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Crop Science 43:358-366 (2003)
© 2003 Crop Science Society of America

GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

Identification of Quantitative Trait Loci for Resistance to Crown Rust in Oat Line MAM17-5

S. Zhu and H. F. Kaeppler*

Plant Breeding and Plant Genetics Program, and Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706, USA

* Corresponding author (hfkaeppl{at}facstaff.wisc.edu)


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Crown rust, caused by the fungus Puccinia coronata Cda. f. sp. avenae Eriksson, is the most damaging disease of oat (Avena sativa L.). Breeding for resistance to crown rust has been an efficient and economical means to control the disease. Most of the resistance genes in recently released oat cultivars have been introgressed from the hexaploid, wild oat species A. sterilis L. The number of effective resistance genes has been rapidly decreasing. Characterization and utilization of new resistance sources are needed to ensure adequate resistance in future oat cultivars. Crown rust resistance in diploid, wild oat accessions was transferred to the hexaploid, cultivated oat line MAM17-5. The objective of this study was to identify the number, position, and effect of quantitative trait loci (QTL) and digenic QTL epistasis controlling crown rust resistance in MAM17-5. A linkage map of 272 molcular markers was used for this analysis. Reaction type and rust severity data were collected on field-grown adult plants from 152 F5:6 recombinant inbred lines derived from the cross, ‘Ogle’/MAM17-5. Composite interval mapping was conducted to identify genomic regions associated with crown rust resistance. Overall, two QTL, Pcq1 on linkage group 28 and Pcq2 on 29, were consistently identified for crown rust resistance in different years. Pcq1 and Pcq2 explained 48.5 to 70.1% and 9.6 to 14.0%, respectively, of the total phenotypic variation for crown rust resistance. Significant digenic, epistatic interactions were detected for QTL controlling rust severity but not reaction type. Marker-assisted selection targeting the major QTL, Pcq1, should be useful for efficient selection of crown rust resistance.

Abbreviations: AFLP, amplified fragment length polymorphism • CIM, composite interval mapping • LOD, log likelihood of odds • QxE, QTL x environment interaction • QTL, quantitative trait locus/loci • RFLP, restriction fragment length polymorphism • RIL, recombinant inbred line • SSR, simple sequence repeat


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
CROWN RUST is recognized as the most widespread and damaging disease of oat (Harder and Haber, 1992; Simons, 1985). The disease reduces both yield and quality of the grain and forage (Ohm and Shaner, 1992). The primary strategy for controlling crown rust is the development of cultivars resistant to or tolerant of the pathogen (Simons, 1985). Control of oat crown rust has been almost exclusively through the use of single-gene resistance. Most of the resistance genes in recently released oat cultivars have been introgressed from the hexaploid, wild oat species, A. sterilis (Martens and Dyck, 1989). These genes, however, have shown limited durability because of the frequent change in pathogenic specialization. The number of effective genes has been rapidly decreasing; therefore, it is important to characterize and utilize other sources of resistance so that novel resistance to crown rust is readily available.

The diploid wild oat species, A. strigosa L., is another important source of resistance; however, it has been difficult to transfer these valuable genes from the diploid to the hexaploid, cultivated A. sativa (Forsberg and Shands, 1969). Crown rust resistance derived from A. strigosa accession CD3820 was eventually transferred to A. sativa selection DCS1789 by a series of bridging crosses and irradiation of monosomic alien substitution lines. Resistance from A. strigosa accession CI3436 was similarly transferred to A. sativa selections, N560 lines and N770 lines (Forsberg, 1990; Sharma and Forsberg, 1977). N560 lines with moderate resistance and good agronomic traits were widely used as breeding stocks since 1968 and successfully contributed crown rust resistance to Wisconsin oat cultivars. No commercial cultivar, however, has yet been derived from N770 lines, which possess a higher level of crown rust resistance, but are tall and weak strawed. An attempt to combine N770-165-2-1, one of the N770 lines, and DCS1789 sources of resistance to crown rust resulted in a set of oat lines designated as MAM lines, which demonstrated an improved level and durability of resistance to crown rust (Moustafa et al., 1992). Cytogenetically stabilized, hexaploid oat MAM lines carrying crown rust resistance genes were subjected to classical inheritance studies. Results indicated that MAM 17-5, one of the MAM lines, carried two dominant resistance genes, believed to have been transferred from A. strigosa (Dilkova, 1995). Only 35 F3 lines derived from a cross, PA8494-4099/MAM17-5, were tested in the study, however. Therefore, further research on the inheritance of resistance in line MAM17-5 is needed to determine the genetic basis of resistance and to utilize this line as a parent in oat breeding crosses.

