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Crop Science 43:319-328 (2003)
© 2003 Crop Science Society of America

GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

Mapping Flowering Time Gene Homologs in Soybean and Their Association with Maturity (E) Loci

I. M. Tasmaa and R. C. Shoemaker*,b

a Dep. of Agronomy, Iowa State Univ., Ames, IA 50011
b USDA-ARS-CICGR, Dep. of Agronomy and Dep. of Zoology/Genetics, Iowa State Univ., Ames, IA 50011

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


   ABSTRACT
TOP
 NOTES
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Time of flowering is a quantitatively inherited character of agronomic importance in soybean [Glycine max (L.) Merr.]. The genetics of flowering time has been extensively studied in the model plant Arabidopsis thaliana (L.) Heynh. The first objective of this study was to map onto the soybean genetic map orthologous genes known to be involved in photoperiod recognition and time of flowering in A. thaliana and compare their location with previously mapped flowering time quantitative trait loci (QTL). The second objective was to associate the mapped homologs with maturity (E) loci by means of near isogenic lines (NILs). Three single-cross soybean populations, consisting of two recombinant inbred line (RIL) populations and one F2 population, were used in the mapping study. One RIL population, IX132, was developed by crossing PI 317.336 and ‘Corsoy’; the second, IX136, by crossing PI 317.334B and Corsoy. Both plant introductions have been reported to be photoperiod-insensitive while the Corsoy parent has been reported to be photoperiod-sensitive. The RIL populations were previously used to map QTL for flowering time, maturity, and photoperiod-insensitivity in soybean. The F2 population was developed from an interspecific cross between G. max (breeding line A81-356022) and G. soja (PI 468.916). Eighteen soybean cDNA clones, identified by BLAST to have high similarities with 18 previously cloned A. thaliana flowering time genes, were used as probes in this study. Ten of the 18 cDNA clones were mapped. The cDNAs were mapped onto linkage groups (LGs) A2 (CRY2), B1 and H (COL1), A1 and B2 (PHYA), C1 (DET1 and LD), D2 (AP2), E and K (PHYB), F (COL2), L (FCA), and Q (CCA1). None of the cDNAs were directly associated with previously mapped QTL for flowering time. Forty-one NILs and two recurrent parents (RPs) were used in the association study. Analyses of these candidate genes using contrasting NILs showed that the FCA homolog was associated with maturity locus E3. That FCA is a strong gene candidate for maturity locus E3 is further supported by map position and phenotypic data. Analyses of NILs suggest that the soybean homolog PHYB may be associated with maturity locus E1. However, current data show they mapped in different LGs.

Abbreviations: DP, donor parent • FLIP, floral initiation process • LB, Luria Bertoni • LD, long day • LG, linkage group • NIL, near isogenic line • PCR, polymerase chain reaction • QTL, quantitative trait loci • RFLP, restriction fragment length polymorphism • RIL, recombinant inbred line • RP, recurrent parent • SD, short day • SSR, simple sequence repeat


   INTRODUCTION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
FLOWERING TIME of most plant species has been reported to be controlled by the interaction between environmental and endogenous cues (Levy and Dean, 1998). Environmental cues such as light duration, light quality, and temperature signal the onset of conditions favorable to the success of reproductive development. The endogenous cues are those that control the developmental competence of the plant.

Studies from the model plant A. thaliana show that flowering time is the result of a sequential action of flowering time and floral identity or floral initiation process (FLIP), genes (Koornneef et al., 1998; Levy and Dean, 1998; Piñeiro and Coupland, 1998). Flowering time genes are those that display major effects on the duration of vegetative development. These genes act before FLIP genes and may activate or repress floral identity genes under different environmental conditions. FLIP genes, on the other hand, switch the fate of meristems from vegetative to floral phase. Mutations of these genes cause primordia that would normally develop as flowers in the wild-type plants to instead form structures with shoot-like characteristics.

Many genes that control flowering time have been identified in different plant species, such as Arabidopsis and pea (Weller et al., 1997; Koornneef et al., 1998; Piñeiro and Coupland, 1998). From Arabidopsis alone, at least 80 loci are reported to affect the timing of flowering (Levy and Dean, 1998). The genes were identified through the analyses of natural variation of different Arabidopsis ecotypes and through characterization of induced mutations (Coupland, 1995; Coupland, 1997). Some of these genes promote flowering while others repress it. Some appear to interact with environmental factors (e.g., photoperiod and temperature) while others appear to act in an autonomous way. On the basis of these observations and data from double mutant studies and transgenic plant analyses, it was proposed that at least four different genetic pathways may control flowering time in Arabidopsis (Levy and Dean, 1998; Koornneef et al., 1998).

