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a Dep. of Agronomy & Horticulture, Univ. of Nebraska, Lincoln, NE 68583
b Dep. of Plant Pathology, Univ. of Nebraska, Lincoln, NE 68583
c Dep. of Horticulture, Texas A&M Univ., Weslaco, TX 78596
d Dep. of Soil & Crop Sciences, Colorado State Univ., Fort Collins, CO 80523
* Corresponding author (jsteadman1{at}unl.edu).
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ABSTRACT |
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 TOPNOTES ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Abbreviations: BCMV, Bean common mosaic virus • BSA, bulked segregant analysis • GGW, golden gate wax • GN, great northern • LG, linkage group • MA, Middle American • RAPD, random amplified polymorphic DNA • RIL, recombinant inbred line • SCAR, sequence characterized amplified region • SR, specific resistance
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INTRODUCTION |
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TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Sources of resistance to bean rust have been identified (Mmbaga and Stavely, 1988; Stavely and Pastor-Corrales, 1989; Echavez et al., 1982; Arnaud-Santana et al., 1993). Resistant bean cultivars and breeding lines have been developed and released (Wood and Keenan, 1982; Stavely and Steinke, 1990; Stavely and McMillan, 1992; Coyne et al., 1994; Stavely et al., 1994). Each breeding line possessed at least two different rust resistance genes (Mmbaga et al., 1996b). Kelly et al. (1996) described and discussed the original and revised assigned symbols for rust resistance genes in beans. Different patterns of specific resistance to individual rust races or pathotypes have been reported as follows: single dominant genes (Coyne and Schuster, 1975; Bravo and Galvez, 1976; Kolmer and Groth, 1984; Augustin et al., 1972; Finke et al., 1986; Park et al., 1999, 2003), a single recessive gene (Zaiter et al., 1989), two genes with epistatic interaction (Finke et al., 1986), two complementary dominant genes (Grafton et al., 1985), and two independent genes (Grafton et al., 1985).
Bulked segregant analysis (BSA) (Michelmore et al., 1991) is an efficient method to rapidly identify molecular markers linked to a specific gene using DNA bulks from F2 plants. This technique was used to detect four different genes (Ur-3, Ur-5, Ur-7, and Ur-11) of Middle American (MA) origin and two genes (Ur-4 and Ur-9) of Andean origin for rust resistance in beans using random amplified polymorphic DNA (RAPD) markers (Haley et al., 1993, 1994; Miklas et al., 1993; Johnson et al., 1995; Park et al., 1999, 2003). Miklas et al. (2002) reported integration of identified rust resistance genes in the bean linkage map. Three important rust resistance genes such as Ur-3, Ur-7, and Ur-11 of MA origin are located on linkage group (LG) 11 (Miklas et al., 2002; Park et al., 2003), while other rust genes Ur-9, Ur-5 and Ur-4 are located on LGs 1, 4, and 6, respectively (Miklas et al., 2002). Pyramiding monogenic resistance genes into a bean cultivar is a strategy recommended to obtain durable rust resistance (Mmbaga et al., 1996b). Those markers linked to rust resistance genes have been utilized to pyramid these genes into a single cultivar, as suggested by Kelly (1995).
Grafton et al. (1985) reported a single dominant resistance gene of Andean origin present in Olathe. This rust resistance gene, along with other sources, was utilized to develop resistant pinto and great northern (GN) bean breeding lines (Stavely and Grafton, 1989; Stavely et al., 1989, 1992). McClean et al. (1994) initially identified RAPD marker OV12.950 linked to Ur-6 for resistance to race 47 at 10.4 cM in a pinto bean cross. On the basis of this result Miklas et al. (2002) mapped Ur-6 on LG 11 of the core bean map. However, markers tightly linked to Ur-6 of Andean origin for specific resistance (SR) to rust present in Olathe have not been reported.
