Genetic differentiation analysis for the identification of complementary parental pools for sorghum hybrid breeding in Ethiopia

Key message The potential for exploiting heterosis for sorghum hybrid production in Ethiopia with improved local adaptation and farmers preferences has been investigated and populations suitable for initial hybrid development have been identified. Abstract Hybrids in sorghum have demonstrated increased productivity and stability of performance in the developed world. In Ethiopia, the uptake of hybrid sorghum has been limited to date, primarily due to poor adaptation and absence of farmer’s preferred traits in existing hybrids. This study aimed to identify complementary parental pools to develop locally adapted hybrids, through an analysis of whole genome variability of 184 locally adapted genotypes and introduced hybrid parents (R and B). Genetic variability was assessed using genetic distance, model-based STRUCTURE analysis and pair-wise comparison of groups. We observed a high degree of genetic similarity between the Ethiopian improved inbred genotypes and a subset of landraces adapted to lowland agro-ecology with the introduced R lines. This coupled with the genetic differentiation from existing B lines, indicated that these locally adapted genotype groups are expected to have similar patterns of heterotic expression as observed between introduced R and B line pools. Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most divergent from introduced B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland-adapted genotypes, indicating the potential for increased heterotic response of their hybrids. However, these groups were also differentiated from the R lines, and hence are different from the existing complementary heterotic pools. This suggests that although these groups could provide highly divergent parental pools, further research is required to investigate the extent of heterosis and their hybrid performance.

Pre-emptive breeding to combine superior eating quality in tropical super sweet corn with resistance to major diseases

This report presents the process and outcomes of a five year project, which employed genetics and breeding approach for integrating disease resistance,agronomy and quality traits that enhances sustainable productivity improvement in sweet corn production. The report outlines a molecular markers based approach to introgress quantitative traits loci that are believed to contribute to resistance to downy mildew, a potentially devastating disease that threatens sweet corn and other similar crops. It also details the approach followed to integrate resistances for other major diseases such as southern rust (caused by Puccinia polysora Underw), Northern Corn Leaf Blight (Exserohilum turcicum) with improved agronomy and eating quality. The report explains the importance of heterosis (hybrid vigour) and combining ability in the development of useful sweet corn hybrids. It also explains the relevance of parental performance to predict its breeding value and the performance of its hybrids.

Sugarcane productivity response to different fallow and soybean residue management practices in the Bundaberg district

GRAIN LEGUME ROTATIONS underpin the sustainability of the Australian sugarcane farming system, offering a number of soil health and environmental benefits. Recent studies have highlighted the potential for these breaks to exacerbate nitrous oxide (N2O) emissions. An experiment was implemented in 2012 to evaluate the impact of two fallow management options (bare fallow and soybean break crop) and different soybean residue management practices on N2O emissions and sugarcane productivity. The bare fallow plots were conventionally tilled, whereas the soybean treatments were either tilled, not tilled, residue sprayed with nitrification inhibitor (DMPP) prior to tillage or had a triticale ‘catch crop’ sown between the soybean and sugarcane crops. The fallow plots received either no nitrogen (N0) or fully fertilised (N145) whereas the soybean treatments received 25 kg N/ha at planting only. The Fallow N145 treatment yielded 8% more cane than the soybean tilled treatment. However there was no statistical difference in sugar productivity. Cane yield was correlated with stalk number that was correlated to soil mineral nitrogen status in January. There was only 30% more N/ha in the above-ground biomass between the Fallow N145 and the Fallow N0 treatment; highlighting poor fertiliser nitrogen use efficiency. Supplying adequate nitrogen to meet productivity requirements without causing environmental harm remains a challenge for the Australian sugar industry. The soybean direct drill treatment significantly reduced N2O emissions and produced similar yields and profitability to the soybean tilled treatment (outlined in a companion paper by Wang et.al. in these proceedings). Furthermore, this study has highlighted that the soybean direct drill technique provides an opportunity to enable grain legume cropping in the sugarcane farming system to capture all of the soil health/environmental benefits without exacerbating N2O emissions from Australian sugarcane soils.

