NIR model development and robustness in prediction of melon fruit total soluble solids

Near infrared spectroscopy (NIRS) can be used for the on-line, non-invasive assessment of fruit for eating quality attributes such as total soluble solids (TSS). The robustness of multivariate calibration models, based on NIRS in a partial transmittance optical geometry, for the assessment of TSS of intact rockmelons (Cucumis melo) was assessed. The mesocarp TSS was highest around the fruit equator and increased towards the seed cavity. Inner mesocarp TSS levels decreased towards both the proximal and distal ends of the fruit, but more so towards the proximal end. The equatorial region of the fruit was chosen as representative of the fruit for near infrared assessment of TSS. The spectral window for model development was optimised at 695-1045 nm, and the data pre-treatment procedure was optimised to second-derivative absorbance without scatter correction. The 'global' modified partial least squares (MPLS) regression modelling procedure of WINISI (ver. 1.04) was found to be superior with respect to root mean squared error of prediction (RMSEP) and bias for model predictions of TSS across seasons, compared with the 'local' MPLS regression procedure. Updating of the model with samples selected randomly from the independent validation population demonstrated improvement in both RMSEP and bias with addition of approximately 15 samples.

Flour yield QTLs in three Australian doubled haploid wheat populations

Flour yield quantitative trait loci (QTLs) were identified in 3 Australian doubled haploid populations, Sunco × Tasman, CD87 × Katepwa, and Cranbrook × Halberd. Trial data from 3 to 4 sites or years were available for each population. QTLs were identified on chromosomes 2BS, 4B, 5AL, and 6BL in the Sunco × Tasman population, on chromosomes 4B, 5AS, and 6DL in the CD87 × Katepwa population, and on chromosomes 4DS, 5DS, and 7AS in the Cranbrook × Halberd population. In the Sunco × Tasman cross the highest genetic variance was detected with the QTL on chromosome 2B (31.3%), in the CD87 × Katepwa cross with the QTL on chromosome 4B (23.8%), and in the Cranbrook × Halberd cross with the QTL on chromosome 5D (18%). Only one QTL occurred in a similar location in more than one population, indicating the complexity of the flour yield character across different backgrounds.

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.

Detection of nitrogen deficiency in wheat from spectral reflectance indices and basic crop eco-physiological concepts

We tested the capacity of several published multispectral indices to estimate the nitrogen nutrition of wheat canopies grown under different levels of water supply and plant density and derived a simple canopy reflectance index that is greatly independent of those factors. Planar domain geometry was used to account for mixed signals from the canopy and soil when the ground cover was low. A nitrogen stress index was developed, which adjusts shoot %N for plant biomass and area, thereby accounting for environmental conditions that affect growth, such as crop water status. The canopy chlorophyll content index (CCCi) and the modified spectral ratio planar index (mSRPi) could explain 68 and 69% of the observed variability in the nitrogen nutrition of the crop as early as Zadoks 33, irrespective of water status or ground cover. The CCCi was derived from the combination of 3 wavebands 670, 720 and 790 nm, and the mSRPi from 445, 705 and 750 nm, together with broader bands in the NIR and RED. The potential for their spatial application over large fields/paddocks is discussed.

Impact of subsoil constraints on wheat yield and gross margin on fine-textured soils of the southern Victorian Mallee

The APSIM-Wheat module was used to investigate our present capacity to simulate wheat yields in a semi-arid region of eastern Australia (the Victorian Mallee), where hostile subsoils associated with salinity, sodicity, and boron toxicity are known to limit grain yield. In this study we tested whether the effects of subsoil constraints on wheat growth and production could be modelled with APSIM-Wheat by assuming that either: (a) root exploration within a particular soil layer was reduced by the presence of toxic concentrations of salts, or (b) soil water uptake from a particular soil layer was reduced by high concentration of salts through osmotic effects. After evaluating the improved predictive capacity of the model we applied it to study the interactions between subsoil constraints and seasonal conditions, and to estimate the economic effect that subsoil constraints have on wheat farming in the Victorian Mallee under different climatic scenarios. Although the soils had high levels of salinity, sodicity, and boron, the observed variability in root abundance at different soil layers was mainly related to soil salinity. We concluded that: (i) whether the effect of subsoil limitations on growth and yield of wheat in the Victorian Mallee is driven by toxic, osmotic, or both effects acting simultaneously still requires further research, (ii) at present, the performance of APSIM-Wheat in the region can be improved either by assuming increased values of lower limit for soil water extraction, or by modifying the pattern of root exploration in the soil pro. le, both as a function of soil salinity. The effect of subsoil constraints on wheat yield and gross margin can be expected to be higher during drier than wetter seasons. In this region the interaction between climate and soil properties makes rainfall information alone, of little use for risk management and farm planning when not integrated with cropping systems models.

