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Published in Crop Sci. 44:1832-1838 (2004).
© 2004 Crop Science Society of America
677 S. Segoe Rd., Madison, WI 53711 USA

GENOMICS, MOLECULAR GENETICS & BIOTECHNOLOGY

A PCR Marker for Growth Habit in Common Wheat Based on Allelic Variation at the VRN-A1 Gene

J. D. Shermana,*, L. Yanb, L. Talberta and J. Dubcovskyb

a Dep. of Plant Science, Montana State Univ., Bozeman, MT 59718
b Dep. of Agronomy and Range Science, Univ. of California, Davis, CA 95616

* Corresponding author (jsherman{at}montana.edu).


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Growth habit varies among accessions of hexaploid wheat (Triticum aestivum L.). The winter habit genotype (homozygous recessive for vrn-A1, vrn-B1, vrn-D1) requires a cold treatment to induce flowering and is generally planted in the fall. Spring habit genotypes flower in the absence of a vernalization treatment. Spring habit is conferred by a dominant allele at any of the three VRN-1 loci, but varieties carrying the VRN-A1 locus are the most frequent and usually flower earlier. To facilitate selection in populations segregating at the VRN-A1 locus and to assist in genotyping wheat accessions of unknown VRN-1 composition, a PCR-based marker for growth habit would be useful. The VRN-A1 gene was recently cloned allowing for the development of markers for growth habit. In this report, we designed primer sets specific for the VRN-A1 locus, and used them to amplify an 810-bp segment of the VRN-A1 gene between intron 4 and exon 8 from 40 spring wheat lines and 37 winter wheat lines. Three diagnostic nucleotide changes were identified that differentiated the dominant Vrn-A1 and recessive vrn-A1 alleles in 75 out of the 77 genotypes analyzed in this study. One of these differences resulted in the presence of an additional AciI restriction site in the allele for spring growth habit. This difference was exploited to develop a cleavage amplification polymorphic sequence (CAPS) that can be used to determine the allelic state at VRN-A1 in germplasm collections, and as a marker in backcross breeding projects. An additional pair of dominant markers was developed from a different polymorphism.

Abbreviations: CAPS, cleavage amplification polymorphic sequence • CS, Chinese Spring • indel, insertion–deletion • RFLP, restriction fragment length polymorphism • SNP, single nucleotide polymorphism


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
WHEAT PRIMARILY EXISTS as either winter or spring growth habit. Winter wheat requires a vernalization period (4–6 wk at temperatures below 10°C) to induce flowering, while spring wheat flowers without a vernalization treatment. Although there are several genes influencing vernalization treatment (McIntosh et al., 2003), the most common difference between spring and winter wheat genotypes in North America is at the VRN-A1 locus. In common wheat, spring habit is inherited as a dominant trait and winter habit is recessive (Flood and Halloran, 1986).

Spring and winter wheat are grown interchangeably in many regions of the Great Plains, and as a result, breeding criteria for new varieties are similar. However, the two habits have formed isolated gene pools since new spring and winter varieties tend to be developed from varieties of similar habit. In this regard, Barrett and Kidwell (1998) assessed genetic diversity using amplified fragment length polymorphisms (AFLP) for several classes of wheat grown in the Pacific Northwest. Their results showed a clear separation of spring and winter wheat, which was supported by pedigree information (Barrett et al., 1998). Since genetic variance for agronomic traits among progeny lines was correlated with AFLP diversity of parents (Burkhamer et al., 1998), more progeny diversity would be expected in winter by spring crosses.

Several breeding programs have been involved in producing winter x spring crosses. These programs have been interested in increasing genetic diversity and improving certain traits such as yield, winter hardiness, earliness, and drought resistance (Gill et al., 1977; McCuistion, 1978; Kant et al., 2001). Motives for crossing between spring and winter wheat germplasm pools not only include improving diversity for quantitative traits but also include backcrossing for specific genes. In both cases, the inability to determine progeny genotypes easily and reliably at VRN-A1 is a limitation. This is especially true in backcrossing programs, where distinguishing homozygous and heterozygous spring wheat progeny is not possible. A molecular marker for vernalization habit would be valuable in crossing programs involving both growth habits.

