Synthetic Evaluation Project - Nematodes

The project tests synthetic hexaploid wheats for resistance to root-lesion nematodes.

DAN00094 Australian chickpea breeding program

To develop new, high yielding, desi chickpea varieties with improved resistance to Ascochya Blight and Phtyophthora Root Rot.

Isohydric and anisohydric characterisation of vegetable crops. The classification of vegetables by their physiological responses to water stress

Research on the physiological response of crop plants to drying soils and subsequent water stress has grouped plant behaviours as isohydric and anisohydric. Drying soil conditions, and hence declining soil and root water potentials, cause chemical signals—the most studied being abscisic acid (ABA)—and hydraulic signals to be transmitted to the leaf via xylem pathways. Researchers have attempted to allocate crops as isohydric or anisohydric. However, different cultivars within crops, and even the same cultivars grown in different environments/climates, can exhibit both response types. Nevertheless, understanding which behaviours predominate in which crops and circumstances may be beneficial. This paper describes different physiological water stress responses, attempts to classify vegetable crops according to reported water stress responses, and also discusses implications for irrigation decision-making.

Phosphonate applied as a pre-plant dip controls Phytophthora cinnamomi root and heart rot in susceptible pineapple hybrids.

The effectiveness of pre-plant dips of crowns in potassium phosphonate and phosphorous acid was investigated in a systematic manner to develop an effective strategy for the control of root and heart rot diseases caused by Phytophthora cinnamomi in the pineapple hybrids 'MD2' and '73-50' and cultivar Smooth Cayenne. Our results clearly indicate that a high volume spray at planting was much less effective when compared to a pre-plant dip. 'Smooth Cayenne' was found to be more resistant to heart rot than 'MD2' and '73-50', and 'Smooth Cayenne' to be more responsive to treatment with potassium phosphonate. Based on cumulative heart rot incidence over time 'MD2' was more susceptible to heart rot than '73-50' and was more responsive to an application of phosphorous acid. The highest levels of phosphonate in roots were reached one month after planting and levels declined during the next two months. Pre-plant dipping of crowns prior to planting is highly effective to control root and heart rot in the first few months but is not sufficient to maintain health of the mother plant root system up until plant crop harvest when weather conditions continue to favour infection.

Molecular genetics of primary open angle glaucoma and exfoliation syndrome

Glaucoma is the second leading cause of blindness worldwide. It is a group of optic neuropathies, characterized by progressive optic nerve degeneration, excavation of the optic disc due to apoptosis of retinal ganglion cells and corresponding visual field defects. Open angle glaucoma (OAG) is a subtype of glaucoma, classified according to the age of onset into juvenile and adult- forms with a cut-off point of 40 years of age. The prevalence of OAG is 1-2% of the population over 40 years and increases with age. During the last decade several candidate loci and three candidate genes, myocilin (MYOC), optineurin (OPTN) and WD40-repeat 36 (WDR36), for OAG have been identified. Exfoliation syndrome (XFS), age, elevated intraocular pressure and genetic predisposition are known risk factors for OAG. XFS is characterized by accumulation of grayish scales of fibrillogranular extracellular material in the anterior segment of the eye. XFS is overall the most common identifiable cause of glaucoma (exfoliation glaucoma, XFG). In the past year, three single nucleotide polymorphisms (SNPs) on the lysyl oxidase like 1 (LOXL1) gene have been associated with XFS and XFG in several populations. This thesis describes the first molecular genetic studies of OAG and XFS/XFG in the Finnish population. The role of the MYOC and OPTN genes and fourteen candidate loci was investigated in eight Finnish glaucoma families. Both candidate genes and loci were excluded in families, further confirming the heterogeneous nature of OAG. To investigate the genetic basis of glaucoma in a large Finnish family with juvenile and adult onset OAG, we analysed the MYOC gene in family members. Glaucoma associated mutation (Thr377Met) was identified in the MYOC gene segregating with the disease in the family. This finding has great significance for the family and encourages investigating the MYOC gene also in other Finnish OAG families. In order to identify the genetic susceptibility loci for XFS, we carried out a genome-wide scan in the extended Finnish XFS family. This scan produced promising candidate locus on chromosomal region 18q12.1-21.33 and several additional putative susceptibility loci for XFS. This locus on chromosome 18 provides a solid starting point for the fine-scale mapping studies, which are needed to identify variants conferring susceptibility to XFS in the region. A case-control and family-based association study and family-based linkage study was performed to evaluate whether SNPs in the LOXL1 gene contain a risk for XFS, XFG or POAG in the Finnish patients. A significant association between the LOXL1 gene SNPs and XFS and XFG was confirmed in the Finnish population. However, no association was detected with POAG. Probably also other genetic and environmental factors are involved in the pathogenesis of XFS and XFG.

