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Crop Science 42:1459-1464 (2002)
© 2002 Crop Science Society of America

CROP BREEDING, GENETICS & CYTOLOGY

Genetic Linkage in Soybean

Classical Genetic Linkage Groups 6 and 8

A. Assibi Mahamaa, Kim S. Lewersb and Reid G. Palmer*,a

a USDA-ARS-CICGR and Dep. of Agronomy and Zoology/Genetics, Iowa State Univ., Ames, IA 50011
b USDA-ARS-PSI-SARL, Bldg. 006 BARC-West, 10300 Baltimore, MD 20705

* Corresponding author (rpalmer{at}iastate.edu)


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
Mapping mutants of classical linkage groups 6 and 8 (CLGs 6 and 8) in soybean [Glycine max (L.) Merr.] can enhance the identification of important agronomic traits. Genetic data suggest that CLGs 6 and 8 may belong to the same linkage group. Our objectives were to determine if CLGs 6 and 8 are the same or different linkage groups and to determine the gene order. Genotypes containing mutants of CLGs 6 and 8 and mutants of other CLGs were crossed in various combinations. Data for the different characters were collected from F2 populations and F2:3 families. Recombination values confirmed that CLG 6 characters, Df2 and Y11 were linked (R = 27.0 ± 5.9), Df2 was linked to Ms1 (CLG 8) (R = 24.8 ± 1.2) and to W1 (CLG 8) (R = 36.4 ± 1.3), and Y11 was linked to Ms1 (R = 31.7 ± 1.4). F2 data suggested that Y11 segregated independently of W1, while F2:3 data indicated the two were linked (R = 38.4 ± 3.2). Our data indicated that CLGs 6 and 8 belong to the same linkage group, which is molecular linkage group F (MLG F), and chromosome 13. Y11 and Adh1 are at the ends of the chromosome segment studied, and Y23 is located between Ms6 and St5. Recombination values among the other loci of CLG 8, and between them and loci of other CLGs were consistent with published values. This information will be useful in the reassignment of CLGs, ordering of loci, and will enhance molecular genetic linkage mapping in soybean.

Abbreviations: CLG(s), Classical Linkage Group(s) • MLG, Molecular Linkage Group • EC, Enzyme Commission


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
SOYBEAN classical linkage group 8 (CLG 8), currently defined by seven gene loci (Adh1, Ms1, Ms6, St5, W1, Wm, andY23), has been assigned to the nucleolus-organizing region (NOR) or satellite chromosome (Sadanaga and Grindeland, 1984), which was identified as chromosome 13 (Singh and Hymowitz, 1988). Through molecular mapping, 18 of the 20 classical linkage groups have been associated with a molecular linkage group. Cregan et al. (1999) assigned the flower color locus, W1, to molecular linkage group F (MLG F), which enabled the integration of CLG 8 with MLG F. However, CLGs6 has not been associated with a molecular linkage group. Mutants on CLGs 6 and 8 could be associated with yield or seed weight quantitative trait loci (QTL) (Mansur et al., 1993; Orf et al., 1999), and Adh1 could be associated with flooding tolerance QTL (VanToai et al., 2001). Therefore mapping mutants of CLGs 6 and 8 can enhance the identification of genes affecting important agronomic traits.

Factors such as the type of genetic data, environment, genetic background, genotype x environment interaction, and the linkage phase can influence recombination and result in a range of recombination values. The differences between recombination values obtained from backcross data, F2 populations, and F2:3 families have been documented (Allard, 1956; Haldane, 1919; Immer, 1930, 1934; Mather, 1936). Recombination values calculated from coupling data can differ significantly from those calculated from repulsion data (Butler, 1968; Immer, 1930, 1934; Mather, 1951).