A long-term goal would be to combine the A. strigosa-derived crown rust resistance genes with genes from other species such as A. sterilis as a means to enhance durability of crown rust resistance in oat. A gene pyramiding strategy such as this, however, has not been frequently implemented because if multiple genes are incorporated, and all confer complete resistance, the presence of a single gene may mask the phenotypic effect of any other resistance gene. Conventional methods have largely depended on the availability of rust cultures having the appropriate virulence combinations to test the breeding lines. Identification of molecular markers linked to the resistance alleles could be used for marker-assisted selection and gene pyramiding without having to rely on the availability of rust cultures having the appropriate virulence.

Quantitative traits, including quantitative resistance, could be resolved into discrete Mendelian factors (Paterson et al., 1988). Identification of QTL for disease resistance in oat has been limited, although there are a number of examples of QTL detection for resistance in other crops (Messmer et al., 2000; William et al., 1997; Qi et al., 1998). In past studies mapping resistance genes in oat, the reaction types were almost exclusively divided into two categories: resistant and susceptible, even for some cases in which continuous variation was observed. In those cases, the data were used to fit a one-locus or two-locus genetic model. As a result, loci with smaller effects would not be identified in those studies.

This study was conducted to identify the number, position, and effect of QTL and digenic QTL epistasis controlling crown rust resistance in MAM17-5 by means of 152 recombinant inbred lines (RIL) derived from the cross, Ogle/MAM17-5. Information obtained from this research should be useful for comparison with other mapped rust resistance genes to gain a better understanding of the organization of rust resistance genes in the hexaploid oat genome. Tightly linked markers would be particularly valuable in physical mapping of genes and ultimately in map-based gene cloning. The final goal of the QTL analysis is to pyramid resistance genes in MAM17-5 with other resistance genes into a single line by marker-assisted selection to improve the durability of resistance.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
Plant Materials
Two hexaploid, cultivated oat genotypes, ‘Ogle’ (CI9401) and MAM17-5, with contrasting responses to the crown rust pathogen were used as parents to produce a mapping population. MAM17-5 is a crown rust resistant line, its resistance genes believed to originate from the diploid, wild oat accessions CI3436 and CD3820 of A. strigosa (Dilkova, 1995). Ogle is a well-known oat cultivar lacking current crown rust resistance. The mapping population of the 152 F5:6 recombinant inbred lines (RIL) was derived using the single-seed-descent method from the cross, Ogle/MAM17-5.

Evaluations for Crown Rust Resistance
Crown rust resistance evaluations were made at the West Madison Agricultural Experiment Station, Madison, WI, in 1999 and 2000. The 152 RILs and the two parents, Ogle and MAM17-5 (controls), were planted into a three-replication plot trial for two growing seasons. Each plot consisted of two 3-m rows with row spacing of 30 cm. Approximately 600 seeds were planted in each plot. A randomized complete block design was used. Planting was 2 wk later in 1999, because of wet weather, than in 2000. Additionally, significantly more rain occurred during the oat growing season in 2000 than in 1999.

