Identification of QTL for sugar-related traits in a sweet x grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population

QTL for stem sugar-related and other agronomic traits were identified in a converted sweet (R9188) × grain (R9403463-2-1) sorghum population. QTL analyses were conducted using phenotypic data for 11 traits measured in two field experiments and a genetic map comprising 228 SSR and AFLP markers grouped into 16 linkage groups, of which 11 could be assigned to the 10 sorghum chromosomes (SBI-01 to SBI-10). QTL were identified for all traits and were generally co-located to five locations (SBI-01, SBI-03, SBI-05, SBI-06 and SBI-10). QTL alleles from R9188 were detected for increased sucrose content and sugar content on SBI-01, SBI-05 and SBI-06. R9188 also contributed QTL alleles for increased Brix on SBI-05 and SBI-06, and increased sugar content on SBI-03. QTL alleles from R9403463-2-1 were found for increased sucrose content and sucrose yield on SBI-10, and increased glucose content on SBI-07. QTL alleles for increased height, later flowering and greater total dry matter yield were located on SBI-01 of R9403463-2-1, and SBI-06 of R9188. QTL alleles for increased grain yield from both R9403463-2-1 and R9188 were found on SBI-03. As an increase in stem sugars is an important objective in sweet sorghum breeding, the QTL identified in this study could be further investigated for use in marker-assisted selection of sweet sorghum.

An assessment of the genetic relationship between sweet and grain sorghums, within Sorghum bicolor ssp. bicolor (L.) Moench, using AFLP markers

Compared to grain sorghums, sweet sorghums typically have lower grain yield and thick, tall stalks which accumulate high levels of sugar (sucrose, fructose and glucose). Unlike commercial grain sorghum (S. bicolor ssp. bicolor) cultivars, which are usually F1 hybrids, commercial sweet sorghums were selected as wild accessions or have undergone limited plant breeding. Although all sweet sorghums are classified within S. bicolor ssp. bicolor, their genetic relationship with grain sorghums is yet to be investigated. Ninety-five genotypes, including 31 sweet sorghums and 64 grain sorghums, representing all five races within the subspecies bicolor, were screened with 277 polymorphic amplified fragment length polymorphism (AFLP) markers. Cluster analysis separated older sweet sorghum accessions (collected in mid 1800s) from those developed and released during the early to mid 1900s. These groups were emphasised in a principle component analysis of the results such that sweet sorghum lines were largely distinguished from the others, particularly by a group of markers located on sorghum chromosomes SBI-08 and SBI-10. Other studies have shown that QTL and ESTs for sugar-related traits, as well as for height and anthesis, map to SBI-10. Although the clusters obtained did not group clearly on the basis of racial classification, the sweet sorghum lines often cluster with grain sorghums of similar racial origin thus suggesting that sweet sorghum is of polyphyletic origin within S. bicolor ssp. bicolor.

Identification of small juvenile scombrids from northwest tropical Australia using mitochondrial DNA cytochrome b sequences

Small juveniles of the nine species of scombrids in Australian waters are morphologically similar to one another and, consequently, difficult to identify to species level. We show that the sequence of the mitochondrial DNA cytochrome b gene region is a powerful tool for identification of these young fish. Using this method, we identified 50 juvenile scombrids collected from Exmouth Bay, Western Australia. Six species of scombrids were apparent in this sample of fish: narrow-barred Spanish mackerel (Scomberomorus commerson), Indian mackerel (Rastrelliger kanagurta), frigate tuna (Auxis thazard), bullet tuna (Auxis rochei), leaping bonito (Cybiosarda elegans), and kawakawa (Euthynnus affinis). The presence of Indian mackerel, frigate tuna, leaping bonito, and kawakawa is the first indication that coastal waters may be an important spawning habitat for these species, although offshore spawning may also occur. The occurrence of small juvenile S. commerson was predicted from the known spawning patterns of that species, but other mackerel species (Scomberomorus munroi, Scomberomorus queenslandicus, Scomberomorus semifasiciatus) likely to be spawning during the sampling period were not detected among the 50 small juveniles analyzed here.

