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Detailed Mapping of the Species Cytoplasm-Specific (scs) Gene in Durum Wheat
Kristin J. Simonsa, Sarah B. Gehlhara, Shivcharan S. Maana, and Shahryar F. Kianianaa Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58105
Corresponding author: Shahryar F. Kianian, 470G Loftsgard Hall, North Dakota State University, Fargo, ND 58105., s.kianian{at}ndsu.nodak.edu (E-mail)
Communicating editor: J. A. BIRCHLER
| ABSTRACT |
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The compatibility-inducing action of the scsti (species cytoplasm-specific gene derived from Triticum timopheevii) and Vi (vitality) genes can be observed when a durum (T. turgidum) nucleus is placed in T. longissimum cytoplasm. These two genes restore compatibility between an otherwise incompatible nucleus and cytoplasm. The objective of this study was to localize the scsti gene on a linkage map of chromosome 1A, which could eventually be used to clone the gene. The mapping population consisted of 110 F2 individuals derived from crossing a Langdon-T. dicoccoides chromosome 1A substitution line with a euplasmic (normal cytoplasm) line homozygous for the scsti gene. Through a series of testcrosses the genotypes of the 110 individuals were determined: 22 had two copies, 59 had one copy, and 29 had no copy of the scsti gene. Data from RFLP, AFLP, and microsatellite analysis were used to create a linkage map. The flanking marker loci found for the scsti gene were Xbcd12 and Xbcd1449-1A.2 with distances of 2.3 and 0.6 cM, respectively. Nearly 10% of individuals in this population were double recombinant for a genetic interval of <3 cM. A blistering phenotype reminiscent of the phenotype observed in maize brittle-1 mutable was also evident in these individuals. The higher frequency of double recombination within this region and seed-blistering phenotype could be an indication of a transposable element(s) in this locus.
MOST cultivated wheats are polyploid in nature. Common bread wheat, Triticum aestivum L. (2n = 6x = 42), is hexaploid, consisting of three different genomes designated as AABBDD. Durum wheat, T. turgidum L. var. durum (2n = 4x = 28), is a tetraploid consisting of two genomes, AABB. Wild Triticum species have various ploidy levels. Examples include the tetraploids, T. dicoccoides (Körn. Ex Asch. & Graebner) (2n = 4x = 28, AABB) and T. timopheevii Zhuk. (2n = 4x = 28, AAGG), and the diploid T. longissimum (S. & M.) Bowden (2n = 2x = 14, SlSl). Wild wheat species are an invaluable source of novel genes for cultivated wheat, including genes for high grain protein content and pest resistance (![]()
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In the past, restoration of fertility (Rf) genes was used to overcome hybrid sterility induced by incompatibility, but Rf genes do not work in all situations (![]()
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Plants other than wheat demonstrate evidence of nuclear-cytoplasmic incompatibility and compatibility. The most commonly observed phenotype is cytoplasmic male sterility (cms; ![]()
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Molecular genetic research of nuclear-cytoplasmic interaction genes in wheat has been limited. ![]()
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Studies of the scs genes may lead to a better understanding of wheat evolution and easier introgression of agronomically important genes from wild to cultivated wheat. Determination of the sequence would provide more immediate and far-reaching information about the gene itself, the sequence surrounding it, its function, and its role in the evolution of wheat. This information may, in turn, broaden our knowledge of nuclear-cytoplasmic interactions in plants. The first step toward cloning this gene is to produce a segregating population for the gene and identify flanking markers. Thus, the objective of this study was to determine a more precise location of scsti with respect to various DNA-based markers in a euplasmic mapping population. This mapping population could also provide the means for saturation mapping of the region surrounding this locus. The long-term goal of this project is to employ these markers to enable cloning of the scsti gene.
| MATERIALS AND METHODS |
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Population development:
A segregating population of 129 euplasmic individuals was developed to find markers associated with the scsti gene (Fig 1). This F2 population was generated by crossing an intervarietal chromosomal substitution line, Langdon-T. diccocoides 1A (abbreviated LDN[Dic1A]), developed by ![]()
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The F2 individuals were planted in the greenhouse in the fall of 1998. The greenhouse conditions were optimized for the growth and reduction of environmental stress to the durum wheat plants. The plants were first exposed to a 24-hr light cycle until heading, at which point the light regime was switched to a 16-hr light cycle. Parental and check durum lines, such as prevalent cultivars "Ben" and "Maier," were also planted as controls to observe environmental effects.
One head of each individual F2 plant was self-pollinated and at least two alternate heads were used for testcrossing to determine genotype (Fig 1). Each male head for testcrossing was used to pollinate at least one female head. The seed produced from each male head was kept separate. The testcross line was alloplasmic in that it had a T. longissimum cytoplasm and a T. turgidum nucleus [(lo) durum]. The testcross line also was hemizygous for the scsti gene [(lo) scsti -]. Resulting ratios of plump to shriveled seed were used to determine the genotype of the male parents (Fig 1). All plump seed indicated two copies of the scsti gene in the F2 individual. Three plump seeds to one shriveled seed indicated one copy of the scsti gene. One plump to one shriveled seed indicated no copy of the scsti gene. Various formulas from ![]()
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Genotypic analysis:
Tissue was collected from the 129 F2 individuals before jointing and flash frozen in liquid nitrogen. DNA was extracted according to the protocol of ![]()
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Microsatellite primers were chosen for their location near the centromere on chromosome 1A (![]()
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2 hr at 70 W, allowing the 100-bp standard to run near the bottom of the gel. The DNA was visualized by silver staining with the Promega (Madison, WI) Silver Sequence DNA sequencing system kit.