An acceptable level of crown rust epidemic in the field plots was obtained by three strategies: (i) planting spreader rows of mixed susceptible varieties with different maturity around the whole trial; the mix consisted of ‘Bay’ (late maturing Wisconsin cultivar) and ‘Pacer’ (early maturing cultivar from Michigan); (ii) artificial inoculation of the spreader rows with composite spores of Midwest common races provided by the USDA-ARS, Cereal Disease Laboratory, St. Paul, MN; (iii) planting 10 to 14 d later than spreader rows and other oat breeding materials. When the pustules were clearly seen on the flag leaves of the susceptible control Ogle (approximate Zadoks Growth Stage 61) (Zadoks et al., 1974), other lines were evaluated for reaction type and assigned a severity rating. For reaction type, the modified method of Murphy (1935) was used and is based on a 1-to-5 scale. On this scale, 1 represents little or no visible reaction; 2, no visible sporulation, but abundant flecks or necrotic spots; 3, sparse small sporulating pustules, and surrounded by prominent chlorotic spots; 4, many small sporulating pustules, and often surrounded by chlorotic areas; and 5, many medium to large pustules, and generally with little or no chlorosis. The modified method of Peterson et al. (1948) was used to assess rust severity by visually assessing the area of leaf occupied by rust pustules. This method is based on 1-to-8 scale, where 1 = 0%, 2 = ~1%, 3 = ~2%, 4 = ~4%, 5 = ~8%, 6 = ~16%, 7 = ~25%, and 8 = ~40% or more, of leaf area occupied by rust pustules. Five individuals were randomly chosen in each plot, flag leaves were read, and ratings averaged to generate a single reading for each plot. The evaluation was conducted once in 1999 and twice, 5 d apart, in 2000. Since days to heading and plant height could potentially affect the host-parasite interaction, both traits were also recorded in 1999 and 2000.

DNA Marker Analysis and Framework Map Construction
Amplified fragment length polymorphism (AFLP) analysis was performed according to the protocol provided by the manufacturer (Gibco-BRL Life Technology, Inc., Gaithersburg, MD) with minor modifications. Microsatellite or simple sequence repeat (SSR) analysis was performed according to Chin et al. (1996), except that the separation and detection of the amplified products were done on polyacrylamide sequencing gels. Restriction fragment length polymorphism (RFLP) analysis followed a standard protocol (Zhu, 2002). For identification of QTL, a framework linkage map with 272 molecular markers was developed from the most informative markers (Zhu, 2002), and the map was used in this study. The genetic distance in the map, however, was in Haldane's centimorgan units preferred by PlabQTL (Utz and Melchinger, 1996).

Data Analysis
Analysis of variance for trait data was performed by the General Linear Model Procedure (Proc GLM) of SAS (SAS Institute Inc., 1990). Broad sense heritability was calculated as h2 = {sigma}2g/, where {sigma}2g = /, {sigma}2gy = /Reps, and {sigma}2e = MSerror. Mean values across replications were calculated for each trait for each RIL. These values were used to determine phenotypic correlations in the RIL population and to conduct QTL analysis. Pearson correlation coefficients were calculated by the Correlation Procedure (Proc Corr) of SAS. The significance of genotype x year and genotype x reading interactions was examined.

Computer program PlabQTL (Utz and Melchinger, 1996) was used in QTL analysis. To determine the critical log likelihood of odds (LOD) threshold, permutation tests were performed with 1000 random reshuffles of observation recommended by Churchill and Doerge (1994). All regions with LOD >3.5, corresponding to an experiment-wise error rate of 0.05, from the QTL analysis were considered significant and included in the final model. Composite interval mapping (CIM) (Zeng, 1994) with the cov SELECT option was used for QTL detection. CIM is an extension of interval mapping with some selected markers also fitted in the model as cofactors to control the genetic variation of other possibly linked or unlinked QTL. An F-to-enter value of 7.0 was used for the step-wise regression to preselect cofactors. The cov SELECT option uses all markers in the pre-selection as cofactors. The QTL position, given as centimorgans from the top of a linkage group, was determined when the LOD score reached its maximum. A support interval with a LOD fall-off of 1.0 was given for each QTL. QTL with an overlapping support interval are assumed to be the same QTL. The additive effect of a QTL was calculated by PlabQTL as (mean of the homozygous MAM17-5 class - mean of the homozygous Ogle class)/2. The additive x additive epistasis was estimated by the Model AA command. QTL x environment interactions were finally examined by the ENV option. The phenotypic variance explained by the QTL model was estimated by the adjusted coefficient of determination (R2adj), which accounts for the number of predictors in the final model. The phenotypic variance explained by an individual QTL or an individual QTL x QTL interaction (predictor) was calculated as R2i = Partial R2i x R2adj/; n = total number of predictors in the final model. Partial R2i– partial coefficient of determination estimated for the ith predictor.