Identification and immunogenicity of an immunodominant mimotope of Avibacterium paragallinarum from a phage display peptide library

Avibacterium paragallinarum is the causative agent of infectious coryza. The protective antigens of this important pathogen have not yet been clearly identified. In this paper, we applied phage display technique to screen the immunodominant mimotopes of a serovar A strain of A. paragallinarum by using a random 12-peptide library, and evaluated the immunogenicity in chickens of the selected mimotope. Polyclonal antibody directed against A. paragallinarum strain 0083 (serovar A) was used as the target antibody and phage clones binding to this target were screened from the 12-mer random peptide library. More than 50% of the phage clones selected in the third round carried the consensus peptide motif sequence A-DP(M)L. The phage clones containing the peptide motif reacted with the target antibody and this interaction could be blocked, in a dose-dependent manner, by A. paragallinarum. One of the peptide sequences, YGLLAVDPLFKP, was selected and the corresponding oligonucleotide sequence was synthesized and then inserted into the expression vector pFliTrx. The recombinant plasmid was transferred into an expression host Escherichia coli GI826 by electroporation, resulting in a recombinant E. coli expressing the peptide on the bacterial surface. Intramuscular injection of the epitope-expressing recombinant bacteria into chickens induced a specific serological response to serovar A. A. paragallinarum. The chickens given the recombinant E. coli showed significant protection against challenge with A. paragallinarum 0083. These results indicated a potential for the use of the mimotope in the development of molecular vaccines for infectious coryza.

Characterization of disease resistance gene candidates of the nucleotide binding site (NBS) type from banana and correlation of a transcriptional polymorphism with resistance to Fusarium oxysporum f.sp. cubense race 4

Most plant disease resistance (R) genes encode proteins with a nucleotide binding site and leucine-rich repeat structure (NBS-LRR). In this study, degenerate primers were used to amplify genomic NBS-type sequences from wild banana (Musa acuminata ssp. malaccensis) plants resistant to the fungal pathogen Fusarium oxysporum formae specialis (f. sp.) cubense (FOC) race 4. Five different classes of NBS-type sequences were identified and designated as resistance gene candidates (RGCs). The deduced amino acid sequences of the RGCs revealed the presence of motifs characteristic of the majority of known plant NBS-LRR resistance genes. Structural and phylogenetic analyses grouped the banana RGCs within the non-TIR (homology to Toll/interleukin-1 receptors) subclass of NBS sequences. Southern hybridization showed that each banana RGC is present in low copy number. The expression of the RGCs was assessed by RT-PCR in leaf and root tissues of plants resistant or susceptible to FOC race 4. RGC1, 3 and 5 showed a constitutive expression profile in both resistant and susceptible plants whereas no expression was detected for RGC4. Interestingly, RGC2 expression was found to be associated only to FOC race 4 resistant lines. This finding could assist in the identification of a FOC race 4 resistance gene.

Genotypic variation in seedling root architectural traits and implications for drought adaptation in wheat (Triticum aestivum L.)

Root system characteristics are of fundamental importance to soil exploration and below-ground resource acquisition. Root architectural traits determine the in situ space-filling properties of a root system or root architecture. The growth angle of root axes is a principal component of root system architecture that has been strongly associated with acquisition efficiency in many crop species. The aims of this study were to examine the extent of genotypic variability for the growth angle and number of seminal roots in 27 current Australian and 3 CIMMYT wheat (Triticum aestivum L.) genotypes, and to quantify using fractal analysis the root system architecture of a subset of wheat genotypes contrasting in drought tolerance and seminal root characteristics. The growth angle and number of seminal roots showed significant genotypic variation among the wheat genotypes with values ranging from 36 to 56 (degrees) and 3 to 5 (plant-1), respectively. Cluster analysis of wheat genotypes based on similarity in their seminal root characteristics resulted in four groups. The group composition reflected to some extent the genetic background and environmental adaptation of genotypes. Wheat cultivars grown widely in the Mediterranean environments of southern and western Australia generally had wider growth angle and lower number of seminal axes. In contrast, cultivars with superior performance on deep clay soils in the northern cropping region, such as SeriM82, Baxter, Babax, and Dharwar Dry exhibited a narrower angle of seminal axes. The wheat genotypes also showed significant variation in fractal dimension (D). The D values calculated for the individual segments of each root system suggested that, compared to the standard cultivar Hartog, the drought-tolerant genotypes adapted to the northern region tended to distribute relatively more roots in the soil volume directly underneath the plant. These findings suggest that wheat root system architecture is closely linked to the angle of seminal root axes at the seedling stage. The implications of genotypic variation in the seminal root characteristics and fractal dimension for specific adaptation to drought environment types are discussed with emphasis on the possible exploitation of root architectural traits in breeding for improved wheat cultivars for water-limited environments.

