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Genome Res. 2005 Apr; 15(4): 526–536.
PMCID: PMC1074367

Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels


Plant genomes, in particular grass genomes, evolve very rapidly. The closely related A genomes of diploid, tetraploid, and hexaploid wheat are derived from a common ancestor that lived <3 million years ago and represent a good model to study molecular mechanisms involved in such rapid evolution. We have sequenced and compared physical contigs at the Lr10 locus on chromosome 1AS from diploid (211 kb), tetraploid (187 kb), and hexaploid wheat (154 kb). A maximum of 33% of the sequences were conserved between two species. The sequences from diploid and tetraploid wheat shared all of the genes, including Lr10 and RGA2 and define a first haplotype (H1). The 130-kb intergenic region between Lr10 and RGA2 was conserved in size despite its activity as a hot spot for transposon insertion, which resulted in >70% of sequence divergence. The hexaploid wheat sequence lacks both Lr10 and RGA2 genes and defines a second haplotype, H2, which originated from ancient and extensive rearrangements. These rearrangements included insertions of retroelements and transposons deletions, as well as unequal recombination within elements. Gene disruption in haplotype H2 was caused by a deletion and subsequent large inversion. Gene conservation between H1 haplotypes, as well as conservation of rearrangements at the origin of the H2 haplotype at three different ploidy levels indicate that the two haplotypes are ancient and had a stable gene content during evolution, whereas the intergenic regions evolved rapidly. Polyploidization during wheat evolution had no detectable consequences on the structure and evolution of the two haplotypes.

Comparative analysis of related genomes can reveal the molecular mechanisms of genome evolution. Species from the grass family provide an excellent model for such studies, as extensive genetic colinearity among several grass species has been described despite very heterogenous genome sizes and evolutionary divergence times of over 60 million years (for review, see Devos and Gale 2000; Keller and Feuillet 2000). Recent large-scale comparative studies in maize, sorghum, rice, barley, and wheat have revealed a mosaic organization of conserved and nonconserved genes at orthologous loci and many small rearrangements (Dubcovsky et al. 2001; Ramakrishna et al. 2002; Song et al. 2002; Brunner et al. 2003; Gu et al. 2003, 2004; Ilic et al. 2003; Guyot et al. 2004). Interestingly, intraspecific comparative studies in maize have also shown disruption of colinearity, not only in the intergenic regions, but also in the gene space (Fu and Dooner 2002; Song and Messing 2003). The partial absence of microcolinearity observed between grass species, as well as between inbred maize cultivars, is a rich resource for the identification of molecular mechanisms involved in genome evolution.

The wheat A genomes that diverged from a common ancestor living about 0.5–3 million years ago (Mya) (Huang et al. 2002; Wicker et al. 2003a) are particularly suitable for comparative analysis. The A genomes are found in modern wheat species of different ploidy such as Einkorn wheat (Triticum monococcum, diploid), Emmer wheat (T. turgidum, tetraploid), and bread wheat species (T. aestivum, hexaploid) (Feldman 2001). A number of recent studies have demonstrated rapid and massive local changes in wheat genomes after polyploidization (Liu et al. 1998; Ozkan et al. 2001). Therefore, the comparison at the molecular level of wheat A genomes at different ploidy levels could also give insight into the molecular consequences of the “genomic shock” following hybridization of complete genomes. The development of large insert bacterial artificial chromosome (BAC) libraries from diploid wheat T. monococcum DV92 (AA, Lijavetzky et al. 1999), tetraploid wheat T. turgidum subsp. durum cv. Langdon (AABB, Cenci et al. 2003), and the donor of the D genome Aegilops tauschii (Moullet et al. 1999) has allowed the isolation and sequencing of large wheat genomic fragments. Recent studies have compared orthologous loci in the three A, B, and D homoeologous wheat genomes (Gu et al. 2004; Kong et al. 2004), which diverged 2.5–4 Mya (Huang et al. 2002). Rapid genome evolution was observed that was mostly due to insertion of retroelements after the divergence of the three subgenomes. A comparison of the A genome of tetraploid (cv. Langdon with Au genome from T. urartu) with the Am genome of the diploid T. monococcum DV92 that diverged 0.5–3 Mya (Huang et al. 2002; Wicker et al. 2003a), has recently revealed rapid genome divergence in the intergenic regions even between these closely related genomes (Wicker et al. 2003a). Conservation was restricted to small regions and a large proportion of the sequence, which contains mainly repetitive elements, was completely different, providing evidence for a dynamic and rapid evolution. So far, none of the previous comparative studies have included orthologous sequences from hexaploid wheat, and the evolution of A genomes derived from T. urartu in different polyploid backgrounds has not been investigated. Two BAC libraries from hexaploid wheat have been recently constructed from the cultivars Chinese Spring (Allouis et al. 2003) and Renan (B. Chalhoub, unpubl.), allowing such analysis.

