Power of the joint segregation analysis method for testing mixed major-gene and polygene inheritance models of quantitative traits

Understanding the genetic architecture of quantitative traits can greatly assist the design of strategies for their manipulation in plant-breeding programs. For a number of traits, genetic variation can be the result of segregation of a few major genes and many polygenes (minor genes). The joint segregation analysis (JSA) is a maximum-likelihood approach for fitting segregation models through the simultaneous use of phenotypic information from multiple generations. Our objective in this paper was to use computer simulation to quantify the power of the JSA method for testing the mixed-inheritance model for quantitative traits when it was applied to the six basic generations: both parents (P-1 and P-2), F-1, F-2, and both backcross generations (B-1 and B-2) derived from crossing the F-1 to each parent. A total of 1968 genetic model-experiment scenarios were considered in the simulation study to quantify the power of the method. Factors that interacted to influence the power of the JSA method to correctly detect genetic models were: (1) whether there were one or two major genes in combination with polygenes, (2) the heritability of the major genes and polygenes, (3) the level of dispersion of the major genes and polygenes between the two parents, and (4) the number of individuals examined in each generation (population size). The greatest levels of power were observed for the genetic models defined with simple inheritance; e.g., the power was greater than 90% for the one major gene model, regardless of the population size and major-gene heritability. Lower levels of power were observed for the genetic models with complex inheritance (major genes and polygenes), low heritability, small population sizes and a large dispersion of favourable genes among the two parents; e.g., the power was less than 5% for the two major-gene model with a heritability value of 0.3 and population sizes of 100 individuals. The JSA methodology was then applied to a previously studied sorghum data-set to investigate the genetic control of the putative drought resistance-trait osmotic adjustment in three crosses. The previous study concluded that there were two major genes segregating for osmotic adjustment in the three crosses. Application of the JSA method resulted in a change in the proposed genetic model. The presence of the two major genes was confirmed with the addition of an unspecified number of polygenes.

Breeding for low input conditions and consequences for participatory plant breeding: Examples from tropical maize and wheat

Participatory plant breeding (PPB) has been suggested as an effective alternative to formal plant breeding (FPB) as a breeding strategy for achieving productivity gains under low input conditions. With genetic progress through PPB and FPB being determined by the same genetic variables, the likelihood of success of PPB approaches applied in low input target conditions was analyzed using two case studies from FPB that have resulted in significant productivity gains under low input conditions: (1) breeding tropical maize for low input conditions by CIMMYT, and (2) breeding of spring wheat for the highly variable low input rainfed farming systems in Australia. In both cases, genetic improvement was an outcome of long-term investment in a sustained research effort aimed at understanding the detail of the important environmental constraints to productivity and the plant requirements for improved adaptation to the identified constraints, followed up by the design and continued evaluation of efficient breeding strategies. The breeding strategies used differed between the two case studies but were consistent in their attention to the key determinants of response to selection: (1) ensuring adequate sources of genetic variation and high selection pressures for the important traits at all stages of the breeding program, (2) use of experimental procedures to achieve high levels of heritability in the breeding trials, and (3) testing strategies that achieved a high genetic correlation between performance of germplasm in the breeding trials and under on-farm conditions. The implications of the outcomes from these FPB case studies for realizing the positive motivations for adopting PPB strategies are discussed with particular reference for low input target environment conditions.

Diversity of Phytophthora clandestina isolated from subterranean clover in southern australia: Analysis of virulence and RAPD profiles

The virulence spectrum of 112 isolates of Phytophthora clandestina collected from 56 sites in four subterranean clover-growing states in southern Australia was determined using differential cultivars of subterranean clover. Five races were detected, with race 0 in all states except New South Wales, race 1 in all states, race 2 only in Victoria, race 3 only in New South Wales, and race 4 in Victoria and Western Australia. The level of genotypic diversity among the different P. clandestina populations was investigated using five RAPD primers. Among 30 bands amplified, only two were polymorphic. This enabled identification of four multilocus RAPD genotypes. Three of the four genotypes occurred in all four states. Races 2 and 3 occurred with RAPD genotypes 1 and 2 only whereas races 0 and 1 occurred in all four multilocus RAPD genotypes. These results indicate that the pathogenicity spectrum of P. clandestina can change rapidly.