Effect of the puroindoline locus and environment on Chinese fresh noodle texture

Grain produced from doubled-haploid (DH) wheat lines, developed from a hard- and a soft-grained wheat cultivar, were bulked according to Pinb (puroindoline b) genotypes for an assessment of Chinese fresh noodle texture by a trained taste panel. Each DH line was designated as 'soft' or 'hard' grained, based on a PCR amplification of the wildtype, soft allele, or the mutant, hard allele. Theoretically, the soft and hard grain bulks represented respective Pinb alleles and an independent assortment of unlinked alleles from the parents, Sunco and Chuanyu 12. Grains from the parents and DH lines were grown at 2 locations in Queensland, Australia, and one in Sichuan, China. The grains were milled and processed for a taste panel evaluation in Chengdu, Sichuan. Results suggest the Pinb alleles had a significant effect on noodle softness and explained 30% of the variation; the 'soft' Pinb allele conferred a softer noodle texture. Location had a significant effect on noodle smoothness; wheat grain grown at Biloela, Queensland, produced a smoother noodle texture than grain grown in Sichuan. The effect of location confirms the importance of environment as a variable for this quality character. This investigation exemplifies the utility of Pinb markers for specifically altering Chinese Fresh Noodle texture.

Graze to grain - measuring and modelling the effects of grazed pasture leys on soil nitrogen and sorghum yield on a Vertosol soil in the Australian subtropics

Highly productive sown pasture systems can result in high growth rates of beef cattle and lead to increases in soil nitrogen and the production of subsequent crops. The nitrogen dynamics and growth of grain sorghum following grazed annual legume leys or a grass pasture were investigated in a no-till system in the South Burnett district of Queensland. Two years of the tropical legumes Macrotyloma daltonii and Vigna trilobata (both self regenerating annual legumes) and Lablab purpureus (a resown annual legume) resulted in soil nitrate N (0-0.9 m depth), at sorghum sowing, ranging from 35 to 86 kg/ha compared with 4 kg/ha after pure grass pastures. Average grain sorghum production in the 4 cropping seasons following the grazed legume leys ranged from 2651 to 4012 kg/ha. Following the grass pasture, grain sorghum production in the first and second year was < 1900 kg/ha and by the third year grain yield was comparable to the legume systems. Simulation studies utilising the farming systems model APSIM indicated that the soil N and water dynamics following 2-year ley phases could be closely represented over 4 years and the prediction of sorghum growth during this time was reasonable. In simulated unfertilised sorghum crops grown from 1954 to 2004, grain yield did not exceed 1500 kg/ha in 50% of seasons following a grass pasture, while following 2-year legume leys, grain exceeded 3000 kg/ha in 80% of seasons. It was concluded that mixed farming systems that utilise short term legume-based pastures for beef production in rotation with crop production enterprises can be highly productive.

