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a Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, 97331
b Department of Crop and Soil Sciences, Michigan State University, East Lansing, MI, 48824
* Corresponding author (kellyj{at}msu.edu)
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Abbreviations: AFLP, amplified fragment length polymorphism • BN, Bunsi/Newport • DI, disease incidence • DSI, disease severity index • HN, Huron/Newport • I, disease incidence bulk • MAS, marker-assisted selection • M, multi-trait bulk • MT, multi-trait • MTB, multi-trait bulking • MRF, Montcalm Research Farm • QTL, quantitative trait loci • RAPD, random amplified polymorphic DNA • RIL, recombinant inbred line • ROX, resistance to oxalate • S, disease severity bulk • SCF, Sanilac Cooperator Farm
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Avoidance mechanisms, such as an open porous canopy, can play a major role in the development of disease in the field (Fuller et al., 1984; Steadman et al., 1973; Miklas et al., 2001). Agronomically undesirable avoidance mechanisms, such as early flowering or decreased canopy width, may reduce white mold infection levels, but place a crucial restraint on the ability of breeders to select for high-yielding genotypes (Kolkman and Kelly, 2002). Moreover, the apparent difficulty of detecting desirable phenotypes, because of environmental or plant avoidance characteristics, hinders normal selection procedures for important quantitative traits and increases the value of marker-assisted selection (MAS) in breeding for resistance to white mold in common bean.
Quantitative trait loci for resistance to white mold in the field have been identified in bean by means of diverse mapping populations. Two QTL were identified in an ‘A 55’/‘G 122’ recombinant inbred line (RIL) population on linkage groups B1 and B7 of the integrated bean linkage map (Freyre et al., 1998), corresponding to the fin (growth habit) and Phs (seed storage protein) locus regions, respectively (Miklas et al., 2001). The QTL on B7 was confirmed as a region conferring physiological resistance via the greenhouse straw test. The QTL on B1 was associated with canopy porosity, and was located near the fin gene for determinate growth habit in large-seeded Andean bean genotypes (Miklas et al., 2001). Quantitative trait loci for resistance to white mold in the field as well as physiological resistance, determined by the straw test, have also been identified in a ‘PC-50’/‘XAN-159’ RIL population (Park et al., 2001). In general, markers linked to QTL for resistance to white mold in the field were located on B4, B7, B8, and B11. The most significant marker locus for resistance to white mold in the field was found on B7 and accounted for 12% of the phenotypic variation in a multiple regression analysis. Quantitative trait loci for plant height and porosity over the furrow were also identified in several of the regions associated with resistance to white mold.
Selective genotyping (Lander and Botstein, 1989) and bulked segregant analysis (Michelmore et al., 1991) have been utilized to screen large numbers of polymorphic markers efficiently, without having to genotype entire populations. Selective genotyping has successfully identified QTL for resistance to common bacterial blight [caused by Xanthomonas axonopodis pv. phaseoli (Smith) Vauterin et al.] in bean (Miklas et al., 1996). In a computer simulation study, the detection of markers linked to QTL for the trait of interest was improved when alternate DNA bulks were used for traits that were correlated with the main trait of interest. The use of alternative multiple traits that are related to the traits of interest has been effective in identifying QTL that may not be detected through screening extreme phenotypes (Ronin et al., 1998). A single set of DNA bulks composed solely of small numbers of lines with extreme phenotypes may not adequately represent resistant genotypes in a population segregating for resistance to white mold where both agronomic avoidance and physiological resistance mechanisms are expressed. DNA pooling strategies based on a priori knowledge of the population should help resolve useful markers linked to QTL, and discern the location of the QTL (Wang and Paterson, 1994). Selective genotyping and DNA pooling methods are also important in reference to genetically narrow populations that are the most useful for QTL studies, but not suitable or amenable for saturated linkage map development.