The objective of this study was to identify RAPD markers tightly linked to Ur-6 for SR to race 51 by BSA in an F2 population from the MA common bean cross Olathe (resistant) x GN Nebr.#1 sel.27 (susceptible). Merits of sequence characterized amplified region (SCAR) markers over RAPDs have been reported (Paran and Michelmore, 1993; Melotto et al., 1996). Thus, our additional goal was to convert the most tightly linked RAPD marker to Ur-6 into a SCAR marker on the basis of a specific forward and reverse 24-mer primer pair. We then determined the presence or absence of these identified RAPD and SCAR markers in 70 MA and Andean bean genotypes with or without Ur-6.
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MATERIALS AND METHODS |
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TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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One hundred F2 plants and 88 F3 families (12 to 16 plants per F3), along with their parents Olathe and Nebr.#1 sel.27, were planted in the greenhouse on 16 Feb. 1998 and 18 Aug. 1998, respectively. Twelve of the 100 F3 families were not planted because of a lack of seeds. Fifty-seven MA and 13 Andean common bean cultivars–breeding lines were also planted in a completely randomized design with two replications in the greenhouse on 4 Feb. 2003. Two or four plants were grown per clay pot containing equal parts by volume of sand, sphagnum peat moss, vermiculite, and sharpsburg silty clay loam soil. Peters 20N:10P:20K Peat-Lite Special (Scotts-Sierra Horticultural Products Co., Marysville, OH) water soluble fertilizer was applied weekly. The chemical Orthene 75 s soluble powder (active ingredient Acephate: O,S-dimethyl acetyl-phosphophoromidothioate) (Valent Co., Walnut Creek, CA) was applied biweekly to control white flies [Bemisia tabaci (Gennadius)]. Approximate day/night greenhouse temperatures were 26 ± 2/22 ± 2°C in each experiment. Lengths of natural days/nights ranged from 13/11 to 15/9 h in each experiment.
Inoculation
Race 51 of the bean rust pathogen, collected from the USA, was used for inoculation of 57 MA and 13 Andean bean cultivars–lines as well as 100 F2 plants and 88 F3 families. Race 51 was chosen because in our preliminary screening of SR to several races of the rust pathogen, Olathe was resistant to race 51, whereas Nebr.#1 sel.27 was susceptible. A water suspension of approximately 2 x 104 urediniospores/mL with 40 µL/L of Tween-20 [polyoxyethylene (20) sorbitan monolaurate] was prepared for inoculation. The abaxial leaf surfaces of two unifoliolate leaves in each plant were inoculated at 7 d after planting with the rust spore suspension using the inoculation technique of Stavely (1983). Inoculated plants were incubated in a misting chamber at 20 to 22°C for 16 h and then transferred from the chamber to greenhouse benches. Rust reactions on the unifoliolate leaves of each plant were recorded at 14 d after inoculation using the disease rating scale described by Stavely et al. (1983). Resistant reactions included no visible symptom (immune), necrotic spots without sporulation (a hypersensitive reaction), and/or small uredinia less than 300 µm in diameter. A susceptible reaction produced uredinia larger than 300 µm in diameter.
Bulked Segregant Analysis Using RAPD
Noninoculated fully expanded trifoliolate leaves of 100 F2 plants along with their parents as well as 70 bean cultivars and breeding lines were collected at 21 d after planting. Total genomic DNA was extracted from the lyophilized leaf tissue using the method of Skroch and Nienhuis (1995). A total of 680 random 10-mer primers (Operon Technologies, Alameda, CA) were used for the RAPD analysis (Williams et al., 1990). Polymerase chain reactions (PCR) were performed on 96-well plates in a MJ Research thermocycler (model PTC-0100; MJ Research, Waltham, MA). PCR protocols and the composition of the final volume of reactants were similar to those described by Skroch and Nienhuis (1995). Molecular size markers from a 100-base pair ladder (Life Technologies, Grand Island, NY) were used to estimate the length of RAPD markers. The name of each RAPD marker is derived from an "O" prefix for Operon primers, the letters identifying the Operon kit, Operon primer number, and the approximate length of the marker.