   RESULTS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
Phenotypic Evaluations of the Parents and the Mapping Population
Significant genotype x environment (G x E) interaction was identified for reaction type, severity rating, days to heading, and plant height. Therefore, data for these traits from 1999 and 2000 were analyzed separately for QTL mapping. Reaction type and rust severity were recorded twice, 5 d apart, in 2000. No significant genotype x reading interaction was found for reaction type. No QTL reading interaction was detected in further analysis, although significant genotype-by-reading interaction was identified for rust severity. Therefore, the average of the two readings for 2000 was used in the following analysis.

Analysis of variance indicated that highly significant differences were present between the two parents and among the 152 RILs for all evaluated traits. Reaction type and severity rating were consistently higher for Ogle, while days to heading and plant height were consistently lower for Ogle than for MAM17-5 (Table 1), corroborating that the two parents differed in genes controlling these traits. Reaction type and severity rating for the 152 RILs showed a relatively continuous distribution with most of the individual lines falling between the two parental types, although the distributions were nonnormal (Table 1 and Fig. 1). The results suggested that no clear transgressive segregation existed for these two traits in the current study, and that resistance could be treated as a quantitative trait.


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  		Table 1. Mean reaction type (RT) to Puccinia coronata, severity (S), days to heading (Hd), and plant height (Ht) of the two parents and recombinant inbred lines (RILs) in different environments.

 


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  		Fig. 1. Frequency distributions of reaction type scores, rust severity ratings, days to heading, and plant height for the 152 recombinant inbred lines from the cross, Ogle/MAM17-5. Reaction type was recorded based on a 1-to-5 scale, where 1 is highly resistant and 5 is susceptible. Severity was rated based on a 1-to-8 scale in which 1 is 0% leaf area covered by pustules and 8 is approximately 40% or more leaf area covered. Days to heading means days from planting to heading. The values next to the x axis are the upper limit of each category.

 
A strong correlation was found among reaction types and severity ratings (Table 2). Both days to heading and plant height had no significant correlation with field reaction type, whereas they did have a small but significant (P < 0.05–0.01) negative relationship with severity (r = -0.18 to -0.35).


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  		Table 2. Phenotypic correlation coefficients between the traits of reaction type, severity, days to heading, and plant height.

 
The broad sense heritabilities of reaction type, severity, days to heading, and plant height were estimated from data from three replications of each year in 1999 and 2000. The heritabilities for reaction type and days to heading were higher with h2 = 0.82 and 0.83, respectively, whereas relatively lower for severity and plant height with h2 = 0.52 and 0.34, respectively. This is likely due to the high error variance and G x E interaction for severity and plant height. The relatively low heritabilities for severity and plant height indicate that only a subset of QTL are likely to be detected.

QTL for Resistance to Crown Rust Based on Reaction Type
Composite interval mapping was used to more precisely map QTL for resistance to crown rust. Three QTL were identified for resistance to crown rust on the basis of reaction type in the Ogle/MAM17-5 mapping population by CIM (Table 3; Fig. 2). Two of the QTL, Pcq1 tightly linked to an AFLP marker e8m2-13 and located on linkage group 28, and Pcq2 tightly linked to a RFLP markers bcd1280a and on linkage group 29, were detected consistently in both 1999 and 2000. The third QTL, Pcq3 located on linkage group 16, was found to be significant only in 2000. The negative signs of QTL effects indicated that resistance alleles were all contributed by MAM17-5, which was in agreement with the absence of clear transgression in the RILs.