Cannibalism contributes significantly to the diet of cultured sand crabs, Portunus pelagicus (L.): A dual stable isotope study

The significance of cannibalism in the diet of juvenile pond-cultured blue swimmer crabs (Portunus pelagicus (L.)) was investigated using dual stable isotope analysis of carbon and nitrogen. In a laboratory feeding experiment, δ15N demonstrated a constant trophic shift (Δδ15N ≈+ 1.6‰), and therefore seemed to be a reliable indicator for assessing trophic position for P. pelagicus. This agrees with previously reported trends. Difference in growth rate did not seem to influence δ15N values. In contrast, δ13C did not display consistent shifts between trophic levels (range of Δδ13C: + 1 to + 1.7‰). The results from the pond experiment showed that larger individuals had a more enriched δ15N than smaller individuals, which, when compared to the results from the laboratory experiment, indicates that larger individuals were at a higher trophic level. This is most likely due to cannibalism prevailing in the pond rather than a direct result of faster growth rate. Cannibalistic behaviour might further increase growth, resulting in the observed positive correlation between size and δ15N.

DNA markers linked to yield, yield components, and morphological traits in autotetraploid lucerne (Medicago sativa L.)

We have mapped and identified DNA markers linked to morphology, yield, and yield components of lucerne, using a backcross population derived from winter-active parents. The high-yielding and recurrent parent, D, produced individual markers that accounted for up to 18% of total yield over 6 harvests, at Gatton, south-eastern Queensland. The same marker, AC/TT8, was consistently identified at each individual harvest, and in individual harvests accounted for up to 26% of the phenotypic variation for yield. This marker was located in linkage group 2 of the D map, and several other markers positively associated with yield were consistently identified in this linkage group. Similarly, markers negatively associated with yield were consistently identified in the W116 map, W116 being the low-yielding parent. Highly significant positive correlations were observed between total yield and yield for harvests 1-6, and between total yield and stem length, tiller number, leaf yield/plant, leaf yield/5 stems, stem yield/plant, and stem yield/5 stems. Highly significant QTL were located for all these characters as well as for leaf shape and pubescence.

Urana subterranean clover (Trifolium subterraneum L. var. subterraneum)

Urana is a hardseeded, moderately early flowering F-5-derived crossbred subterranean clover of var. subterraneum [( Katz. et Morley) Zohary and Heller] developed by the collaborating organisations of the National Annual Pasture Legume Improvement Program. It has been selected for release as a new cultivar on the basis of its high winter and spring herbage production and overall field performance relative to other subterranean clovers of similar maturity. Urana is recommended for sowing in Western Australia, New South Wales, Victoria, South Australia and Queensland. It is best suited to well-drained, moderately acidic soils in areas with a growing season of 5 - 7 months, which extends into mid-October. Urana is suited to phase farming and crop rotations. It has been granted Plant Breeders Rights in Australia.

Identification of two distinct bovine parainfluenza virus type 3 genotypes

The partial gene sequencing of the matrix (M) protein from seven clinical isolates of bovine parainfluenza virus type 3 (BPIV-3), and the complete sequencing of a representative isolate (Q5592) was completed in this study. Nucleotide sequence analysis was initiated because of the failure of in-house BPIV-3 RT-PCR methods to yield expected products for four of the isolates. Phylogenetic reconstructions based on the nucleotide sequences for the M-protein and the entire genome, using all of the available BPIV-3 nucleotide sequences, demonstrated that there were two distinct BPIV-3 genotypes (BPIV-3a and BPIV-3b). These newly identified genotypes have implications for the development of BPIV-3 molecular detection methods and may also impact on BPIV-3 vaccine formulations.

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.