Lucerne biology and genetic improvement - an analysis of past activities and future goals in Australia

Breeding methodologies for cultivated lucerne (Medicago sativa L.), an autotetraploid, have changed little over the last 50 years, with reliance on polycross methods and recurrent phenotypic selection. There has been, however, an increase in our understanding of lucerne biology, in particular the genetic relationships between members of the M. sativa complex, as deduced by DNA analysis. Also, the differences in breeding behaviour and vigour of diploids versus autotetraploids, and the underlying genetic causes, are discussed in relation to lucerne improvement. Medicago falcata, a member of the M. sativa complex, has contributed substantially to lucerne improvement in North America, and its diverse genetics would appear to have been under-utilised in Australian programs over the last two decades, despite the reduced need for tolerance to freezing injury in Australian environments. Breeding of lucerne in Australia only commenced on a large scale in 1977, driven by an urgent need to introgress aphid resistance into adapted backgrounds. The release in the early 1980s of lucernes with multiple pest and disease resistance (aphids, Phytophthora, Colletotrichum) had a significant effect on increasing lucerne productivity and persistence in eastern Australia, with yield increases under high disease pressure of up to 300% being recorded over the predominant Australian cultivar, up to 1977, Hunter River. Since that period, irrigated lucerne yields have plateaued, highlighting the need to identify breeding objectives, technologies, and the germplasm that will create new opportunities for increasing performance. This review discusses major goals for lucerne improvement programs in Australia, and provides indications of the germplasm sources and technologies that are likely to deliver the desired outcomes.

Differentiation of peanut seedborne potyviruses and curcumoviruses by RT-PCR

Seedborne peanut viruses pose important constraints to peanut production and safe movement of germ plasm. They also pose a risk of accidental introduction into previously disease-free regions. We have developed reverse transcription-polymerase chain reaction (RT-PCR) assays based on identical cycling parameters which identified peanut stripe, Peanut mottle, Peanut stunt, and Cucumber mosaic viruses through production of specific DNA fragments of 234 bp, 327 bp, 390 bp, and 133 bp, respectively. Assay sensitivity in the picogram range was achieved. The two potyviruses and two cucumoviruses could be differentiated using duplex RT-PCR assays. These assays should be useful for testing peanut leaves or seeds for virus identification in epidemiological studies, seed testing or in post-entry quarantine.

Promoters for pregenomic RNA of banana streak badnavirus are active for transgene expression in monocot and dicot plants

Two putative promoters from Australian banana streak badnavirus (BSV) isolates were analysed for activity in different plant species. In transient expression systems the My (2105 bp) and Cv (1322 bp) fragments were both shown to have promoter activity in a wide range of plant species including monocots (maize, barley, banana, millet, wheat, sorghum), dicots (tobacco, canola, sunflower, Nicotiana benthamiana, tipu tree), gymnosperm (Pinus radiata) and fern (Nephrolepis cordifolia). Evaluation of the My and Cv promoters in transgenic sugarcane, banana and tobacco plants demonstrated that these promoters could drive high-level expression of either the green fluorescent protein (GFP) or the beta -glucuronidase (GUS) reporter gene (uidA) in vegetative plant cells. In transgenic sugarcane plants harbouring the Cv promoter, GFP expression levels were comparable or higher (up to 1.06% of total soluble leaf protein as GFP) than those of plants containing the maize ubiquitin promoter (up to 0.34% of total soluble leaf protein). GUS activities in transgenic in vitro-grown banana plants containing the My promoter were up to seven-fold stronger in leaf tissue and up to four-fold stronger in root and corm tissue than in plants harbouring the maize ubiquitin promoter. The Cv promoter showed activities that were similar to the maize ubiquitin promoter in in vitro-grown banana plants, but was significantly reduced in larger glasshouse-grown plants. In transgenic in vitro-grown tobacco plants, the My promoter reached activities close to those of the 35S promoter of cauliflower mosaic virus (CaMV), while the Cv promoter was about half as active as the CaMV 35S promoter. The BSV promoters for pregenomic RNA represent useful tools for the high-level expression of foreign genes in transgenic monocots.

