| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
a Plant Science Department, South Dakota State University, Brookings, SD 57007
b Crop and Soil Science Department, Michigan State University, East Lansing, MI 48824
c USDA-ARS, 605 Airways Blvd., Jackson, TN 38331
d Department of Agronomy, Iowa State University, Ames, IA 50011
e Department of Crop Sciences, University of Illinois, Urbana, IL 61801
* Corresponding author (bdiers{at}uiuc.edu).
 |
ABSTRACT |
|---|
 TOPNOTES ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
|---|
Abbreviations: cM, centimorgan • LG, linkage group • NIL, near isogenic line • QTL, quantitative trait locus • SCN, soybean cyst nematode • SSR, simple sequence repeat marker
|
INTRODUCTION |
|---|
|
TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
|---|
Genetic studies indicate that ‘Peking’, PI 90763, and PI 88788 have major genes in common that provide resistance to SCN Race 3 (Rao Arelli and Anand, 1988). Further research by Rao Arelli et al. (1992) indicates that Race 3 SCN resistance in PI 88788 is inherited by three genes, with one recessive and two dominant. The genetic evidence indicates that one of the dominant genes is at a previously unreported locus which was designated Rhg5 (Rao Arelli, 1994) the second gene is Rhg4, which maps close to the i gene (Matson and Williams, 1965), and the recessive gene is rhg2. Genetic mapping efforts have since shown that PI 88788 has a major QTL on LG G (Concibido et al., 1997), and a second minor QTL on LG C2 (Diers et al., 1997a). The QTL on LG G maps to the same region where a major resistance locus was mapped in PI 437654 (Webb et al., 1995), Peking, PI 90763, PI 89772, and PI 209332 (Concibido et al., 1997; Concibido et al., 1996; Yue et al., 2001). The resistance gene in this region has been designated rhg1 in the literature and Cregan et al. (1999b) reported a linkage of 0.4 centimorgans (cM) between the simple sequence repeat (SSR) marker Satt309 and rhg1 in crosses with Peking and PI 209332 as sources of SCN resistance.
Although many QTL have been mapped in soybean, few have been confirmed in additional populations in the same or different genetic backgrounds. The confirmation of QTL after initial mapping is a critical step before the selection of the QTL with markers in breeding programs. Near isogenic line populations are particularly useful for QTL confirmation because they are developed to segregate for QTL in an otherwise homogeneous background. Populations of NIL can be formed quickly by identifying lines in inbred mapping populations that were derived from plants that were heterozygous for the region containing the QTL. Plants from within these lines would be individually harvested to form populations of NIL (Haley et al., 1994).
There is great interest in conducting marker-assisted selection (MAS) for SCN resistance genes since screening with nematodes is tedious and expensive. Soybean PI 88788 continues to be a widely used source of SCN resistance, and mapping of additional SCN resistance genes from this source is necessary. The mapping of these genes will allow efficient MAS in germplasm developed with PI 88788 resistance. The objective of our research was to map and confirm SCN resistance QTL in Bell, a cultivar carrying resistance from PI 88788.
|
MATERIALS AND METHODS |
|---|
|
TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
|---|
Three populations that segregate for the region containing the LG J SCN resistance QTL were developed to confirm this QTL. Each population was developed from one of three lines from the original F4 population. These three lines were selected because each was derived from a plant heterozygous for the region on LG J. These lines were segregating for the SSR markers Satt431, Satt244, and Satt547 on LG J. In addition, the allele at rhg1 in each line was predicted to be fixed based on results from the SSR marker Satt309, which is closely linked to rhg1. The F4–derived lines were advanced to the F7 generation as bulks and the NIL populations were developed by threshing individual F7 plants from the selected lines. There were 48 lines in both NIL populations 1 and 2 (NIL1, NIL2), and 56 lines in NIL population 3 (NIL3).
