Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.” Abstract Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

New strawberry breeding lines – Enhanced phytochemical composition and bioaccessibility

Screening of phytochemicals has been of interest in strawberry genotypes as there is emerging evidence from epidemiological and clinical studies that consumption of phytochemical-rich strawberry cultivars may provide health benefits. The aim of the present study was (1) to quantify selected phytochemicals in new strawberry breeding lines (BL) and (2) to assess the in vitro bioaccessibility of phytochemicals as an initial measure to predict their bioavailability.

Commercial-scale Alternaria brown spot resistance screening as the first step in breeding new mandarins for Australia

Rapid screening tests and an appreciation of the simple genetic control of Alternaria brown spot (ABS) susceptibility have existed for many years, and yet the application of this knowledge to commercial-scale breeding programs has been limited. Detached leaf assays were first demonstrated more than 40 years ago and reliable data suggesting a single gene determining susceptibility has been emerging for at least 20 years. However it is only recently that the requirement for genetic resistance in new hybrids has become a priority, following increased disease prevalence in Australian mandarin production areas previously considered too dry for the pathogen. Almost all of the high-fruit-quality parents developed so far by the Queensland-based breeding program are susceptible to ABS necessitating the screening of their progeny to avoid commercialisation of susceptible hybrids. This is done effectively and efficiently by spraying 3-6 month old hybrid seedlings with a spore suspension derived from a toxin-producing field isolate of Alternaria alternate, then incubating these seedlings in a cool room at 25°C and high humidity for 5 days. Susceptible seedlings show clear disease symptoms and are discarded. Analysis of observed and expected segregation ratios loosely support the hypothesis for a single dominant gene for susceptibility, but do not rule out the possibility of alternative genetic models. After implementing the routine screening for ABS resistance for three seasons we now have more than 20,000 hybrids growing in field progeny blocks that have been screened for resistance to the ABS disease.

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.

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.

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.

Pollinator limitation and the effect of breeding systems on plant reproduction in forest fragments

Reproduction of plants in fragmented habitats may be limited because of lower diversity or abundance of pollinators, and/or variation in local plant density. We assessed natural fruit set and pollinator limitation in ten species of woody plants in natural and restored fragments in the Pondicherry region of southern India, to see whether breeding system of plants (self-compatible and self-incompatible) affected fruit set. We tested whether the number of flowering individuals in the fragments affected the fruit set and further examined the adult and sapling densities of self-compatible (SC) and self-incompatible (SI) species. We measured the natural level of fruit set and pollinator limitation (calculated as the difference in fruit set between hand cross-pollinated and naturally pollinated flowers). Our results demonstrate that there was a higher level of pollinator limitation and hence lower levels of natural fruit set in self-incompatible species as compared to self-compatible species. However, the hand cross-pollinated flowers in SC and SI species produced similar levels of fruit set,further indicating that lower fruit set was due to pollinator limitation and not due to lack of cross-compatible individuals in the fragments. There was no significant relation between number of flowering individuals and the levels of natural fruit set, except for two species Derris ovalifolia, Ixora pavetta. In these species the natural fruit set decreased with increasing population size, again indicating pollinator limitation. The adult and sapling densities in self-compatible species were significantly higher than inself-incompatible species. These findings indicate that the low reproductive output in self-incompatible species may eventually lead to lower population sizes. Restoration of pollinator services along with plant species in fragmented habitats is important for the long-term conservation of biodiversity. (C) 2009 Elsevier Masson SAS. All rights reserved.