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Published in Crop Sci 39:1702-1706 (1999)
© 1999 Crop Science Society of America
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Crop Science 39:1702-1706 (1999)
© 1999 Crop Science Society of America

CELL BIOLOGY & MOLECULAR GENETICS

Development of Arm Specific RAPD Markers for Rye Chromosome 2R in Wheat

Mark S. Brunella, Adam J. Lukaszewskib and Richard Whitkusb

a Dep. of Biology, P.O. Box 10037, Lamar Univ., Beaumont, TX 77710 USA
b Dep. of Botany and Plant Sciences, Univ. of California, Riverside, CA 92521 USA

brunellms{at}hal.lamar.edu


    ABSTRACT
 TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 REFERENCES
 
Rye (Secale cereale L.) chromosome 2R carries several genes for resistance to biotic and abiotic stresses, which could be used in wheat (Triticum aestivum L.) improvement. To make these genes accessible in breeding, translocations of 2R to wheat chromosome 2B have been generated. To compensate for the lack of clearly identifiable cytological markers on chromosome 2R, random amplified polymorphic DNAs (RAPDs) were employed as markers. Wheat lines homozygous for centric translocations 2RS.2BL and 2BS.2RL were screened with 489 primers, resulting in 65 clear and reproducible RAPD polymorphisms. To assign the polymorphisms to individual arms of chromosomes 2R and 2B, the arms of the translocations were separated by centric misdivision and the resulting progeny with desired chromosome constructs were rescreened. As a result, 17 markers were assigned to chromosome arm 2RS, 15 to 2RL, and the remaining 33 most likely located on 2B. Preliminary mapping studies (not shown here) have indicated that some of these markers are evenly distributed along the chromosome arms. These markers should be useful for the localization of translocation breakpoints in recombinant wheat-rye chromosomes.

Abbreviations: RAPD, random amplified polymorphic DNA


    INTRODUCTION
 TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 REFERENCES
 
RYE has long been considered an excellent source of germplasm for the genetic improvement of bread wheat. Rye is tolerant to abiotic stresses such as drought and cold, and its genetic pool contains a wide array of genes for resistance to many pests and diseases of wheat (Zeller and Hsam, 1983).

Of the seven chromosomes of rye, chromosome 1R (and especially its short arm) has been extensively used in wheat breeding. Translocations 1RS.1AL and 1RS.1BL are common in commercial cultivars and breeding stocks all over the world (Rabinovitch, 1998). The 1RS arm carries several genes for resistance to pests and pathogens of wheat and appears to have a positive effect on yield, at least in some genetic backgrounds (Carver and Rayburn, 1994; Moreno-Sevilla et al., 1995; McKendry et al., 1996) but is detrimental to breadmaking quality (Zeller et al., 1982). Extensive cytogenetic manipulations of this arm have been performed to reduce or eliminate the quality defect (Koebner and Shepherd, 1986; Lukaszewski, 1993, 1995, 1997, unpublished data).

In recent years, it has been observed that a centric translocation of the long arm of rye chromosome 2R to wheat, 2BS.2RL, also had a positive effect on yield of wheat (Fritz and Sears, 1991). Preliminary screening of the disomic additions of rye chromosomes to wheat indicated that chromosome 2R increased water-use efficiency and positively affected rooting characteristics of the recipient wheat line (Lahsaiezadeh et al., 1983; Shah, 1992). Moreover, chromosome 2R carries genes for resistance to tanspot and Hessian fly (Hatchett et al., 1993; Lee et al., 1996) and wheat leaf and stem rusts (D. McVey and A.J. Lukaszewski, 1992, unpublished). It appeared, therefore, that chromosome 2R was a good candidate for cytological manipulations, whereby segments of rye chromatin containing loci responsible for the desirable characteristics would be introgressed into wheat.

