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Primary Trisomics and SSR Markers as Tools to Associate Chromosomes with Linkage Groups in Soybean.

A PRIMARY TRISOMIC INDIVIDUAL carries the normal complement of chromosomes plus an additional copy of one chromosome. Primary trisomics provide a way to associate genes and linkage groups with their respective chromosomes. In diploid species including maize (Zea mays L.) (Rhoades and McClintock, 1935), tomato (Lycopersicon esculentum Mill.) (Rick and Barton, 1954), barley (Hordeum vulgare L.) (Tsuchiya, 1967), and rice (Oryza sativa L.) (Khush et al., 1984), a complete set of primary trisomic individuals (each chromosome is trisomic in one member of the set) has allowed the establishment of cytogenetic maps. The trisomic sets have been useful in positioning classical genes and molecular markers on specific chromosomes by the use of modified genetic ratios associated with trisomic inheritance or by dosage effects from the extra chromosome (Tsuchiya, 1983; Carlson, 1988; Khush et al., 1984, McCouch et al., 1988; and Young et al., 1987).

In soybean [Glycine max (L.) Merr.], the complete set of primary trisomics (2x + 1 = 41) has been difficult to establish because mitotic metaphase chromosomes are morphologically indistinguishable. Early attempts by soybean cytologists resulted in the characterization of five trisomics (Gwyn and Palmer, 1989; Gwyn et al., 1985; Palmer, 1976; Sadanaga and Grindeland. 1984; Skorupska et al., 1989). In a species with small chromosome size and few differences in the morphology of mitotic metaphase chromosomes, pachytene chromosome analysis was shown to be a useful tool in the identification of individual chromosomes (Singh and Hymowitz, 1991). This approach was used to construct the first cytological map of soybean on the basis of chromosome length and euchromatin and heterochromatin distribution. As a result of the work of Singh and Hymowitz (1991), Ahmad et al. (1992), and Ahmad and Hymowitz (1994), 13 of the possible 20 primary trisomics were identified by pachytene chromosome analysis. Recently, these same researchers completed the characterization of the complete set of soybean primary trisomics (Xu et al. 2000).

In soybean, the association of linkage groups with specific chromosomes via trisomic analysis is in its initial stages. Hedges and Palmer (1991) associated the isozyme marker Dial (diaphorase) with Tri D (trisomic D). Tri D was identified as Triplo 4 by pachytene analysis by Singh and Hymowitz (1991). Sadanaga and Grindeland (1984) associated the w1 (flower color) locus (classical linkage group 8) with the satellite chromosome using Tri S which is now referred to as Triplo 13 (Singh and Hymowitz, 1991). More recently, Xu et al. (2000) confirmed the presence of w1 on Triplo 13 and also placed v2 (variegated leaf) on chromosome 5. They also associated eu1 (urease null), lx1 (lipoxygenase null), and p2 (puberulent) on chromosomes 5, 13, and 20, respectively.

DNA marker technology has progressed rapidly in soybean. In the past few years, much interest has focused on the development of polymerase chain reaction (PCR) based single locus DNA markers with multiple alleles. The highly polymorphic nature (i.e., multiallelism) of simple sequence repeat (SSR) or microsatellite DNA markers is quite clear as evidenced by initial work of Akkaya et al. (1992) and Morgante and Olivieri (1993). Subsequent reports (Rongwen et al., 1995; Maughan et al., 1995; Powell et al., 1996; Diwan and Cregan, 1997) have described highly polymorphic microsatellite loci with as many as 26 alleles. SSR markers are the latest addition to the molecular genetic map of soybean that has developed over the past 10 yr. The first such map, published by Keim et al. (1990), was based upon 150 restriction fragment length polymorphism (RFLP) loci and contained 26 linkage groups. Subsequent reports by Shoemaker and Olson (1993), Shoemaker and Specht (1995), Mansur et al. (1996), Keim et al. (1997), and Cregan et al. (1999) have added greatly to the number of available DNA markers and their assembly into linkage maps with a total length of between 2400 and 3000 centimorgans (cM). The most recent map (Cregan et al., 1999) was actually a compilation of three maps based upon the genotyping of plants in three mapping populations. A total of more than 1400 DNA markers was positioned in this work, of which more than 600 were SSR markers. This resulted in the assembly of 20 consensus linkage groups. In some instances, two or more linkage groups on one map were joined not on the basis of a significant statistical association between markers in the groups, but on the basis of markers in common with a single linkage group in another population. Nonetheless, the final distillation into 20 molecular linkage groups led to the assumption that these groups corresponded to the 20 soybean chromosomes.