Among the 80 Arabidopsis flowering time genes reported so far, at least 25 have been cloned and characterized (Koornneef et al., 1998; Levy and Dean, 1998). In addition, several genes from studies of other aspects of plant development, such as light perception and hormone metabolism, have been cloned and found to play roles in the regulation of flowering time. These genes have also been labeled as flowering time genes.

Cloned flowering time genes have been mapped in several different plant species. In barley (Hordeum vulgare L.), homologs of three Arabidopsis genes [CONSTANTS (CO), TERMINAL FLOWER 1 (TFL1), and GIGANTEA (GI)] were found to map closely to previously identified flowering time QTL (Christodoulou et al., 2001). However, they did not correspond precisely to the QTL peak. A study in rice (Oryza sativa L.) also reported that homologs of the flowering time genes, GIGANTEA (GI) from Arabidopsis, and PNZIP from Pharbitis nil (L.) Choisy [= Ipomoea nil (L.) Roth], were associated with the previously detected flowering time QTL (Thompson et al., 2001). The authors concluded that presence of flowering time gene homologs in both the rice and barley genomes suggests that there is a considerable conservation of the flowering time genetic pathways. This information provides support for the continued use of this candidate gene approach.

In soybean, at least seven genes have been reported to affect flowering time and maturity (Cober et al., 1996a). The genes are known as the E-series: E1, E2, E3, E4, E5, E6, and E7 [Bernard, 1971; Buzell, 1971; Buzell and Voldeng, 1980; McBlain and Bernard, 1987; Bonato and Vello, 1999; Cober and Voldeng, 2001). McBlain et al. (1987) reported these loci interact with photoperiod in the control of flowering. Under natural daylength, the dominant alleles tend to delay flowering time and maturity, but the magnitude of each gene's effect can be different (Cober et al., 1996a).

Several QTL associated with flowering time and maturity have been mapped in soybean. A large-effect QTL controlling flowering time, maturity, and photoperiod-insensitivity was mapped on LG C2 (Tasma et al., 2001). The QTL was found to be located in the same location in two populations. This QTL explained as much as 47% of total phenotypic variance and was also found to closely map to the pubescent color locus T (Tasma et al., 2001). Smaller-effect QTL were located on other LGs (A2, G, J, and L) in both populations. These QTL explained up to 17.8% of total phenotypic variance. Keim et al. (1990) reported that five markers on linkage groups C1, C2, and D1 were associated with maturity (including time of flowering) in an F2 population derived from a cross between G. max and G. soja. The observed QTL explained 17 to 23% of total phenotypic variance. Using a ‘Minsoy’ x ‘Noir 1’ population, Mansur et al. (1996) also reported a major QTL for flowering time on LG C2 and minor QTL for maturity on LG L and M. Lee et al. (1996) reported QTL for maturity traits were found on LG K, based on an F2 population derived from a cross between PI 97100 and ‘Coker 237’. The observed QTL explained 26 to 31% of phenotypic variance.

In this study, we mapped candidate genes for flowering time traits in A. thaliana onto the soybean genetic map. In addition, we compared the candidate's map location with flowering time QTL previously identified (Tasma et al., 2001). Finally, we examined the relationship between candidate gene sequences and the known maturity (E) loci.


   MATERIALS AND METHODS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
Plant Materials
Mapping Populations
Three populations were used in this study: two RIL populations and one F2 population. The RIL population, IX132, was developed by crossing PI 317.336 and Corsoy. The RIL population, IX136, was developed by crossing PI 317.334B and Corsoy. Both plant introductions are reported to be photoperiod-insensitive (Gutrie, 1972; Nissly et al., 1981; Metz et al., 1985). The Corsoy parent, on the other hand, is reported to be photoperiod-sensitive. These RIL populations were previously used to map QTL for flowering time, maturity, and photoperiod-insensitivity in soybean (Tasma et al., 2001).