The expression of resistance to white mold in the field is usually highly influenced by many traits affecting the final phenotype (Kolkman and Kelly, 2002). Identifying QTL for resistance to white mold would therefore greatly facilitate the progress in developing improved cultivars, and improve on our understanding of the complex relationship between physiological resistance and avoidance mechanisms. The use of selective genotyping for a trait as complex as resistance to white mold, however, may be hindered by the limitation of a set of DNA bulks on the basis of disease reaction alone. The objectives of this research were to (i) discover QTL conferring resistance to white mold in navy bean, (ii) determine if a Multi-trait bulking (MTB) strategy, where multiple traits were used to develop contrasting DNA bulks for use in selective genotyping, was an efficient approach for QTL identification, and (iii) determine if agronomic traits, particularly growth habit, were associated with QTL for avoidance to white mold in bean in the field.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Both the BN and HN populations and parental genotypes were evaluated for resistance to white mold in three or four field environments, respectively, in Michigan (Montcalm and Sanilac) from 1996 to 1998. In each experiment, the two center rows of each four-row plot were planted with the experimental line, and the two outer border rows were planted with Midland, a highly white mold susceptible cultivar. Standard agronomic practices were applied to ensure good crop growth and development at all sites. Field sites were chosen that had a history of white mold and natural infestation was relied on for disease development. Irrigation was periodically used at the Montcalm site to promote crop growth and uniform disease pressure during the main flowering period.
Plots were rated for DSI by means of a "quarter scale" (Hall and Phillips, 1996) shortly before harvest using the following formula:
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Disease incidence (DI) was calculated as the percentage of 30 individual plants with white mold infection. Genotypes were also evaluated throughout the growing season for a number of agronomic traits, such as growth habit [determinate (Type I); indeterminate (Type II)]. Days to flowering was determined as the number of days after planting when 50% of the plants had at least one open flower. Mid-season canopy height and width measurement were averaged over six individual samples per plot. Branching pattern was evaluated on a basis of a 1-to-5 scale, where 1 = acute upright branching, and 5 = obtuse prostrate branching. Days to maturity was measured as the number of days after planting when 90% of the pods were physiologically mature and drying down. Lodging was determined at maturity on a 1-to-5 scale, where 1 = no lodging, and 5 = excessive lodging. Plots were harvested at maturity, and seed yield and seed size (the weight of 100 seeds) were adjusted to 18% moisture content by weight (Kolkman and Kelly, 2002).
Physiological resistance in both populations was determined indirectly, by screening the populations for ROX in the greenhouse. The BN population was evaluated for ROX in an RCBD with four replications over time with four seedling samples per entry in each replication. The HN population was evaluated three times for ROX with three replications in a RCBD, using five seedling samples per entry in each replication. Briefly, 20-d-old seedlings (second trifoliate emerging) were cut at the base of the stem, placed in a 20 mM oxalate solution (pH 4.0), and rated for wilting symptoms after 12 to 15 h by a 1-to-6 scale (Kolkman and Kelly, 2000).
All field and greenhouse experiments were analyzed as RCBDs, by PROC GLM (SAS Institute, 1995) with both genotypes and environments considered as random effects. An analysis of variance of resistance and agronomic traits, and a chi-square analysis for growth habit were reported previously (Kolkman and Kelly, 2002). Estimates of heritability for ROX were calculated on an entry-mean basis (Hallauer and Miranda, 1988). The 90% confidence intervals for heritability estimates were determined on the basis of Knapp et al. (1985).
