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.

Fine Mapping of qDor7, a Major QTL Affecting Seed Dormancy in Sorghum (Sorghum bicolor (L.) Moench)

Seed dormancy is a key domestication trait for major crops, which is acquired in long-term systems development processes and enables the survival of plants in adverse natural conditions. It is a complex trait under polygenic control and is affected by endogenous and environmental factors. In the present study, a major seed dormancy QTL in sorghum (Sorghum bicolor (L.) Moench), qDor7, detected previously, was fine mapped using a large, multi-generational population. The qDor7 locus was delimited to a 96-kb region which contains 16 predicted gene models. These results lay a solid foundation for cloning qDor7. In addition, the functional markers tightly linked to the seed dormancy QTL may be used in marker-assisted selection for seed dormancy in sorghum.

Effect of nitrogen on the skin colour and other quality attributes of ripe ‘Kensington Pride’ mango (Mangifera indica L.) fruit

Near-ripe ‘Kensington Pride’ mango (Mangifera indica L.) fruit with green skin colour generally return lower wholesale and retail prices. Pre-harvest management, especially nitrogen (N) nutrition, appears to be a major causal factor. To obtain an understanding of the extent of the problem in the Burdekin district (dry tropics; the major production area in Australia), green mature ‘Kensington Pride’ mango fruit were harvested from ten orchards and ripened at 20 ± 0.5 O C. Of these orchards, 70% produced fruit with more than 25% of the skin surface area green when ripe. The following year, the effect of N application on skin colour and other quality attributes was investigated on three orchards, one with a high green (HG) skin problem and two with a low green (LG) skin problem. N was applied at pre-flowering and at panicle emergence at the rate of 0,75,150,300 g per tree (soil applied) or 50 g per tree as foliar N for the HG orchard, and 0,150,300,450 g per tree (soil applied) or 50 g per tree (foliar) for the LG orchards. In all orchards the proportion of green colour on the ripe fruit was significantly (P<0.05) higher with soil applications of 150 g N or more per tree. Foliar sprays resulted in a higher proportion of green colour than the highest soil treatment in the HG orchard, but not in the LG orchards. Anthracnose disease severity was significantly (P<0.05) higher with 300 g of N per tree or foliar treatment in the HG orchard, compared with no additional N. Thus, N can reduce mango fruit quality by increasing green colour and anthracnose disease in ripe fruit.

Egg parasitoids of the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), from south-east Queensland

Field surveys of egg parasitoids of the diamondback moth, Plutella xylostella, were conducted at Redlands and Gatton, south-east Queensland. Eggs of P. xylostella were present all year round in both localities, and parasitized eggs were consistently found between late spring and early winter. Percent parasitism in the range 30–75% was recorded on many occasions, although rates less than 10% were more common. The major parasitoids included Trichogrammatoidea bactrae Nagaraja and Trichogramma pretiosum Riley. Laboratory evaluation showed that the T. pretiosum from Gatton has a high capacity to parasitize P. xylostella eggs under suitable conditions. This study represents the first record of egg parasitoids of P. xylostella from Australia.

Homologues of the maize rust resistance gene Rp1-D are genetically associated with a major rust resistance QTL in sorghum

As part of a comparative mapping study between sugarcane and sorghum, a sugarcane cDNA clone with homology to the maize Rp1-D rust resistance gene was mapped in sorghum. The cDNA probe hybridised to multiple loci, including one on sorghum linkage group (LG) E in a region where a major rust resistance QTL had been previously mapped. Partial sorghum Rp1-D homologues were isolated from genomic DNA of rust-resistant and -susceptible progeny selected from a sorghum mapping population. Sequencing of the Rp1-D homologues revealed five discrete sequence classes: three from resistant progeny and two from susceptible progeny. PCR primers specific to each sequence class were used to amplify products from the progeny and confirmed that the five sequence classes mapped to the same locus on LG E. Cluster analysis of these sorghum sequences and available sugarcane, maize and sorghum Rp1-D homologue sequences showed that the maize Rp1-D sequence and the partial sugarcane Rp1-D homologue were clustered with one of the sorghum resistant progeny sequence classes, while previously published sorghum Rp1-D homologue sequences clustered with the susceptible progeny sequence classes. Full-length sequence information was obtained for one member of a resistant progeny sequence class ( Rp1-SO) and compared with the maize Rp1-D sequence and a previously identified sorghum Rp1 homologue ( Rph1-2). There was considerable similarity between the two sorghum sequences and less similarity between the sorghum and maize sequences. These results suggest a conservation of function and gene sequence homology at the Rp1 loci of maize and sorghum and provide a basis for convenient PCR-based screening tools for putative rust resistance alleles in sorghum.

