Crop Science 40:1445-1452 (2000)
© 2000 Crop Science Society of America
CELL BIOLOGY & MOLECULAR GENETICS
Molecular Markers Useful for Detecting Resistance to Brown Stem Rot in Soybean
K.L.E. Klosa,
M.M. Paza,
L.Fredrick Mareka,
P.B. Creganc and
R.C. Shoemakerb
a Dep. of Agronomy, Iowa State Univ., Ames, IA 50011 USA
b USDA-ARS-CICGR and Dep. of Agronomy and Dep. of Zoology/Genetics, Iowa State Univ., Ames, IA 50011 USA
c USDA-ARS, Soybean and Alfalfa Research Lab., Beltsville, MD 20705 USA
rcsshoe{at}iastate.edu
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ABSTRACT
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Brown stem rot (BSR) causes vascular and foliar damage in soybean [Glycine max (L.) Merr.]. Identification of plants resistant to BSR by inoculation with Phialophora gregata (Allington & W.W. Chamberlain) W. Gams is laborious and unreliable because of low heritability. Molecular markers linked to the resistance gene could be used to screen for resistant individuals and hasten the development of BSR resistant genotypes. The objective of this study was to develop molecular markers for efficient identification of BSR resistant plants in a breeding program. Seventeen resistant and 29 susceptible cultivars and plant introductions as well as recombinant inbred lines derived from a cross between BSR 101 and PI 437.654 were assayed by PCR-based markers derived from RFLPs K375I-1 and RGA2V-1, Satt244, or developed from bacterial artificial chromosome (BAC) sequences. The DNA markers that were developed tag the BSR locus and are informative in a diverse range of soybean germplasm. Markers detected different banding patterns between resistant and susceptible genotypes. The PCR-based markers will most likely be useful in screening for BSR resistance and allow soybean breeders to transfer rapidly resistance derived from Rbs3 to improved cultivars or soybean lines. The markers are relatively easy-to-use, inexpensive, and highly informative. Soybean breeding efforts can now be designed to incorporate the use of marker information when parental genotypes possess contrasting banding patterns.
Abbreviations: BSR, brown stem rot • MAS, marker-assisted selection • PCR, polymerase chain reaction • PI, plant introduction • RAPD, random amplified polymorphic DNA • RFLP, restriction fragment length polymorphism • RIL, recombinant inbred line • SSR, simple sequence repeat
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INTRODUCTION
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BROWN STEM ROT is a devastating fungal disease of soybean (Glycine max) caused by Phialophora gregata, a soil-borne fungus. The pathogen infects host plants through the roots and causes vascular and foliar injury to the susceptible plants (Allington and Chamberlain, 1948; Mengistu and Grau, 1986). The disease is prevalent in soybean producing regions of the northern USA and Canada (Sinclair and Backman, 1989) and has been estimated to cause a yield reduction of over 20 million bushels each year in the north central states alone, depending upon environmental conditions (Doupnik, 1993).
Host resistance is the main means of controlling BSR. Plant introductions (PIs) have been identified as sources of non-allelic BSR resistance genes: PI 84946-2 for Rbs1 (Sebastian and Nickell, 1985) and Rbs3 alleles (Eathington et al., 1995); PI 437.833 for Rbs2 (Hanson et al., 1988); and PI 437.970 for Rbs3 (Willmot and Nickell, 1989). Other resistance genes may exist. Multiple genes may control BSR resistance in Asgrow A3733 which are not derived from known sources of resistance (Waller et al., 1991). Nelson et al. (1989) identified three resistant lines: PI 424.285A; PI 424.353; and PI 424.611A from more than 3400 accessions from the USDA Soybean Germplasm Collection. Bachman et al. (1997) screened 559 soybean accessions from China and found 13 accessions with resistance to BSR. Most of the publicly released BSR resistant cultivars and breeding lines are derived from PI 84946-2, including BSR101 which has the Rbs3 allele (Eathington et al., 1995). Under conditions where P. gregata infection affects yield, Sebastian et al. (1985) found that in soybean lines derived mostly from PI 84946-2, BSR resistance was associated with a 12 to 16% yield advantage.