DNA Isolation and Marker Amplification
Plant tissue was harvested from parental genotypes and from approximately 10 F3:7 greenhouse grown plants for each line in the BN population, and 10 greenhouse grown F5:7 plants for each line in the HN population. DNA was extracted from the plant tissue by a miniprep procedure (Edwards et al., 1991; Haley et al., 1994b). Parental genotypes of the BN population were screened via PCR with approximately 600 Operon random 10-mer primers (Operon Technology, Alameda, CA) for the presence of polymorphic bands, using Gibco Taq DNA polymerase (Invitrogen, Carlsbad, CA; Miklas et al., 1993; Haley et al., 1994a). The parents were also screened twice with 111 random amplified polymorphic DNA (RAPD) primers from the integrated bean linkage map (Freyre et al., 1998), using Gibco Taq DNA polymerase and Stoffel fragment Taq DNA polymerase (Perkin Elmer, Foster City, CT). PCR was conducted in a 96-well PTC-100 Programmable Thermal Controller (MJ Research, Inc., Waltham, MA) programmed for 3 cycles of 1 min at 94°C, 1 min at 35°C, and 2 min at 72°C; 34 cycles of 1 min at 94°C, 1 min at 40°C, and 2 min at 72°C with the final step extended by 1 s for each of the 34 cycles, and a final extension cycle of 5 min at 72°C (Haley et al., 1994a). RAPD markers are identified by the name of the Operon primer, followed by the size of the polymorphic fragment. Parental genotypes were also screened for polymorphic bands with eight AFLP primer pair combinations (Vos et al., 1995) and polyacrylamide gel electrophoresis was used to separate AFLP fragments. Fragments were visualized by a silver staining procedure, according to the directions of a commercial silver staining kit (Promega, Madison, WI), with the addition that both the fix–stop and developing solution were partially frozen (Barrett and Kidwell, 1998). The first three letters of the AFLP marker names indicate the EcoRI +3 (+ANN) selective nucleotides, while the second three letters indicate the MseI + 3 (+CNN) selective nucleotides used in this study. The number following the six-letter enzyme–primer combination represents the size of the polymorphic fragment generated by the specific marker in reference to a 10 and 25 base pair ladder.
Selective Genotyping and DNA Pooling
Selective genotyping of individuals, on the basis of both single-trait and multiple-trait DNA pooling strategies, was utilized to create three sets of DNA bulks in the BN population. Resistant and susceptible DNA bulks were created from the combined analysis across environments. Two sets of single-trait resistant and susceptible DNA bulks were created by pooling together three to five genotypes of either extreme of DSI or DI phenotypes, where selected genotypes were among 4 to 10% of the total population with either the highest or lowest DSI and DI ratings (Table 1). Only two of the genotypes in each resistant bulk were common between the resistant DSI and DI bulks, as well as in the susceptible DSI and DI bulks, to maximize the opportunity of identifying significant markers.
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Markers polymorphic in the parental genotypes and bulks were used for genotypic screening of the entire BN population. Markers were tested for segregation distortion and identified via analysis of variance and correlation analysis (SAS Institute, 1995) to indicate linkage between markers and to confirm linkage to ROX, resistance to white mold in the field, and genes influencing agronomic traits. Markers from the integrated linkage map that were polymorphic between Bunsi and Newport were confirmed as anchor points to the core map by verification of the polymorphic band size found between Bunsi and Newport, and the parental genotypes of the core map, BAT93 and Jalo EEP558 (Freyre et al., 1998), and subsequently screened on the entire BN population. RAPD and AFLP markers that were identified as significant in the BN population were screened in the HN population.