The leaf rust resistance gene Lr10 was recently isolated (Feuillet et al. 2003) using a combination of subgenome map-based cloning (Stein et al. 2000; Wicker et al. 2001) and haplotype studies (Scherrer et al. 2002). Lr10 is closely associated with a second resistance gene analog (RGA2), but the two genes are very different from each other at the molecular level (Feuillet et al. 2003). Analysis of the wheat gene pool by Southern hybridization revealed the presence of two groups of lines with distinct haplotypes (H1 and H2) at the Lr10 locus, defined by the presence (H1) or absence (H2) of the two full-length Lr10 and RGA2 genes on chromosome 1A (Scherrer et al. 2002). Thus, the Lr10 resistance locus differs from most resistance loci in plants, where clusters of closely related genes are present, but is similar to the Arabidopsis RPM1 locus (Grant et al. 1995). The RPM1 locus also exists in two stable haplotypes in the Arabidopsis gene pool that are defined by the presence or absence of the gene.

Studies of molecular haplotype diversity in plants are limited and so far restricted to a few species, such as Arabidopsis, soybean, barley, and maize (Collins et al. 2001; Nordborg et al. 2002; Charlesworth et al. 2003; Zhu et al. 2003; for review, see Rafalski and Morgante 2004). To assess the molecular basis and mechanisms of genomic rearrangements during evolution of the Lr10 locus in the two different haplotypes, we have compared BAC sequences at the orthologous Lr10 loci of the A genomes from diploid, tetraploid, and hexaploid wheat species. These comparisons revealed that the two haplotypes were very stable during evolution from diploid to tetraploid and hexaploid wheat, although conservation was restricted to the gene space, whereas intergenic sequences diverged rapidly. A large deletion and inversion was found at the origin of the H2 haplotype that, despite gene loss, was highly conserved during wheat evolution.


Contig establishment at the Lr10 locus in tetraploid and hexaploid wheat

We have isolated BAC clones from the orthologous Lr10 loci on chromosome 1AS from T. turgidum subsp. durum cv. Langdon and T. aestivum cv. Renan, which belong to the H1 and H2 haplotypes, respectively (Fig. 1). Seven BAC clones were identified from the tetraploid Langdon BAC library (data not shown) using the probes rga1NBS and rga2NBS2, which are derived from the Lr10 and RGA2 genes, respectively (Scherrer et al. 2002) and are specific for the A genome. Previous hybridization studies have shown that H2 lines (including Renan) have no Lr10 gene, only part of RGA2 on chromosome 1A and a full copy of RGA2 on chromosome 1D (Scherrer et al. 2002). No specific primers could be designed for the partial fragment of RGA2 on chromosome 1A. Therefore, the hexaploid Renan BAC library was screened by PCR of pooled BAC DNA with two primer pairs, one amplifying specifically the RGA2 copy on the D genome (DF/DR) and the other one amplifying both RGA2 copies on the A and D genomes (ADF/ADR). In this way, we could identify three BACs from the A genome by screening for amplification with the primers ADF/ADR but not with DF/DR (data not shown). Based on DNA hybridizations with probes derived from the T. monococcum DV92 sequence (Wicker et al. 2001), physical contigs were established for the tetraploid and hexaploid wheat species. Hybridization experiments of NotI fingerprints of both tetraploid and hexaploid BAC clones revealed that the order of the probes was conserved in both wheat species (Fig. 1). However, the Lr10 and RGA2 probes corresponding to the 5′ end of both genes were not detected in the hexaploid Renan (H2 haplotype). The probe F467 derived from low-pass sequencing of the T. monococcum DV92 BAC clone 111I4 (Stein et al. 2000) was found on two NotI fragments on the T. turgidum BAC, suggesting a duplication in cv. Langdon. In addition, the distance between RGA2 and MWG2245 (Stein et al. 2000) was shorter in the hexaploid H2 haplotype, indicating a large deletion, including the Lr10 gene in Renan. Based on these results, one BAC clone from cv. Langdon (BAC 1156G16) and one BAC clone from cv. Renan (BAC 930H14) were selected for complete sequencing (Fig. 1). A total of 187,054 bp of sequence was assembled with a 9.18-fold coverage for the Langdon 1156G16 BAC clone. For the cv. Renan BAC 930H14, a total of 154,778 bp of sequence was assembled with a similar coverage.