Molecular markers close to a gene of interest may be useful for selection in breeding programs, especially for agronomic traits which are difficult to analyze, e.g., disease resistance, insect resistance, and quantitative traits (Lawson et al., 1997; Mohan et al., 1997; Heer et al., 1998). Selection of genotypes resistant to BSR by inoculating plants with isolates of P. gregata is laborious and time-consuming. Moreover, assessment of BSR incidence is rendered difficult by seasonal and environmental variation (Nicholson et al., 1973). Soybean breeding efforts to transfer BSR resistance to improved cultivars or soybean lines have been hampered by the low heritability
of the trait (Sebastian et al., 1985). Several examples of the application of molecular markers in breeding programs have been presented. Simple sequence repeat (SSR) markers have been used for assessing heterosis in rice breeding (Liu and Wu, 1998). Random amplified polymorphic DNA (RAPD) and sequence characterized amplified region (SCAR) markers were utilized to characterize anthracnose resistance in common bean (Young et al., 1998) and rust resistance in sunflower (Helianthus annuus L.; Lawson et al., 1998).
Marker-assisted selection (MAS) could facilitate the development of BSR resistant genotypes. MAS is more efficient than selection based on the phenotype for a trait with low heritability (Van Berloo and Stam, 1999). Gene introgression can readily be followed using molecular markers, which are not influenced by the environmental conditions in which plants are grown. Lewers et al. (1999) identified and mapped molecular markers linked with BSR resistance in the soybean cultivar BSR 101. This study is a follow-up to Lewers et al. (1999) in an attempt to develop breeder-friendly markers. Here we report the development and evaluation of nine new DNA markers that can detect BSR resistance in a diverse range of soybean germplasm and discuss their utility in soybean breeding programs.
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Materials and methods
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Genomic DNA Extraction
Forty-six BSR resistant or susceptible genotypes (Table 1)
were identified by querying GRIN data [The Germplasm Resources Information Network (GRIN), 1999] through SoyBase ACEDB version 4.3 (http://genome.cornell.edu/cgi-bin/WebAce/webace?db=soybase; verified April 26, 2000). Most BSR resistant genotypes were derived from PI 84946-2 and possess the Rbs3 or Rbs1 allele. Cultivars and PIs with other sources of resistance were also included (Table 1). Seed for each genotype was obtained from R. Nelson, curator of the USDA Soybean Germplasm Collection, Urbana, IL, or from the R. Shoemaker laboratory, Dept. of Agronomy, Iowa State University, Ames, IA. Seedlings were grown in the greenhouse and DNA was isolated by a method adapted from Saghai-Maroof et al. (1984). The first trifoliate was harvested, freeze-dried, and ground. The DNA was extracted from 750 mg dried tissue with CTAB buffer followed by chloroform:isoamyl alcohol (24:1) separation and precipitated with 2/3 volume isopropanol, rinsed with 80% (v/v) ethanol:15 mM ammonium acetate solution. After being air-dried, the DNA was resuspended in 1x TE (Tris-EDTA) buffer.
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Table 1 BSR resistant and susceptible germplasm analyzed for the nine PCR-based markers. The allele(s) responsible for BSR resistance is given in parentheses when known
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PCR Primer Design
PCR primers were selected from DNA sequences by OLIGO software (National Biolabs, St. Paul, MN). Oligonucleotide primers for K375.sp1 and BSR3.sp1 were designed by means of the DNA sequences of RFLP probes K375 and RGA2, respectively.
The Gm_ISb001 soybean genomic library (Marek and Shoemaker, 1997) was probed with the K375 RFLP probe to identify bacterial artificial chromosome (BAC) clones having homology to the region of interest. The BACs identified were sequenced from both ends and these sequences were used to develop primers for PCR. PCR amplification products were evaluated for fragment size polymorphism between BSR101 and PI437.654. PCR products not polymorphic in amplification fragment size were screened for restriction site polymorphisms by restriction enzyme digests. Markers polymorphic between BSR101 and PI437.654 were considered for further evaluation of their utility in detecting polymorphism at theRbs3 locus. Satt244, a SSR marker, was developed according to procedures described in Akkaya et al. (1995) and Cregan et al. (1999). Soybean SSRs were developed both from SSR containing sequences available in GenBank and from genomic subclones of Williams soybean DNA. SSR containing subclones were identified by colony hybridization screening using labeled oligonucleotide probes. Positive clones were rescreened and then sequenced to locate the SSR. Primers were developed for more than 600 SSR markers including Satt244. The primers were tested against Williams DNA and 10 additional soybean genotypes. Primers that identified a polymorphism between G. max (A81-356022) and G. soja (PI 468.916) were mapped in a F2-derived mapping population. Because Satt244 mapped to a region of linkage group J identified by Lewers et al. (1999) to be significantly correlated with BSR resistance in BSR101, it was chosen for further testing to screen for resistance in a wide range of germplasm.