In addition to the synthesis of a linkage map containing 20 molecular linkage groups, Cregan et al. (1999) reported the association of 18 of the 20 classical linkage groups (Palmer and Shoemaker, 1998) with a molecular linkage group based on in situ segregation or linkage reports in the literature. Only classical linkage group 6 was not associated with a molecular linkage group. Thus, while the molecular and classical linkage maps are now substantially integrated, no association of these maps with specific soybean chromosomes has been made. It is therefore the objective of this paper to demonstrate the use of SSR markers to associate consensus molecular linkage groups with their respective soybean chromosome.

MATERIALS AND METHODS

Plant Materials

Triplo 13

A plant (UT95-135, Xu et al., 2000) identified as trisomic for chromosome 13 (Triplo 13) was used as the female parent in a cross with an experimental line that was homozygous for the lx1 (lipoxygenase null) gene. Root-tip squashes were used to identify trisomic [F.sub.1] plants. The [F.sub.1] seeds were germinated in a greenhouse sand bench at the Univ. of Illinois, Urbana, IL, and actively growing root tips were collected at 7 to 10 d after seeding and chromosomes were counted as described by Xu et al. (2000). [F.sub.2] seeds were collected from a single trisomic [F.sub.1] plant and a chip was removed from each of the seeds to determine the presence (Lx1-) or absence (lx1lx1) of lipoxygenase as described by Hildebrand and Hymowitz (1981). A total of 63 [F.sub.2] plants was grown in the greenhouse at Beltsville, MD, and DNA was isolated from each as described by Keim et al. (1988).

Triplo 5

A plant (UT95-109, Xu et al., 2000) identified as trisomic for chromosome 5 (Triplo 5) was used as the female parent in a cross with an experimental line that was homozygous for the mutant alleles ti (Kunitz trypsin inhibitor null), eu1 (urease null), and sp1 (beta amylase null) (Singh et al., 1998). Root-tip squashes were used to identify trisomic [F.sub.1] plants at the Univ. of Illinois as described above. [F.sub.2] seeds were collected from a single trisomic [F.sub.1] plant. A total of 56 [F.sub.2] plants was grown in the greenhouse at Beltsville, MD. DNA was isolated from the leaf tissue as described above. Plants were allowed to mature and seeds were collected from each plant. A sample of [F.sub.3] seeds from each of the 56 [F.sub.2] plants was used to determine the presence (Eu1-) or absence (eu1 eu1) of seed urease as described by Kloth et al. (1987).

Simple Sequence Repeat Marker Analysis

DNA of the parents used to produce the Triplo 13 [F.sub.1] from which the [F.sub.2] plants arose was not available. Therefore, to determine which SSR markers were polymorphic in this cross, two SSR markers from each of the 20 linkage groups defined by Cregan et al. (1999) were initially used to assay six plants from each set of [F.sub.2] plants using [sup.32]P-labeled PCR products separated on DNA sequencing gels as described by Cregan and Quigley (1997). Additional loci were used if necessary to identify at least one polymorphic locus per linkage group. In the case of the Triplo 5 population, the SSR allele present in the ti eu1 sp1 experimental line was compared with that of the cultivar Clark to identify polymorphic loci. Clark was used because the Triplo 5 parent used to create the [F.sub.2] population had been backcrossed into the cultivar Clark 63.

Once polymorphic markers were identified, a group of 20 [F.sub.2] plants from each population was assayed to identify loci that deviated significantly from 1:2:1 (homozygous for the SSR allele contributed by the female parent: heterozygous: homozygous for the SSR allele contributed by the male parent). It was assumed that the anticipated excess of genotypes in one homozygous class along with the deficiency in the other would allow the putative identification of SSR loci mapping to the trisomic chromosome. Following the identification of SSR markers showing a putative association with either Triplo 13 or Triplo 5, each of these markers was used to genotype the entire population of [F.sub.2] plants derived from the appropriate Triplo cross. The data obtained from the genotyping of the entire [F.sub.2] populations were analyzed by [chi square] for goodness of fit to a 1:2:1 segregation ratio and to a 6:11:1 segregation ratio. The latter ratio would be expected with trisomic inheritance and 50% female transmission of the extra chromosome (Singh, 1993). When the [chi square] analysis indicated significant deviation from a 1:2:1 ratio at a given SSR locus, other markers in the same linkage group were used to genotype the complete set of plants from the appropriate [F.sub.2] population.