A VRN-A1 marker also would be useful in genotyping spring germplasm. It is often the case that VRN-A1 genotype is not known in untested germplasm materials, as spring habit may be due to dominate alleles at other VRN loci (McIntosh et al., 2003). Dominant spring alleles at these loci result in genotypes that do not require cold treatment to flower but have differences in flowering time. The effect of the different VRN-1 genes on flowering is difficult to distinguish from other genes that also influence flowering time in wheat (e.g., response to photoperiod). A simple distinguishing test to determine allelic state at VRN-A1 would be useful in applied wheat breeding programs.

The VRN-A1 vernalization locus has been mapped in Triticum monococcum L. and associated with RFLP markers (Dubcovsky et al., 1998). VRN-A1 was also mapped in the deletion-bin maps of T. aestivum (Sarma et al., 1998; Sutka et al., 1999). These mapping projects identified RFLP markers that were tightly linked to the VRN-A1 locus. Unfortunately, RFLPs often show low levels of polymorphism between improved cultivars (Bryan et al., 1999). Iwaki et al. (2002) converted an RFLP marker linked to the orthologous VRN-B1 locus on chromosome 5B into a dCAPS marker. RFLP markers linked to vernalization also have been used to identify BAC clones in barley, rice and T. monococcum and to clone the VRN-A1 using a map-based cloning approach (Dubcovsky et al., 2001; Yan et al., 2003). The positional cloning showed that wheat APETALA1 (AP1) homolog was the VRN-A1 gene in diploid wheat, and this was confirmed by expression studies during vernalization (Yan et al., 2003). Trevaskis et al. (2003) and Danyluk et al. (2003) confirmed a similar expression profile of AP1 in common wheat. The VRN-A1 sequence information obtained from the previous studies provides the opportunity to develop a PCR marker within the gene for the spring versus winter allele. That opportunity is the focus of this paper.


   MATERIALS AND METHODS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
Plant Materials
Triple Dirk isogenic line carrying the VRN-A1 allele for spring growth habit and recessive vrn-B1 and vrn-D1 alleles for winter growth habit at the other loci was provided by R.E. Allan at Washington State University. Triple Dirk C is an isogenic winter line with recessive vrn-1 alleles at all three loci. (Pugsley, 1971; Stelmakh, 1987; Storlie et al., 1998). All other accessions were obtained from the USDA National Small Grains Collection (Aberdeen, ID) or from Montana breeding lines (Table 1). All plant materials were maintained in a greenhouse where temperature ranged from 18 to 25°C with a daylength of 16 h. Spring wheat accessions of unknown genotype were crossed with the Triple Dirk line with the VRN-A1 allele. Resulting F2s were tested for growth habit by growing 96 individuals from each cross under greenhouse conditions without vernalization.


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  		Table 1. List of spring and winter accessions comparing reported habit with VRN-A1 intron sequence.

 


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  		Fig. 2. Consensus sequences for winter and spring genotypes of the region amplified by VRN-A1-specific primers (indicated in bold-italic letters at the beginning and end of the sequence). Dots in the sequence from the spring varieties indicate identical bases with the sequences from the winter varieties. The three differences found between the ‘s’ and ‘w’ haplotypes are indicated by bold letters. AciI restriction sites are underlined. The location of the allele specific primer 361W-F is indicated in underlined italic letters.

 
Molecular Protocols
Genomic DNA was isolated from 40 spring wheat lines and 37 winter wheat lines as described by Riede and Anderson (1996). Each individual was maintained in the greenhouse to confirm growth habit.

Sequence of VRN-A1 was available from T. monococcum BAC 231A16 (GenBank AY188331, Yan et al., 2003). A probe for the VRN-A1 gene excluding the conserved MADS-box domain was amplified from BAC 231A16 by means of primers TmExon4-F and Tm3'UTR-R (Table 2). This probe was used to screen the BAC library of the tetraploid variety Langdon (Cenci et al., 2003) and a partial EcoRI BAC library of the D genome from Aegilops tauschii subsp. strangulata (Eig.) Tzvelev AL8/78-2-2 from Armenia (J. Dvorak, M.-C. Luo, and H.B. Zhang, unpublished). The PCR products amplified from the A, B, and D-genome BACs were sequenced, and the intergenome polymorphisms were used to design A-genome specific primers.


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  		Table 2. VRN–1 primer sequences. Polymorphic bases are underlined.