An F2 population was developed from an interspecific cross between G. max (breeding line A81-356022) and G. soja (PI 468.916). This population was used to construct the USDA/ISU public map (Shoemaker and Olson, 1993; Shoemaker and Specht, 1995) and the soybean consensus map (Cregan et al., 1999). The development of the populations was reported previously (Keim et al., 1990; Tasma et al., 2000). Population sizes were 101 (IX132), 100 (IX136), and 60 progeny (G. max x G. soja).

Near-Isogenic Lines
Two sets of NILs were used. The first set comprised the L-lines developed at the University of Illinois, Urbana-Champaign (Bernard et al., 1991), and the second set comprised the OT-lines developed at the Plant Research Center, Ottawa, ON, Canada. The L-lines were developed using RP cultivars ‘Clark’ and ‘Harosoy’ and were obtained from Dr. Randall Nelson (USDA-ARS/University of Illinois, Urbana-Champaign). The OT-lines were developed using Harosoy and were obtained from Dr. Elroy Cober (Eastern Cereal and Oilseed Research Center, ON, Canada). The NILs contain different allele combinations of the E loci (Table 1). The rationale behind the usefulness of the NILs for mapping the molecular and classical genetic markers has been reported (Muehlbauer et al., 1988; Young et al., 1988; Muehlbauer et al., 1989; Muehlbauer et al., 1991).


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  		Table 1. Genotypes and recurrent parents of near isogenic lines used in this study.

 
Identification of Candidate Flowering Time Genes
From a literature review, we identified cloned flowering time genes to be used in this study (e.g., PHYA, PHYB, CRY2, CO, and FCA) (Table 2). Soybean clones (Table 3) were then selected based upon similarity of the soybean expressed sequence tag sequences to those sequences of the cloned flowering time genes as determined by using BLASTx (Altschul et al., 1990) against the GenBank nonredundant database with default parameters (Table 3).


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  		Table 2. Characteristics of flowering time genes used in this study.

 

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  		Table 3. Soybean cDNA clones used as probes in this study and BLAST results of the cDNA sequences. All queries were made using BLASTx against the nonredundant database with default parameters (BLOSUM62 Matrix).

 
PCR Amplification of cDNA Clones
The cDNA clones were obtained from Incyte Genomics (St. Louis, MO) (Table 3). The clones were cultured in a Luria Bertoni (LB) plate medium containing the antibiotic ampicillin (0.1 µg/µL). A single colony was then picked and cultured in a 5-mL LB medium containing ampicillin and was incubated in a shaker (250 revolutions m-1) at 37°C overnight. The cDNA insert of each clone was amplified by polymerase chain reaction (PCR). We used either a single colony or an overnight bacterial-LB culture containing a particular cDNA clone as template in the PCR amplification. Generally, we used T3 and T7 promoter primers (Gibco BRL, Rockville, MD) to amplify the inserts since most cDNA clones were constructed in the pBluescript vector (Gibco BRL). cDNA clones constructed in a pSPORT1 vector (Gibco BRL), were amplified using SP6 and T7 primer pairs (Gibco BRL). All primers were synthesized at the Iowa State University DNA facility. A 100-µL total PCR reaction was set up containing 1.5 mM MgCl2, 0.2 mM each of T3 and T7 (or SP6 and T7) primers, 100 µM of each nucleotide, 1 x PCR buffer (containing 50 mM of KCl, 10 mM of Tris-HCl pH 8.3), two units of Taq DNA polymerase (Gibco BRL), and a single bacterial colony or a 10-µL overnight bacterial culture containing the respective cDNA clone. An initial 4-min treatment at 94°C was conducted before the cycling began. Cycling consisted of 45-s denaturation at 94°C, 1-min primer annealing at 52°C, and 2-min DNA extension at 72°C for 30 cycles on a MJ Research PTC-100 thermocycler. At the end of the cycles, an additional 5-min DNA extension at 72°C was performed. The PCR product was diluted with sterile water to a concentration of 25 ng per µL. The amplified cDNA inserts were then used as probes in the restriction fragment length polymorphism (RFLP) analyses.