Introgressions of alien chromatin into wheat are usually done by X-ray induced translocations, whole arm translocations resulting from misdivision-fusion of univalents, or by induced homoeologous recombination (Knott, 1987). X-ray induced translocations are random; hence most are non-compensating. Centric translocations introduce entire arms of chromosomes which often contain, in addition to the loci of interest, undesirable loci with adverse effects on the agronomic performance of the recipient wheat cultivar. As a consequence, centric translocations of 1RS in wheat are an exception rather than the rule in the introduction of alien chromatin.

Since rye is a cultivated species with a gene pool well adapted to modern agronomic practices, it is possible that the introduction of another complete rye chromosome arm into wheat would have an overall positive effect. This, however, requires that the introduced rye arm is genetically equivalent to the replaced wheat arm. In chromosome 2R, the long arm appears to meet this criterion. The short arm is partially homoeologous to the short arms of both group 2 and 6 chromosomes of wheat (Naranjo et al., 1987; Devos et al., 1993) and as such, it is not capable of fully compensating for the absence of either one. Centric translocation of 2RS was indeed found to reduce yield of wheat (Gupta et al., 1989). Induced homoeologous recombination is the method of choice to accomplish a successful transfer of chromatin.

In interspecific transfers into wheat, homoeologous recombination is induced by manipulation of the Ph1 locus on chromosome 5B. Resulting recombinant chromosomes are, as a rule, single breakpoint translocations (Lukaszewski, 1995). Once an adequate number of such translocations is accumulated, they are screened to identify the location of the breakpoint relative to the locus of interest. Two reciprocal recombinants with breakpoints flanking the locus of interest and as close to it as possible are selected, combined in one plant and allowed to cross over in the presence of the wild-type allele of the Ph1 locus to produce a very short interstitial insertion of alien chromatin in wheat (Sears, 1981). Screening of the single breakpoint recombinants is a tedious and long process. Conventionally, this was done by the analysis of meiotic pairing of the primary recombinants with tester chromosomes (Sears, 1977). Molecular markers offer a quicker method of screening but they may not always be available for the particular chromosome arms used as donors and recipients of transfers.

The molecular technique of RAPDs (Williams et al., 1990) has been widely used to generate markers for specific chromosomes or chromosome arms, and to identify alien chromosome inserts harboring genes of economic interest. Such studies have been conducted with grasses (Iqbal and Rayburn, 1995; Nair et al., 1996; Barcaccia et al., 1997; Komatsuda et al., 1997) and other crops species (Bai et al., 1995; Frello et al., 1995; Mikkelsen et al., 1996).

Because of the genetic content of rye chromosome 2R and its potential value in wheat breeding, a project has been undertaken to transfer the desirable characteristics from that chromosome to wheat. While the cytogenetic aspect of this work is slowly taking its course, a set of RAPD markers was developed for the arms of 2R, which will later facilitate the localization of the translocation breakpoints in the primary recombinant chromosomes.


    Materials and methods
 TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 REFERENCES
 
Plant Material
Centric translocations of chromosome 2R from rye S. cereale cv. Blanco to chromosome 2B of wheat were produced in cv. Chinese Spring (CS) by centric breakage-fusion (Lukaszewski, 1997, unpublished) and transferred to cv. Pavon by backcrosses. After BC7 the translocation heterozygotes were self pollinated and among their progeny, translocation homozygotes and their 2B disomic sibs were isolated and grown. For each translocation, four to five translocation homozygotes and four to five 2B disomics as controls were isolated. The DNAs isolated from these lines were used for the detection of polymorphisms.

To assign the source of polymorphism differentiating the pairs of lines to specific chromosome arms, the chromosome arms of the two translocations were separated by centric misdivision in the progeny of plants with chromosome constitution 20'' + 2RS.2BL'' + 2BS.2RL'', in the same fashion as with the 1RS.1BL translocation previously reported (Lukaszewski, 1993). All cytological analyses used C-banding for chromosome identification.