Weiss (1970) reported a recombination value of 12.1 ± 0.7 between the Y11 and Df2 loci that established soybean CLG 6. The first reported study involving loci of classical CLG 8 was by Palmer (1976), for Ms1 and W1. However, many of the soybean studies looked at linkage between two loci at a time. This manner of studying linkage can result in a range of significantly different map distances due to factors mentioned earlier. Variation in recombination values in soybean has been documented (Hildebrand et al., 1980; Kiang et al., 1985; Palmer et al., 1998b; Pfeiffer, 1993; Pfeiffer and Vogt, 1990; Yu and Kiang, 1990). While this can result in the assignment of loci to linkage groups, it makes the unambiguous assignment of gene order difficult. Palmer and Chen (1998) classified F2:3 families and reported recombination values of 24.7 ± 2.2 for Df2 -Y11, 35.3 ± 3.0 for W1 - Ms1, 40.7 ± 2.8 for Df2 - Ms1, 42.1 ± 4.3, for Y11 - W1, and 39.3 ± 5.3 for Y11 - Ms1. On the basis of classification of F2 populations, Mahama and Palmer (1998) reported recombination values of 37.1 ± 2.4 for Df2 - W1, and 28.5 ± 2.5 for Df2 - Ms1. These reports suggest that classical linkage groups 6 and 8 may be the same linkage group. Although recombination values of various loci pair vary, they are in general agreement in loci placement, hence the consensus classical linkage map of Palmer and Hedges (1993). Though a consensus map has been constructed, the gene order of some loci of CLG 8, and the independence of CLG 6 and CLG 8 is not confirmed. Our objectives were to determine if CLGs 6 and 8 are the same or different linkage groups, and to determine the gene order.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
In this study, genetic marker types were constructed that comprised various combinations of mutant loci of classical linkage groups 6 and 8, as well as mutant loci of the other linkage groups. The majority of the loci combinations were in coupling phase linkage. To obtain segregating populations, standard cross-pollination techniques (Walker et al., 1979) were used. Male-sterile plants of the genotype ms1ms1 and ms6ms6 were used as the female parents. Fertile plants (of genotype St5st5) in segregating families, identified by progeny testing, were used as pollen parents. F2 seeds were produced from F1 plants grown at the University of Puerto Rico/Iowa State University soybean nursery. The soil type is a very-fine, kaolinitic, isohyperthermic Typic Hapludox. Data for the different characters were collected from F2 populations and F2:3 families grown at the Bruner Farm near Ames, IA. The soil type is a Clarion-Nicollet Loam soil type (fine-loamy, mixed, superactive, mesic, Typic Hapludoll and fine-loamy, mixed, supeactive. mesic Aquic Hapludoll). All loci express complete dominance except the Y11 locus, which expresses incomplete dominance. Homozygous recessive (y11y11) plants are lethal, dying shortly after germination.

Segregation data for the alcohol dehydrogenase (EC 1.2.3.4) locus were obtained from F2 seeds following the starch gel electrophoresis procedure of Cardy and Beversdorf (1984) with modifications (Mahama et al., 1995). Seedlings from sampled seeds were transplanted to the field at the Bruner Farm, in rows 1 m apart, with 0.45 m between seedlings, and segregation data collected for the other traits. Family rows were classified for flower color and plant color 6 wk after planting. At maturity F2 plants were visually classified on the basis of pod set, as fertile (mostly three-seeded pods at all nodes) or sterile (no pods or occasional out-crossed pods at a few nodes). Dwarf (df2df2) and yellow (y23y23) plants among tall green plants in the field are difficult to classify accurately for fertility–sterility because they set few or no pods. Mature flower buds (with petals showing just above the sepals) were collected from each plant separately and placed into vials containing 70% (v/v) ethanol. The anthers were squashed and pollen dispersed in a drop of 1% (v/v) I2KI solution (Jensen, 1962). Plants were classified as fertile (Ms1-) or sterile (ms1 ms1) by counting pollen grains stained with I2KI at x100 magnification. At maturity, F2 plants were individually threshed. F2:3 progenies from self-pollination of F2 plants were grown the following season. Approximately 50 to 60 seeds per progeny row were planted in 3-m-long rows, spaced 0.7 m apart. Progeny rows were classified for segregation of the various traits. Phenotypic descriptions of the marker loci used in this study are presented in Table 1 . List of crosses made is shown in Table 2 .


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  		Table 1. Phenotypic description of alleles of soybean genes studied to evaluate classical genetic linkage groups 6 and 8.

 

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  		Table 2. List of soybean crosses used to generate segregation populations for evaluating linkages between classical linkage groups 6 and 8.