 
The A-genome specific primers VA1-F and VA1-R (Table 2) were used to amplify the distal part of the VRN-A1 gene from spring and winter wheat lines (Table 1). PCR conditions were as described by Talbert et al. (1994) with annealing temperature of 55°C. The genome-specific PCR products from 40 spring lines and 37 winter lines were cleaned by Wizard PCR preps (Promega, Madison, WI) and cloned into pGEM-T vector (Promega) by means of TOP10F' (Invitrogen, Carlsbad CA) competent cells. Plasmids with the correct inserts were isolated with Wizard SV Plus Minipreps (Promega) and sequenced in both directions using the T7 and SP6 primers. Sequences were aligned using ClustalW (http://workbench.sdsc.edu; verified 27 April 2004).

Allele-specific primers for the spring and winter alleles of VRN-A1 (361S-F and 361W-W, Table 2) were labeled with IRDye800 (LI-COR, Lincoln, NE) for use with IR2 DNA Analyzer (LI-COR).


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
Development of A Genome Specific Primers
Twelve positive BAC clones were identified in the screening of the tetraploid BAC library of Langdon (Cenci et al., 2003) by hybridization with the VRN-1 specific probe. These twelve BACs were assembled into two groups by HindIII fingerprinting, and then confirmed by Southern blot hybridization with the VRN-1 probe. Langdon BACs 1256C17 and 1225D16 were selected to represent each of the two different groups from Langdon, and BAC clone 22J2 was selected from the partial D genome BAC library. Genomic sequences between exon 4 and the end of the genes were obtained by means of primers TmExon4-F and Tm3'UTR-R (Table 2) from BACs 1256C17, 1225D16, and BAC 22J2 (GenBank AY466448, AY466447, AY466446). BAC 1256C17 sequence was the more similar to the A genome of T. monococcum (AY188331) indicating that BAC 1256C17 corresponded to the A genome and BAC 1225D16 to the B genome. This genome assignment was confirmed by amplification of nulli-tetrasomic lines from homeologous group five using primers specific for the BAC 1256C17 sequence (Fig. 1 , see below).



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  		Fig. 1. PCR amplification of primers VA1-F and VA1-R. DNAs were digested with restriction enzyme HinfI. Normal Chinese Spring in the first lane is followed by nulli-tetrasomic lines missing chromosomes 5A, 5B, and 5D, respectively. Note that there is no amplification product in the nulli-5A line, confirming that the primers are A-genome specific. The band size after restriction with HinfI was 690 bp as predicted by the A genome sequence.

 
Comparisons among these sequences revealed numerous differences among the three genomes, which were used to design genome specific primers. The VRN-A1-specific forward primer VA1-F was located in intron 4. The sequence of this primer differed from the B and D genome sequences at positions 20 and 25 (Table 2, underlined). The VRN-A1-specific reverse primer VA1-R was located in the 3'UTR. The sequence of this primer differed from the B genome sequence at positions 10 and 20 (Table 2, underlined), but only at position 20 from the D genome.

The VRN-A1-specific primers amplified an 810-bp region in Chinese Spring and nullisomic-tetrasomic lines lacking chromosomes 5B and 5D, but not in the line lacking chromosome 5A, confirming the A-genome specificity of these primers (Fig. 1).

Polymorphisms Differentiating Alleles for Spring and Winter Growth Habit
VRN-A1-specific primersVA1-F and VA1-R were used to amplify, clone, and sequence the 0.8-kb fragment from the VRN-A1 gene from different spring and winter accessions (Table 1). To confirm that the cloned products were from the A-genome copy before sequencing, the PCR products from the clones were digested with HinfI. This restriction enzyme cuts only once within the VRN-A1 gene but twice within the VRN-B1 and VRN-D1 genes.

Comparison of the VRN-A1 sequences from 40 accessions with spring growth habit and 37 accessions with winter growth habit showed two main haplotypes that differed in two 1-bp indels and one single nucleotide polymorphism (SNP, Fig. 2) . Other sequence differences were observed in some of the lines, but were not consistent among growth habit groups. Since only one clone from each accession was analyzed, these differences could be sequencing artifacts. Conversely, the differences composing the two haplotypes were seen in all accessions. All the accessions with a winter growth habit, except Triple Dirk C, had the same haplotype (Fig. 2, top), which will be referred to hereafter as the "w" haplotype. Thirty-seven out of the 40 accessions with a spring growth habit have the alternative haplotype (Fig. 2, bottom), which will be referred to hereafter as the "s" haplotype. Lines Egypt NA 101, Gular, and S-1 were confirmed to have a spring growth habit, but have the w haplotype (Table 1). Spring growth habit may be due to dominant alleles at other vernalization loci (Flood and Halloran, 1986). To determine the VRN-A1 genotype for these three accessions, they were each crossed with the tester line Triple Dirk homozygous for the dominant VRN-A1 allele. If the lines had a spring allele at a VRN locus other than VRN-A1 then a portion of the F2 progeny would have a winter growth habit, whereas if these three lines had the dominant VRN-A1 allele, then all the progeny would have a spring growth habit. In each of the three cases tested, a portion of the F2 progeny were winter. Therefore, Egypt NA 101, Gular, and S-1 are homozygous recessive for vrn-A1 and their spring growth habit was determined by a dominant allele at one of the other vernalization genes. Chinese Spring was an exception to the association between the dominant VRN-A1 allele and the s haplotype among the accessions with a spring growth habit (Table 1). Chinese Spring had the s haplotype but is known to carry a recessive vrn-A1 allele. Its spring growth habit is determined by a dominant VRN-D1 allele.