Figure 1.
Physical maps of BAC clones from the Lr10 orthologous loci in diploid, tetraploid, and hexaploid wheat. All probes indicated are derived from the T. monococcum DV92 sequence (Wicker et al. 2001) except for 930F and 930R, which are PCR-amplified BAC end ...

Sequence organization at the Lr10 locus in tetraploid and hexaploid wheat

The tetraploid and hexaploid BAC sequences were annotated based on comparison with the diploid T. monococcum DV92 sequence analyzed by Wicker et al. (2001). The 187,054-bp sequence of tetraploid wheat is comprised of 8% genic regions and 55.3% identifiable, repetitive elements. Class I LTR retrotransposons are the most abundant elements, and Angela LTR retrotransposons represent >48% of all repetitive sequences. The 154,778-bp sequence of hexaploid wheat is comprised of 11.5% genic regions and 33.3% repetitive elements. Angela LTR retrotransposons represent >50% of all repeats and are mainly located in a single region of ∼25 kb between the 3′ end of RGA2 (RGA2-b) and NLL1 (Fig. 2). The only class II elements identified in the three orthologous sequences are CACTA transposons (Wicker et al. 2003b). Five genes (ACT, CCF, CCF(p), RGA2, and Lr10), of which one is a putative gene (CCF(p)), were found in the Langdon BAC 1156G16 sequence (Fig. 2). Orthologs of all five genes have been previously identified in T. monococcum DV92 (Wicker et al. 2001; Guyot et al. 2004; Fig. 2). The ACT, CCF, and CCF(p) genes were also present in the orthologous Renan BAC 930H14 sequence. In this sequence, three additional genes were detected (NLL1, A5HY, and NLL2), for which orthologs also exist in the orthologous region of T. monococcum DV92. The NLL1 gene was described by Wicker et al. (2001), whereas NLL2 was recently identified by Guyot et al. (2004). The A5HY gene, which was identified in T. monococcum by low-pass sequencing (data not shown), encodes a conserved domain of cytochrome P450s, proteins usually involved in oxidative degradation of various compounds. The best BLASTP hit for this protein is an aldehyde-5-hydroxylase (e value of e-159).

Figure 2.
Schematic representation of the sequence organization and detailed comparison at the Lr10 orthologous loci in diploid, tetraploid, and hexaploid wheat. (A.) Organization of the orthologous loci in T. monococcum and T. turgidum and comparison of the genomic ...