Two different DNA bulks were prepared from equal volumes of standardized DNA (10 ng/µL) from eight homozygous resistant and eight homozygous susceptible F2 plants selected on the basis of F3 phenotypic data for the reaction to race 51 of the bean rust pathogen, respectively. The 680 primers were used to simultaneously screen between the two different DNA bulks from resistant and susceptible F2 plants, and between the parents Olathe and GN Nebr.#1 sel.27. Twenty-six primers generated marker polymorphisms between the DNA bulks from resistant and susceptible plants, and they were tested subsequently in the F2 population of the cross Olathe and Nebr.#1 sel.27. Two primers were tested in 70 bean cultivars/breeding lines for determining the presence or absence of coupling-phase markers linked to Ur-6.
Converting RAPD to SCAR Markers
To develop a SCAR marker for the RAPD marker OBC06.300, the DNA fragment of the RAPD marker was excised and purified with the GENECLEAN II Kit (Q-BIO gene, Carlsbad, CA). Insertion of the purified RAPD fragment into the pCR 2.1- TOPO and cloning of the transformed plasmid were conducted with the TOPO TA Cloning Kit (Invitrogen, Carlsbad, California). The cloned plasmid was harvested using the GenElute Plasmid Miniprep Kit (Sigma, St. Louis, MO). The RAPD fragment was sequenced with the M13 reverse and forward primers at the DNA sequencing and synthesis facility of the Iowa State University Office of Biotechnology (Ames, IA). A specific forward and reverse 24-mer primer pair was designed on the basis of the forward and reverse sequences of the RAPD fragment. The forward and reverse primer pair was synthesized at the Operon Technologies. PCR was performed on 96-well plates in the MJ Research thermocycler. PCR protocols and the composition of the final volume of reactants were similar to those described by Rubio et al. (2001) with an annealing temperature of 65°C. The specific forward and reverse 24-mer primer pair was tested in the F2 population of the cross Olathe and Nebr.#1 sel.27. The primer pair was also tested in 70 MA and Andean bean cultivars/lines for determining the presence or absence of the SCAR marker linked to Ur-6.
Linkage Analysis
To test the genetic hypothesis of a single dominant gene controlling rust resistance the chi-square test was used to test goodness-of-fit to a 3:1 resistant to susceptible ratio in the F2 generation or a 1:2:1 segregation of nonsegregating for rust resistance, segregating, and nonsegregating for rust susceptibility in the F3 generation. To detect segregation distortion of markers, the F2 population marker data was tested for goodness-of-fit to a 3:1 ratio.
Because of the dominant character of RAPD and SCAR markers, the linkage analysis of seven coupling- or five repulsion-phase markers with the Ur-6 locus for SR to rust was separately performed on the data for 100 F2 plants of the cross Olathe x Nebr.#1 sel.27 by MAPMAKER version 3.0 (Lander et al., 1987). On the basis of a logarithm of odds (LOD) score of 3.0 and a linkage threshold of 0.4, LGs were displayed by the Group command. To establish a LG, a subset of markers was initially selected on the basis of LOD scores and pairwise linkages. The best linkage order within the subset was calculated by the Compare command and then, additional markers were inserted by the Try command. LOD scores of at least 2.0 were considered different between the most and second most likely position for the marker. The Ripple command was finally used to check the marker order. Map distances (centimorgan, cM) between ordered loci of marker and gene were calculated using recombination fractions and the Kosambi mapping function (Kosambi, 1944).