Linkage Analysis
Linkage and linkage order of markers were determined with MAPMAKER/EXP (Lander et al., 1987), using the Kosambi mapping function (Kosambi, 1944), a minimum LOD score of 3.0, and a maximum recombination frequency of 0.30. Growth habit was included as a phenotypic marker in linkage map construction. Quantitative trait loci for DSI, DI, and associated agronomic traits across environments in the BN population (P < 0.01) were sought on the constructed linkage groups via interval mapping with the QTL Cartographer software program (Basten et al., 1999). Threshold LOD scores (95%) for individual traits were determined with this program through a permutation test, with 1000 permutations (Churchill and Doerge, 1994). Significant markers that were most closely associated with major QTL are reported, along with corresponding R2 values determined via analysis of variance in combined and individual environments (SAS Institute, 1995). Markers associated with DSI, ROX, and yield, in the BN population were tested for significance and corresponding R2 values in the HN population by analysis of variance. The effect of single markers on phenotypic trait was determined by a t test (SAS Institute, 1995). Multiple stepwise regression including markers linked to QTL for DSI and agronomic traits (P < 0.15) associated with DSI along with corresponding R2 values were calculated by PROC REG (SAS Institute, 1995).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Approximately 100 of the 600 random 10-mer primers where polymorphic between Bunsi and Newport. Of those markers, only 13 were polymorphic between the single or multitrait bulks. Only eight of the 111 primers from the integrated bean map were polymorphic between Bunsi and Huron. Overall, 24 polymorphic markers, including growth habit, in the BN population mapped to four linkage groups (Fig. 1), for a total genetic length of 220 cM. The first linkage group had seven markers, with four markers that were anchored to B2 of the integrated linkage map (Freyre et al., 1998). The second linkage group was composed of nine markers, with an anchor marker, H12.1050, and a second putative anchor marker, I07.1200, in common with B7 (Beebe et al., 1998; Freyre et al., 1998). The third and fourth linkage groups each had only one marker in common with B3 and B8, respectively; therefore, additional markers are needed to anchor these groups to the integrated linkage map. No DSI or yield QTL were associated with either B3 or B8.
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B7 was the most important linkage group, where markers were significantly associated with DSI, days to flowering, lodging, seed size, and yield (Fig. 3; Table 2). Two of the most important markers, aggctt85 and aacctt130, contributed up to 16.8 and 15.8% of the phenotypic variability for DSI, respectively. Aacctt130 was also associated with days to flowering (R2 = 13.9%). A potential QTL region for architectural traits was also located on B7. Marker I07.1200 was associated with branching pattern (R2 = 9.1%), lodging (R2 = 9.1%), and seed size across environments (R2 = 19.5%). Alleles for reduced DSI [aggctt85 (repulsion phase linkage); aacctt130], shorter days to flowering (aacctt130), narrower branching pattern (I07.1200), and reduced lodging (I07.1200) were all derived from the Bunsi parent. The proximity of aacctt130 and I07.1200 indicates that avoidance traits may be linked to DSI, or a general avoidance trait in the region that could have had a pleiotropic effect on reducing disease levels.
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The region of B7 associated with resistance appears to be the same region associated with yield in the BN population, and is supported by high LOD scores (Fig. 3; Table 2). Most of the markers significantly associated with yield across environments in this linkage group included I07.1200 (R2 = 36.5%), aacctt130 (R2 = 34.4%), G17.820 (R2 = 27.2%), and aggctt85 (R2 = 24.9%). The most significant marker for yield, I07.1200, was also the most significant marker for seed size. All alleles for increased yield and seed size were contributed by the Bunsi parent. Other genes located on this region of B7, include those for seed lectins and the leghaemoglobbin (LegH) gene (Freyre et al., 1998). Because of the complex interaction of yield potential and microclimate suitable for white mold development, B7 has a unique role in improving yield and resistance to white mold in the field.
Single- and Multitrait Bulking
Both single- and multitrait bulking strategies identified markers linked to QTL conferring resistance to white mold. The markers most closely associated with QTL for DSI on B2 were derived from both single-trait bulks, DSI and DI, as well as the MT bulk (Table 2). Alternatively, only one of the eight molecular markers in B7 was detected in all three sets of DNA bulks. Four of the markers were identified by both the DI and MT bulks, while two markers, I07.1200 and aacctt130, were identified by the MT bulks only. All eight molecular markers on B7 were identified by the MT bulks. The single-trait DSI bulk alone would not have identified the most closely linked markers to the QTL conferring resistance to white mold on B7. Testing for multiple traits that are correlated with the characteristic of interest was suggested as a useful method in the identification of markers linked to QTL (Ronin et al., 1998). The additional single-trait DI bulk, and the MT bulks were critical in identification of markers of this important linkage region. The DSI values in the selected individuals within the resistant MT bulks were higher than those of the single-trait resistant DSI bulk (Table 1), and indicate that the resistant DSI bulk may have included genotypes with greater avoidance mechanisms that significantly reduced yield but were potentially commercially unproductive. A similar pattern occurred between the DI bulks and the MT bulks, where the MT resistant bulk included genotypes with higher DI values, ranging from 23.3 to 41.1% (compared with <25% DI for the resistant bulk), and the susceptible bulks included genotypes with slightly lower DI values, ranging from 78.5 to 88.5% (compared with >82% DI for the susceptible bulks). Genotyping a chosen set of individuals with specific phenotypes, on the basis of a priori knowledge of the traits that are segregating in the population that may affect the desired phenotype, was an efficient method to detect markers linked to the resistance phenotype which would not have been detected in the single-trait DSI bulks alone.