Soybean rotation and crop residue management to reduce nitrous oxide emissions from sugarcane soils

NITROUS OXIDE (N2O) IS a potent greenhouse gas and the predominant ozone-depleting substance in the atmosphere. Agricultural nitrogenous fertiliser use is the major source of human-induced N2O emissions. A field experiment was conducted at Bundaberg from October 2012 to September 2014 to examine the impacts of legume crop (soybean) rotation as an alternative nitrogen (N) source on N2O emissions during the fallow period and to investigate low-emission soybean residue management practices. An automatic monitoring system and manual gas sampling chambers were used to measure greenhouse gas emissions from soil. Soybean cropping during the fallow period reduced N2O emissions compared to the bare fallow. Based on the N content in the soybean crop residues, the fertiliser N application rate was reduced by about 120 kg N/ha for the subsequent sugarcane crop. Consequently, emissions of N2O during the sugarcane cropping season were significantly lower from the soybean cropped soil than those from the conventionally fertilised (145 kg N/ha) soil following bare fallow. However, tillage that incorporated the soybean crop residues into soil promoted N2O emissions in the first two months. Spraying a nitrification inhibitor (DMPP) onto the soybean crop residues before tillage effectively prevented the N2O emission spikes. Compared to conventional tillage, practising no-till with or without growing a nitrogen catch crop during the time after soybean harvest and before cane planting also reduced N2O emissions substantially. These results demonstrated that soybean rotation during the fallow period followed with N conservation management practices could offer a promising N2O mitigation strategy in sugarcane farming. Further investigation is required to provide guidance on N and water management following soybean fallow to maintain sugar productivity.

High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Water availability is a major limiting factor for wheat (Triticum aestivum L.) in rain-fed agricultural systems worldwide. Root architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root traits in wheat breeding programs has been largely limited due to the lack of suitable phenotyping methods. The aim of this research was to develop a low-cost high-throughput phenotyping method to facilitate selection for desirable root traits. We developed a method to assess ‘seminal root angle’ and ‘seminal root number’ in seedlings – two proxy traits associated to root architecture of mature wheat plants (1). The method involves measuring the angle between the first pair of seminal roots and the number of roots of wheat seedlings grown in transparent pots (Figure 1). Images captured at 5 to 10 days after sowing are analyzed to calculate seminal root angle and number. Performing this technique under “speed breeding” conditions (plants grown at a density of 600 plants / m2, under controlled temperature and constant light) allows the selection based on the desired root traits of up to 5 consecutive generations within 12 months. Alternatively, when focusing only on germplasm screening, up to 52 successive phenotypic assays can be conducted within 12 months. This approach has been shown to be highly reproducible, it requires little resource (time, space, and labour) and can be used to rapidly enrich breeding populations with desirable alleles for narrow root angle and a high number of seminal roots to indirectly target the selection of deeper root system with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with the climate model projections, especially in summer rainfall dominant regions including some Australian, Indian, South American and African cropping regions, where winter crops mainly rely on deep stored water.

Integrating Rapid Phenotyping and Speed Breeding to Improve Stay-Green and Root Adaptation of Wheat in Changing, Water-Limited, Australian Environments

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons. A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to be quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland “speed breeding” method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in bi-parental populations and to identify novel QTL for stay-green and root traits. We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments.

Strategies to limit the impact of nematode pressure on sugarcane productivity in the Isis

Two trials were done in this project. One was a continuation of work started under a previous GRDC/SRDC-funded activity, 'Strategies to improve the integration of legumes into cane based farming systems'. This trial aimed to assess the impact of trash and tillage management options and nematicide application on nematodes and crop performance. Methods and results are contained in the following publication: Halpin NV, Stirling GR, Rehbein WE, Quinn B, Jakins A, Ginns SP. The impact of trash and tillage management options and nematicide application on crop performance and plant-parasitic nematode populations in a sugarcane/peanut farming system. Proc. Aust. Soc. Sugar Cane Technol. 37, 192-203. Nematicide application in the plant crop significantly reduced total numbers of plant parasitic nematodes (PPN) but there was no impact on yield. Application of nematicide to the ratoon crop significantly reduced sugar yield. The study confirmed other work demonstrating that implementation of strategies like reduced tillage reduced populations of total PPN, suggesting that the soil was more suppressive to PPN in those treatments. The second trial, a variety trial, demonstrated the limited value of nematicide application in sugarcane farming systems. This study has highlighted that growers shouldn’t view nematicides as a ‘cure all’ for paddocks that have historically had high PPN numbers. Nematicides have high mammalian toxicity, have the potential to contaminate ground water (Kookana et al. 1995) and are costly. The cost of nematicide used in R1 was approx. $320 - $350/ha, adding $3.50/t of cane in a 100 t/ha crop. Also, our study demonstrated that a single nematicide treatment at the application rate registered for sugarcane is not very effective in reducing populations of nematode pests. There appears to be some levels of resistance to nematodes within the current suite of varieties available to the southern canelands. For example the soil in plots that were growing Q183 had 560% more root knot nematodes / 200mL soil compared to plots that grew Q245. The authors see great value in investment into a nematode screening program that could rate varieties into groups of susceptibility to both major sugarcane nematode pests. Such a rating could then be built into a decision support ‘tree’ or tool to better enable producers to select varieties on a paddock by paddock basis.

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.