The diploid and tetraploid wheat lines studied here have the same haplotype structure (H1) at the Lr10 locus, as they each comprise full-length RGA2 and Lr10 genes (Scherrer et al. 2002; Fig. 2A) as well as the three genes ACT, CCF, and CCF(p) (Fig. 2). All of the genes are conserved in order and orientation. The size of the large intergenic region between Lr10 and RGA2 is nearly identical (around 130 kb) in both sequences (Fig. 2A). In the haplotype H2 of the hexaploid cv. Renan, the genes ACT, CCF, CCF(p), A5HY, and NLL2 (Fig. 2B) are conserved in the same order and orientation as in the H1 haplotype. However, major differences are observed in the RGA2/NLL1 interval. First, in the hexaploid sequence (H2), 2.5 kb of RGA2, corresponding to the 5′ half of the gene, are missing. The remaining part (bases 2537–4769) is split into two parts, RGA2-a and RGA2-b, which are separated from one another by >46 kb (Fig. 2B). In addition, RGA2-a is inverted compared with the original gene sequence. The gene fragment RGA2-a comprises the last 73 bp of the second exon, the second intron, and the first 352 bp of the third and last exon of RGA2 (bases 2538–3272 of the complete RGA2 gene). The gene fragment RGA2-b comprises the remaining part of the last exon (bases 3273–4769 bp). The second major difference to the sequence of the H1 haplotype is the complete absence of Lr10 in the hexaploid H2 sequence, confirming previous hybridization experiments (Scherrer et al. 2002). Finally, the two haplotypes differ in the position of the NLL1 gene between the RGA2 fragments, and the inverted orientation of NLL1 and RGA2-a compared with the order observed in the H1 sequences. This suggests that the T. aestivum H2 haplotype originated from the H1 haplotype after extensive rearrangements including deletions, inversions, and insertions.

A gene-rich region is highly conserved in the three homoeologous A genomes

At the three orthologous loci, the first 31 kb of common sequence correspond to a gene-rich region with three genes (ACT, CCF, and CCF(p)) (Fig. 3) and a partial gene (RGA2) that are conserved in order and orientation. The sizes of the intergenic regions are short, the largest being 14.6 kb between ACT and CCF in the T. monococcum DV92 sequence (Fig. 3). Nucleic acid sequences of all the genes are highly conserved, as there is >89.8% identity between the orthologous genes, independent of haplotype and ploidy level (data not shown). In addition, sequences ranging from 5 bp to >6.8 kb are also conserved in the intergenic regions with >80% of identity at the nucleic acid level (Fig. 3). The conserved regions downstream of the genes are, in general, shorter (from 5 to 1.3 kb) than the upstream regions (from 28 to 6.8 kb). For both the ACT and CCF genes, the conserved 5′ upstream regions are longer in T. turgidum and T. aestivum (1.3 and 6.8 kb, Fig. 3) than in T. turgidum/T. aestivum and T. monococcum (<750 bp in both). In T. aestivum (haplotype H2), only the bases 3273–4769 of RGA2 (RGA2-b), corresponding to the last 1496 bp of the last exon, are found at the same position as in T. monococcum and T. turgidum (haplotype H1). Nevertheless, the 1496 bp of sequence is highly conserved (>96% of sequence identity). In addition, 1.3 kb downstream of the stop codon of RGA2 are conserved, in all three genomes, with >90% identity (Fig. 3), whereas 4.6 kb are conserved upstream of the start codon of RGA2 only in the diploid and tetraploid species. A similar conservation of both upstream and downstream regions was found for Lr10 (data not shown) in the H1 haplotype, and the gene sequence itself is even more highly conserved (>99% identity). Such conservation in the gene and regulatory sequences of both Lr10 and RGA2 indicates a strong selective pressure that maintains them intact and functional in the species of the H1 haplotype. To study whether selective pressure acts on the functional RGA2 gene, and to assess whether this is also true for the partial RGA2 sequence found in the hexaploid wheat cultivar, we have compared the last exon (exon 3) of RGA2 (nucleotides 2920–4769) in T. monococcum, T. turgidum, and T. aestivum. Estimation of the synonymous (Ks) vs. nonsynonymous (Ka) substitution rates yielded a Ka/Ks ratio of 0.125 and revealed strong purifying selection on the H1 sequences with a functional allele (T. monococcum and T. turgidum). In contrast, the Ka/Ks ratio of 0.35 calculated for exon 3 in the T. aestivum (H2) sequence indicates relaxation of the selection on the partial gene.