DNA Extraction
Total genomic DNA extraction followed the selective precipitation method of Murray and Thompson (1980), with several modifications. Leaves from each plant were powdered by grinding in liquid nitrogen, followed by addition of 2 mL extraction buffer per gram fresh tissue. Extraction buffer consisted of 0.1 M Tris-HCl, CTAB (mixed alkyltrimethyl-ammonium bromide, 20 g/L), 1.4 M NaCl, 20 mM EDTA, 0.5 mM polyvinylpyrrolidone (PVP-40), 6 mM L-ascorbic acid, and 28 mM 2-mercaptoethanol. Grinding continued until a thin slurry resulted. To improve the purity of the final product, 25 mg activated charcoal (Kodak Norit 211) per gram fresh tissue was added to the slurry (Vroh bi et al., 1996). The homogenate was transferred to a 15-mL tube and incubated at 60°C for 30 min, followed by 10 min at room temperature.

After one extraction with an equal volume of 24:1 (v/v) chloroform/octanol, 1/10 volume of CTAB (10 g/L)/0.7 M NaCl was added to each preparation. Following two additional chloroform/octanol extractions, DNA was precipitated with 1.4 volume of CTAB precipitation buffer (consisting of 50 mM Tris-HCl, CTAB [10 g/L], and 10 mM EDTA). Following centrifugation, the pellet was resuspended in high salt TE (consisting of 10 mM Tris-HCl, 1 mM EDTA, and 1 M NaCl), allowing 24 h for dissolution. DNA was precipitated by the addition of 2 volumes of cold absolute ethanol, followed by centrifugation at 16 000 x g for 10 min at room temperature. The pellets were washed twice: first with 76% (v/v) ethanol/0.2 M sodium acetate for 20 min, and then with 76% ethanol/10 mM ammonium acetate for 20 min. The pellets were air dried and resuspended overnight in 200 µL TE (10 mM Tris-HCl, 1 mM EDTA). Next, two phenol–chloroform–isoamyl alcohol (25:24:1) extractions and one chloroform–octanol extraction were performed. Ammonium acetate was added to the solution (reaching 2.5 M), followed by precipitation with 2 volumes of absolute ethanol. The DNA was then pelleted, air-dried, and resuspended in 200 µL TE. DNA concentrations were measured with a Hoefer TKO 100 DNA Fluorometer (Hoefer Scientific Instruments, San Francisco) following manufacturer's protocols. The final concentration of each sample DNA was adjusted to 10 ng/µL with sterile-filtered water and stored at -20°C.

Random Amplified Polymorphic DNAs
RAPD markers (Williams et al., 1990) were generated in 25 µL reactions consisting of 0.65 U Taq DNA Polymerase (GibcoBRL), 1x Taq DNA Polymerase Buffer (GibcoBRL), 2 mM MgCl2 (GibcoBRL, Gaithersburg, MD), 0.1 mM (each) dNTP (Amersham Pharmacia Biotech, Piscataway, NJ), 25 ng sample DNA, and 0.2 µM (5 pmoles) decamer primer (Operon Technologies, Inc., Alameda, CA). All dilutions were made with sterile-filtered water. Amplifications were performed in a PTC-100 thermal controller (MJ Research , Inc., Watertown, MA) programmed for 2 min at 94°C, followed by 45 cycles of 1 min at 94°C, 1 min at 38°C, and 2 min at 72°C. This was followed by 13 min at 72°C. All DNAs were screened with 489 primers.

Amplification products were separated by size on denaturing 6% (w/v) polyacrylamide gels (3 M urea, 38 x 50 cm), run at 500 V for 17 h. To facilitate the binding and repelling of the gel necessary for subsequent staining, the glass plates were prepared according to Konecny and Redinbaugh (1997). Amplification products were visualized by silver staining (Bassam et al., 1991). Subsequent to air-drying for several hours, RAPD polymorphisms were scored and photographed using Kodak Tech Pan 2415 black and white film. A 100-bp DNA ladder (GibcoBRL) was used as a molecular size standard on all gels.


