Progress 09/15/02 to 09/14/05
Outputs
The long-term goal of this project was to precisely characterize the nature of quantitative resistance in the barley/stripe rust system. Significant progress was made in answering two fundamental questions. 1. How does population size influence estimates of QTL number, effect, and interactions? The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible
parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods - resampling, selective genotyping, and selective phenotyping - to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping vs. phenotyping. 2. Are the same QTL associated with different components of resistance? As an intermediate step in the preparation of near-isogenic lines representing
individual QTL alleles and combinations of QTL alleles in a homogeneous genetic background, we developed a set of QTL introgression lines in a susceptible background. These intermediate barley near-isogenic (i-BISON) lines represent disease resistance QTL combined in one-, two-, and three-way combinations in a susceptible background. We measured five components of disease resistance on the i-BISON lines: latent period, infection efficiency, lesion size, pustule density, and speed of pustule formation. The most notable differences between the target QTL introgressions and the susceptible controls were infection efficiency, lesion size, pustule density, and speed of pustule formation. On average, the QTL introgressions had longer latent periods than the susceptible parent (Baronesse) did. They also had significantly more resistant differences than Baronesse for the other components. There were significant differences in magnitudes of effect of different QTL alleles. The 4H QTL allele
had the largest effect, followed by the alleles on 1H and 5H. Pyramiding multiple QTL alleles led to higher levels of resistance in terms of infection efficiency, lesion size, pustule density, and speed of pustule formation.
Impacts
This research will help plant breeders and pathologists to efficiently develop durably disease resistant crop varieties. Fungicides are useful in the battle against plant diseases, but the best defense is genetics. However, not all types of genetic resistance are equally effective. Plant disease resistance can be classified as qualitative or quantitative. Qualitative resistance leads to no disease symptoms and a false sense of security. The evolution of virulence in the pathogen population will almost certainly overcome whatever qualitative resistance is deployed. Quantitative resistance, on the other hand, can lead to a lasting peace. Quantitative resistance is more complicated to achieve, due to complex inheritance, but it is more durable. We have made significant contributions to identifying and using genes that confer quantitative resistance to barley stripe rust. We can now offer these genes, with the molecular breeding tools to rapidly cross them into susceptible
varieties, to the breeding community. Barley growers, processors, and consumers will benefit from the development of varieties with quantitative resistance to stripe rust. The results of our research can also serve as a model to breeders and consumers of all plants and plant products: barley explores the frontiers of science and other crops follow.
Publications
- Vales, M.I., C. C. Schon, F. Capettini, X. M. Chen, A. E. Corey, D. E. Mather, C. C. Mundt, K. L. Richardson, J. S. Sandoval-Islas, H. F. Utz, and P. M. Hayes. 2005. Effect of population size on the estimation of QTL: A test using resistance to barley stripe rust. Theor. Appl. Genet. In press.
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Progress 01/01/04 to 12/31/04
Outputs
The long-term goal of our project is to precisely characterize the nature of quantitative resistance in the barley/stripe rust system. Adult plant resistance was characterized using a population of 409 doubled haploid (DH) lines developed from the F1 of the cross of BCD47 (QR) and Baronesse (susceptible). QTL analyses were performed on these data using options available in QTL Cartographer. QTL x environment interaction was due to changes in magnitude of response and no QTL x QTL interaction was detected. BCD47 was the principal donor of BSR resistance QTL alleles, but Baronesse also contributed BSR resistance alleles, accounting for the presence of transgressive segregants. Subpopulations of different sizes were generated using three different methods: selective genotyping, selective phenotyping, and random sampling to evaluate the effect of population size in the estimation of QTL parameters. In all cases, the number of QTL increased as the population size
increased. The method of choice to select a smaller population for QTL studies will depend on the effort and cost balance between genotyping and phenotyping of a particular population for a particular trait. In general, the size of the population is more important than the number of evaluation environments in the estimation of QTL parameters. However, the use of environments that maximize the heritability of the trait is of crucial importance to maximize the number of QTL detected and the proportion of phenotypic variance explained. A manuscript will be submitted shortly. The second step in QTL characterization is construction of near-isogenic lines (the BISON) that allow for trait dissection and finer structure characterization. The target QTL regions are on chromosomes 1H, 4H ,and 5H. We have also created BISON for all possible combinations of QTL: 1Hx4H, 1Hx5H, 4Hx5H, and 1Hx4Hx5H. We also developed a separate germplasm construct for a major gene on chromosome 7H. The BISON lines
have been characterized in controlled environment experiments. Data analyses are in progress. Preliminary analysis of these data indicates correspondence between the seedling and adult stages, supporting our previous findings. We have increased the saturation of markers in the 4H QTL area thanks to a unique collaboration with our colleague Dr. Kazuhiro Sato, who is the leader of the Japanese Barley Genome Project, based at Okayama University. In this collaboration, we are engaged in the map-based cloning of rice blast resistance QTL that we have mapped in the ORO population. Via this collaboration, we have access to the barley and rice EST mapping data of the Japanese project. The germplasm for developing the breakpoint-NILs is at the F2 stage. Marker assisted selection on a large number of F2 lines will allow us to identify and select lines homozygous for the resistance donor allele (BCD47) for small sections of the broad QTL region.