Peanut stripe potyvirus resistance in peanut (Arachis hypogaea L.) plants carrying viral coat protein gene sequences

Peanut (Arachis hypogaea L.) lines exhibiting high levels of resistance to peanut stripe virus (PStV) were obtained following microprojectile bombardment of embryogenic callus derived from mature seeds. Fertile plants of the commercial cultivars Gajah and NC7 were regenerated following co-bombardmentwith the hygromycin resistance gene and one of two forms of the PStV coat protein (CP) gene, an untranslatable, full length sequence (CP2) or a translatable gene encoding a CP with an N-terminal truncation (CP4). High level resistance to PStV was observed for both transgenes when plants were challenged with the homologous virus isolate. The mechanism of resistance appears to be RNA-mediated, since plants carrying either the untranslatable CP2 or CP4 had no detectable protein expression, but were resistant or immune (no virus replication). Furthermore, highly resistant, but not susceptible CP2 T0 plants contained transgene-specific small RNAs. These plants now provide important germplasm for peanut breeding, particularly in countries where PStV is endemic and poses a major constraint to peanut production.

Near infrared reflectance as a rapid and inexpensive surrogate measure for fatty acid composition and oil content in peanuts (Arachis hypogaea L.)

The fatty acid composition of ground nuts (Arachis hypogaea L.) commonly known as peanuts, is an important consideration when a new variety is being released. The composition impacts on nutrition and, importantly, self-life of peanut products. To select for suitable breeding material, it was necessary to develop a rapid, non-derstructive and cost-efficient method. Near infrared spectroscopy was chosen as that methodology. Calibrations were developed for two major fatty-acid components, oleic and linoleic acids and two minor components, palmitic and stearic acids, as well as total oil content. Partial least squares models indicated a high level of precision with a squared multiple correlation coefficient of greater than 0.90 for each constitutent. Standard errors for prediction for oleic, linoleic, palmitic, stearic acids and total oil content were 6.4%, 4.5%, 0.8%, 0.9% and 1.3% respectively. The results demonstrated that reasonable calibrations could be developed to predict oil composition and content of peanuts for a breeding programme.

SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ≥0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal-Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.

Genetic erosion and changes in distribution of sorghum (Sorghum bicolor L. (Moench)) landraces in north-eastern Ethiopia

Ethiopia is believed to be the centre of origin and domestication for sorghum, where sorghum remains one of the main staple crops. Loss of biodiversity is occurring at an alarming rate in Ethiopia and crops, including sorghum, have long been recognized as vulnerable to genetic erosion. A major collection of sorghum germplasm was made in 1973 by Gebrekidan and Ejeta from north-eastern Ethiopia. A new collection of landraces was made in 2003, and these were field evaluated at Sirinka in 2004 along with representative samples from the 1973 collection. Farmer surveys and soil and climate surveys were also performed. Preliminary analysis demonstrated that some important landraces have disappeared either locally or regionally in the past 30 years and many other landraces have become marginalized. Landraces which are less preferred in terms of agronomic value and end use, and introductions, have become increasingly important. Late maturing landraces were found to be particularly vulnerable, with a number disappearing altogether. Farmers have become more risk averse, and factors such as declining soil fertility, more frequent drought and unreliable rainfall, and increased pest infestation have contributed to a change in farmer landrace selection. Data are presented on the variability and unique characters of some of the Ethiopian landraces, and implications for conservation are discussed.