The lines in both the original F4 population and the NIL populations were evaluated for resistance to SCN populations PA3 (HG type 7, race 3) and PA14 (HG type 1.3.5.6.7, race 14) in a greenhouse using five plants from each line according to Diers et al. (1997b). In addition, a second resistance test was done on the NIL populations with PA14. The cultivar Hutcheson was included as a susceptible control for each evaluation. A female index (FI) was calculated for each plant using the formula (Golden et al., 1970):
 |
Hutcheson was used as the susceptible check because it provides a consistent susceptible reaction. Because the five plants from each line were not randomized in the SCN tests, the five plants were treated as subsamples in the data analysis. Pearson product-movement correlations calculated with PROC CORR (SAS, 1988) were used to compare the means of lines for resistance to the two SCN populations.
Molecular Marker and QTL Analysis
The lines in the F4 population were initially tested with 21 restriction fragment length polymorphism (RFLP) and 18 simple sequence repeat (SSR) markers. These markers were selected based on their reported association with SCN resistance in other genetic backgrounds (Chang et al., 1997; Concibido et al., 1994; Concibido et al., 1997; Cregan et al., 1999b; Mahalingam and Skorupska, 1995; Mudge et al., 1997; Webb et al., 1995). An additional 672 SSR markers were used to screen four SCN resistant and four susceptible genotypes in an attempt to identify markers that are likely associated with new resistance QTL from PI 88788. This screening was done by testing PI 88788, the cultivars Fayette, Jack, and Bell, which have resistance from PI 88788, and the susceptible genotypes ‘Williams’, ‘Hardin’, Colfax, and LN80-10398. These genotypes were selected because Fayette was developed by backcrossing using Williams as a recurrent parent and PI 88788 as a donor parent; Fayette crossed with Hardin resulted in the development of Jack, and Bell was selected from a cross between LN80-10398 with Fayette. The entire F4 population was tested with 15 markers that were identified as incorporated from PI 88788 into the SCN resistant cultivars. The NIL populations were tested with only the SSR markers Satt431, Satt244, and Satt547, which map near the LG J QTL.
Genomic DNA was extracted from 10 bulked seedlings per line using a modified CTAB method (Kisha et al., 1997). Genotypic data for RFLP markers were obtained following the protocol described by Diers and Osborn (1994). Simple sequence repeat marker analysis was done with DNA primers developed by Dr. Perry Cregan, USDA-ARS. Polymerase chain reactions (PCR) were performed according to Cregan and Quigley (1997). The PCR products were analyzed by electrophoresis in 3% metaphor (FMC BioProducts, Rockland, ME) agarose gels or 6% (w/v) nondenaturing polyacrylamide gels (Wang et al., 2003).
For the F4 population, linkage and map distances among the selected markers were determined using the computer program JoinMap (Stam, 1993) with the Kosambi (1944) mapping function and a minimum likelihood of odds (LOD) score of 4.0. The composite interval mapping (CIM) method (Zeng, 1994) was applied to detect QTL with the computer program package QTL-CARTOGRAPHER (Basten et al., 1994, 1999). The CIM was run with model 6 of the Zmapqtl program and a window size of 10 cM for all analyses. The threshold of the LOD score for declaring a putative QTL significant was obtained using 1000 permutations, which is a way to determine experimentwise significance levels and comparisonwise probabilities (Churchill and Doerge, 1994; Doerge and Churchill, 1996). Estimates of the R2 value and additive effects for each QTL at its peak LOD position were obtained from the output of QTL analysis using the program Zmapqtl in QTL-CARTOGRAPHER (Basten et al., 1999). These R2 values were obtained by fitting a model including all putative QTL for the respective trait simultaneously.
Single-marker analysis was performed by analysis of variance with PROC GLM in SAS (SAS, 1988) for the NIL and F4 populations. In addition, single-marker analysis was done for the F4 population using linear regression with the LRmapqtl program of QTL-CARTOGRAPHER (Basten et al., 1999). The markers with the greatest R2 values at each independent QTL in the F4 population were tested in pairs with two-factor analysis of variance with PROC GLM to test for epistatic interactions. The marker with the greatest R2 value from each independent QTL was included in a multivariate model with PROC GLM to estimate the total phenotypic variance 
explained by the QTL.