Codominant Cleavage Amplification Polymorphic Sequence (CAPS) Marker
The lines with the w haplotype have a T at position 457, whereas the lines with the s haplotype have a C at this position generating an additional recognition site for restriction enzyme AciI (Fig. 2). The s haplotype has five recognition sites for AciI and the w haplotype four (Fig. 2). Digestion of the PCR product from VRN-A1-specific primers VA1-F and VA1-R with AciI resulted in a 532-bp fragment in the accessions with the ‘w’ haplotype and in a 456-bp fragment in the accessions with the s haplotype (Fig. 3) .



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  		Fig. 3. PCR product amplified by VRN-A1-specific primers and digested with restriction enzyme AciI. The growth habit of each variety is indicated below the photograph. The PCR product from the winter varieties is 76 bp larger than the PCR product from the spring varieties, which have an additional AciI restriction site. The varieties used in this figure except HiLine are not part of Table 1: H-HiLine, E-Era, V-Vanguard, F-Federation, Re-Red Egyptian, R-Rocky, Mt-MTW94410, R-Reeder, Ru-Russ, No-Norstar, P-Pilot, Ph-Pronghorn, 3-PI372129.

 
Allele-Specific Dominant Markers
The two-step procedure required for the CAPS marker and the additional cost of the restriction enzyme could be a limitation in high throughput screenings in breeding programs. For these cases, allele specific primers were designed based on the 1-bp indel at position 361 (Fig. 2). Primer 361S-F had an A at the 3' end of the primer that matched the ‘s’ haplotype, whereas primer 361W-F had a T at the 3' end, characteristic of the w haplotype (Table 2). Each of these two primers in combination with the A specific primer VA1-R produced a dominant marker for each of the two different haplotypes.

Since the allele-specific primers differ only in 1 bp they might require optimization of the PCR conditions. During the optimization process, the PCR products can be digested with HinfI to confirm the A-genome origin of the amplification product (no HinfI site within this A genome segment) and with AciI to confirm the amplified haplotype (s haplotype: 116 + 264 bp, w haplotype: 360 bp). Figure 4 shows the PCR amplifications of DNAs from 20 spring (1–20) and 10 winter (21–30) F2 plants from the cross Newana x Redwin. The PCR products were amplified with the spring haplotype-specific primer 361S-F/VA1-R and then digested with restriction enzyme AciI. The presence of the 116-bp band confirmed that the PCR product was from the s haplotype. No PCR products were detected in the winter accessions.



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  		Fig. 4. PCR products from F2 plants from the cross Newana x Redwin amplified by IRDye800-labeled primers 361SF and VA1-R and run on a Licor DNA Analyzer. Products were digested with restriction enzyme AciI to confirm that they originated in the A genome. Note that the specific primers for the ‘s’ allele amplified a product only from the 20 spring plants (1–20). The band is absent in the 10 winter individuals (21–30). Digestion with AciI produced the expected band of 116 bp, confirming the presence of a different ‘s’-specific polymorphism in the PCR products. M indicates the molecular weight marker.

 

   DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
Perfect markers, which show no recombination with the phenotype, have been designed for the dwarfing, hardness, and waxy loci in wheat (Ellis et al., 2002; Gioux and Morris, 1997; Tranquilli et al., 1999; McLauchlan et al., 2001). In these cases, the perfect marker is for the sequence difference that causes the different phenotypes. The advantage of perfect markers is that they are completely linked to the phenotype.