Chromolaena odorata (L.) King and Robinson (Asteraceae)

Chromolaena, or Siam weed, is a serious problem in several tropical and sub-tropical areas around the world. In our own region, it is a serious weed in New Guinea, East Timor and Indonesia and is also under an eradication regime in North Queensland. The chapter summarises current knowledge about the taxonomy, biology, distribution, ecology, impacts and control of the weed. Biological control has been a major multinational initiative against this weed in recent years and these efforts are described in some detail. Interestingly agents have not been universally effective because of weed biotype differences and climate. Considerable success has been achieved in New Guinea, principally with the tephritid fly Cecidocares connex and by the efforts of Michael Day, Rachel McFadyen and Graham Donnelly from Alan Fletcher Research Station.

Ocean dispersal modelling for propagules of pond apple (Annona glabra L.)

Pond apple invades riparian and coastal environments with water acting as the main vector for dispersal. As seeds float and can reach the ocean, a seed tracking model driven by near surface ocean currents was used to develop maps of potential seed dispersal. Seeds were ‘released’ in the model from sites near the mouths of major North Queensland rivers. Most seeds reach land within three months of release, settling predominately on windward-facing locations. During calm and monsoonal conditions, seeds were generally swept in a southerly direction, however movement turns northward during south easterly trade winds. Seeds released in February from the Johnstone River were capable of being moved anywhere from 100 km north to 150 km south depending on prevailing conditions. Although wind driven currents are the primary mechanism influencing seed dispersal, tidal currents, the East Australian Current, and other factors such as coastline orientation, release location and time also play an important role in determining dispersal patterns. In extreme events such as tropical cyclone Justin in 1997, north east coast rivers could potentially transport seed over 1300 km to the Torres Strait, Papua New Guinea and beyond.

Germination, emergence, and persistence of Sonchus oleraceus, a major crop weed in subtropical Australia.

Sonchus oleraceus (common sowthistle) is a dominant weed and has increased in prevalence in conservation cropping systems of the subtropical grain region of Australia. Four experiments were undertaken to define the environmental factors that favor its germination, emergence, and seed persistence. Seeds were germinated at constant temperatures between 5 and 35C and water potentials between 0 and -1.4 MPa. The maximum germination rate of 86-100% occurred at 0 and -0.2 MPa, irrespective of the temperature when exposed to light (12 h photoperiod light/dark), but the germination rate was reduced by 72% without light. At water potentials of -0.6 to -0.8 MPa, the germination rate was reduced substantially by higher temperatures; no seed germinated at a water potential >-1.0 MPa. Emergence and seed persistence were measured over 30 months following seed burial at 0 (surface), 1, 2, 5, and 10 cm depths in large pots that were buried in a south-eastern Queensland field. Seedlings emerged readily from the surface and 1 cm depth, with no emergence from below the 2 cm depth. The seedlings emerged during any season following rain but, predominantly, within 6 months of planting. Seed persistence was short-term on the soil surface, with 2% of seeds remaining after 6 months, but it increased with the burial depth, with 12% remaining after 30 months at 10 cm. Thus, a minimal seed burial depth with reduced tillage and increased surface soil water with stubble retention has favored the proliferation of this weed in any season in a subtropical environment. However, diligent management without seed replenishment will greatly reduce this weed problem within a short period.

Understanding and management of resistance to Group M, L and I Herbicides

This project will develop better understanding of resistance to glyphosate, paraquat and Group I herbicides to better inform weed management. The project will develop a range of tools for farm advisors to improve their confidence in decision making with respect to reducing the risk of glyphosate, Group I and paraquat resistance. These will include risk assessments, case studies and scenario exploring tools. The project will discuss with commercial providers the potential for new herbicide registrations. The project will establish farm advisor learning groups to work on the application of the research in local areas where resistance is already a major problem and to improve adoption of research outcomes from this and other projects.