The GIBCO BRL (Gaithersburg, MD) kit for amplified fragment length polymorphisms (AFLPs) was used with several modifications. First, 350 ng instead of 250 ng of DNA was digested for 2 hr at 37° followed by inactivation of the enzyme for 15 min at 70°. The ligation step was done as described, but the product was diluted only 1:5 with TE buffer. The preamplification step was done as directed with 2.5 µl of diluted ligated DNA in a 25.5-µl reaction. The preamplification product was diluted 1:25 with TE buffer. The selective amplification used 2.5 µl of the diluted preamplified product, 1 µl 10x PCR buffer, 0.3 µl 50 mM MgCl2, 0.09 µl selected primer containing EcoRI adapter sequence, 2.25 µl selected primer containing MseI adapter sequence, 3.76 µl water, and 0.5 units platinum Taq polymerase (GIBCO BRL). The results were visualized by silver staining with the Promega Silver Sequence DNA sequencing system kit.
Linkage:
A linkage map containing the scsti gene was generated using Mapmaker 3.0b (![]()
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| RESULTS |
|---|
Population development and genotypic determination:
The T. turgidum nucleus is incompatible with the T. longissimum cytoplasm, producing nonviable progeny. This incompatibility is improved by scsti. Alloplasmic lines of T. turgidum with T. longissimum cytoplasm [(lo) durum] that have the scsti gene have improved embryo-endosperm compatibility but are male sterile (Fig 2). The Vi gene, located on the short arm of chromosome 1B (1BS), in conjunction with the scsti gene restores male fertility and seed viability (Fig 2). In the absence of the Vi gene, alloplasmic plants that are hemizygous for the scsti gene have normal vigor, are male sterile, and produce a 1:1 ratio of viable to aborted seed when crossed to normal durum wheat (Fig 2). In the absence of the scsti gene, alloplasmic plants with the Vi gene are weak, but fertile (Fig 2). In the absence of both scsti and Vi genes, the T. turgidum nucleus is incompatible with the T. longissimum cytoplasm. Therefore, addition of these two nuclear genes overcomes a number of deleterious phenotypes.
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The initial F2 euplasmic population segregating for the scsti gene consisted of 129 individuals. Testcrosses allowed genotypes to be determined for 50 of the 129 individuals at a 90% level of confidence (Table 1). After planting eight plump seeds from the testcross progeny and crossing the plants with euplasmic durum ([d]- -), the genotypes for 60 additional individuals were determined at the 90% level of confidence (Table 1). The remaining 19 individuals could not be assigned a genotype due to a lack of seed produced from the testcrosses. Twenty-nine individuals were obtained with (d)- -, 59 with (d)scsti -, and 22 with (d)scsti scsti. The F2 population fit the expected segregation ratio for scsti of 1:2:1 with a chi-squared value of 1.47. This evidence supports the idea of a single gene that follows Mendelian inheritance.
Genotypic analysis:
Microsatellites, RFLPs, and AFLPs were the three types of markers used to screen the parents and score the initial population. Of the five microsatellites screened, two were polymorphic, producing five polymorphic bands. Of the 47 RFLP clones screened, 19 were polymorphic, producing 48 polymorphic bands. Of the 64 AFLP combinations screened, the 8 combinations that produced at least three polymorphic bands each were used to screen a subset (107 individuals) of the initial population. In total the 8 AFLP combinations produced 40 polymorphic bands.
Linkage:
All scores from the markers were entered into Mapmaker 3.0b. Thirty-seven marker loci were grouped with the scsti genotype. Thirty-four of the 37 markers fit the expected codominant 1:2:1 ratio or the dominant 3:1 ratio. Marker loci were successfully ordered, resulting in a skeletal map with six markers spaced over chromosome 1A for a total length of 93.5 cM (LOD > 4.0, Fig 3). The remaining 30 markers were placed in regions using the "try" command (Fig 3).
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The region containing the scsti gene was mapped in more detail and loci flanking the scsti gene, Xbcd12 and Xbcd1449-1A.2, were identified (Fig 3). The distance between these flanking loci was 1.4 cM before placing scsti and 14.0 cM after placement of the scsti gene, indicating that this locus was showing more double recombinants than expected (Fig 4). Graphic genotyping identified 11 individuals that appeared to have crossovers flanking both sides of the scsti gene. Removal of the scsti genotypes of these 11 individuals resulted in a map with distances of 2.3 and 0.6 cM from the scsti gene for the loci, Xbcd12 and Xbcd1449-1A.2, respectively (Fig 3). A comparison of the detailed maps before and after removing these 11 individual genotypes demonstrates the degree of difference (Fig 3).