RESULTS AND DISCUSSION

Triplo 13

The initial screening of 20 [F.sub.2] plants was undertaken with SSR markers from only six linkage groups. Early in the screening, a possible association was indicated between linkage group F and chromosome 13 by apparent deviations from a 1:2:1 ratio obtained from the analysis of segregation data with SSR markers GMRUBP and Satt030 (Table 1). The analysis of the complete population of 63 plants with Satt030 resulted in a segregation ratio of 24:34:5 and a highly significant [chi square] value indicating deviation from a 1:2:1 ratio (Table 2). Six additional loci on linkage group F yielded similar deviation from 1:2:1 segregation. None of the seven loci deviated from the expectation of 6:11:1 trisomic inheritance (Table 2). The deviation of these loci from the 1:2:1 ratio plus the fit to 6:11:1 confirmed the association of chromosome 13 with linkage group F. The molecular marker phenotypes of 32 of the 63 plants at the Sat_090 locus are shown in Fig. 1.

[ILLUSTRATION OMITTED]
Table 1. Simple sequence repeat markers used in the initial analysis
of 20 [F.sub.2] plants from populations derived from trisomic [F.sub.1]
plants from crosses of Triplo 13 x lx1 and Triplo 5 x ti eu sp1,
segregation ratios obtained, and [chi square] probability for goodness
of fit to a 1:2:1 ratio.

Triplo and   Linkage    [F.sub.2]    [chi square]
SSR marker    group    Segregation   probability

Triplo 13
  SOYGPATR     C1        5:12:3         0.55
  GMGLPSI2     I         4:12:3         0.49
  GMRUBP       F        10:9:1          0.02
  Sat_022      D2        5:11:3         0.64
  Satt022      N         7:9:5          0.67
  Satt030      F         8:11:1         0.08
  SOYLBC       O         6:6:5          0.45

Triplo 5
  GMABAB       N         5:10:4         0.92
  Sat_044      K         8:9:3          0.26
  Sat_064      G         8:7:5          0.26
  Satt002      D2        6:10:3         0.61
  Satt005      D1b       5:8:7          0.55
  Satt006      L         6:11:3         0.58
  Satt030      F         7:8:5          0.55
  Satt073      A1       13:7:0         <0.001
  Satt076      L         4:11:4         0.79
  Satt079      C2        5:12:3         0.55
  Satt089      A2        7:9:2          0.25
  Satt100      C2        3:14:3         0.20
  Sct_001      J         4:9:6          0.79
  Sct_028      C2        5:14:1         0.09
  SOYGPATR     C1        5:10:3         0.72
Table 2. Simple sequence repeat markers used in the analysis of
complete populations of [F.sub.2] plants derived from trisomic
[F.sub.1] plants from crosses of and Triplo 13 x lxl and Triplo 5 x
ti eu sp1, segregation ratios obtained, [chi square] probability for
goodness of fit to a 1:2:1 and 6:11:1 ratio, and the specific [F.sub.2]
plant that were homozygous for the least frequent homozygous marker
class. The SSR loci on each triplo are listed in the order they appear
on the soybean linkage map (Cregan et al., 1999).

                                [chi square]        Plant no. of
                               for probability    [F.sub.2] plants
                                 goodness of        in the under-
             Link-   Segre-        fit to           represented
Triplo and    age    gation                         homozygous
SSR marker   group    ratio    1:2:1    6:11:1    recessive class

Triplo 13
  Satt569      F     24:34:5   0.0027    0.43    18, 44, 45, 48, 70
  Satt193      F     24:34:5   0.0027    0.43    18, 44, 45, 48, 70
  Satt030      F     24:34:5   0.0027    0.43    18, 44, 45, 48, 70
  Satt343      F     24:34:5   0.0027    0.43    18, 44, 45, 48, 70
  Satt657      F     20:38:5   0.0074    0.71    3, 28, 35, 46, 68
  Sat_090      F     22:36:5   0.0054    0.93     1, 3, 28, 33, 68
  Sat_074      F     22:38:3   0.0008    0.64        1, 33, 68

Triplo 5
  Satt276     A1     27:26:3   <0.001    0.05        30, 38, 52
  Satt364     A1     26:27:3   <0.001    0.10        30, 38, 60
  Satt471     A1     25:27:2   <0.001    0.14        30, 38, 52
  Satt300     A1     26:27:3   <0.001    0.10        30, 38, 60
  Satt155     A1     25:28:3   <0.001    0.18        30, 38, 60
  Satt073     A1     24:29:3   <0.001    0.29        30, 38, 60
  Satt385     A1     27:27:2   <0.001    0.05          30, 38
  Satt545     A1     24:29:3   <0.001    0.29        27, 30, 38