Traffic and residue cover effects on infiltration

Wheel traffic can lead to compaction and degradation of soil physical properties. This study, as part of a study of controlled traffic farming, assessed the impact of compaction from wheel traffic on soil that had not been trafficked for 5 years. A tractor of 40 kN rear axle weight was used to apply traffic at varying wheelslip on a clay soil with varying residue cover to simulate effects of traffic typical of grain production operations in the northern Australian grain belt. A rainfall simulator was used to determine infiltration characteristics. Wheel traffic significantly reduced time to ponding, steady infiltration rate, and total infiltration compared with non-wheeled soil, with or without residue cover. Non-wheeled soil had 4-5 times greater steady infiltration rate than wheeled soil, irrespective of residue cover. Wheelslip greater than 10% further reduced steady infiltration rate and total infiltration compared with that measured for self-propulsion wheeling (3% wheelslip) under residue-protected conditions. Where there was no compaction from wheel traffic, residue cover had a greater effect on infiltration capacity, with steady infiltration rate increasing proportionally with residue cover (R-2 = 0.98). Residue cover, however, had much less effect on infiltration when wheeling was imposed. These results demonstrated that the infiltration rate for the non-wheeled soil under a controlled traffic zero-till system was similar to that of virgin soil. However, when the soil was wheeled by a medium tractor wheel, infiltration rate was reduced to that of long-term cropped soil. These results suggest that wheel traffic, rather than tillage and cropping, might be the major factor governing infiltration. The exclusion of wheel traffic under a controlled traffic farming system, combined with conservation tillage, provides a way to enhance the sustainability of cropping this soil for improved infiltration, increased plant-available water, and reduced runoff-driven soil erosion.

Tillage and traffic effects on runoff

Traffic and tillage effects on runoff and crop performance on a heavy clay soil were investigated over a period of 4 years. Tillage treatments and the cropping program were representative of broadacre grain production practice in northern Australia, and a split-plot design used to isolate traffic effects. Treatments subject to zero, minimum, and stubble mulch tillage each comprised pairs of 90-m 2 plots, from which runoff was recorded. A 3-m-wide controlled traffic system allowed one of each pair to be maintained as a non-wheeled plot, while the total surface area of the other received a single annual wheeling treatment from a working 100-kW tractor. Rainfall/runoff hydrographs demonstrate that wheeling produced a large and consistent increase in runoff, whereas tillage produced a smaller increase. Treatment effects were greater on dry soil, but were still maintained in large and intense rainfall events on wet soil. Mean annual runoff from wheeled plots was 63 mm (44%) greater than that from controlled traffic plots, whereas runoff from stubble mulch tillage plots was 38 mm (24%) greater than that from zero tillage plots. Traffic and tillage effects appeared to be cumulative, so the mean annual runoff from wheeled stubble mulch tilled plots, representing conventional cropping practice, was more than 100 mm greater than that from controlled traffic zero tilled plots, representing best practice. This increased infiltration was reflected in an increased yield of 16% compared with wheeled stubble mulch. Minimum tilled plots demonstrated a characteristic midway between that of zero and stubble mulch tillage. The results confirm that unnecessary energy dissipation in the soil during the traction process that normally accompanies tillage has a major negative effect on infiltration and crop productivity. Controlled traffic farming systems appear to be the only practicable solution to this problem.