DNA Extraction, Restriction Digestion, Electrophoresis, and Southern Analysis
DNA was extracted from leaves as described previously (Keim et al., 1988). To identify the RFLP probe-enzyme combinations revealing polymorphism between the parents of the mapping populations, all parental DNAs [PI 317.336, PI 317.334B, Corsoy, G. max (A81-356022) and G. soja (PI 468.916)] were digested with each of nine restriction enzymes (DraI, EcoRI, EcoRV, HhaI, HindIII, PstI, StyI, TaqI, and XhoI) according to the manufacturer (Gibco BRL). The RP and the NIL DNAs were also digested with the same restriction enzymes as those used to digest the parental and mapping progeny DNAs. Digested DNAs were then electrophoresed in 0.8% Ultrapure agarose gel (Gibco BRL) in 1 x TAE buffer (Sambrook et al., 1989) at 22 to 30 V for 16 to 20 h. The DNAs were then transferred (Southern, 1975) onto Zeta-Probe GT nylon membranes (Bio Rad, Hercules, CA), probed, and autoradiographed as described previously (Keim et al., 1990). Following the parental screen analyses, the polymorphic probes were hybridized to the progeny DNA of each population. A Chi-square test was used to determine the segregation ratio if the polymorphic bands fit the expected ratio for each population. The null hypothesis of the tests was that progeny segregated in a 1:1 ratio in populations IX132 and IX136 and a 1:2:1 ratio for the G. max x G. soja population. Only the mapped candidate flowering time gene sequences were used to probe the NIL DNAs and their respective RPs.

Linkage Mapping
Markers used in this study were those reported by Tasma et al. (2001) for the RIL populations IX132 and IX136, and those reported by Cregan et al. (1999), Shoemaker and Olson (1993), and Shoemaker and Specht (1995) for the G. max x G. soja population. Markers were placed on the map using the Mapmaker mapping program (Lander et al., 1987). For grouping the markers, a minimum LOD score of 3.0 and a maximum distance of 40 cM were used as a threshold value to declare linkage in the pairwise loci analysis. The linkage map was constructed using the Haldane map function (Haldane, 1919). The gene orders were assigned using the compare, try, and ripple (minimum LOD score of 3.0) commands.


   RESULTS
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
Candidate Gene Segregation in the Progeny of IX132 and IX136
A total of 14, 11, and 17 gene and restriction enzyme combinations segregated in populations IX132, IX136, and G. max x G. soja, respectively (Tables 4, 5, 6). This represented eight, seven, and nine distinct homologous genes, respectively. Chi-square tests showed almost all the segregating restriction fragments fit the expected segregation ratio (Tables 4, 5, 6). Only two of the segregating restriction fragments (FCA-I and FCA_S) did not fit the expected segregation ratios in population IX132. Only one (AP2_H1) of the markers did not follow the expected segregation ratio in G. max x G. soja population.


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  		Table 4. Chi-square tests of segregation ratios for homologous cloned flowering time gene candidates in population IX132.

 

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  		Table 5. Chi-square tests of segregation ratios for homologous cloned flowering time gene candidates in population IX136.

 

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  		Table 6. Chi-square tests of segregation ratios for homologous cloned flowering time gene candidates in the F2:4 G. max x G. soja population.

 
Location of Candidate Flowering Time Genes in the Soybean Genome
Homologous sequences to four photoperiod recognition genes (PHYA, PHYB, CRY2, and CCA1), five flowering time genes (FCA, DET1, COL1, COL2, and LD), and one floral identity gene (AP2) were mapped. Eight were mapped in population IX132 (Fig. 1). AP2, CCA1, COL2, DET1, FCA, FUS5, and PHYA mapped to single locations. PHYB mapped to two different LGs, E and K (Fig. 1).



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  		Fig. 1. Location of flowering time gene homologs on the soybean genetic map based on data from population IX132 (PI317.336 x ‘Corsoy’). *FCA_I, FCA_T, and FCA_H were also mapped on this site. D = DraI, I = EcoRI, V = EcoRV, Ha = HhaI, H = HindIII, P = PstI, S = StyI, and T = TaqI.

 
Six homologs were mapped in population IX136 (Fig. 2): COL2, DET1, FCA, FUS5, PHYA, and PHYB. As in population IX132, PHYB also mapped to two different LGs (E and K) and was linked to the same markers in both populations (Fig. 2).



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  		Fig. 2. Location of flowering time gene homologs on the soybean genetic map based on data from population IX136 (PI317.334B x ‘Corsoy’). *FCA_I, and FCA_T were also mapped in this site. D = DraI, I = EcoRI, V = EcoRV, Ha = HhaI, H = HindIII, P = PstI, S = StyI, and T = TaqI.