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RESULTS AND DISCUSSION |
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TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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2 = 0.01 and P = 0.91) of number of resistant to susceptible F2 plants to race 51 was observed. It was hypothesized that a single dominant gene controlled SR to race 51. The genetic hypothesis of a single dominant gene for resistance to race 51 was confirmed in the F3 generation based on a satisfactory fit to a 1:2:1 ratio (2 = 1.35 and P = 0.51) of number of families nonsegregating for resistance, segregating for resistance and susceptibility, and nonsegregating for susceptibility. A single dominant gene for SR to race 51 found here agrees with the findings of Grafton et al. (1985) and McClean et al. (1994), who reported that the reaction to races 44 and 47 of the rust pathogen was controlled by a single dominant gene in F2 populations from two pinto bean crosses Olathe x UI-114 and Sierra x Olathe. However, Grafton et al. (1985) also reported two complementary dominant genes controlling resistance to race 44 in an F2 population from a cross Olathe x T-39 and two independent genes conferring resistance to races 44 and 52 in an F2 population from a cross Olathe x Aurora. The symbol Ura was assigned by Grafton et al. (1985) for the dominant resistance gene of Andean origin present in Olathe of the MA background. The Ura gene was subsequently defined as Ur-6 by Kelly et al. (1996). It is known to be independent of other rust resistance genes and is resistant to 58 of 93 races available at USDA-Beltsville (Pastor-Corrales, USDA-Beltsville, personal communication).
RAPD Markers Linked to Ur-6 for Specific Rust Resistance
A total of 680 primers were used for the RAPD analysis of two different bulks developed from resistant and susceptible F2 plants along with their parents Olathe and Nebr.#1 sel.27. Thirty-two RAPD markers were polymorphic for the two different DNA bulks. Twenty displayed an amplified DNA fragment in the resistant bulk that was absent in the susceptible bulk (Fig. 1a)
. Twelve showed an amplified DNA fragment in the susceptible bulk that was absent in the resistant bulk (Fig. 1c). These 32 marker fragments segregated in the F2 population of the cross Olathe x Nebr.#1 sel.27. Of the 32 markers, 11 were identified to be linked to Ur-6 on the basis of linkage analysis. A goodness-of-fit to a 3:1 ratio for band presence to band absence for each of the 11 markers was observed in 100 F2 plants (Table 1).
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Of the five repulsion-phase RAPD markers linked to Ur-6 identified in the F2 population from the cross of Olathe x Nebr.#1 sel.27, two markers OAB18.650 and G5.500 were also polymorphic between the parents BelNeb-RR-1 and A 55 that were utilized to create the RIL population from which the RAPD marker-based linkage map was constructed (Ariyarathne et al., 1999). These two repulsion-phase markers, very loosely linked to the Andean gene in the F2 population, displayed an amplified DNA fragment in the A 55 parent susceptible to rust, whereas they were absent in the BelNeb-RR-1 parent resistant to rust. The two markers OAB18.650 and G5.500 were observed to be located within a distance of 4 cM on LG 11 of the RAPD marker-based linkage map constructed from the RIL population from the cross GN BelNeb-RR-1 x A 55 (Fig. 2), suggesting that Ur-6 was positioned on LG 11 of the map. However, six coupling-phase RAPD markers linked to Ur-6 found in the F2 population here were not noted on the RAPD linkage map.
The Ur-6 location found here confirms the finding of Miklas et al. (2002), who reported that the Andean gene was mapped on LG 11 of the core bean linkage map, on the basis of the result of McClean et al. (1994). Important rust resistance genes of MA origin such as Ur-3, Ur-7, and Ur-11 are located on LG 11 of the core bean map, while other rust genes Ur-9 of Andean origin, Ur-5 of MA origin, Ur-4 of Andean origin, and Ur-12 are located on LGs 1, 4, 6, and 7, respectively (Miklas et al., 2002; Park et al., 2003). However, Ur-6 is located in a different region on LG 11 with respect to the other important rust resistance genes, on the basis of the results of Miklas et al. (2002) and Park et al. (2003). Thus, a total of five rust resistance genes including four of MA origin and one of Andean origin have been mapped on LG 11 of the core bean map.
Development of a SCAR Marker Linked to Ur-6
The coupling-phase RAPD marker OBC06.300 tightly linked to Ur-6 at a distance of 1.3 cM identified in the F2 population from the cross Olathe x Nebr.#1 sel.27 was converted into a SCAR marker on the basis of the specific forward and reverse 24-mer primer pair. The size of the RAPD fragment OBC06.300 was 308 bp based on the sequence data obtained from the DNA sequencing and synthesis facility of the Iowa State University. For generating the SCAR marker, we designed the specific forward and reverse 24-mer primer pair based on the sequence of the RAPD fragment OBC06.300. The sequence of the forward primer was 5'-GAAGGCGAGAAGAAAAAGAAAAAT-3', while that of the reverse primer was 5'-GAAGGCGAGAGCACCTAGCTGAAG-3'. The underlined sequences were the original 10-mer sequence of the OBC06 primer. Melting temperatures of the forward and reverse primers were 58 and 67°C, respectively.