Impacts
Stripe rust is a very serious threat to barley and wheat production throughout the United States. Genetic resistance is essential if farmers are to produce cereals in a sustainable and profitable fashion. The type of resistance we are working with, quantitative resistance, is more likely too be durable and effective than the single resistance genes that lead to boom and bust cycles of resistance and susceptibility. Our data will be an essential tool for dealing with fungal pathogens that are a major threat to American food security.
Publications
- No publications reported this period
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Progress 01/01/03 to 12/31/03
Outputs
This project is on schedule. We have genotyped and phenotyped a large (n = 409) doubled haploid population derived from the cross of BCD47 (quantitatively resistant to barley stripe rust) x Baronesse (susceptible to barley stripe rust). We have generated comprehensive linkage maps that have allowed us to map adult plant resistance QTL, test for QTL interactions, and empirically assess the role of population size in QTL detection. We are currently completing a manuscript summarizing this phase of the research and plan to submit in January, 2004. We are currently collaborating with Dr. Xianming Chen (WSU) on phenotyping seedling resistance in this population and we plan on submitting a paper on this research by summer, 2004. We have developed a set of 42 F6 near-isolines for the 1H, 4H, and 5H QTL regions, and for a qualitative resistance gene on 7H. We are still developing a set of near-isolines for a QTL on 2H were the susceptible parent contributes the resistance
allele. The QTL near- isolines represent the possible single, two-way, and three-way QTL allele combinations. We have measured resistance phenotypes of these near-isolines in preliminary field and controlled environment tests. We have genotyped the near-isolines with markers flanking each QTL region. We are currently using these near-isolines for addressing the question what are the average effects of resistance QTL alleles in a series of controlled environment tests in which we will measure components of quantitative resistance at the seedling and adult plant stages. We anticipate submitting a paper describing these experiments by summer, 2004. We have completed backcrosses of all the near-isolines to Baronesse to create truer isolines. We will perform background genotyping on these lines in order to select candidates with the highest proportion of recurrent parent genome. These candidates will be used as the platform for generating segmental isolines for each QTL region, the first
step towards map-based cloning. We have identified the syntenous regions of rice that correspond to the stripe rust QTL regions and we are mining the rice and barely EST databases for new markers to achieve marker saturation.
Impacts
Stripe rust is a very serious threat to barley and wheat production throughout the United States. Genetic resistance is essential if farmers are to produce cereals in a sustainable and profitable fashion. The type of resistance we are working with, quantitative resistance, is more likely too be durable and effective than the single resistance genes that lead to boom and bust cycles of resistance and susceptibility. Our data will be an essential tool for dealing with fungal pathogens that are a major threat to American food security.
Publications
- No publications reported this period
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Progress 09/15/02 to 12/01/02
Outputs
We have developed, genotyped, and phenotyped a large (n = 409) doubled haploid population derived from the cross of BCD47 (quantitatively resistant) and Baronesse (susceptible). We have generated genetic linkage maps for regions of the genome hypothesized to segregate for quantitative resistance alleles (on chromosomes 4H and 5H) and for regions of the genome where we have found resistance genes (quantitative and qualitative) in other germplasm combinations (chromosomes 1H, 2H,3H, 6H and 7H). We have phenotyped this population in four environments (Toulca, Mexico in 2001 and 2002; Mt. Vernon, WA, 2002; and Pullman, WA, 2002). Our preliminary QTL analyses reveal effects in all regions. We have developed a set of "quasi" isolines for the 1H, 4H, and 5H QTL regions, and for a qualitative resistance gene on 7H. These are "quasi" isolines in that they are homozygotes for the target region (as defined by flanking SSR markers) but they are still segregating in other,
untargeted regions of the genome. We have four lineages for each individual QTL and 1 - 3 lineages for each 2 and 3-QTL allele combination. We are selfing these plants to homozygosity, and using them to assess, in a preliminary fashion, the effects of each QTL resistance allele. We have four lineages representing the qualitative resistance allele in a Baronesse background.
Impacts
The results of this research will help plant breeders to more rapidly and efficiently develop crop varieties with durable resistance and plant pathologists to understand how this resistance operates. The benefit will be more productive and environmentally sound agriculture.
Publications
- No publications reported this period
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