PCR Reaction Conditions
PCR reactions for the BSR3.sp1, K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, and 98P22.sp2 markers were carried out in a 20-µL reaction mixture containing 60 ng of genomic DNA, 0.5 µM of each primer, 1x Gibco-BRL PCR buffer, 1.5 mM MgCl2, 100 µM each of dGTP, dTTP, dATP and dCTP, 0.5 U Taq Polymerase (Gibco-BRL), and 0.5x SCR dye [6% (w/v) sucrose, 100 µM cresol red]. The PCR conditions for BSR3.sp1 and 35E22.sp1 consisted of 94°C for 2 min followed by 35 cycles of 94°C for 1 min (denaturation), 58°C for 45 s (annealing), 72°C for 1 min (extension), and a final extension at 72°C for 5 min. PCR conditions for K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, and 98P22.sp2 were as described above with the exception of the annealing temperatures which were as follows: for K375.sp1, 14H13.sp1 and 30L19.sp1 the annealing temperature was 56°C; and for 21E22.sp1, 21E22.sp2, and 98P22.sp1 it was 62°C. Amplification products of 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, and 98P22.sp2 were digested with RsaI, MspI, HhaI, Hsp92II, HhaI, and EcoRI restriction enzymes, respectively, at 2 U/µL for 1.5 h at 37°C.
SSR analyses were carried out in 20-µL reactions with 60 ng of genomic DNA, 0.15 µM of each primer, 1x Gibco-BRL PCR buffer, 2 mM MgCl2, 200 µM each of dGTP, dTTP, dATP and dCTP, 0.75 U Taq Polymerase (Gibco-BRL), and 0.5x SCR dye [6% (w/v) sucrose, 100 µM cresol red). The thermal cycling conditions for the SSR assay were 94°C for 1 min followed by 45 cycles of 94°C for 30 s, 47°C for 30 s, and 68°C for 30 s.
Amplification and digestion products of these markers were separated using a 2% (w/v) agarose gel in 1x TAE (Tris/acetate/EDTA) and visualized by ethidium bromide staining. The samples were electrophoresed for 3 h at 90 V.
Molecular Marker Evaluation
PCR and enzyme digest products were compared to determine the efficacy of distinguishing BSR resistance in different cultivars and PIs. Restriction enzyme recognition site polymorphisms and polymorphic amplification products were observed between the parents of several mapping populations including the parents of the population segregating for brown stem rot resistance, BSR 101 and PI 437.654. The gene diversity of a locus, defined by Weir (1990) as the amount of polymorphism in homozygous progeny of a self-fertilizing species, has been used as an estimator of the polymorphism information content (PIC) value of a molecular marker (Anderson et al., 1992). The PIC value of a PCR-based marker was calculated as adapted by Weir (1990)(p. 125) from Nei (1987)(p. 106–107):
where Pij is the frequency of the jth PCR pattern for Genotype i.
In addition, PCR analyses using all nine markers were done on a recombinant inbred line (RIL) population derived from a cross between BSR 101 and PI 437.654 (Baltazar and Mansur, 1992) which are resistant and susceptible to BSR, respectively. RILs were screened for BSR resistance by Lewers et al. (1999). For mapping purposes, the banding patterns in the parental genotypes and in the RILs were scored as A or B in 320 RILs. The markers were added to the map reported by Lewers et al. (1999) by Mapmaker 2.0 with the default parameters LOD 3.0 and maximum recombination of 30%. The `TRY' and the `RIPPLE' commands were used to confirm the map (minimum LOD score of 2.0, window size of 3).