    Results and discussion
 TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 REFERENCES
 
In the primary screening of the translocation homozygotes (20'' + 2RS.2BL'' and 20'' + 2BS.2RL'') and their sibs with normal chromosome constitution (no rye chromatin present), 40 of the 489 primers tested produced repeatable polymorphisms, yielding a total of 65 bands. The nature of the materials used suggested that these polymorphisms could have resulted from three sources: from the presence of the arms of rye chromosome 2R in Pavon wheat, from the presence of proximal segments of arms of chromosome 2B from CS in the translocated chromosomes, or from residual introgressions of CS chromatin into Pavon which were not removed by backcrosses.

In theory, seven backcrosses are expected to produce, on the average, sister lines which are genetically over 99% identical. However, because of the uneven distribution of crossing over along chromosome arms in wheat (Lukaszewski and Curtis, 1993), the actual levels of similarity may be quite different. To reduce the effect of the residual variation, four to five translocation homozygotes and four to five of their normal sibs were selected on the assumption that such populations would differ only in presence–absence of the wheat-rye translocation. It would therefore appear that the probability of substantial residual variation as a source of polymorphism was low.

Recombination in wheat is practically absent in the proximal regions of chromosome arms (Lukaszewski and Curtis, 1993). Consequently, transfer of centric translocations from one cultivar to another introduces not only the arms of rye chromosomes but also the proximal regions of the wheat chromosome arms in the translocations. These proximal regions of wheat arms in the translocations were completely linked to the rye chromosome arms and in this study they must have been of CS origin. This could be a source of DNA polymorphism between the translocation lines and their normal sibs or the recipient cultivar.

To assign the polymorphisms to chromosome arms, the arms in the translocated chromosomes were separated from each other by centric misdivision. For this purpose, translocation homozygotes 2RS.2BL and 2BS.2RL were intercrossed. In the resulting progeny, the two translocated chromosomes had no arm in common to support meiotic pairing. As univalents, they misdivided producing series of misdivision products. Among the 100 progeny screened, there were three plants with single copies of chromosome 2R and three with chromosome 2B (in effect, chromosomes reconstructed from the translocations). Chromosome 2B was essentially of CS origin except for the distal segments which presumably were from Pavon. Chromosome 2R was a reconstructed original 2R chromosome of Blanco with some possibility of variation in the number of centromeric units present. In addition to the reconstructed chromosomes 2B and 2R, among the progeny screened there were several plants with telocentric chromosomes 2RS, 2RL, 2BS, or 2BL, with isochromosomes 2RS, 2BS, and 2BL, and centric translocations 2BS.2RS and 2BL.2RL (Fig. 1) . Overall, among 100 progeny screened, 35 had at least one misdivision product. This frequency exceeds that observed in the reconstruction of rye chromosome 1R from its centric translocations (Lukaszewski, 1993).



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Fig. 1 Separation of chromosome arms in centric translocations 2BS.2RL and 2RS.2BL by centric breakage and fusion in plants with chromosome constitution 20'' + 2BS.2RL'' + 2RS.2BL''. From left to right, upper row: T2BS.2RL and T2RS.2BL; lower row: telocentric 2BS, isochromosome 2BS, telocentric 2RL, isochromosome 2RL, isochromosome 2RS, centric translocation T2BL.2RL, reconstructed chromosomes T2R and T2B

 
From among various misdivision products, plants were selected with chromosome constitution 20'' + 2RL'' and 20'' + iso2RS''. These plants were screened with the 40 primers which revealed reproducible DNA polymorphism in the original screening. As the two arms of rye chromosome 2R were present individually in the second screening, and no arms of chromosome 2B were present, either of Pavon origin or recombinant CS/Pavon, it is believed that the second screening allowed allocation of markers to individual chromosome arms of 2R and to the entire 2B chromosome. In this case, a RAPD polymorphism could be clearly assigned to the arm of rye chromosome 2R present in the plant screened. Polymorphisms that were not reproducible between the two screenings suggest that they were likely the result of wheat chromosome 2B.