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  		Table 3. Summary of quantitative trait loci (QTL) for resistance to crown rust based on reaction type in 1999, 2000 and average of the two years. Reaction type data collected on 152 recombinant inbred lines derived from Ogle/MAM17-5 were used. The QTL analysis was conducted using composite interval mapping with a LOD threshold of 3.5.

 


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  		Fig. 2. Linkage groups from the framework linkage map (Zhu, 2002) developed on the cross, Ogle/MAM17-5 (OM), showing significant quantitative trait loci (QTL) for crown rust resistance, days to heading and plant height. Map distances are given in Haldane's centi-Morgan. QTL for crown rust resistance are indicated to the right of linkage groups by crosshatch bars (reaction type) and open boxes (rust severity). QTL for days to heading (Hdq) and plant height (Htq) are indicated to the right of linkage groups by lines. Pcq1, Pcq2, and Pcq3 are QTL controlling reaction type. Pcq1, Pcq2, Pcq3 and Pcq4 are QTL controlling rust severity. Molecular markers beginning with letter ‘e’ are AFLP-type, with ‘am’ are SSR-type, and with others are RFLP-type markers.

 
Q x E interaction was analyzed to determine if the reaction type data of the two years could be combined for QTL mapping. No Q x E was detected, although significant G x E interaction was identified for resistance to crown rust on the basis of reaction type. Following the combining of the 2-yr data, the same three QTL were identified. No epistasis was found among these three QTL. The three QTL were included in the model for simultaneous fit, and the final model explained 87.4% of the total phenotypic variance for reaction type. The first QTL, Pcq1, explained 67.6% of the total phenotypic variance, the second QTL, Pcq2, explained 11.4%, and the third QTL, Pcq3, explained 8.4% (Table 3).

QTL for Resistance to Crown Rust Based on Severity
Four QTL were identified for resistance on the basis of crown rust severity in the mapping population (Table 4; Fig. 2). Three of the QTL located on linkage groups 28, 29, and 16, respectively, were also designated as Pcq1, Pcq2, and Pcq3 since they have overlapped support intervals with the QTL, Pcq1, Pcq2, and Pcq3, controlling reaction type, although they may show different LOD score peaks. Like QTL controlling reaction type, two of the QTL, Pcq1 and Pcq2, were consistently detected in both years. The third QTL, Pcq3, was significant only in 2000. One minor QTL, Pcq4 closely linked to marker e5m1-11 on linkage group 11, was significant only in 1999. By averaging the 2-yr data, three QTL were found to be the same as those detected in 2000. These three QTL on linkage groups 16, 28, and 29 explained 8.5, 51.8, and 14.0%, respectively, of the total phenotypic variance for resistance to crown rust on the basis of severity rating.


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  		Table 4. Summary of quantitative trait loci (QTL) for resistance based on crown rust severity. Severity data collected on 152 recombinant inbred lines derived from Ogle/MAM17-5 were used. The QTL analysis was conducted using composite interval mapping with a LOD threshold of 3.5.

 
Digenic epistasis between Pcq1 and Pcq2 was found to be significant for crown rust severity across both of the years. Significant epistatic effect between Pcq1 and Pcq3 was identified only in 2000. For the 2-yr average data, significant digenic epistases between Pcq1 and Pcq2 and between Pcq1 and Pcq3 were found. By including the two epistatic effects in the model for simultaneous fit, the final model explained 81.2% of the total phenotypic variance for crown rust resistance averaged over the 2-yr data (Table 4). The QTL controlling rust severity should be interpreted on the basis of single year data, however, since significant Q x E interaction was detected.