The analysis of seed lipoxygenase indicated that [F.sub.2] plant numbers 1, 28, 33, 45, and 68 were lipoxygenase nulls. This segregation ratio of 58 Lx1-:5 lx1lx1 deviates significantly ([is less than] 0.001) from a 3:1 ratio that would be anticipated for normal disomic segregation. The 58:5 ratio was a good fit to a 17:1 ratio ([chi square] = 0.68, P = 0.41) that would be expected with trisomic inheritance and 50% female transmission of the trisomic chromosome. This result verifies the location of the Lx1 locus on chromosome 13 as previously reported (Xu et al., 2000). At the Sat_090 locus, [F.sub.2] plant numbers 1, 3, 28, 33, and 68 were homozygous for the under-represented allele. Thus, in four of five instances the molecular phenotype at the Sat_090 locus corresponded with the lipoxygenase null phenotype. This suggests that the Lx1 locus is situated close to Sat_090 because relatively little recombination has occurred between the two loci. In contrast, only one of the five plants that was homozygous for the under-represented allele at the Satt030, Satt193, Satt343, and Satt569 loci were lipoxygenase nulls. These loci are located at the opposite end of linkage group F from the Sat_090 locus (Cregan et al., 1999).

Triplo 5

The 20 plants were screened with SSR markers from 13 of the 20 linkage groups and the segregation tested for goodness of fit to a 1:2:1 ratio. Marker Sct_028 yielded a segregation ratio of 5:14:1 with a [chi square] value of 4.8 (P = 0.09) suggesting a possible deviation from 1:2:1 segregation and the association between chromosome 5 and linkage group C2. However, tests of two additional loci on linkage group C2 (Satt079 and Satt100) did not support this association (Table 1). It might be desirable to genotype a larger number of plants initially to avoid false positive associations such as occurred in the case of Sct_028. However, as demonstrated in this instance, false positives were quickly identified by analysis of the population with other loci in the same linkage group.

The initial genotyping of 20 plants with Satt073 gave skewed segregation and the [chi square] value for goodness of fit to a 1:2:1 ratio indicated highly significant deviation (Table 1). The analysis of the complete population of 56 [F.sub.2] plants with Satt073 resulted in a segregation ration of 24:29:3 and a highly significant [chi square] for deviation from a 1:2:1 ratio (Table 2). Seven additional loci on linkage group A1 showed deviation from 1:2:1 segregation and good fit to 6:11:1 segregation (Table 2) and thus confirmed the association of chromosome 5 with linkage A1. The molecular marker phenotypes of 28 of the 56 plants at the Satt300 locus are shown in Fig. 1.

In addition to the molecular marker data, the [F.sub.3] seed produced by each [F.sub.2] plant was characterized for the presence of seed urease. [F.sub.2] plant numbers 30, 38, and 60 were urease nulls. Thus, the ratio of urease normal: urease nulls was 53:3 which is a highly significant (P = 0.0007) deviation from the expected 3:1 segregation ratio for a single gene. In contrast, this segregation fit trisomic 17:1 segregation (P = 0.68). This result suggests that the urease gene is on linkage group A1. The plant number of each of the individual plants in the underrepresented homozygous recessive class for each SSR locus is given in Table 2. In the case of Satt364, Satt300, Satt155, and Satt073, [F.sub.2] plant numbers 30, 38, and 60 were in the under-represented homozygous recessive class. The exact correspondence of homozygosity at the marker loci and at the urease locus suggests that the urease gene is located relatively near these molecular marker loci. Thus, it is not surprising that Satt364, Satt300, Satt155, and Satt073 are mapped to an interval that spans only 6.5 cM on the University of Utah linkage group A1-U07 (Cregan et al., 1999). However, Satt471 also maps to this interval but at this locus, plants 30, 38, and 52 were in the under-represented homozygous class. A close examination of the USDA/Iowa St. Univ. and the Univ. of Utah maps (Cregan et al., 1999) indicates disagreement in the ordering of loci in this part of MLG A1. It is possible that Satt461 is outside of the interval defined by Satt364-Satt073. If this were the case, then the discrepancy between the individual plants in the under-represented homozygous class at Satt461 versus Satt364, Satt300, Satt155, and Satt073 would be possible. In fact, the same three plants (numbers 30, 38, and 52) that were homozygous for the male parent allele at Satt471 were also homozygous at Satt276. Satt276 is distal to the Satt364-Satt073 interval and suggests that Satt471 is also distal to this interval. The lack of exact correspondence between molecular marker phenotype and the urease phenotype for loci Satt385, Satt545 (Table 2) could readily result from recombination because these loci are relatively distant from the Satt364-Satt073 interval.