 
Seven genes were mapped in the G. max x G. soja population (Fig. 3): COL1, COL2, CRY2, FCA, LD, PHYA, and PHYB. Consistent with data from populations IX132 and IX136, PHYB was again mapped on two LGs (E and K). However, PHYA and COL1 also mapped in two LGs (A1 and B2 for PHYA; B1 and H for COL1) (Fig. 3).



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  		Fig. 3. Location of flowering time gene homologs on the soybean genetic map based on data from G. max x G. soja population. D = DraI, I = EcoRI, V = EcoRV, Ha = HhaI, H = HindIII, P = PstI, S = StyI, T = TaqI. Only a portion of the map in each linkage group (LG) is shown. Other markers in each LG are not shown.

 
The map locations of candidate genes were found to be consistent across populations (Fig. 1, 2, 3). PHYA (LG B2), PHYB (LGs E and K), and FCA (LG L) were mapped in all three populations and all were found to be linked with the same markers. DET1 (LG C1), FUS5 (LG E), and COL2 (LG F) were mapped only in populations IX132 and IX136 and were also mapped to consistent locations. The genes mapped in only one population include AP2 (LG D2 of IX132), CCA1 (LG Q of IX132), COL1 (LGs B1 and H of G. max x G. soja), CRY2 (LG A2 of G. max x G. soja), and LD (LG C1 of G. max x G. soja).

Correlation of Flowering Time Gene Homologs and the Maturity (E) Loci
Among 10 cloned flowering time genes used to probe 41 NILs and RPs, only two were found to yield polymorphisms. These were homologs of FCA and PHYB. An example of a polymorphism observed from this study is shown in Fig. 4. The FCA probe was polymorphic on NILs L71-920, L74-441, L80-5914, L63-2404, L63-3270, and L80-5879 with respect to their RP, Clark (Table 7, Fig. 4). Restriction endonucleases showing polymorphisms in these NILs were StyI, TaqI, and HindIII. Each NIL genotype and the respective RP are shown in Table 7. The pattern of polymorphisms among the various NILs is consistent with the association of FCA with maturity locus E3. FCA mapped to LG L in all three populations (IX132, IX136, and G. max x G. soja). E3 also maps on LG L (Cregan et al., 1999) proximal to FCA. Thus, FCA may correspond to the maturity locus E3.



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  		Fig. 4. Polymorphisms observed between NILs (L71-920 and L74-441) and their respective RP ‘Clark’ including the donor parent ‘Oni Hadaka’ using homologous gene sequence FCA as probe. DNAs were digested with a restriction endonuclease StyI. Arrows indicate polymorphic bands. Numbers on the left side of the picture indicate the lambda marker size in kilobase.

 

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  		Table 7. Homologous gene sequences associated with flowering time and genotypes of corresponding polymorphic near isogenic lines and recurrent parents.

 
The soybean homolog of PHYB was polymorphic on NIL L66-531 with respect to its RP Clark and on NILs L67-2324 and L71-1116 with respect to their RP Harosoy (Table 7). Restriction endonucleases showing polymorphisms were HhaI and HindIII. The analysis of NILs shows an association between the candidate gene PHYB sequence and maturity locus E1. However, PHYB was mapped on LGs E and K in all three populations. E1, on the other hand, was mapped on LG C2 (Cregan et al., 1999). All other candidate flowering time gene sequences were found to be monomorphic across all NILs used in this study.

Correlation of Map Positions with QTL
No direct association between map position of candidate genes and flowering QTL were observed within the populations studied. Once FCA and PHYB sequence homologs were placed on the linkage maps QTL analyses were performed again and no flowering time QTL was discovered in the region of these genes. A small effect QTL for days to R3 was observed on LG L (Tasma et al., 2001) but its position is distance from the FCA homolog. However, based on reports from other studies, an indirect association of the mapped flowering time gene candidate and the QTL can be inferred. These will be discussed in a later section.


   DISCUSSION
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
In this study we mapped 10 flowering time gene homologs in soybean. The identification of gene homologs in soybean suggests that homologous flowering time gene sequences found in Arabidopsis have corresponding sequences in soybean that may affect flowering, and these sequences may be conserved across other plant genera. The sequences were distributed on nine soybean LGs. Seven of the homologous sequences were detected in only one LG. Three, however, were detected in two LGs, suggesting that they represent duplicate loci.