The marker SOBC06.308, the name of the SCAR marker amplified with the specific forward and reverse primer pair, is shown in Fig. 1b. The marker SOBC06.308 was present in the resistant parent Olathe and the DNA bulk from resistant F2 plants, whereas it was absent in the susceptible parent GN Nebr.#1 sel.27 and the DNA bulk from susceptible F2 plants. The SCAR marker fragment segregated in the F2 population of the cross Olathe x GN Nebr.#1 sel.27. A goodness-of-fit to a 3:1 ratio for band presence to band absence for the marker SOBC06.308 was observed in 100 F2 plants (Table 1). The integrated location of the Ur-6 locus and the loci of six coupling-phase markers including the SCAR marker is shown in Fig. 2. The marker SOBC06.308 showed no recombination with the RAPD marker OBC06.300 in the F2 population, and thus, the SCAR and RAPD markers were observed at the same locus on the LG. The marker SOBC06.308 was also closely linked to Ur-6 at 1.3 cM. The results confirm that the SCAR marker SOBC06.308 was derived from the RAPD marker OBC06.300. This is the first report of a coupling-phase SCAR marker linked to Ur-6 in common bean.
No recombination between the RAPD marker OBC06.300 and the SCAR marker SOBC06.308 was expected. However, Melotto et al. (1996) observed a few recombinations between the RAPD marker OW13.690 and the SCAR marker SW13 linked to the I gene in a N84004/Michelite population. Adam-Blondon et al. (1994) reported a codominant SCAR marker linked to the Are gene for resistance to anthracnose in bean, caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.Scrib. For rust resistance, Correa et al. (2000) developed SCAR markers SCARBA08 and SCARF10 linked to Ur-Ouro Negro at 4.3 and 6.0 cM, respectively, on LG 4 of the core map.
Survey of RAPD and SCAR Markers in Diverse Bean Germplasm
We investigated the presence or absence of the SCAR marker SOBC06.308 as well as RAPD markers OBC06.300 and OAG15.300 in 33 MA pinto bean cultivars–breeding lines (Table 2). In combination with Ur-3 or Ur-11 of MA origin, Ur-6 was widely utilized in developing rust resistant pinto bean breeding lines including two BelDak (Stavely and Grafton, 1989) and six BelDakMi breeding lines (Stavely et al., 1992). All BelDak and BellDakMi bean lines were observed to be resistant to race 51. The presence of the two RAPD and one SCAR markers was associated with BelDak-RR-1 and 2 possessing Ur-6. Also, these three marker fragments were amplified in BelDakMi-RR-1, 2, 5, 10, 14, and 18 (genotype = Ur-6), while no marker fragment was amplified in BelDakMi-RR-4 (genotype = ur-6). Along with either Ur-5 or Ur-11, this Andean gene is currently being used to develop rust resistant pinto bean breeding lines in Colorado bean breeding programs. The presence of the markers was consistently associated with all 10 Colorado lines mostly resistant to race 51. The gene was incorporated into several elite pinto bean cultivars such as Apache, Bill Z, Burke, Topaz, and Kodiak (Wood et al., 1989). The RAPD and SCAR marker fragments were present in the five bean cultivars resistant to race 51. Other susceptible pinto cultivars or lines without the gene, except UI-111, lacked the marker fragments. These results would be expected because of the tight linkage of the markers with the gene. Thus, the RAPD and SCAR markers could be useful in breeding and selecting the Andean gene for rust resistance in MA pinto bean germplasm.