The positioning of the Eu locus on linkage group A1 represents the first association of a classical genetic marker with this linkage group. Cregan et al. (1999) putatively associated classical linkage groups or individual classical loci with 18 of the 20 consensus linkage groups. A1 and M were the only linkage groups with which no classical locus was associated.

The recently published linkage map of the soybean genome positioned more than 600 SSR markers in three separate mapping populations and then aligned homologous linkage groups from the three populations to produce 20 consensus linkage groups (Cregan et al., 1999). One of the mapping populations, the Minsoy x Noir 1, Univ. of Utah population used in this work was considered to be particularly reliable because it has four times more individuals than the other two populations. Nonetheless, in the case of linkage group F, two portions of the linkage group remained statistically unassociated. The two portions were joined on the basis of markers in common with a single linkage group in the other two mapping populations. Thus, it would be extremely useful to verify independently this joining of the two groups of linked markers that make up linkage group F. Indeed, this was accomplished by the association with chromosome 13 of both SSR locus Sat_074, which maps to one part of the Univ. of Utah linkage group F, and the loci Satt030, Satt193, Satt343, Satt569, and Satt657 which map to the second part of linkage group F.

The combined use of primary trisomics and-SSR markers to associate linkage groups with chromosomes functioned well in the work reported herein. This positive result is partially a function of the single locus nature of SSR markers. In contrast to RFLP loci, soybean SSR loci map to a single locus. Up to 19 independent RFLP loci have been mapped by specific RFLP probes (Mansur et al., 1996). While most soybean RFLP probes map to only two or three positions in the genome, this multilocus characteristic would make the unambiguous association of linkage group and chromosome somewhat problematic.

A second characteristic of SSR loci that make them an attractive tool for the association of chromosomes and linkage groups is the highly polymorphic nature of SSR loci. Thus, the likelihood that a given locus will be polymorphic in a particular population is greater with SSR markers than with any other marker type. The populations used in the current study were created by crossing experimental lines that were fairly similar in their genetic backgrounds. The genetic backgrounds of the two genotypes carrying Triplo 13 and Triplo 5, respectively, were related to the cultivar Clark. Likewise, the genotypes used as the donors of the urease null and the lipoxygenase null were related to Clark. As a result, only about 15% of the SSR markers tested were polymorphic in the initial assay used to identify polymorphic SSR loci. A higher level of polymorphism would expedite the process of associating linkage groups with chromosomes. At this time, the 20 soybean primary trisomics are being backcrossed into the cultivar Clark 63 so that each can be examined in a common genetic background. In order to provide a high level of SSR length polymorphism, each of the primary trisomics are being crossed with Glycine soja PI 407287. PI 407287 is a vigorous genotype that produces completely fertile hybrids with cultivated soybean (Cregan et al., 1989). Crosses of PI 407287 have been made to each of the 20 primary trisomics. Cytological studies to identify trisomic [F.sub.1] plants are currently underway at the University of Illinois. In defining 20 consensus linkage groups, Cregan et al. (1999) assumed each to be associated with a separate chromosome. In the near future, it is anticipated that this assumption will be tested by the use of the newly developed complete set of soybean primary trisomics.

ACKNOWLEDGMENTS

The authors thank Ms. Sarah Hyatt and Mr. DaRel Barksdale for their excellent technical assistance during the course of the work reported here. This research was supported in part by funds from United Soybean Board (USB Grants #8207and 9222) to PBC. Research at the University of Illinois supported in part by the Illinois Agricultural Experiment Station, Illinois Soybean Program Operating Board grant 97-23-182-3HY and C-FAR grant 1-5-95411.

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Abbreviations: cM, centimorgan; PCR, polymerase chain reaction; MLG, molecular linkage group; RFLP, restriction fragment length polymorphisms; SSR, simple sequence repeat.

P. B. Cregan,(*) K. P. Kollipara, S. J. Xu, R. J. Singh, S. E. Fogarty, and T. Hymowitz

P.B. Cregan and S.E. Fogarty, Soybean Genomics and Improvement Laboratory, Bldg. 006, Room 100, BARC-West, USDA-ARS, Beltsville, MD 20705; K.P. Kollipara, S.J. Xu, R.J. Singh, and T. Hymowitz, Dep. of Crop Sciences, Univ. of Illinois, Urbana, IL 61801. Received 25 April 2000. (*) Corresponding author (creganp@ba.ars.usda.gov).
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Title Annotation:simple sequence repeat
Author:Cregan, P. B.; Kollipara, K. P.; Xu, S. J.; Singh, R. J.; Fogarty, S. E.; Hymowitz, T.
Publication:Crop Science
Article Type:Statistical Data Included
Geographic Code:1USA
Date:Jul 1, 2001
Words:4997
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