Using combinations of NILs, the candidate gene sequence FCA was found to be associated with maturity locus E3. Six NILs (L71-920, L74-441, L80-5914, L63-3270, L63-2404, and L80-5879) carried the e3 allele compared with their respective Clark (Table 7, Fig. 4). Using the soybean FCA probe, a polymorphism was found between all six L-lines and Clark (Fig. 4), suggesting the polymorphisms are due to genetic variation in the genome region including the contrasting e3 and E3 alleles. Thus, from this analysis we infer that FCA may be maturity locus E3 or may be tightly linked to E3. The candidate gene PHYB was also found to be polymorphic in three NILs and seems to be associated with maturity locus E1. However, the map positions of PHYB and E1 do not support this observation.

Supporting this conclusion was the discovery that the FCA soybean homolog was mapped on LG L and was detected in approximately the same locations in all three populations used in this study (Fig. 1, 2, 3). E3 was mapped on LG L by Cregan et al. (1999). FCA and E3 both are located near simple sequence repeat (SSR) marker Satt006. Mansur et al. (1996) discovered a minor effect QTL for flowering time (days to R1) and maturity (days to R8) on LG L, also linked with SSR marker Satt006. Yamanaka et al. (2001) found a major QTL (FT3) for flowering time on LG L very tightly linked with SSR marker Satt373. The soybean FCA homolog mapped close to Satt373 in all three populations used in this study (Fig. 1, 2, 3). It is possible that some effects of the minor QTL observed by Mansur et al. (1996), and the major QTL FT3, observed by Yamanaka et al. (2001), may be due to the E3 locus.

No flowering time (days to R1) QTL were detected on LG L using these RIL populations (Tasma et al., 2001). It is possible that we have failed to detect flowering time QTL at the candidate gene loci in these populations. Simulation studies show not all QTL will be detected in a small population (100 to 200 progeny) (Beavis, 1997). In addition, due to distances between informative markers, a small-effect QTL may not have been detected. Thus, some of the homologs mapped in this study may have had an undetectable effect on flowering time in these soybean populations. Alternatively, in these populations FCA is not a flowering time factor. We also have no evidence that E3 is segregating in these populations that may account for the lack of a QTL at the FCA location.

A degree of common functionality has been demonstrated between FCA of Arabidopsis and the maturity locus E3 of soybean with regard to their response to inductive and noninductive daylengths. In Arabidopsis, FCA promotes flowering independent of photoperiod (photoperiod-insensitive) (Levy and Dean, 1998; Piñeiro and Coupland, 1998). E3 was also reported as a major locus conferring photoperiod-insensitivity in soybean (Saindon et al., 1989). In addition, under natural daylength, the dominant late maturity E3 allele was reported to delay maturity the least compared with the effects of dominant alleles of other maturity loci with respect to the recessive (early maturing) alleles. This supports the insensitive nature of the E3 locus. Cober et al. (1996b) also reported the E3 allele was the least sensitive to changes in light quality in response to long daylength compared to other E loci. Thus, based upon their responses to inductive and noninductive photoperiods, FCA in Arabidopsis and the maturity locus E3 in soybean demonstrate similar functions. This observation and the similar map locations of the soybean FCA homolog and E3 on LG L make the soybean FCA homolog a strong candidate for the soybean maturity locus E3.

Analysis of NILs also indicated PHYB is associated with the maturity locus E1. In support of this observation, the map position of E1 (LG C2) was proximal to a QTL for flowering time (Tasma et al., 2001). However, in this study PHYB did not map to LG C2 but mapped to two other LGs (E and K).

The mapping of this gene to two locations suggests that we may have mapped PHYB paralogs. Soybean is recognized as an ancient polyploid and is reported to be rich in duplicated loci (Shoemaker et al., 1996). That LG E and LG K contain homeologous regions (i.e., RFLP markers in common) provides further support that the two mapped PHYB are duplicated loci. A similar situation was observed between homeologous regions on LGs B1 and H (Shoemaker et al., 1996) where duplicate copies of the COL1 homolog were mapped.