Figure 3.
Schematic comparison of the 31-kb gene-rich region conserved on the proximal side of the Lr10 locus in T. monococcum, T. turgidum, and T. aestivum. The four genes ACT, CCF, CCF(p), and RGA2 located in this gene-rich region are represented by black boxes. ...

The large intergenic regions between RGA2 and Lr10 evolved differentially in T. monococcum and T. turgidum of the H1 haplotype

The intergenic regions between RGA2 and Lr10 in T. monococcum and T. turgidum are mainly comprised of nested repetitive elements (Fig. 2A). Repetitive elements represent 64% of the T. turgidum interval and 83% of the T. monococcum interval, which is higher than the content of repetitive elements in the complete sequences of both species (54% in T. turgidum and 70% in T. monococcum). This suggests preferential insertion of repetitive elements in this intergenic region. The largest complete elements common to both species are a Jorge CACTA transposon of 15.6 kb (Jorge_AF326781-1 and Jorge_1156G16-1) and a Fatima LTR retrotransposon of 9.1 kb (Fatima_AF326781-2 and Fatima_1156G16-1). These elements are true orthologs, as they are found in both species at corresponding positions, indicating that they were present already in the common ancestor. In addition, five foldback elements (three MITES and two LITES) (Fig. 2A) located in RGA2, the Jorge element and downstream of Lr10, respectively, are also conserved in both sequences. These data indicate that these elements inserted between RGA2 and Lr10 in the common ancestor of the H1 lines before the divergence of the A genome in the T. monococcum and T. urartu lineages. Both Jorge and Fatima elements are interrupted by other elements in diploid wheat, but only Jorge is interrupted in the tetraploid sequence (Fig. 2A). In total, 35.7 kb are conserved between the RGA2 and Lr10 genes at the two orthologous loci of the H1 haplotype structure. This represents only 27% of the two intergenic regions, despite their almost identical length (130 kb).

The presence of the conserved Jorge and Fatima elements both in T. monococcum DV92 and T. turgidum cv. Langdon allowed the comparison of base substitution rates in repetitive elements vs. genes in this region. The average substitution rate of the complete sequences of the two repetitive elements calculated as described in San Miguel et al. (1998) is 0.032. The synonymous substitution rates of the coding sequences of three complete genes (CCF, Lr10, and RGA2) are 0.054, 0.050, and 0.019, respectively. RGA2 appears to have evolved more slowly than the repetitive elements. However, the data show that the other two genes appear to have evolved faster than the repetitive elements, and highlight the high variability of synonymous substitution rates in different genes. Recently, such a large variability in substitution rates was also found in a set of 24 genes in rice (Ma and Bennetzen 2004).

Insertion times were estimated for nine complete LTR retroelements in the RGA2/Lr10 intergenic region in the T. monococcum and T. turgidum sequences using an average base substitution of 6.5 × 10-9 mutations per site per year (Gaut et al. 1996) and following the method used by SanMiguel et al. (1998). This revealed a “recent” group (0.08–1.5 Mya) and a more “ancient” group (2.3–3.9 Mya) of retrotransposon insertions. The old group is comprised of one element conserved in both sequences (Fatima_AF326781-2 and Fatima_1156G16-1) and two Angela elements (Am2 and Ad9). Although Am2 is only present in T. monococcum and Ad9 only in T. turgidum, both are interrupted by conserved elements (Jorge and Fatima) (Fig. 2A). Therefore, these Angela elements were most likely already present in the common ancestor of the two species and subsequently deleted from one of them. Although Fatima_AF326781-2 and Fatima_1156G16-1 are true orthologs (i.e., they inserted in the common ancestor), their calculated insertion times are slightly different (3.3 and 2.3 Mya, respectively) (Fig. 2A). This can be explained by the fact that the LTRs of this element are short (490 bp), compared with an average LTR size of 1438 bp for Angela elements, and this resulted in a calculated substitution rate with a higher standard deviation (SD) (in both sequences, SD was at least 0.85 million years). The more recent group of retrotransposon insertions comprises five elements with insertion times ranging from 0.08 to 1.9 Mya, four of them in T. monococcum (Da, Am7, Am8, and Ba) and only one in T. turgidum (Ad7), with Am7 being the most recent insertion (0.08 Mya). None of these elements are common to both sequences, indicating either that they inserted after the divergence of the wheat A genomes, or that they were present in a common ancestor and were subsequently deleted from one of the two species. The divergence of the wheat A genomes is estimated to have occurred 0.5 to 3 Mya ago (Huang et al. 2002; Wicker et al. 2003a). Genome divergence is thus in the range of the calculated insertion times of the four remaining “recent” elements (on average 1.5 Mya), but there may be differences in evolution rates between LTR sequences and other sequences (SanMiguel et al. 1998). We cannot, therefore, exclude the possibility that these elements inserted after the species divergence.