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Results
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Marker Identification
The method of location-specific molecular marker development, utilizing DNA sequences from RFLP probes and BACs, was successful at generating markers which mapped to the region of interest on soybean linkage group J (Fig. 1B)
. Twenty-nine PCR primer sets developed from BAC end sequences were discarded from further evaluation in this study due to lack of polymorphism between BSR101 and PI437.654. The markers BSR3.sp1, and K375.sp1 (Table 2) , developed from RFLP probe sequences were polymorphic in PCR amplification size between BSR101 and PI437.654. Two PCR primer sets developed from BAC sequences were observed to amplify fragments polymorphic in size between BSR101 and PI437.654 (data not shown), but these polymorphisms were not reproducible under stringent PCR conditions and so were discarded from further evaluation. Polymorphism between BSR101 and PI437.654 was observed in six markers (14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, and 98P22.sp2) developed from BAC end sequences after restriction enzyme digest of the PCR product (Table 2). This study demonstrates the utility of BAC library sequences in conjunction with an experimental population segregating for the gene of interest as a source of new markers that are polymorphic among a large group of genotypes.
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Fig. 1 Soybean Linkage Group J from the BSR101 by PI437.654 recombinant inbred line population showing: A. Marker association with brown stem rot resistance as measured by foliar disease severity, and B. Map locations of new markers in relation to RGA2V-1 and K375I-1. Associations are illustrated by a curve from QTL Cartographer. The horizontal bar indicates significance at
. Adapted from Lewers et al. (1999)
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Segregation Analysis
RILs derived from a cross between BSR 101 and PI 437.654 were analyzed to confirm the usefulness of markers to monitor BSR resistance during inbreeding, i.e., to confirm linkage with Rbs3. A total of 320 RILs were assayed with BSR3.sp1, K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, 98P22.sp2, and Satt244. The marker scores were used to map the nine new markers against one another and to place them in relation to the molecular genetic map reported by Lewers et al. (1999) with the same set of RILs. Lewers et al. (1999) mapped markers associated with one major and one minor QTL in linkage group J (Fig. 1A). A major gene (Rbs3) and a second gene with a minor effect control BSR resistance in BSR101 (Eathington et al., 1995). We believe that markers identified in this study are at the major QTL (Rbs3) that was mapped by Lewers et al. (1999) between RGA2V-1 and G8.15V-1 of linkage group J (Fig. 1). BSR3.sp1 was mapped near marker RGA2V-1. The K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, and 98P22.sp2 markers mapped within the cluster of markers AAGATG152E, AAGATG152M, K375I-1, and ACAAGT260. Satt244 was mapped near the RFLP markers K005V-2 and G815V-1. All of these markers are in the region of linkage group J identified to have the maximum correlation with BSR resistance controlled byRbs3, in BSR 101 (Fig. 1; Lewers et al., 1999).
The BSR3.sp1, K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, 98P22.sp2, and Satt244 markers were successful at differentiating among resistant and susceptible RILs. Three hundred twenty RILs were inoculated with Phialophora gregata in a glasshouse by Lewers et al. (1999) and rated for foliar disease severity from 0 (healthy) to 10 (all leaflets dead or missing). We compared their foliar severity results with our marker evaluation of the RIL population. Figure 2
shows the number of RILs within each BSR disease rating that were scored for the `A' allele (derived from the resistant parent) or the `B' allele. This figure indicates the number of RILs which would have been incorrectly classified as resistant by the marker allele score as the selection criteria. For example BSR3.sp1 identified 148 RILs as potentially resistant on the basis of the `A' allele, but 41 of these have disease severity ratings of 5 or greater (susceptible to highly susceptible). 30L19.sp1 identified 132 potentially resistant RILs, and 34 of these were rated 5 or greater in the greenhouse disease severity screen. A set of 44 RILs was identified as highly resistant and a set of 49 RILs as highly susceptible to BSR based on foliar symptoms in relation to the parental genotypes (Lewers et al., 1999). These markers were able to identify highly resistant genotypes with an accuracy of 90% or greater, and susceptible genotypes with a greater than 85% accuracy (Table 3)
. These markers will be particularly useful for monitoring soybean populations segregating for Rbs3.