Multiple host use by a sap-sucking membracid: population consequences of nymphal development on primary and secondary host plant species

Aconophora compressa is a gregarious, sap-sucking insect that uses multiple host plant species. Nymphal host plant species (and variety) significantly affected nymphal survival, nymphal development rate and the subsequent size and fecundity of adults, with fiddlewood ( Citharexylum spinosum ) being significantly best in all respects. Nymphs that developed on a relatively poor host ( Duranta erecta var “geisha girl”) and which were moved to fiddlewood as adults laid significantly fewer eggs (mean ± SE = 836 ± 130) than those that developed solely on fiddlewood (1,329 ± 105). Adults on geisha girl, regardless of having been reared as nymphs on fiddlewood or geisha girl, laid significantly fewer eggs (342 ± 83 and 317 ± 74, respectively) than adults on fiddlewood. A simple model that incorporates host plant related survival, development rate and fecundity suggests that the population dynamics of A. compressa are governed mainly by fiddlewood, the primary host. The results have general implications for understanding the population dynamics of herbivores that use multiple host plant species, and also for the way in which weed biological control host testing methods should be conducted.

Quality Assessment of a Forest Inventory Based on Airborne Laser Scanning

In this study, a quality assessment method based on sampling of primary laser inventory units (microsegments) was analysed. The accuracy of a laser inventory carried out in Kuhmo was analysed as a case study. Field sample plots were measured on the sampled microsegments in the Kuhmo inventory area. Two main questions were considered. Did the ALS based inventory meet the accuracy requirements set for the provider and how should a reliable, cost-efficient and independent quality assessment be undertaken. The agreement between control measurement and ALS based inventory was analysed in four ways: 1) The root mean squared errors (RMSEs) and bias were calculated. 2) Scatter plots with 95% confidence intervals were plotted and the placing of identity lines was checked. 3) Bland-Altman plots were drawn so that the mean difference of attributes between the control method and ALS-method was calculated and plotted against average value of attributes. 4) The tolerance limits were defined and combined with Bland-Altman plots. The RMSE values were compared to a reference study from which the accuracy requirements had been set to the service provider. The accuracy requirements in Kuhmo were achieved, however comparison of RMSE values proved to be difficult. Field control measurements are costly and time-consuming, but they are considered to be robust. However, control measurements might include errors, which are difficult to take into account. Using the Bland-Altman plots none of the compared methods are considered to be completely exact, so this offers a fair way to interpret results of assessment. The tolerance limits to be set on order combined with Bland-Altman plots were suggested to be taken in practise. In addition, bias should be calculated for total area. Some other approaches for quality control were briefly examined. No method was found to fulfil all the required demands of statistical reliability, cost-efficiency, time efficiency, simplicity and speed of implementation. Some benefits and shortcomings of the studied methods were discussed.

Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time

Nested association mapping (NAM) offers power to dissect complex, quantitative traits. This study made use of a recently developed sorghum backcross (BC)-NAM population to dissect the genetic architecture of flowering time in sorghum; to compare the QTL identified with other genomic regions identified in previous sorghum and maize flowering time studies and to highlight the implications of our findings for plant breeding. A subset of the sorghum BC-NAM population consisting of over 1,300 individuals from 24 families was evaluated for flowering time across multiple environments. Two QTL analysis methodologies were used to identify 40 QTLs with predominately small, additive effects on flowering time; 24 of these co-located with previously identified QTL for flowering time in sorghum and 16 were novel in sorghum. Significant synteny was also detected with the QTL for flowering time detected in a comparable NAM resource recently developed for maize (Zea mays) by Buckler et al. (Science 325:714-718, 2009). The use of the sorghum BC-NAM population allowed us to catalogue allelic variants at a maximal number of QTL and understand their contribution to the flowering time phenotype and distribution across diverse germplasm. The successful demonstration of the power of the sorghum BC-NAM population is exemplified not only by correspondence of QTL previously identified in sorghum, but also by correspondence of QTL in different taxa, specifically maize in this case. The unification across taxa of the candidate genes influencing complex traits, such as flowering time can further facilitate the detailed dissection of the genetic control and causal genes.

Responses of tribolium castaneum to olfactory cues from cotton seeds, the fungi associated with cotton seeds, and cereals

We tested, in an olfactometer, whether or not Tribolium castaneum Herbst (Coleoptera: Tenebrionidae) responds preferentially to the volatiles that emanate from the fungi associated with cotton [Gossypium hirsutum L. (Malvaceae)] seed over those that emanate from cereals, because cereals are usually portrayed as the primary resources of these beetles. Pairwise comparisons were conducted between cotton seed, wheat (Triticum aestivum L.), and sorghum [Sorghum bicolor (L.) Moench] (both Poaceae); volatiles were tested from intact seeds and from both water and ethanol extracts. The results demonstrate that T. castaneum is attracted more strongly to cotton seeds with its lint contaminated with fungi, than to the conventional resources of this species (i.e., wheat and sorghum). Further tests prove that it is the fungus on the lint that produces the active volatiles, because the beetles did not respond to sterilized cotton lint (i.e., without the fungi typically associated with it when cotton seed is stored). Tests with five fungal cultures (each representing an unidentified species that was isolated from the field-collected cotton lint) were variable across the cultures, with only one of them being significantly attractive to the beetles. The others were not attractive and one may even have repulsed the beetles. The results are consistent with the beetles having a strong ecological association with fungi and suggest it would be worth investigating the ecology of T. castaneum from this perspective. © 2012 The Netherlands Entomological Society.