Mapping quantitative trait loci for resistance to Pratylenchus thornei from synthetic hexaploid wheat in the International Triticeae Mapping Initiative (ITMI) population

Root-lesion nematode (Pratylenchus thornei) is a serious pathogen of wheat in many countries. The International Triticeae Mapping Initiative (ITMI) population of recombinant inbred lines (RILs) was assessed for resistance to P. thornei to determine the chromosome locations of the resistance genes. The ITMI population is derived from a cross between the resistant synthetic hexaploid wheat W-7984 and a susceptible bread wheat cultivar Opata 85. Two years of phenotypic data for resistance to P. thornei were obtained in replicated glasshouse trials. Quantitative trait locus (QTL) analysis was performed using available segregation and map data for 114 RILs. A QTL on chromosome 6DS showed consistent effects for reduced nematode numbers (partial resistance) across years and accounted for 11% and 23% of the phenotypic variation. A second QTL for P. thornei resistance on chromosome 2BS accounted for an additional 19% and 5%. Restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers associated with the QTLs are physically located in regions rich in major genes at the distal ends of the short chromosome arms of 6D and 2B. SSR markers with potential for marker-assisted selection of P. thornei resistance effective in different genetic backgrounds have been identified.

Testing the simulation capability of APSIM-ORYZA under different levels of nitrogen fertiliser and transplanting time regimes in Korea

APSIM-ORYZA is a new functionality developed in the APSIM framework to simulate rice production while addressing management issues such as fertilisation and transplanting, which are particularly important in Korean agriculture. To validate the model for Korean rice varieties and field conditions, the measured yields and flowering times from three field experiments conducted by the Gyeonggi Agricultural Research and Extension Services (GARES) in Korea were compared against the simulated outputs for different management practices and rice varieties. Simulated yields of early-, mid- and mid-to-late-maturing varieties of rice grown in a continuous rice cropping system from 1997 to 2004 showed close agreement with the measured data. Similar results were also found for yields simulated under seven levels of nitrogen application. When different transplanting times were modelled, simulated flowering times ranged from within 3 days of the measured values for the early-maturing varieties, to up to 9 days after the measured dates for the mid- and especially mid-to-late-maturing varieties. This was associated with highly variable simulated yields which correlated poorly with the measured data. This suggests the need to accurately calibrate the photoperiod sensitivity parameters of the model for the photoperiod-sensitive rice varieties in Korea.

The development of an improved PCR-based marker system for Sw-5, an important TSWV resistance gene of tomato

Sw-5 is an important disease resistance gene of tomato, providing broad resistance to Tomato spotted wilt virus (TSWV). A cleaved amplified polymorphic sequence (CAPS) marker, closely linked to the gene, has been reported. Although the Sw-5 locus has been characterised, a gene-specific marker has not been developed. This paper presents a PCR-based marker-system that consists of the co-amplification of a dominant marker representing the Sw-5 gene sequence, and the modified CAPS marker as a positive control and indicator of genotype.

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.

Growth responses of sugarcane to mycorrhizal spore density and phosphorus rate

Arbuscular mycorrhizal (AM) fungi, commonly found in long-term cane-growing fields in northern Queensland, are linked with both negative and positive growth responses by sugarcane (Saccharum spp.), depending on P supply. A glasshouse trial was established to examine whether AM density might also have an important influence on these growth responses. Mycorrhizal spores (Glomus clarum), isolated from a long-term cane block in northern Queensland, were introduced into a pasteurised low-P cane soil at 5 densities (0, 0.06, 0.25, 1, 4 spores/g soil) and with 4 P treatments (0, 8.2, 25, and 47 mg/kg). At 83 days after planting, sugarcane tops responded positively to P fertilizer, although responses attributable to spore density were rarely observed. In one case, addition of 4 spores/g led to a 53% yield response over those without AM at 8 mgP/kg, or a relative benefit of 17 mg P/kg. Root colonisation was reduced for plants with nil or 74 mg P/kg. For those without AM, P concentration in the topmost visible dewlap (TVD) leaf increased significantly with fertiliser P (0.07 v. 0.15%). However, P concentration increased further with the presence of AM spores. Irrespective of AM, the critical P concentration in the TVD leaf was 0.18%. This study confirms earlier reports that sugarcane is poorly responsive to AM. Spore density, up to 4 spores/g soil, appears unable to influence this responsiveness, either positively or negatively. Attempts to gain P benefits by increasing AM density through rotation seem unlikely to lead to yield increases by sugarcane. Conversely, sugarcane grown in fields with high spore densities and high plant-available P, such as long-term cane-growing soils, is unlikely to suffer a yield reduction from mycorrhizal fungi.

