyramiding strategies through close collaboration with Pacific Seeds. These strategies have been developed by Department of Primary Industries and Fisheries (DPI&F) researchers in two previous GRDC projects, DAQ356 and DAQ537. The gene pyramids will be incorporated into elite breeding material using techniques and technologies developed by DPI&F. These include the use of DNA markers. If successful, a range of elite lines/commercial hybrids containing strategic resistance gene pyramids will be available to growers. These lines will provide the industry with a directed strategy to manage the sunflower rust pathogen and reduce the risk of outbreaks of the disease.

Influence of climate variability and stocking strategies on greenhouse gas emissions (GHGE), production and profit of a northern Queensland beef cattle herd

Previous studies of greenhouse gas emissions (GHGE) from beef production systems in northern Australia have been based on models of ‘steady-state’ herd structures that do not take into account the considerable inter-annual variation in liveweight gain, reproduction and mortality rates that occurs due to seasonal conditions. Nor do they consider the implications of flexible stocking strategies designed to adapt these production systems to the highly variable climate. The aim of the present study was to quantify the variation in total GHGE (t CO2e) and GHGE intensity (t CO2e/t liveweight sold) for the beef industry in northern Australia when variability in these factors was considered. A combined GRASP–Enterprise modelling platform was used to simulate a breeding–finishing beef cattle property in the Burdekin River region of northern Queensland, using historical climate data from 1982–2011. GHGE was calculated using the method of Australian National Greenhouse Gas Inventory. Five different stocking-rate strategies were simulated with fixed stocking strategies at moderate and high rates, and three flexible stocking strategies where the stocking rate was adjusted annually by up to 5%, 10% or 20%, according to pasture available at the end of the growing season. Variation in total annual GHGE was lowest in the ‘fixed moderate’ (~9.5 ha/adult equivalent (AE)) stocking strategy, ranging from 3799 to 4471 t CO2e, and highest in the ‘fixed high’ strategy (~5.9 ha/AE), which ranged from 3771 to 7636 t CO2e. The ‘fixed moderate’ strategy had the least variation in GHGE intensity (15.7–19.4 t CO2e/t liveweight sold), while the ‘flexible 20’ strategy (up to 20% annual change in AE) had the largest range (10.5–40.8 t CO2e/t liveweight sold). Across the five stocking strategies, the ‘fixed moderate’ stocking-rate strategy had the highest simulated perennial grass percentage and pasture growth, highest average rate of liveweight gain (121 kg/steer), highest average branding percentage (74%) and lowest average breeding-cow mortality rate (3.9%), resulting in the lowest average GHGE intensity (16.9 t CO2e/t liveweight sold). The ‘fixed high’ stocking rate strategy (~5.9 ha/AE) performed the poorest in each of these measures, while the three flexible stocking strategies were intermediate. The ‘fixed moderate’ stocking strategy also yielded the highest average gross margin per AE carried and per hectare. These results highlight the importance of considering the influence of climate variability on stocking-rate management strategies and herd performance when estimating GHGE. The results also support a body of previous work that has recommended the adoption of moderate stocking strategies to enhance the profitability and ecological stability of beef production systems in northern Australia.

Breeding and fecundity of the endemic Australian gudgeon, sleepy cod Oxyeleotris lineolatus (Steindachner 1867) (Eleotridae)

Sleepy cod (Oxyeleotris lineolatus Steindachner) is a tropical species of eleotrid native to northern Australia. A related species, sand or marbled goby, is the highest priced freshwater fish in Asia, and a market for a similar fish exists in expatriate Chinese communities. Sleepy cod breed when minimum temperatures reach 24 °C for more than 3 days. During the breeding season the genital papilla is broad and flattened in females compared to the triangular papilla of males and juveniles. Spawning pairs were usually of approximately equal size. Females could spawn up to 10 times during one breeding season. Wet weather increased the frequency of spawning. Eggs were usually laid hanging from the underside of a surface. Most spawning occurred between 05:00 and 10:00 h. Females attended egg masses immediately after spawning, after which males cared for eggs until hatching, 3–5 days later. Agitation of the egg mass was essential for development. The mean number of eggs per spawning was 43 130. Larvae commenced feeding 2–5 days after hatching, on plankton from 100 to 250 m in size. A spawning trap used to collect egg masses is described. The breeding biology of sleepy cod is considered to be an adaptation to the monsoonal tropics.

Risk management strategies using seasonal climate forecasting in irrigated cotton production: a tale of stochastic dominance.

Decision-making in agriculture is carried out in an uncertain environment with farmers often seeking information to reduce risk. As a result of the extreme variability of rainfall and stream-flows in north-eastern Australia, water supplies for irrigated agriculture are a limiting factor and a source of risk. The present study examined the use of seasonal climate forecasting (SCF) when calculating planting areas for irrigated cotton in the northern Murray Darling Basin. Results show that minimising risk by adjusting plant areas in response to SCF can lead to significant gains in gross margin returns. However, how farmers respond to SCF is dependent on several other factors including irrigators’ attitude towards risk.