Characterization of north-eastern Australian environments using APSIM for increasing rainfed maize production

Recurring water stresses are a major risk factor for rainfed maize cropping across the highly diverse agro-ecological environments of Queensland (Qld) and northern New South Wales (NNSW). Enhanced understanding of such agro-ecological diversity is necessary to more consistently sample target production environments for testing and targeting release of improved germplasm, and to improve the efficiency of the maize pre-breeding and breeding programs of Qld and New South Wales. Here, we used the Agricultural Production Systems Simulator (APSIM) – a well validated maize crop model to characterize the key distinctive water stress patterns and risk to production across the main maize growing regions of Qld and NNSW located between 15.8° and 31.5°S, and 144.5° and 151.8°E. APSIM was configured to simulate daily water supply demand ratios (SDRs) around anthesis as an indicator of the degree of water stress, and the final grain yield. Simulations were performed using daily climatic records during the period between 1890 and 2010 for 32 sites-soils in the target production regions. The runs were made assuming adequate nitrogen supply for mid-season maize hybrid Pioneer 3153. Hierarchical complete linkage analyses of the simulated yield resulted in five major clusters showing distinct probability distribution of the expected yields and geographic patterns. The drought stress patterns and their frequencies using SDRs were quantified using multivariate statistical methods. The identified stress patterns included no stress, mid-season (flowering) stress, and three terminal stresses differing in terms of severity. The combined frequency of flowering and terminal stresses was highest (82.9%), mainly in sites-soils combinations in the west of Qld and NNSW. Yield variability across the different sites-soils was significantly related to the variability in frequencies of water stresses. Frequencies of water stresses within each yield cluster tended to be similar, but different across clusters. Sites-soils falling within each yield cluster therefore could be treated as distinct maize production environments for testing and targeting newly developed maize cultivars and hybrids for adaptation to water stress patterns most common to those environments.

QTL for root angle and number in a population developed from bread wheats (Triticum aestivum) with contrasting adaptation to water-limited environments

Root architecture traits in wheat are important in deep soil moisture acquisition and may be used to improve adaptation to water-limited environments. The genetic architecture of two root traits, seminal root angle and seminal root number, were investigated using a doubled haploid population derived from SeriM82 and Hartog. Multiple novel quantitative trait loci (QTL) were identified, each one having a modest effect. For seminal root angle, four QTL (-log10(P) >3) were identified on 2A, 3D, 6A and 6B, and two suggestive QTL (-log10(P) >2) on 5D and 6B. For root number, two QTL were identified on 4A and 6A with four suggestive QTL on 1B, 3A, 3B and 4A. QTL for root angle and root number did not co-locate. Transgressive segregation was found for both traits. Known major height and phenology loci appear to have little effect on root angle and number. Presence or absence of the T1BL.1RS translocation did not significantly influence root angle. Broad sense heritability (h 2) was estimated as 50 % for root angle and 31 % for root number. Root angle QTL were found to be segregating between wheat cultivars adapted to the target production region indicating potential to select for root angle in breeding programs. © 2013 Springer-Verlag Berlin Heidelberg.

The critical role of extreme heat for maize production in the United States

Statistical studies of rainfed maize yields in the United States(1) and elsewhere(2) have indicated two clear features: a strong negative yield response to accumulation of temperatures above 30 degrees C (or extreme degree days (EDD)), and a relatively weak response to seasonal rainfall. Here we show that the process-based Agricultural Production Systems Simulator (APSIM) is able to reproduce both of these relationships in the Midwestern United States and provide insight into underlying mechanisms. The predominant effects of EDD in APSIM are associated with increased vapour pressure deficit, which contributes to water stress in two ways: by increasing demand for soil water to sustain a given rate of carbon assimilation, and by reducing future supply of soil water by raising transpiration rates. APSIM computes daily water stress as the ratio of water supply to demand, and during the critical month of July this ratio is three times more responsive to 2 degrees C warming than to a 20% precipitation reduction. The results suggest a relatively minor role for direct heat stress on reproductive organs at present temperatures in this region. Effects of elevated CO2 on transpiration efficiency should reduce yield sensitivity to EDD in the coming decades, but at most by 25%.