Increasing profits and reducing risks in crop production using participatory systems simulation approaches

The development of cropping systems simulation capabilities world-wide combined with easy access to powerful computing has resulted in a plethora of agricultural models and consequently, model applications. Nonetheless, the scientific credibility of such applications and their relevance to farming practice is still being questioned. Our objective in this paper is to highlight some of the model applications from which benefits for farmers were or could be obtained via changed agricultural practice or policy. Changed on-farm practice due to the direct contribution of modelling, while keenly sought after, may in some cases be less achievable than a contribution via agricultural policies. This paper is intended to give some guidance for future model applications. It is not a comprehensive review of model applications, nor is it intended to discuss modelling in the context of social science or extension policy. Rather, we take snapshots around the globe to 'take stock' and to demonstrate that well-defined financial and environmental benefits can be obtained on-farm from the use of models. We highlight the importance of 'relevance' and hence the importance of true partnerships between all stakeholders (farmer, scientists, advisers) for the successful development and adoption of simulation approaches. Specifically, we address some key points that are essential for successful model applications such as: (1) issues to be addressed must be neither trivial nor obvious; (2) a modelling approach must reduce complexity rather than proliferate choices in order to aid the decision-making process (3) the cropping systems must be sufficiently flexible to allow management interventions based on insights gained from models. The pro and cons of normative approaches (e.g. decision support software that can reach a wide audience quickly but are often poorly contextualized for any individual client) versus model applications within the context of an individual client's situation will also be discussed. We suggest that a tandem approach is necessary whereby the latter is used in the early stages of model application for confidence building amongst client groups. This paper focuses on five specific regions that differ fundamentally in terms of environment and socio-economic structure and hence in their requirements for successful model applications. Specifically, we will give examples from Australia and South America (high climatic variability, large areas, low input, technologically advanced); Africa (high climatic variability, small areas, low input, subsistence agriculture); India (high climatic variability, small areas, medium level inputs, technologically progressing; and Europe (relatively low climatic variability, small areas, high input, technologically advanced). The contrast between Australia and Europe will further demonstrate how successful model applications are strongly influenced by the policy framework within which producers operate. We suggest that this might eventually lead to better adoption of fully integrated systems approaches and result in the development of resilient farming systems that are in tune with current climatic conditions and are adaptable to biophysical and socioeconomic variability and change. (C) 2001 Elsevier Science Ltd. All rights reserved.

International Grassland Congress Outlook: An historical review and future expectations

Features of the history of the International Grassland Congress are mentioned. Aspects of a number of failed themes in grassland science are described with respect to molecular biology, intensive systems of ruminant production, carbohydrate use in plant growth, plant succession and range condition, and stocking method. Future expectations are focused on meeting a balance of objectives, maintaining reductionist science, taking new initiatives in plant improvement and in the development of animal production systems, and reducing barriers to international trade. The adoption of grassland science depends upon the growth of new learning, especially through cyclical interaction between scientists and farmers.

Development of a generic crop model template in the cropping system model APSIM

The Agricultural Production Systems slMulator, APSIM, is a cropping system modelling environment that simulates the dynamics of soil-plant-management interactions within a single crop or a cropping system. Adaptation of previously developed crop models has resulted in multiple crop modules in APSIM, which have low scientific transparency and code efficiency. A generic crop model template (GCROP) has been developed to capture unifying physiological principles across crops (plant types) and to provide modular and efficient code for crop modelling. It comprises a standard crop interface to the APSIM engine, a generic crop model structure, a crop process library, and well-structured crop parameter files. The process library contains the major science underpinning the crop models and incorporates generic routines based on physiological principles for growth and development processes that are common across crops. It allows APSIM to simulate different crops using the same set of computer code. The generic model structure and parameter files provide an easy way to test, modify, exchange and compare modelling approaches at process level without necessitating changes in the code. The standard interface generalises the model inputs and outputs, and utilises a standard protocol to communicate with other APSIM modules through the APSIM engine. The crop template serves as a convenient means to test new insights and compare approaches to component modelling, while maintaining a focus on predictive capability. This paper describes and discusses the scientific basis, the design, implementation and future development of the crop template in APSIM. On this basis, we argue that the combination of good software engineering with sound crop science can enhance the rate of advance in crop modelling. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta)

Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.