Two out of the 77 accessions analyzed here did not show the expected association between the dominant VRN-A1 allele and the corresponding marker, indicating that these mutations are probably not directly responsible for the differences in growth habit. The two 1-bp indels are located within introns 4 and 6, and it is unlikely that they would affect the regulation of the VRN-A1 transcription. The single SNP that differentiates the two haplotypes is located within the seventh exon and generates an amino acid difference, a valine in the w haplotype and an alanine in the s haplotype. However, an alanine amino acid is also present at the same position in the VRN-1 sequences from winter T. monococcum accession G1777 (Yan et al., 2003) and winter T. tauschii accession AL8/78-2-2 used to construct the D genome BAC library (GenBank AY466446). These results suggest that the valine to alanine amino acid difference is not sufficient to explain the change between winter and spring growth habit. However, it would be interesting to investigate if this amino acid difference in the VRN-A1 protein in hexaploid wheat has any effect on flowering time.

In diploid wheat T. monococcum, no amino acid differences in the VRN-A1 proteins were found between accessions with spring and winter growth habit. The differences in growth habit were associated with deletions in the promoter regions (Yan et al., 2003). A more detailed study of the allelic variation in the promoter region of the VRN-A1 gene in hexaploid wheat will be necessary to establish the relationship between the haplotypes found in this study and the differences in the regulatory regions of the VRN-A1 gene.

Although the polymorphisms discovered in this study are probably not the direct cause of the differences between spring and winter growth habit, they were associated with growth habit in a wide range of germplasm (Table 1). The three spring accessions with the w haplotype were shown to carry a recessive vrn-A1 allele and alleles for spring growth habit at different VRN-1 loci, and so were not real exceptions (Table 1). The only two real exceptions were Chinese Spring and Triple Dirk C, which have the recessive vrn-A1 allele but showed the three mutations characteristic of the s haplotype. A simple explanation for these observations is that the separation of the s and w haplotypes occurred before the mutation that originated the change in growth habit, and that those mutations occurred in VRN-A1 genes with the s haplotype. Thus far, all springs have the s haplotype and most accessions with the recessive vrn-A1 allele winters have the w haplotype. The close association between haplotypes and growth habit support the conclusions of Yan et al. (2003) that the wheat AP1 gene is the vernalization gene VRN-1.

Breeding Applications
The results from the Newanan x Redwin population indicates the feasibility of using these markers to screen populations segregating for the VRN-A1 gene. Even though these markers are based on polymorphisms that are not the cause of the differences in growth habit, the probability of a recombination between this marker and a different part of the VRN-1 gene is extremely small. Yan et al. (2003) did not find a single recombinant within the VRN-A1 gene in a segregating population of 6190 gametes. The large regions of repetitive elements flanking the VRN-A1 gene (at least 50 kb in one side and 165 kb on the other) might contribute to the low recombination frequency observed in this region. Therefore, for this type of application these markers would probably be as reliable as a perfect marker.

The CAPS marker is the better option for applications that require a codominant marker. For example, in a marker assisted backcrossing programs to convert a spring line into a winter growth habit, the CAPS marker can be used to differentiate the VRN-A1 homozygous and heterozygous spring plants. The CAPS marker also can be used to select homozygous plants for the spring haplotype in an F2 segregating population, to fix the spring growth habit. However, if the breeding objective were to enrich very large segregating populations for one of the alleles, the allele specific primers would probably be a cheaper option. These markers do not require a restriction enzyme digestion after the PCR, minimizing time and cost.

These molecular markers also could be useful in characterizing spring lines of unknown genotype. As an example of this application, the CAPS marker was used to characterize seven spring accessions (Fig. 3). All these accessions had the s haplotype suggesting that they carry the dominant spring allele for the VRN-A1 locus. The five winter lines included as controls showed the expected w haplotype (Fig. 3).

The CAPS marker also can be used to screen large germplasm collections and identify spring accessions carrying alleles for spring growth habit different from VRN-A1. The identification of lines Egypt NA 101, Gular, and S-1 carrying spring alleles different from VRN-A1 is a good example of this type of application. The quantification of the frequencies of the different spring alleles in different regions of the world might provide an insight on the adaptive value of the different VRN-1 alleles to different environments.


   ACKNOWLEDGMENTS
 
The authors express their gratitude to Dr. J. Dvorak, and M.-C. Luo for providing access to the D genome BAC library. The authors acknowledge financial support from USDA- IFAFS competitive grant 2001-04462 and USDA-NRI grant 2003-00929.

Received for publication November 20, 2003.


   REFERENCES
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 




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