Of the 65 polymorphic DNA bands in the original screening, 17 were observed when iso2RS was present and 2RL or 2B were absent (Table 1 ; Fig. 2) . These bands, therefore, must be located on 2RS. Similarly, 15 polymorphic bands observed in the original screening were observed with 2RL present and 2RS or 2B absent; these must be located on rye chromosome arm 2RL. Of the 65 polymorphic bands repeatedly detected in the original screening, 33 were not observed among the plants with the misdivision products, but were present only with 2B. It is assumed that these bands are located on the recombined arms of chromosome 2B present in the original centric translocation. However, there is a low probability that some of these may in fact be due to the presence of the residual introgressions of CS chromatin on chromosomes other than 2B.


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Table 1 RAPD markers differentiating chromosomes 2B, 2RS, and 2RL

 


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Fig. 2 Representative RAPD polymorphisms specific to wheat chromosome 2B (A), rye chromosome arm 2RL (B), and rye chromosome arm 2RS (C). Arrows and numbers indicate molecular size of marker in bp. Designations below lane labels refer to the random primers used to amplify the polymorphisms

 
As mentioned earlier, chromosome 2R carries loci for leaf and stem rust resistance (D. McVey and A.J. Lukaszewski, 1992, unpublished), Hessian fly resistance (Lee et al., 1996, see below) and appears to affect rooting and water-use characteristics of wheat. All of these traits could be used in wheat breeding if appropriate chromosome translocations were available. Individual arms of rye chromosome 2R have been successfully recombined with its wheat homoeologues and 31 recombinants of 2RS and 70 recombinants of 2RL were isolated (Lukaszewski, 1996, unpublished) and Rybka et al. (1999). Most of these recombinants are with chromosome 2B of Pavon; the remaining are with 2A and 2D. Depending on their distribution along the chromosomes, 32 RAPD markers associated with 2R plus a similar number of markers, which seem associated with chromosome 2B give a hypothetical density distribution of about one marker every 2 to 2.5 cM. While the exact distribution of the markers is not yet known, preliminary screening of recombinant chromosome 2BS.2RL-2BL#14 with the most proximal translocation breakpoint (about 74% of the relative arm's length away from the centromere) showed that of the 29 markers tested, 17 were located in the proximal 74% of the arm and 12 in the distal 26% of the arm. This suggests that the identified markers may be scattered along the chromosome arms and a fairly precise discrimination among the translocation breakpoints will be possible.

In an earlier study (Lee et al., 1996), the 2RL arm with a Hessian fly resistance locus was tagged with a rye-specific probe. However, that probe was developed using primers derived from a repetitive rye sequence. Such probes may be very useful for the identification of any segment of rye chromatin in wheat, but will lack sufficient specificity to differentiate among different translocation breakpoints in recombined wheat-rye chromosomes. Conversely, all tests of recombinants of 2RS and 2RL with wheat have demonstrated clearly that the RAPD markers were specific to segments of 2R and could be placed on genetic maps of 2R (data not shown). However, since rye chromosomes other than 2R have not been tested, there remains a remote possibility that they may be located on other rye chromosomes as well.

The RAPD technique provides a rich source of markers for use in wheat improvement. Preliminary mapping studies involving the markers developed here have indicated that many of the markers are evenly dispersed over the arms of 2R. This set of well-spaced markers on 2R will permit the localization of translocation breakpoints in recombinant wheat-rye chromosomes.


    NOTES
 TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 REFERENCES
 
This research was supported in part by grant No. 96N01 from the Southwest Consortium on Plant Genetics and Water Resources.

Received for publication October 30, 1998.


    REFERENCES
 TOP
 NOTES
 ABSTRACT
 INTRODUCTION
 Materials and methods
 Results and discussion
 REFERENCES
 




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