QTL for Days to Heading and Plant Height
Days to heading and plant height may be related to crown rust development since the traits showed small, but statistically significant, correlation coefficients with severity rating (Table 2). Three QTL, Hdq1 and Hdq2 located on linkage group 6 and Hdq3 located on linkage group 7, were identified for days to heading. One of them, Hdq3, was consistently detected in both years, and the other two QTL were only detected in one of the two years (Table 5; Fig. 2). Different signs of QTL effects indicated that the MAM17-5 allele at the QTL, Hdq1 and Hdq2, contributed early maturity, whereas the Ogle allele at Hdq3 contributed early maturity. The two QTL Hdq1 and Hdq3 for days to heading together explained only 23.1% of the total phenotypic variance following combining of data from the two years (Table 5). Four QTL in total were identified for plant height, and one of them, Htq3 located on linkage group 7, was consistently detected in both years. Another QTL was only found by combining data from the two years, and the other two were only detected in one of the two years (Table 6; Fig. 2). No significant, digenic epistasis was found between the QTL identified for either days to heading or plant height. Significant Q x E interaction was detected for both traits, however. The effects of QTL in 2000 were, in general, greater than the effects in 1999.


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  		Table 5. Summary of quantitative trait loci (QTL) for days to heading based on 152 F5:6 recombinant inbred lines derived from Ogle/MAM17-5. The QTL analysis was conducted using composite interval mapping with a LOD threshold of 3.5.

 

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  		Table 6. Summary of quantitative trait loci (QTL) for plant height based on 152 F5:6 recombinant inbred lines derived from Ogle/MAM17-5. The QTL analysis was conducted using composite interval mapping with a LOD threshold of 3.5.

 

   DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
Validation of the Number of QTL for Crown Rust Resistance in MAM17-5
Composite interval mapping was used to map QTL for resistance to crown rust in a more precise manner. Three QTL controlling reaction type, and four QTL controlling rust severity, were putatively identified, but only two QTL, Pcq1 and Pcq2, were consistently detected for the two traits and for both years (Table 3 and 4). Therefore, a conclusion could be made that two QTL controlled crown rust resistance in MAM17-5, which is in agreement with a previous result (Dilkova, 1995).

The bimodal-like distribution of the resistance traits (Fig. 1), however, suggested that there might be only one QTL controlling each of the resistance traits. Moreover, the possibility exists that two QTL, Pcq1 and Pcq2, could merge into one, since the two QTL were located on two small linkage groups (Fig. 2). Two validation analyses were conducted to support the conclusion of at least two QTL controlling crown rust resistance in MAM17-5. First, determination of a linkage relationship between two small linkage groups, 28 and 29, was conducted by MAPMAKER. No evidence of linkage was found even though a genetic distance threshold of 50 cM was used. This suggested that the QTL would span more than 50 cM if two QTL, Pcq1 and Pcq2, located on linkage groups, 28 and 29, merge into one QTL. A QTL with a support interval of more than 50 cM is rare. The other analysis involved examining the existence of a second QTL using only RILs with one of the two parental genotypes at major QTL detected. Pcq1 on linkage group 28 was the major QTL controlling crown rust resistance and tightly linked to marker e8m2-13. The RILs could be divided into two groups on the basis of their genotypes at locus e8m2-13 (Fig. 3). Only RILs with MAM17-5 genotypes were analyzed by PlabQTL. A second QTL for resistance was detected to explain the residual variation among the RILs with MAM17-5 genotypes at locus e8m2-13 and to be located on linkage group 29, thus supporting our original conclusion.



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  		Fig. 3. Frequency distribution of reaction type averaged on 1999 and 2000 relative to the number of recombinant inbred lines (RILs) with either of the parental genotypes at marker locus e8m2-13. Means of the two RIL classes with either of the genotypes are showed by arrows. The values next to the x axis are the upper limit of each category.

