Genetic characterization of root architectural traits in barley (Hordeum vulgare L.) using SNP markers.

Increasing attention is paid to providing new tools to breeders for targeted breeding for specific root traits that are beneficial in low-fertility, drying soils; however, such information is not available for barley (Hordeum vulgare L.). A panel of 191 barley accessions (originating from Australia, Europe, and Africa) was phenotyped for 26 root and shoot traits using the semi-hydroponic system and genotyped using 21 062 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS). The population structure analysis of the barley panel identified six distinct groups. We detected 1199 significant (P<0.001) marker-trait associations (MTAs) with r2 values up to 0.41. The strongest MTAs were found for root diameter in the top 20 cm and the longest root length. Based on the physical locations of these MTAs in the barley reference genome, we identified 37 putative QTLs for the root traits, and three QTLs for shoot traits, with nine QTLs located in the same physical regions. The genomic region 640-653 Mb on chromosome 7H was significant for five root length-related traits, where 440 annotated genes were located. The putative QTLs for various root traits identified in this study may be useful for genetic improvement regarding the adaptation of new barley cultivars to suboptimal environments and abiotic stresses.

Development of a novel semi-hydroponic phenotyping system for studying root architecture.

A semi-hydroponic bin system was developed to provide an efficient phenotyping platform for studying root architecture. The system was designed to accommodate a large number of plants in a small area for screening genotypes. It was constructed using inexpensive and easily obtained materials: 240L plastic mobile bins, clear acrylic panels covered with black calico cloth and a controlled watering system. A screening experiment for root traits of 20 wild genotypes of narrow-leafed lupin (Lupinus angustifolius L.) evaluated the reliability and efficiency of the system. Root architecture, root elongation rate and branching patterns were monitored for 6 weeks. Significant differences in both architectural and morphological traits were observed among tested genotypes, particularly for total root length, branch number, specific root length and branch density. Results demonstrated that the bin system was efficient in screening root traits in narrow-leafed lupin, allowing for rapid measurement of two-dimensional root architecture over time with minimal disturbance to plant growth and without destructive root sampling. The system permits mapping and digital measurement of dynamic growth of taproot and lateral roots. This phenotyping platform is a desirable tool for examining root architecture of deep root systems and large sets of plants in a relatively small space.

Forecasting aphid outbreaks and epidemics of Cucumber mosaic virus in lupin crops in a Mediterranean-type environment.

Cucumber mosaic virus (CMV) causes a serious disease of narrow-leafed lupin (Lupinus angustifolius). It is seed-borne in lupin and seed-infected plants act as the primary virus source for secondary spread by aphid vectors within crops. Infection with CMV causes yield losses of up to 60% in epidemic years, but has little impact on yield in years when spread is limited. Aphids also cause sporadic yield losses due to direct feeding damage. A simulation model was developed to forecast aphid outbreaks and epidemics of CMV in lupin crops growing in the 'grainbelt' of south-west Australia, which has a Mediterranean-type climate. The model uses rainfall during summer and early autumn to calculate an index of aphid build-up on weeds, crop volunteers and self-regenerating annual pastures in each 'grainbelt' locality before the growing season commences in late autumn. The index is used to forecast the timing of aphid immigration into crops. The subsequent aphid build-up and movement within the crop, spread of CMV from virus-infected source plants within the crop, yield losses and percentage of harvested seed-infected are then calculated. The model evaluates the effects of different sowing dates, percentages of CMV infection in seed sown and plant population densities on virus spread. The model simulations were validated with 14 years' field data from six different sites in the 'grainbelt', representing a wide range of pre-growing season rainfall scenarios, sowing dates, percentages of infection in seed sown and plant population densities. The model was incorporated into a decision support system (DSS) for use by lupin farmers and agricultural consultants in planning CMV management and targeting sprays against aphids to prevent direct feeding damage. The inputs required from the user are lupin cultivar, anticipated emergence date, percentage CMV infection in seed sown, plant density and location. The output consists of a personalised risk forecast for the user and includes predictions for date of first aphid arrival, aphid numbers, CMV spread, final virus incidence, yield loss due to infection and percentage infection in harvested seed. Predictions from the DSS are accessible via an Internet site and from other information sources. The model can serve as a template for modelling similar virus/aphid vector pathosystems in other regions of the world, especially those with Mediterranean-type climates.

Modeling the Risk of Entry, Establishment, Spread, Containment, and Economic Impact of Tilletia indica, the Cause of Karnal Bunt of Wheat, Using an Australian Context.

ABSTRACT Modeling techniques were developed to quantify the probability of Tilletia indica entering and establishing in Western Australia (WA), and to simulate spread, containment, and the economic impact of the pathogen. Entry of T. indica is most likely to occur through imports of bulk grain or fertilizer (0.023 +/- 0.017 entries per year and approximately 0.009 +/- 0.009 establishments per year). Entry may also occur through straw goods, new or second-hand agricultural machinery, and on personal effects of travelers who have visited regions with infected plants. The combined probability of entry and establishment of T. indica, for all pathways of entry, is about one entry every 25 years and one establishment every 67 years. Alternatively, sensitivity analysis does show that increases in quarantine funding can reduce the probability of entry to about one entry every 50 years and less than one establishment every 100 years. T. indica is spread efficiently through contaminated farm machinery, seed and soil, rain, air currents, and animals. Depending on the rate of spread of the pathogen and the amount of resources allocated for detection, the time until first detection could range from 4 to 11 years and the economic impact could range from 8 to 24% of the total value of wheat production in WA.