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Fig. 2 BSR foliar disease severity ratings (0 = healthy to 10 = most severe) (x axis) and the number of RILs possessing the `A' allele or the `B' allele (y axis) for BSR markers BSR3.sp1, K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, 98P22.sp2, and Satt244. The `A' allele corresponds to that derived from the resistant parent. The `B' allele corresponds to that derived from the sensitive parent
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Table 3 Polymorphism information content (PIC) values and frequency of BSR101 parental allele (`A') in 44 recombinant inbred lines scored as highly resistant to brown stem rot on the basis of foliar symptoms; the frequency of PI437.654 parental allele (`B') in 49 lines scored as highly susceptible, for nine DNA markers on the basis of 46 genotypes
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Evaluation in Soybean Germplasm
The DNA markers, BSR3.sp1, K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, 98P22.sp2, and Satt244, which were developed on the basis of polymorphism between BSR101 and PI437.654, were evaluated in a set of cultivars, PIs, and ancestral genotypes identified as resistant or susceptible to brown stem rot on the basis of GRIN data (Fig. 3)
. The markers differed in the degree of polymorphism observed among the set of genotypes evaluated. The PIC values (Table 3) signify the possible usefulness of the markers as a means of detecting a polymorphism between two soybean cultivars. The largest PIC value was observed for Satt244 and the smallest for 98P22.sp2. A larger PIC value indicates a greater likelihood that polymorphism will be observed between any two genotypes. In a soybean breeding program to transfer BSR resistance due to the Rbs3 gene, a susceptible cultivar could be used as one parent and a resistant cultivar with a dissimilar PCR banding pattern could be used as the other parent. The marker 35E22.sp1 had the second lowest PIC value, yet it is apparent in a comparison of the banding patterns of resistant and susceptible genotypes that this marker may, along with 21E22.sp1, 21E22.sp2, and 30L19.sp1, be one of the most useful as predictor of resistance in a germplasm screening program (Fig. 3). None of the markers differentiated among the different genes for BSR resistance. Many of the BSR resistant soybean lines included in this study have theRbs3 allele (Table 1). Soybean lines L78-4049 and PI 437.833 have BSR resistance alleles Rbs1 and Rbs2, respectively; and PI 84946-2 has both Rbs1 and Rbs3 (Eathington et al., 1995; Hanson et al., 1988; Willmot and Nickell, 1989; Sebastian and Nickell, 1985). The source of BSR resistance in the remainder of the lines is unknown, but may be due to the presence of one or more alleles for BSR resistance, possibly including Rbs3. No marker or combination of markers from this set could be identified which would differentiate among resistant lines with different alleles (Fig. 3). Therefore, the use of these markers in a breeding program for BSR resistance requires a parent whose resistance is known to be due to the Rbs3 gene, or a test of linkage between resistance and the marker in the segregating progeny. For example, a marker screening program in the progeny of a cross between L78-4094 and any of the susceptible genotypes in Fig. 3, determined on the basis of the polymorphic 35E22.sp1 marker, would not select BSR resistant lines because L78-4094 is resistant due to the Rbs1 allele (Table 1).
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Fig. 3 Amplification banding patterns of BSR3.sp1, K375.sp1, 14H13.sp1, 21E22.sp1, 21E22.sp2, 30L19.sp1, 35E22.sp1, 98P22.sp2, and Satt244 markers in 46 soybean cultivars and PIS which are resistant or susceptible to BSR .
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The greenhouse or field screening procedure for evaluating BSR resistance involves inoculating plants with the causal pathogen and obtaining foliar and stem ratings for disease severity. This method is lengthy, often involves destructive sampling, and disease symptoms are affected by environmental conditions. Our objective was to develop breeder-friendly markers for efficient identification of BSR resistant plants in any soybean population possessing one of the major BSR resistance genes. The markers developed in this study will most likely be useful for screening BSR resistance and allow soybean breeders to rapidly transfer resistance derived from Rbs3 to improved cultivars or new and improved soybean lines. The markers described here are easy-to-use, inexpensive, and highly informative. These markers may also be used to more precisely identify the location of the resistance gene for the purpose of map-based cloning.The Germplasm Resources Information Network 1999
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ACKNOWLEDGMENTS
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The authors want to thank Dr. Kim S. Lewers and Clay Baldwin for their help in developing the PCR assay of K375.sp1 marker.
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NOTES
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Research supported by Iowa Soybean Promotion Board. Contribution of the North Central Region USDA-ARS, Project 3236 of the Iowa Agric. and Home Economics Stn. (Journal Paper no. J-18668), Ames, IA 50011-1010. Names are necessary to report factually on the available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable.
Received for publication November 19, 1999.
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ABSTRACT
INTRODUCTION