 
Data Analyses
Kramer and Burnham (1947) presented maximum likelihood estimation coefficients for calculating linkage intensity values and combining linkage intensity values from backcross, F2, and F2:3 genetic data for repulsion phase linkage, following the method of scoring by Fisher (1946). Making the necessary substitutions for recombination value and sign change, we derived the appropriate coefficients for coupling phase linkage. Coefficients were entered into a spreadsheet and used to calculate chi-square values to test independence of loci pair, and the corresponding recombination values as percentage recombination. Coupling, repulsion, F2, and F2:3 data were analyzed separately. Wherever applicable for any loci pair, F2 and F2:3 coupling and repulsion data were combined and analyzed following the method of scoring (Fisher, 1946). Similarly, recombination values between the Y11 locus and the other loci were calculated following the method of Weiss (1970) for repulsion data. Appropriate coefficients were derived for F2 and F2:3 coupling data as shown below by means of appropriate maximum likelihood estimation coefficients derived following the method of Mather (1935)(1951). The maximum likelihood estimator for recombination frequency is the value of p that would satisfy the equation below.

The F2 phenotypic classes involving Y11 and gene loci are a = Y11Y11 A-, b = Y11y11 A-, c = Y11Y11 aa, and d = Y11y11 aa, in a 3:6:1:2 ratio, where A-, is either W1-, or Ms1- or Df2-, or T- and aa is either w1w1, or ms1ms1, or df2df2 or tt.

The expectations of these classes are, respectively,

The maximum likelihood equation for estimating recombination values from Weiss (1970) is

The amount of information per individual, i, is obtained from the following equation:

The standard errors, S.E., for recombination values were calculated by the formula S.E. = (1/I)1/2, where I is the total amount of information for all plants, n, classified.

For coupling data, the maximum likelihood equation used for estimating recombination values is

The amount of information per individual, i, is obtained from the following equation:

The standard errors, S.E., for recombination values were calculated by the formula S.E. = (1/I)1/2, where I is the total amount of information for all plants, n, classified.

For coupling phase linkage, the F2:3 phenotypic classes involving Y11 and gene loci are e = Y11 Y11 A A, f =Y11 Y11 A a, g = Y11 y11 A A, and h = Y11 y11 A a in a 1:2:2:4 ratio, where A A, is either W1W1, or Ms1Ms1, or Df2Df2, or T T and A a is either W1w1, or Ms1ms1, or Df2df2, or T t.

The expectations of these classes are, respectively,

The maximum likelihood equation for estimating recombination values is

The amount of information per individual, i, is obtained from the following equation:

The standard errors, S.E., for recombination values were calculated by the formula S.E. = (1/I)1/2, where I is the total amount of information for all plants, n, classified.


   RESULTS AND DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
CONCLUSIONS
 REFERENCES
 
Recombination values were calculated from classification of F2 populations (Table 3) and F2:3 families (Table 4) , and from the combination of F2 and F2:3 data (Table 5) . We did not obtain segregation data to enable estimation of linkage between St5 - Adh1, but Uncu (2001) reported a recombination value of 32%. From repulsion data, Weiss (1970) reported linkage between Y11 and Df2, with a recombination frequency of 12%. Our F2 and F2:3 coupling data indicated linkage, although our values are greater (27 and 26%). Palmer and Chen (1998) also reported a recombination frequency of 25% from coupling data. The recombination frequencies among loci of CLG 8 are similar to those reported in the literature. Close linkages were observed for loci pair Mm – W1, W1 – Ms6, and Y23 – St5, with recombination frequencies of, 3, 4, and 3%, respectively. These values agreed with the values of 0 to 2.2% reported by others (Buzzell, 1975, 1976; Buzzell et al., 1977) for Wm – W1, 2.5 to 5% reported by Ilarslan et al. (1999); Lewers and Palmer (1993); Palmer et al. (1998a); and Skorupska and Palmer (1989) for W1 – Ms6, and 1 to 7% reported by Lewers and Palmer (1993), and Palmer et al. (1990)(1998a) for Y23 – St5. The recombination values in this study suggested moderately close linkages between W1 – Y23, St5, Adh1, and between Ms6 – Y23, St5, and Adh1, and confirm values reported by others (Bult et al., 1989; Kiang, 1990; Kiang and Chiang, 1987; Lewers and Palmer, 1993; Palmer and Kaul, 1983; Palmer et al., 1990).


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  		Table 3. Percentage recombination values for loci pair calculated from F2 soybean progeny data used for evaluating classical linkage groups 6 and 8.