An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [viz. S. pyramidalis P. Beauv., S. natalensis (Steud.) Dur and Schinz, S. fertilis (Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified polymorphic DNA (RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD profiling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51490 for S. pyramidalis and S. natalensis; UBC43310.2000.2100 for S. fertilis and S. africanus; and ORA20850 and UBC43470 for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the 'S. indicus complex'. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species (major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

Identification of quantitative trait loci for resistance to two species of root-lesion nematode (Pratylenchus thornei and P. neglectus) in wheat

Pratylenchus thornei and P. neglectus are two species of root-lesion nematode that cause substantial yield losses in wheat. No commercially available wheat variety has resistance to both species. A doubled-haploid population developed from a cross between the synthetic hexaploid wheat line CPI133872 and the bread wheat Janz was used to locate and tag quantitative trait loci (QTLs) associated with resistance to both P. thornei and P. neglectus. Wheat plants were inoculated with both species of nematode in independent replicated glasshouse trials repeated over 2 years. Known locations of wheat microsatellite markers were used to construct a framework map. After an initial single-marker analysis to detect marker-trait linkages, chromosome regions associated with putative QTLs were targetted with microsatellite markers to increase map density in the chromosome regions of interest. In total, 148 wheat microsatellite markers and 21 amplified fragment length polymorphism markers were mapped. The codominant microsatellite marker Xbarc183 on the distal end of chromosome 6DS was allelic for resistance to both P. thornei and P. neglectus. The QTL were designated QRlnt.lrc-6D.1 and QRlnn.lrc-6D.1, for the 2 traits, respectively. The allele inherited from CPI133872 explained 22.0-24.2% of the phenotypic variation for P. thornei resistance, and the allele inherited from Janz accounted for 11.3-14.0% of the phenotypic variation for P. neglectus resistance. Composite interval mapping identified markers that flank a second major QTL on chromosome 6DL (QRlnt.lrc-6D.2) that explained 8.3-13.4% of the phenotypic variation for P. thornei resistance. An additional major QTL associated with P. neglectus resistance was detected on chromosome 4DS (QRlnn.lrc-4D.1) and explained a further 10.3-15.4% of the phenotypic variation. The identification and tagging of nematode resistance genes with molecular markers will allow appropriate allele combinations to be selected, which will aid the successful breeding of wheat with dual nematode resistance.

Simple sequence repeat markers associated with three quantitative trait loci for black point resistance can be used to enrich selection populations in bread wheat

Black point in wheat has the potential to cost the Australian industry $A30.4 million a year. It is difficult and expensive to screen for resistance, so the aim of this study was to validate 3 previously identified quantitative trait loci (QTLs) for black point resistance on chromosomes 2B, 4A, and 3D of the wheat variety Sunco. Black point resistance data and simple sequence repeat (SSR) markers, linked to the resistance QTLs and suited to high-throughput assay, were analysed in the doubled haploid population, Batavia (susceptible) × Pelsart (resistant). Sunco and Pelsart both have Cook in their pedigree and both have the Triticum timopheevii translocation on 2B. SSR markers identified for the 3 genetic regions were gwm319 (2B, T. timopheevii translocation), wmc048 (4AS), and gwm341 (3DS). Gwm319 and wmc048 were associated with black point resistance in the validation population. Gwm341 may have an epistatic influence on the trait because when resistance alleles were present at both gwm319 and wmc048, the Batavia-derived allele at gwm341 was associated with a higher proportion of resistant lines. Data are presented showing the level of enrichment achieved for black point resistance, using 1, 2, or 3 of these molecular markers, and the number of associated discarded resistant lines. The level of population enrichment was found to be 1.83-fold with 6 of 17 resistant lines discarded when gwm319 and wmc048 were both used for selection. Interactions among the 3 QTLs appear complex and other genetic and epigenetic factors influence susceptibility to black point. Polymorphism was assessed for these markers within potential breeding material. This indicated that alternative markers to wmc048 may be required for some parental combinations. Based on these results, marker-assisted selection for the major black point resistance QTLs can increase the rate of genetic gain by improving the selection efficiency and may facilitate stacking of black point resistances from different sources.