|
RESULTS AND DISCUSSION |
|---|
|
TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
|---|
|
The single-factor marker analysis using SAS and QTL Cartographer identified regions on LGs G, J, and C2 that were significantly (P < 0.01) associated with resistance to PA3 and PA14 (data not shown). The significant regions on LG G and J were also significant (experiment wise P < 0.05) with CIM for both PA3 and PA14 (Table 1). Of the 15 markers identified from the screening of resistant and susceptible genotypes, seven mapped near the QTL on LG J, two mapped near rhg1, and the remaining mapped to six other linkage groups. None of the markers on the other linkage groups were significantly associated with SCN. The regions on the other linkage groups were likely incorporated into the resistant lines by chance or because they conferred an agronomic advantage.
|
|
The second QTL mapped to LG J between markers Satt547 and Satt431 (Fig. 2, Table 1). The LOD peaks for the two SCN populations are about 5 cM apart, however, our mapping resolution is insufficient to determine whether the same locus or two different loci control resistance to the SCN populations. Although a QTL providing SCN resistance from PI 88788 has not been previously reported on this linkage group, a QTL conferring Race 3 resistance from PI 90763 and PI 209332 has been mapped in this region (Concibido et al., 1997).
Single-marker analysis revealed that marker Satt277 on LG C2 was significantly associated with resistance for PA3 and PA14. The CIM method, however, failed to detect any significant QTL at this location. The only previous report of a QTL providing SCN resistance in this region was by Diers et al. (1997a). This was a preliminary report of mapping SCN resistance QTL in the same F4 population described in the current study.
A three-factor analysis was done with PROC GLM of SAS (SAS, 1988) using a model that included Satt309, Satt431, and Satt277, the most significant markers on LG G, J, and C2. For both PA3 and PA14, only the markers Satt309, and Satt431 were significant (P < 0.05) in the analysis. The two significant markers together explained 87% of the phenotypic variance for PA3 and 64% of the phenotypic variance for PA14. No significant resistance interactions were found between any pairs of markers in the two-way and three-way analyses of variance for either SCN population.
Rao-Arelli et al. (1992) reported that PI 88788 has the SCN resistance gene Rhg4, which is closely linked to the i gene (Matson and Williams, 1965). The i gene controls seed coat color and has been mapped to LG A2 (Shoemaker and Specht, 1995). We tested the markers A085I-1 and GMENOD2B that flank i and did not uncover evidence of a QTL conferring resistance to either SCN population in this region. It is possible that PI 88788 had a resistance allele near i, but the gene was not transferred in the development of Bell or its parent Fayette. However, during the development of Fayette, Bernard (per. com, 1999) did not observe evidence of linkage between SCN resistance and seed coat color. Rao Arelli et al. (1992) also did not find evidence of linkage between black seed color from PI 88788 and its resistance to SCN Race 3.
Near Isogenic Line Populations
The NIL populations were developed from lines derived from F4 plants that were heterozygous for the region on LG J that carries the SCN resistance QTL. Because these F4 plants are inbred, the NILs in each population should segregate on average for only 12.5% of the genome, allowing the effect of the LG J QTL to be tested in a relatively homogeneous background. Based on segregation of Satt309, lines in NIL1 and NIL3 populations are predicted to be homozygous for the susceptibility allele at rhg1, whereas lines in the NIL2 population are predicted to be homozygous for the resistance allele at rhg1. These predictions are consistent with the overall means of these populations, with NIL1 and NIL3 having greater mean FI for both SCN populations than NIL2 (Table 2).
|
= 0.05 for only NIL2 (Table 3), and both Satt244 and Satt547 were significant for NIL3 (data not shown). There was no significant association between any of the markers tested on LG J and resistance to PA3 across all three populations or in any of the individual populations.
|
= 0.05, lines homozygous for the Bell allele for Satt431 showed greater resistance than lines homozygous for the Colfax allele in all populations (Table 3). In the F4 population, the effect of the LG J QTL was greater for PA14 than PA3 (Table 1), which is consistent with the NIL results. Based on these confirmation results, the SCN resistance QTL on LG J is designated as cqSCN-003 under the category of confirmed QTL at the Soybase website (http://soybase.ncgr.org/). The prefix cq designates that this QTL has been confirmed according to the rules developed by the Soybean Genetics Committee. Based on this convention, rhg1 has been given the designation cqSCN-001 and Rhg4 has been given the designation cqSCN-002. In the analysis across NIL populations, there was no significant interaction between marker classes for Satt431 and NIL population for either PA3 or PA14. This indicates that the effect of this QTL is independent of whether rhg1 is present in the background. The difference in average FI between the NIL1 and 3, and the relatively high FI value for NIL2 with PA14, suggests that there are still SCN resistance QTL in the Bell that have not been mapped.