Resistance to Oxalate
Genotypic variation for ROX was significant (P < 0.10) for the BN population, and across the three combined tests (P < 0.01) for the HN population. Estimates of heritability for ROX were low [0.19 (90% confidence interval: 0 to 0.37); BN population] to moderate [0.56 (90% confidence interval: 0.18 to 0.73); HN population] across tests. Previous heritability estimates for physiological resistance have generally been low to moderate (Miklas et al., 2001; Miklas and Grafton, 1992; Park et al., 2001). Resistance to oxalate was previously found to be correlated with DSI in the field in a group of adapted, relatively high-yielding advanced lines (Kolkman and Kelly, 2000). Surprisingly, there was a very low correlation (r = 0.18; P < 0.10) between the ROX scores and DSI in the BN population, and no significant correlation between ROX and DSI in the HN population. A lack of correlation between physiological resistance, as measured via an excised stem test, and resistance to white mold in the field has been previously reported in a Bunsi-derived population, and was considered to have been due to avoidance mechanisms confounding the relationship (Miklas and Grafton, 1992).
A number of agronomic traits, including growth habit, days to flowering, canopy height and width, branching pattern, lodging, and days to maturity were found previously to be significantly associated with DSI in the field (Kolkman and Kelly, 2002). The combination of a large number of agronomic avoidance mechanisms, as well as potential non-oxalate related defense mechanisms, may have contributed to the lack of correlation between ROX and DSI in the field in the segregating populations. Many markers on B7 were significantly associated with ROX (Fig. 3), including H12.1050 (R2 = 15.5%), aacctt130 (R2 = 15.6%), and growth habit (R2 = 21.7%), accounting for a decrease in ROX of 0.24 for both H12.1050 and aacctt130, and 0.27 for growth habit, and were associated with the Bunsi parent. The QTL for ROX on B7, in addition to QTL for DSI and avoidance traits, such as days to flowering, branching pattern, and lodging, support the concept that it is possible to select simultaneously for physiological disease resistance and avoidance mechanisms in common bean.
Determinate Growth Habit
The growth habit phenotype in the BN population was, unexpectedly, mapped to the distal region of B7 (Fig. 1). The determinate growth habit fin gene in large-seeded genotypes is located on B1 (Koinange et al., 1996), yet the 15 RAPD markers on B1 of the integrated linkage map were monomorphic between the Bunsi and Newport parents. Differing origins of the determinate growth habit in bean populations previously used to map this phenotype and in the mapping population used in this study may account for the contrasting results. Wide crosses of the Andean gene pool as the source for the determinate growth habit, were previously used to map the fin gene (Koinange et al., 1996) as the determinate growth habit is a common trait in Andean germplasm (Kelly, 2000). Alternatively, the determinate growth habit in genotypes of the Middle American gene pool exists mainly in cultivated materials of the navy bean market class and is relatively rare in more exotic, Middle American germplasm (Kelly, 2000).