 
Genetic Basis of Phenotypic Correlation
Correlated traits are often associated with the pleiotropic effect of the same QTL or linkage of different QTL as has been reported for heading date and plant height in barley (Qi et al., 1998) and oat (Siripoonwiwat et al., 1996; Holland et al., 1997). Three QTL, Pcq1, Pcq2 and Pcq3, controlled both reaction type and rust severity (Table 3 and 4). The pleiotropic effects of these regions and/or the linkage of resistance genes resulted in significant phenotypic correlation (r = 0.62– 0.78, P < 0.001) observed between reaction type and rust severity.

Most QTL identified for crown rust resistance in this study were located on either small fragments or sparsely marked regions of a linkage group. Therefore, it has been difficult to determine whether the same gene has pleiotropic effects or whether tightly linked genes are being mapped as the same QTL. This could not be resolved by this QTL mapping study. Further research remains to be conducted by either adding more markers to the QTL regions on the basis of marker linkage relationships from other maps of oat or other crop species, or using a larger mapping population.

Days to heading and plant height were significantly correlated in this study (Table 2). As a result, they were found to be controlled by the same QTL, Hdq3 or Htq3. The allelic effects were also in the same direction for the QTL of both traits. Moreover, this QTL was consistently identified as located at 56 cM from the top of linkage group 7 in both years for both traits (Table 5 and 6). This result suggested that the QTL, Hdq3, for days to heading might have a pleiotropic effect on plant height rather than linkage of two QTL, Hdq3 and Htq3.

Days to heading and plant height had significant negative relationships with rust severity (Table 2). No pleiotropic effect of the same QTL, or linkage of different QTL was detected between these two traits and severity in either 1999 or 2000, however. Reasons for this could be the following. The linkage map used for this study did not completely cover the whole genome of oat (Zhu, 2002). Since 11 markers were not linked to any other markers, they could not be used in composite interval mapping for this QTL analysis. Theoretically, the number of QTL for each of the traits would be underestimated. In fact, one of the unlinked markers (e5m3-2) was found to be significantly (P < 0.0001) associated with both days to heading and plant height using single factor analysis (data not shown). Moreover, the low heritability (0.34) of plant height indicated low power of QTL identification for this trait. It was possible that some QTL with small effects for these traits could be linked to, or overlapped with each other; however, these have not been detected.

Comparison with QTL or Genes from Other Studies
One locus, Pca, conferring resistance to at least nine isolates of P. coronata, was found to be linked to isu2192, which was mapped to linkage group A of the diploid map developed from A. strigosa/A. wiestii (Rayapati et al., 1994). The strigosa parent contributed the resistance, and five resistance genes, Pc81, Pc82, Pc83, Pc84 and Pc85, were later assigned to this locus (Yu and Wise, 2000). The QTL, Pcq2, was detected tightly linked to bcd1280a and located on linkage group 29 in this study. Marker bcd1280a was found cosegregating with isu2192 (data not shown). Moreover, crown rust resistance in MAM17-5 was believed to be derived from A. strigosa (Dilkova, 1995). Therefore, Pcq2 may belong to the same gene family as the Pca locus.

The QTL Pcq3 in this study was mapped to linkage group 16, which appears homeologous to linkage group 15 of the Kanota/Ogle (KO) map (Zhu, 2002). Linkage groups 13 and 15 of the KO map were identified as homeologous (O'Donoughue et al., 1995). It was interesting that there was also a QTL for crown rust resistance mapped on linkage group 13 of the KO map in another study (Bush and Wise, 1996). The QTL Pcq4 controlling rust severity was mapped on linkage group 11, which was identified as homologous to linkage group 33 of the KO map (Zhu, 2002). Linkage groups 33 and 36 of the KO map were identified as homeologous (O'Donoughue et al., 1995). There was at least one QTL for crown rust resistance mapped in another study to a linkage group, believed to be homeologous to linkage group 36 of the KO map (Chen et al., 2000). Marker locus UMN145 linked to Pc91 (Rooney et al., 1994) was not used in the KO map, but was mapped to linkage group 15 of the Ogle/MAM17-5 map, which was clearly homeologous to linkage group 36 of the KO map (Zhu, 2002).

