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Integrated disease management of cereals through development of tolerance in wheat. - IF01118

The challenge of increasing production of food and fuel, whilst reducing environmental impact, can only be achieved by making more efficient use of resources – particularly land, nitrogen and water. Preventing waste and losses caused by crop diseases is essential for efficient resource use and to minimise greenhouse gas emissions per unit of production. Disease control depends predominantly on fungicide treatment and breeding crop varieties which are resistant to disease. However, pathogens constantly evolve new insensitive and virulent strains to overcome fungicides and resistance. The development of crop varieties which are more tolerant of disease would complement host resistance and chemical control as part of a durable integrated control strategy.
Disease tolerance is the heritable capacity of a crop to maintain yield in the presence of disease - tolerant varieties lose less yield to important foliar pathogens, per unit of leaf area affected by symptoms. Tolerance has declined in UK wheat varieties introduced over recent decades, which has contributed to the upward pressure on fungicide use. Indirect selection in plant breeding programmes for ‘source’ and ‘sink’ traits associated with high fungicide-treated yield appears to have selected against tolerance (where source is the capacity of the crop to produce carbohydrate and protein, and sink is the capacity to store these products in the grain). However, recent evidence in wheat has shown that the general association between high yield potential and low tolerance is not due to an inevitable genetic or physiological linkage, so it should be possible to produce varieties which are both high yielding and disease tolerant.

The objectives and methods of the proposed project are:
Objective 1: Identify sources of tolerance to major diseases in UK-adapted cereal germplasm.
Wheat varieties and lines from a wide gene pool will be screened for tolerance in field experiments in years 1 and 2. The breeding programme for resource-poor countries at The International Centre for Maize and Wheat Improvement (CIMMYT) in Mexico selects for high yield in the absence of fungicide treatment, which selects indirectly for varieties with disease resistance and tolerance. So the germplasm tested will include lines, which are adapted to UK conditions, selected from progeny of crosses between wheat from the CIMMYT programme and UK wheat. Progeny from crosses between UK varieties known to contrast in tolerance will also be tested, together with varieties known to contain segments of chromosomes from wild grass relatives (introduced by conventional plant breeding methods). The latter will serve to identify wheat parents (and hence mapping populations) contrasting for tolerance.

Objective 2: Screen for tolerance traits in promising crosses identified in objective 1, using phenotypic and genotypic analysis.
The wheat lines which contrast most for tolerance (objective 1) will be studied in field experiments in year 3, to identify traits which are associated with good tolerance and high yield potential. The effects of these individual traits and trait combinations will be explored by mathematical modelling, to check that traits are associated with tolerance by physiological mechanisms, not just by random chance. Using the model, combinations of traits can be explored that maximise tolerance with a minimal effect on potential yield. In year 4, the traits associated with tolerance will be phenotyped in large numbers of wheat lines in the most promising mapping population according to results in years 1 to 3, to identify locations on chromosomes (quantitative trait loci; QTL) associated with high expression of each trait. QTL can ultimately be used by plant breeders to select for desirable traits.

Objective 3: Assess the benefit of tolerance deployment on durability of disease control within an integrated system. Work packages will quantify the impact of tolerance on: (i) fungicide use under varying seasonal disease pressure and host resistance, (ii) the economic and environmental benefits of disease prediction schemes, and (iii) its effect on pathogen adaptation and hence its effect on the sustainability of disease control.

The work will integrate with research at institutes in Ireland and France, and will utilise expertise and germplasm from UK plant breeders. The main deliverables from the project will be identification of the key physiological traits which determine disease tolerance in high-yielding, UK-adapted germplasm, and evidence for the impact of tolerance deployment as part of an integrated disease control strategy. Uptake from the project into pre-competitive industry/government funded research and breeding programmes will be underpinned by identification of QTL for the key traits and wheat lines expressing the key traits to a high degree. Crop varieties with improved tolerance would result in: (i) a more sustainable balance between disease control by crop genetic improvement and by fungicides, and (ii) improved economic and carbon efficiency. There is evidence that tolerance is effective against a range of pathogen species, so the work will help to 'future proof' against new disease threats resulting from climate change.
7. (b) Objectives

The three objectives below are as stated in the Defra Project Specification. This section gives a short overview of the aims (expressed as hypotheses to be tested) and approaches within each objective. The rationale, materials and methods, timescale and deliverables of each work package are then described in detail in the following sections.

Objective 1: Identify sources of tolerance to major diseases in UK-adapted cereal germplasm

Work package 1(i): Tolerance screen of UK adapted (day-length sensitive) wheat lines derived from CIMMYT x UK parents, and from parents known to contrast for tolerance.
Hypothesis: Germplasm selected for yield in the absence of fungicide treatment will be more tolerant than cultivars selected for yield with treatment (which is normal practice in UK wheat breeding) and can act as a source for introgression of tolerance traits into UK wheat.

Work package 1(ii): Tolerance screen of UK adapted wheat parents of existing mapping populations, including parents known to be derived from ‘wide’ crosses and parents containing alien segments of chromosome from wild relatives.
Hypothesis: Crosses between diverse wheat parents will generate progeny with wider tolerance variation than the limited range of wheat lines tested for tolerance previously.

Work package 1(iii): Test the potential for PCR-based quantification of tolerance.

Objective 2: Screen for tolerance traits in promising crosses identified in objective 1, using phenotypic and genotypic analysis

Sub-objective 2a: Identify tolerance traits compatible with high yield, by phenotypic analysis
Work package 2(i): Quantification of candidate tolerance traits, by detailed growth analysis of wheat lines (identified in work package 1(i)) contrasting strongly for tolerance.
Hypothesis: Genetic variation in sub-traits related to source (HAD) and sink capacity can be exploited to select for tolerance traits compatible with high yield.

Work package 2(ii): Corroborate traits found to be correlated with tolerance in experiments, by mechanistic mathematical modelling.
Hypothesis: Disease tolerance is determined by a balanced combination of physiological traits. Physiological modelling based on experimental data can help to identify optimal trait combinations, which are compatible with high yield in the absence of disease

Sub-objective 2b: Associate tolerance traits with quantitative trait loci (QTL)
Work package 2(iii): Phenotype corroborated tolerance traits in large numbers of wheat lines, to identify QTL.

Objective 3: Assess the benefit of tolerance deployment on durability of disease control within an integrated system

Work package 3(i): Quantify the impact of tolerance on fungicide use under varying seasonal disease pressure and host resistance
Hypothesis: Tolerance will reduce the need for growers to be ‘risk averse’ in their fungicide treatment decisions, thus reducing over-treatment.

Work package 3(ii): Quantify the impact of tolerance on the economic and environmental benefits of disease prediction schemes.
Hypothesis: Tolerance will increase the value of disease prediction (which may seem counter-intuitive), by reducing the adverse consequences of false negative predictions.

Work package 3(iii): Quantify the impact of tolerance on pathogen evolution and hence on the sustainability of disease control
Hypothesis: Tolerance will benefit durability of host resistance, by making the use of partial resistance more acceptable, and slow selection for fungicide insensitivity, thus prolonging the life of modes of action.

Time-Scale and Cost
From: 2011

To: 2015

Cost: £653,474
Contractor / Funded Organisations
University of Nottingham, Rothamsted Research (BBSRC), A D A S UK Ltd (ADAS), SAC Commercial Ltd
Sustainable Farming Systems