Comparison of Results from F4 and Near Isogenic Line Populations
We have observed a reduced effect of cqSCN-003 in the NIL populations compared to the effect observed in the F4 population. It is common to observe inflated QTL effects in mapping studies when relatively small populations are used (Melchinger et al., 1998; Beavis, 1994). A factor that may have inflated the effect of cqSCN-003 was segregation distortion between the regions containing rhg1 and cqSCN-003 (Table 4). If only lines homozygous for each region were considered, the combined segregation of markers from both regions did not fit expectations (
2 = 18.4, P < 0.01) in the F4 population. The distorted segregation was largely the result of fewer lines than expected carrying the resistance allele for Satt309 (Satt309-R) and the susceptibility allele for Satt431 (Satt431-S). The fewer lines than expected in the Satt309-R Satt431-S class would have inflated the difference between the homozygous classes for Satt431 because most Satt431-S lines also carried the susceptibility allele for Satt309 (Satt309-S). This distortion would have made the Satt431-S lines more susceptible than expected based only on the segregation of cqSCN-003. When each marker was evaluated independently, Satt309 deviated from a 1:1 segregation (2 = 6.5, P < 0.05) with fewer lines than expected carrying the resistance allele from Bell. In contrast, segregation of Satt431 did not significantly differ from expected (2 = 0.18, P < 0.5).
|
Webb et al. (1995) observed a strikingly similar segregation distortion in a soybean population developed from crossing the SCN resistant PI 437654 with the cultivar BSR101. They found that segregation of the region containing rhg1, where Satt309 maps, did not segregate independently from a region on LG M, where a second SCN QTL mapped in their population. Similar to our finding, they observed fewer than expected lines carrying both the resistance allele at rhg1 and the allele from the susceptible parent at the second region. Further study is needed to uncover possible mechanisms causing this segregation distortion.
In our study, we have confirmed that cqSCN-003 provides resistance to PA14. Marker assisted selection for cqSCN-003 and rhg1 can be useful for breeders when selecting for SCN resistance with the PI 88788 background since cqSCN-003 can provide greater resistance than is obtained with rhg1 alone. Further work is need to determine the prevalence of cqSCN-003 in elite breeding material and to determine whether there is sufficient polymorphism among elite lines for markers linked to this gene.
|
NOTES |
|---|
|
TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
|---|
Received for publication March 28, 2003.
|
REFERENCES |
|---|
|
TOPNOTESABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONREFERENCES |
|---|
Related articles in Crop Science:
This article has been cited by other articles:
|
|
 |
|
  J. L. De Bruin and P. Pedersen Response of Old and New Soybean Cultivars to Heterodera glycines Ichinohe Agron. J., August 11, 2008; 100(5): 1347 - 1353. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Ishii and K. Yonezawa Optimization of the Marker-Based Procedures for Pyramiding Genes from Multiple Donor Lines: I. Schedule of Crossing between the Donor Lines Crop Sci., March 1, 2007; 47(2): 537 - 546. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. Patzoldt, C. R. Grau, P. A. Stephens, N. C. Kurtzweil, S. R. Carlson, and B. W. Diers Localization of a Quantitative Trait Locus Providing Brown Stem Rot Resistance in the Soybean Cultivar Bell Crop Sci., May 27, 2005; 45(4): 1241 - 1248. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| The SCI Journals | Agronomy Journal | Vadose Zone Journal | |||
| Journal of Natural Resources and Life Sciences Education |
Soil Science Society of America Journal | ||||
| Journal of Plant Registrations | Journal of Environmental Quality |
The Plant Genome | |||