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We conducted the survey of the RAPD and SCAR markers in 13 Andean beans (Table 2). Golden Gate Wax (GGW), resistant to race 51, possessed the coupling-phase markers tightly linked to Ur-6. This result is consistent with the finding of Stavely et al. (1983), who reported that the wax bean cultivar also possessed Ur-6 originally identified by Ballantyne (1978). However, the three markers were also present in six Andean cultivars without Ur-6. The marker fragments were absent in other six susceptible Andean beans lacking the gene. This would be expected because the gene is originally from the Andean gene pool. Miklas et al. (1993) and Haley et al. (1993) reported similar results that Andean beans lacking Ur-4 had a marker linked to the Andean gene, and MA beans without Ur-5 possessed a marker linked to the MA gene. Survey information of the remaining coupling-phase linked RAPD markers, except OAC03.600, to Ur-6 in 70 MA and Andean beans was similar to that of the most closely linked RAPD and SCAR markers, and thus, was not included.
The RAPD and SCAR markers were generally regarded as gene pool specific on the basis of the analysis of our marker survey (Table 2). Miklas et al. (1993) and Park et al. (2003) reported a gene pool specificity and usefulness of their identified markers for Ur-4 and Ur-7 in MA bean germplasm, respectively. A race specificity was also observed within the Andean gene pool (Haley et al., 1993). However, Haley et al. (1994) and Melotto et al. (1996) reported no gene pool or race specificity on the basis of marker surveys in a MA and Andean bean collection, and utility of their linked markers for Ur-3 and I for BCMV resistance across MA and Andean bean gene pools.
Grafton et al. (1985) reported an additional rust resistance gene Urc present in Olathe. Kelly et al. (1996) assumed that two rust resistance genes, Urc and Ur-7, present in GN1140 were the same. Park et al. (2003) reported that two coupling-phase markers, OAD12.550 and OAF17.900, that cosegregated with Ur-7 on LG 11 were present in Olathe, whereas they were absent in GGW possessing Ur-6. The markers were not linked to Ur-6 in the F2 population of the cross Olathe x Nebr.#1 sel.27 (Park et al., 2003). Our RAPD and SCAR markers on LG 11 amplified from Olathe and GGW were absent in GN1140 carrying Ur-7 as well as US-5, from which the rust resistance of GN1140 was derived (Table 2). Thus, we conclude that Ur-6 and Ur-7 are distinct and loosely linked on LG 11. This marker information surveyed in key cultivars is indirect evidence that Urc and Ur-7 are the same gene. Olathe, Bill Z, and BelDak-RR-1 having Ur-6 are candidates to have Ur-7 because of the presence of the markers for Ur-7, whereas GGW and BelDakMi-RR-1, which possess Ur-6, lack Ur-7.
For the MA gene pool, coupling-phase RAPD markers linked to four different rust resistance genes have been developed: OI19.460 linked to Ur-5 in Mexico 309 (Haley et al., 1993), OK14.620 linked to Ur-3 in Aurora (Haley et al., 1994), OAC20.490 linked to Ur-11 in PI181996 (Johnson et al., 1995), and OAD12.550 linked to Ur-7 in GN1140 (Park et al., 2003). Similarly, two different rust resistance genes from the Andean gene pool have tightly linked coupling-phase RAPD markers: OA14.1100 linked to Ur-4 in Early Gallatin (Miklas et al., 1993) and OA4.1050 linked to Ur-9 in PC-50 (Park et al., 1999).
Kelly (1995) reported that pyramiding three major rust resistance genes such as Ur-3, Ur-4, and Ur-5 resulted in resistance to 63 of 65 bean races. The coupling-phase RAPD and SCAR markers linked to Ur-6 of Andean origin in Olathe and GGW identified here, along with the markers linked to the above genes, could be utilized to develop a P. vulgaris cultivar or line with different genes pyramided for enhanced broad rust resistance. Recombining resistance genes from both Andean and MA gene pools should provide more durable resistance to rust (Park et al., 1999).
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ACKNOWLEDGMENTS |
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NOTES |
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TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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Received for publication September 24, 2003.
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TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
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