Linkage group A of diploid oat has been identified as corresponding to linkage group 4 of the hexaploid oat KO map (O'Donoughue et al., 1995) and to the homeologous group 1 of Gramineae (Van Deynze et al., 1995). One QTL for crown rust resistance was mapped on linkage group 4 of the KO map, and Ogle provided resistance at this time (Bush and Wise, 1996). A variety of disease resistance genes have been mapped on homeologous group 1 in the Gramineae such as leaf rust (Lr21) and stem rust (Sr33) resistance in wheat (Van Deynze et al., 1995), and powdery mildew (Ml) resistance in barley (Görg et al., 1993). All these results are in agreement with the hypothesis that disease resistance genes could be organized in clusters on a few chromosomes instead of random dispersion throughout the whole plant genome.

QTL for heading date and plant height were identified by using 71-84 F2:6 RILs derived from an interspecific cross, Kanota/Ogle (Siripoonwiwat et al., 1996; Holland et al., 1997). The major QTL identified for days to heading and plant height in this study, Hdq3 and Htq3, respectively, were linked to marker bcd808b and mapped to linkage group 7 of the Ogle/MAM17-5 map, which was homologous to linkage group 28 of the KO map (Zhu, 2002). No QTL for either heading date or plant height was reported on linkage group 28 of the KO map; however, QTL for heading date and plant height were identified on linkage groups 22 and 24 of the KO map (Siripoonwiwat et al., 1996; Holland et al., 1997), which were homeologous to linkage group 28 of the KO map (O'Donoughue et al., 1995). Another report indicated that a dominant dwarf gene, Dw7, was linked to cdo1437 and cdo708 and was placed to linkage group 22 of the KO map (Milach et al., 1997). Linkage group 22 of the KO map has been assigned to the longest satellited chromosome 19 (Phillips et al., 1995). All these findings suggested that the homeologous linkage group related to chromosome 19 could be rich in QTL for days to heading and plant height and as such could serve as a starting point for more intense scrutiny of genomic regions controlling days to heading and plant height.

Utilization of Mapped QTL for Crown Rust Resistance in Plant Breeding
Two QTL, Pcq1 and Pcq2, were consistently detected for both reaction type and rust severity in both years. One major QTL, Pcq1 on linkage group 28, contributed 48.5 to 70.1% of phenotypic variation for resistance. AFLP marker e8m2-13 was tightly linked to this QTL. The RILs could be divided into two groups on the basis of their genotypes at locus e8m2-13 (Fig. 3). These two classes were significantly different in their reaction types. If we consider lines with reaction type not greater than 3.5 to be resistant and greater than 3.5 to be susceptible, none of the lines with the Ogle allele are resistant, and about 6% of the lines with the MAM17-5 allele are susceptible. Therefore, marker-assisted selection targeting the major QTL should be very useful for efficient selection of crown rust resistance. Additionally, the QTL can be transferred into other oat varieties relatively easily since the QTL detected in this study are carried in adapted, cultivated oat.


   ACKNOWLEDGMENTS
 
The authors thank Dr. S. Kaeppler for his useful suggestions on this research, and R. Duerst for his excellent assistance in planting and plot management.


   NOTES
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 NOTES
ABSTRACT
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 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Research was supported by Hatch Grant No. WIS03920 and a Plant Breeding and Genetics Fellowship from Pioneer Hi-Bred International, Inc.

Received for publication March 26, 2002.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 




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S. Zhu, B. G. Rossnagel, and H. F. Kaeppler
Genetic Analysis of Quantitative Trait Loci for Groat Protein and Oil Content in Oat
Crop Sci., January 1, 2004; 44(1): 254 - 260.
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