Early attempts to introgress the determinate growth habit from Andean germplasm into navy bean germplasm through breeding proved to be unsuccessful. Subsequently, the determinate growth habit was introduced into the navy bean by mutagenesis (Kelly, 2000). In support of the hypothesis of a unique Middle-American gene for the determinate growth habit, a recent study showed that a gene for the determinate growth habit in navy bean was located on a linkage group anchored to B9 of the integrated map (Tar'an et al., 2002). Growth habit was placed on a distal end of the linkage group, 32.3 cM from the nearest RAPD marker. Additional markers are being sought to confirm the linkage group origin of the determinate growth habit in navy bean.
Additional phenotypic evidence suggests that there are unique phenotypic differences that distinguish the determinate growth habit of navy beans and that of genotypes of Andean origin. Determinate navy bean cultivars, such as Midland and Newport, are generally very susceptible to white mold (Kolkman and Kelly, 2000), whereas the determinate growth habit has been recognized as a resistance phenotype in larger-seeded Andean bean genotypes (Fuller et al., 1984; Miklas et al., 2001; Park et al., 2001; Steadman et al., 1973). The determinate navy bean cultivar, Seafarer, was found to have a highly concentrated flowering period characterized by a very short flowering duration. Many of the flowers in the main flush of flowers, however, do not set pods (Izquierdo and Hosfield, 1983), but serve as potential inoculation site for white mold. The open porous canopy of determinate genotypes of Andean origin has been characterized as an avoidance mechanism in resistance to white mold in the field in semiarid production areas (Coyne, 1980) but may be a characteristic that could limit yield. In the Midwest region, the indeterminate navy bean is generally higher yielding, with greater yield stability than the determinate navy bean (Kelly et al., 1987). Growth habit was also associated with yield in the BN population, since average yield of the indeterminate RILs was 364 kg ha-1 higher than the determinate RILs, across three environments.
The indeterminate growth habit was previously identified as a predominant phenotype in a multiple-regression model of agronomic traits on DSI in the BN population within and across environments (Kolkman and Kelly, 2002). The regression model of DSI with the agronomic traits measured in the BN population, and including markers linked to QTL for DSI located on B2 (BC20.1800) and B7 (aacctt130 and aggctt85) was reanalyzed across combined environments. The multiple regression model of DSI, where y = -109.5 + 1.3 (canopy width) + 5.0 (aacctt130) - 11.0 (BC20.1800) + 0.9 (days to flowering) confirms the potential use of both markers and phenotypic selection for specific agronomic traits to improve resistance to white mold in bean. Caution must be exercised to prevent the selection of undesirable avoidance that traits such as a narrow canopy reduces yield potential as well as white mold levels (Kolkman and Kelly, 2002). The model explained 59.4% of the variation for DSI, where low DSI included decreased canopy width (27.2%), aacctt130 (16.3%; B7; presence), BC20.1800 (12.4%; B2; absence), and shorter days to flowering (3.5%). The markers located on B7, particularly aacctt130, were most closely associated with DSI, but growth habit was not identified as an important factor in this model. A good strategy for selecting resistance to white mold should include selection for genotypes with medium canopy width, the presence of aacctt130, and the absence of BC20.1800.
Markers associated with QTL for resistance and agronomic traits were found to be relatively robust across environments. The most significant markers identified for DSI, ROX, and yield in the BN population were tested on the HN population (Table 3). On B2, BC20.1800 accounted for 40% of the phenotypic variability for DSI across combined environments and 60.9% in the MRF96 environment. All markers associated with B7 were tested on the HN population, since it was such a significant linkage group in the BN population. The favorable allele of the resistance phenotype was absent for six of the markers tested. Oddly, the band corresponding with the H12.1050 marker was absent from the 28 progeny despite being polymorphic between the parents, which is possibly due to the small sample size evaluated, or a potential chromosomal irregularity. G17.820 was associated with ROX (R2 = 24.3%) and yield (R2 = 47.0%) across combined environments in the HN population. G17.820 was not correlated with DSI, but was associated with growth habit, as in the BN population, and was associated with 13% of the phenotypic variation for ROX in the BN population. Growth habit was not significantly associated with DSI or yield in the HN population.
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Received for publication March 7, 2002.
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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