 

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  		Table 4. Percentage recombination values for loci pair calculated from F2:3 soybean data used for evaluating classical linkage groups 6 and 8.

 

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  		Table 5. Percentage recombination values for loci pair calculated from combined F2 and F2:3 soybean data used for evaluating classical linkage groups 6 and 8.

 
Recombination values between Df2 – Ms1, Df2 – W1, and Y11 – Ms1 suggested linkage, similar to linkages mentioned earlier among loci of CLG 8. Our F2 data suggested independent assortment between Y11 and W1 while F2:3 data indicated linkage (R = 38). These linkage relationships are similar to those reported by Mahama and Palmer (1998) and Palmer and Chen (1998).

The recombination values shown in this study suggested independent assortment between loci of both CLG 6 and 8 and T of CLG 1, Y9 of CLG 14, and Y10, and Y18 which are not assigned to any linkage group at this time (Tables 2, 3, and 4). This is in agreement with their placement on different linkage groups.

We observed variations in recombination values calculated from F2 compared with F2:3 data, between coupling and repulsion data, between values calculated by the same researcher in different experiments, and between values calculated by different researchers. Variation in recombination values has been documented in soybean (Griffin and Palmer, 1987; Palmer and Chen, 1998; Palmer et al., 1998b; Pfeiffer, 1993; Pfeiffer and Vogt, 1990). The recombination values, in general, are in close agreement with those from other reports, as they tend to place loci in the same order on the map. Such consistency confirms a consensus map proposed by Palmer and Hedges (1993).

Our recombination values suggest that, Df2 and Y11 are linked to Ms1 and W1. This indicates that Df2 and Y11 of CLG 6 are in the same linkage group as the Ms1 and W1 loci of CLG 8, and therefore on the same chromosome, with Y11 being distal to Ms1 (Fig. 1) . Comparing the recombination values betweenY23 - St5 andY23 - Adh1, the Adh1 locus is distal to St5. Recombination values between Ms6 -Y23, Ms6 - St5, Ms1 –Y23, and Ms1 – St5 suggest that, St5 may be between Ms6 andY23. Considering the standard errors of the recombination values of these loci pairs (Tables 3 and 4), and the recombination values between Ms6 - St5, and Ms6 – Adh1, however, the gene order Ms6,Y23, St5, Adh1 (Fig. 1) is favored.



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  		Fig. 1. Linkage map and orientation of loci of classical soybean genetic linkage groups 6 and 8. F2 data (repulsion data in bold type) are above the chromosome segment (dark line) and F2:3 (repulsion data in bold italic type) and combined F2 and F2:3 (bold type) data are below the chromosome segment. I means independent assortment.

 

   CONCLUSIONS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
REFERENCES
 
On the basis of calculations of F2, F2:3, and combined F2 and F2:3 data, loci of classical linkage groups 6 and 8 assorted independently of loci of other linkage groups studied. The recombination values calculated in this study are in close agreement with reported values with the exception of the first reported (Weiss, 1970) recombination value calculated between Y11 and Df2, of classical linkage group 6. Our data indicated linkage between Df2 - Ms1, Df2 - W1, Y11 - Ms1, and Y11 - W1, thus indicating that these loci belong to the same linkage group. Following integration of CLG 8 with MLG F and linkage between mutants of CLGs 6 and 8, and the satellite chromosome having been identified as chromosome 13, CLG 6, CLG 8, and MGL F are all on chromosome 13 of the soybean genome. The suggested orientation of loci is Y11 and Adh1 at opposite ends of the chromosome segment studied, withY23 between Ms6 and St5. The reassignment of CLGs 6 and 8 into one linkage group and the ordering of loci will facilitate their integration into and placement on the molecular map (Cregan et al., 1999; Shoemaker and Specht, 1995).


   NOTES
TOP
 NOTES
ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 
This is a joint contribution: J#19403 of the Iowa Agric. and Home Econ. Exp. Stn., Ames, IA, Project No. 3352 and from the USDA-ARS, Corn Insects and Crop Genetics Research Unit, and supported by Hatch Act and State of Iowa. The mention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by Iowa State Univ. or the USDA, and the use of the name by Iowa State Univ. or the USDA implies no approval of the product to the exclusion of others that may also be suitable.

Received for publication October 1, 2001.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS AND DISCUSSION
 CONCLUSIONS
 REFERENCES
 




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