There may be more than two copies of PHYB homologous sequences in the soybean genome. It is possible, therefore, that we have failed to map the PHYB homolog on LG C2. Another possibility is that another gene (possibly an unknown maturity locus) was introduced along with E1, during the NIL development. In that scenario, PHYB could correspond to that unknown locus. We may have identified polymorphisms around this other gene, and it is this other gene that corresponds to PHYB. An additional possibility is that E1 may be duplicated with copies on LG E and/or K where PHYB has been mapped.

Some common gene action is apparent between PHYB and soybean maturity locus E1. In Arabidopsis [a long day (LD) plant], PHYB inhibits floral initiation (Coupland, 1997). The PHYB mutant is classified as an early flowering mutant and flowers earlier than the wild-type plants under both LD and short day (SD) conditions. However, the early phenotype of the mutant is more pronounced in SD conditions (Goto et al., 1991; Mockler et al., 1999). PHYB mutants in sorghum (Ma3R) (Childs et al., 1997) and pea (Iv-1) (Weller and Reid, 1993) both showed early flowering and decreased photoperiod sensitivities. Sorghum is classified as a SD plant and pea is a LD plant. The PHYB mutant in pea flowers early in SD but not in LD (Weller and Reid, 1993), whereas PHYB mutant in sorghum flowers early in LD but not in SD (Pao and Morgan, 1986). Thus, wild-type PHYB inhibits flowering both in LD and SD plants. The flowering inhibition of PHYB, however, appears more apparent in the photoperiod that normally suppresses flowering in the respective plant.

In soybean, E1 also inhibits flowering. Under natural daylength, the presence of E1 delayed flowering 16 to 23 d and maturity 15 to 18 d (Bernard, 1971) compared with the recessive allele, e1. This flowering delay is greater than the effects of other dominant maturity loci (Cober et al., 1996a).

Light quality studies showed that the E1 allele was most sensitive to light quality and required a R:FR ratio approximating that of natural daylight for response to long daylength (Cober et al., 1996b). The E3 and E4 alleles were reported to have the least and intermediate sensitivities to changes in light quality, respectively. The E1e3e4 isoline showed a strong response to long days compared with the e1e3e4 isoline when a R:FR range from 2 to 1 (a R:FR ratio equivalent to natural light) was used but showed very small response with R:FR ratio above two. The E1e3e4 isoline flowered 5 d later than the e1e3e4 isoline at a R:FR ratio of 2, but 15 d later than the e1e3e4 at R:FR ratio of 1. This flowering delay is characteristic of the effect of allele E1 under field conditions (Bernard, 1971; McBlain et al., 1987). A study in Arabidopsis showed that PHYB and at least one other phytochrome mediate light quality responses where LD low R:FR ratio demonstrated accelerated flowering (Halliday et al., 1994). In soybean, on the other hand, long day low R:FR conditions resulted in delayed flowering (Cober et al., 1996b). Cober et al. (1996b) speculated that LD low R:FR conditions may simply elicit more extreme photoperiodic responses, that is, earlier flowering in LD plants and delayed flowering in SD plants. Thus, on the basis of this evidence, there are common characteristics in phenotypes between PHYB in Arabidopsis and maturity locus E1 in soybean.

Even though some phenotypic traits are common between the candidate gene PHYB and the maturity locus E1, and the analysis of NILs indicated an association, the current map positions of these two genes are different. However, we cannot rule out PHYB as a candidate gene for the maturity locus E1. Further investigation may clarify this discrepancy.


   ACKNOWLEDGMENTS
 
The authors thank Dr. Detroy Green for the RIL populations used in this study, Dr. Randall Nelson and Dr. Elroy Cober for providing near isogenic lines, Dr. John Erpelding and Dr. David Grant for technical advice and helpful discussion, Dr. Margie Paz and Mr. Thad Wunder for the excellent technical assistance. This research was supported by the government of Indonesia. Names are necessary to report factually on the available data; however, the USDA neither guarantees nor warrants the standard of the product to the exclusion of others that may also be available.


   NOTES
TOP
 NOTES
ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Joint publication of the USDA-ARS-Corn Insect and Crop Genetics Research Unit and Journal Paper no. J19861 of the Iowa Agriculture and Home Economics Exp. Stn., Ames, IA (project no. 3236).

Received for publication November 19, 2001.


   REFERENCES
TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 




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