Seasonal incidence of Stenodiplosis sorghicola (Coquillett) (Diptera: Cecidomyiidae) and its parasitoids on Sorghum halepense (L.) Pers. in south-eastern Queensland, Australia

To quantify the role of Johnson grass, Sorghum halepense, in the population dynamics of the sorghum midge, Stenodiplosis sorghicola, patterns of flowering of Johnson grass and infestation by sorghum midge were studied in two different climatic environments in the Lockyer Valley and on the Darling Downs in south-eastern Queensland for 3 years. Parasitism levels of S. sorghicola were also recorded. In the Lockyer Valley, Johnson grass panicles were produced throughout the year but on the Darling Downs none were produced between June and September. In both areas, most panicle production occurred between November and March and infestation by S. sorghicola was the greatest during this period. The parasitism levels were between 20% and 50%. After emergence from winter diapause, one to two generations of S. sorghicola developed on S. halepense before commercial grain sorghum crops were available for infestation. Parasitoids recorded were: Aprostocetus diplosidis, Eupelmus australiensis and two species of Tetrastichus. Relationships between sorghum midge population growth rate and various environmental and population variables were investigated. Population size had a significant negative effect (P < 0.0001) on population growth rate. Mortality due to parasitism showed a significant positive density response (P < 0.0001). Temperature, rainfall, open pan evaporation, degree-days and host availability showed no significant effect on population growth rate. Given the phenology of sorghum production in south-eastern Queensland, Johnson grass provides an important bridging host, sustaining one to two generations of sorghum midge. Critical studies relating population change and build-up in sorghum to sorghum midge populations in Johnson grass are yet to be performed.

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.

The assessment of TGGE for the detection of interspecific and intergeneric DNA-marker polymorphism within Solanaceae

RFLP markers are currently the most appropriate marker system for the identification of uncharacterised polymorphism at the interspecific and intergeneric level. Given the benefits of a PCR-based marker system and the availability of sequence information for many Solanaceous cDNA clones, it is now possible to target conserved fragments, for primer development, that flank sequences possessing interspecific polymorphism. The potential outcome is the development of a suite of markers that amplify widely in Solanaceae. Temperature gradient gel electrophoresis (TGGE) is a relatively inexpensive gel-based system that is suitable for the detection of most single-base changes. TGGE can be used to screen for both known and unknown polymorphisms, and has been assessed here, for the development of PCR-based markers that are useful for the detection of interspecific variation within Solanaceae. Fifteen markers are presented where differences between Lycopersicon esculentum and L. pennellii have been detected by TGGE. The markers were assessed on a wider selection of plant species and found to be potentially useful for the identification of interspecific and intergeneric polymorphism in Solanaceous plants.

Molecular characterisation, pathogenesis and fungicide sensitivity of Pythium spp. from table beet (Beta vulgaris var. vulgaris) grown in the Lockyer Valley, Queensland

Table beet production in the Lockyer Valley of south-eastern Queensland is known to be adversely affected by soilborne root disease from infection by Pythium spp. However, little is known regarding the species or genotypes that are the causal agents of both pre- and post-emergence damping off. Based on RFLP analysis with HhaI, HinfI and MboI of the PCR amplified ITS region DNA from soil and diseased plant samples, the majority of 130 Pythium isolates could be grouped into three genotypes, designated LVP A, LVP B and LVP C. These groups comprised 43, 41 and 7% of all isolates, respectively. Deoxyribonucleic acid sequence analysis of the ITS region indicated that LVP A was a strain of Pythium aphanidermatum, with greater than 99% similarity to the corresponding P. aphanidermatum sequences from the publicly accessible databases. The DNA sequences from LVP B and LVP C were most closely related to P. ultimum and P. dissotocum, respectively. Lower frequencies of other distinct isolates with unique RFLP patterns were also obtained with high levels of similarity (>97%) to P. heterothallicum, P. periplocum and genotypes of P. ultimum other than LVP B. Inoculation trials of 1- and 4-week-old beet seedlings indicated that compared with isolates of the LVP B genotype, a higher frequency of LVP A isolates caused disease. Isolates with the LVP A, LVP B and LVP C genotypes were highly sensitive to the fungicide Ridomil MZ, which suppressed radial growth on V8 agar between approximately four and thirty fold at 5 μg/mL metalaxyl and 40 μg/mL mancozeb, a concentration far lower than the recommended field application rate.