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| DISCUSSION |
|---|
The evidence presented points toward a phenomenon in which a large number of apparent double crossovers are observed. This phenomenon may be observed as the result of a "hotspot" of recombination, gene conversion, somatic crossing over, different frequencies of chromosome transmission, gamete selection, or change in the allelic state of scsti possibly induced by transposable elements. The chromosome pairing was cytologically checked on a sib of the F1 individual and appeared normal.
To test for a hotspot of recombination near scsti, the number of recombination events per map unit between each marker was graphed (Fig 4). The number of recombination events between Xbcd1072 and Xbcd22 more than doubles when the scsti genotypic data are included in the analysis. This increase demonstrates that a change in the allelic state of scsti is responsible for the difference. The recombination across the chromosome based on the markers used in this study was graphed (Fig 5) and compared to the published recombination distribution of wheat chromosome 1A (![]()
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By looking at the recombination distribution, it was observed that the number of recombinations around scsti seemed high. We expected 1 in 2500 (0.0004) double recombinants between the two codominant markers flanking scsti, but observed 11 in 110 (0.1000). Gene conversion was also considered, but we would not expect this event to occur with this high a frequency and cannot explain all instances, since double recombination occurred in five individuals showing homozygosity in the flanking markers. Somatic crossing over is one mechanism by which these double recombinants could arise. A few plants that had chimeric tillers (two tillers each producing different ratios of plump to shriveled seeds) were observed in the F2 population. The observed frequency of chimeric plants is fairly low: 2 of the 110 individuals in the mapping population. The observed frequency of double crossovers for scsti is too high to be explained by this phenomenon.
Different frequencies of chromosomal transmission or gamete selection were also contemplated. For these events to explain the amount of apparent double recombinants, one should observe an overall increase in one genotype. When observing the 11 aberrant individuals, the trend is toward having a scsti locus vs. not having one. Looking at the overall number of the genotypes in each class, particularly scstiscsti vs. - -(null), the trend is toward having more nulls. These two trends do not match, which leads to the conclusion that the scsti locus is not causing gametic selection or different chromosomal transmission frequencies.
The selfed seed from these 11 F2 individuals, their testcross seed, and seed from the genotypic checks were also examined for abnormalities. Some seed seemed to be partially plump and partially shriveled or "blistered" in phenotype, but this shriveling was primarily limited to the nongerminating end of the seed (Fig 2). The environment does not appear to be an instigator of the blistering phenotype, because not all the seeds from a single cross were blistered nor were the seeds from the plants on either side of the crosses that exhibited the blistering. A similar blistering phenotype has been observed in maize with regard to a maize brittle-1 mutable (bt-1m) gene (![]()
Evidence has been found to support the presence of active retrotransposons and transposons in wheat. ![]()
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If a transposition event involving scsti had occurred, one may expect to observe a change in the allelic state of scsti. ![]()
6 inches as compared to nearly 5 feet for the wild-type genotype. The scsd allele originated from (lo)scsti- when it was transferred to durum cultivars for evaluation of yield (S. S. MAAN, personal communication). In alloplasmic lines presumed to have the scsti allele plants grown from plump seed grew half the height of normal durum and typically did not tiller (our unpublished results). These differences in phenotype may possibly be explained by the changes created from a footprint left after a transposition event.
Previous attempts to flank scsti with molecular markers by using alloplasmic populations have had limited success. In an alloplasmic situation, seeds with scsti produce plump seeds that grow to mature plants, while those without scsti are shriveled and inviable. Thus, selection against one of the genotypes could have affected the mapping results and scarcity of linked markers. In this study, flanking marker loci Xbcd12 and Xbcd1449-1A.2 were found for the scsti gene with distances of 2.3 and 0.6 cM, respectively. These marker loci will form the basic framework for more detailed studies of this important gene.
Most cultivated wheats are polyploid in nature. These allopolyploids arose from stepwise interspecific hybridizations involving diploid ancestors. An important factor in the successful formation of a hybrid combination is the interaction between the nucleus and cytoplasmic genomes. Triticum species differ with regard to compatibility with alien cytoplasms and interspecific nuclear-cytoplasmic interactions produce a variety of phenotypes, including maternally inherited male sterility, delayed maturity, and reduced plant vigor in alloplasmic wheat lines (![]()
| ACKNOWLEDGMENTS |
|---|
We thank Justin B. Hegstad, Kay M. Carlson, and the rest of the Wheat Germplasm Enhancement group for their assistance in making this work possible. We also thank P. McClean and J. Faris and the anonymous reviewers for their suggestions in improving this manuscript and R. L. Phillips for helpful discussion and suggestions on the bt-1m blistering phenotype of maize. This material is based upon the work supported by the United States Department of Agriculture-National Research Initiative grant no. 99-35311-8252, National Science Foundation-Plant Genome Research Program contract agreement no. DBI-9975989, and the North Dakota Wheat Commission to S.F.K.
Manuscript received July 2, 2003; Accepted for publication August 28, 2003.
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