Only 27% of sequence in the RGA2/Lr10 intergenic region is conserved between T. monococcum and T. turgidum. This is the result of independent rearrangements that occurred after the divergence of the wheat A genomes. Comparison of the conserved features identified several molecular mechanisms underlying these rearrangements. In addition to insertions and deletions of LTR retrotransposons, which have also been described in previous studies in wheat (Wicker et al. 2003a; Gu et al. 2004), the pattern of conservation of the Romani retrotransposons provides interesting insight into the evolution of this interval (Fig. 2A). Both T. monococcum and T. turgidum contain a Romani element at corresponding positions, indicating that the element was already present in the common ancestor. In T. monococcum, only a solo-LTR with identical TSDs (Romani_AF326781-1), the result of an intraelement recombination, is present, whereas the complete element is present in the tetraploid wheat sequence (Romani_1156G16-1) (Fig. 2A). A model for the evolution of this Romani element in the two sequences is proposed in Figure 4. Interestingly, Romani in T. turgidum is interrupted by other retroelements in its internal domain. The insertions of these four elements date back 1.8–2.8 Mya (dated according to SanMiguel et al. 1998). It is therefore very likely that at least some of them were already present in the common ancestor of T. monococcum and T. turgidum. Thus, the intraelement recombination in T. monococcum led to the loss of at least 7 kb of genomic DNA (if all elements inserted after the divergence of the two species), and at the most, 33 kb (if all elements were present in the common ancestor). The presence of the two LTRs in T. turgidum has actually been misinterpreted as a duplication of the T. monococcum sequence in T. turgidum, based on hybridization experiments of the tetraploid BAC with the probe F467 (Fig. 1), which hybridized to two NotI fragments. This probe was derived from the internal sequence of the Romani solo-LTR of T. monococcum and detected both LTRs in the T. turgidum sequence.

Figure 4.
Model for the evolution of the Romani element in the T. monococcum and T. turgidum H1 haplotypes. The complete Romani retrotransposon is indicated by rectangles comprising two LTR (dark-gray boxes) and internal sequences (white box). The same Romani element ...

The two haplotypes, H1 and H2, originate from ancient and extensive rearrangements

The presence of the conserved Jorge and Fatima repetitive elements both in T. monococcum and T. turgidum (a total of 24,797 bp) allowed us to estimate the time of divergence between the two species, because these conserved elements must have been identical at the time of divergence. Based on an average base substitution of 6.5 × 10-9 mutations per site per year (Gaut et al. 1996), the two loci diverged ∼2.4 Mya. Similar values for the divergence of the two species were previously obtained by Wicker et al. (2003a) (2.9–3.3 Mya). Based on this divergence time and the synonymous substitution rate of RGA2 between T. monococcum and T. turgidum, a molecular clock of 3.93 × 10-9 mutations per site per year was established for RGA2. Assuming a constant substitution rate in both species, an estimated date of 4 Mya was calculated for the partial deletion and disruption of RGA2 in Renan. Thus, the disruption of RGA2 in Renan is older than the estimated divergence time of the wheat A genomes (2.4 Mya) used in this study. This result indicates an ancient origin of the H2 haplotype and is in agreement with the presence of this haplotype at different ploidy levels.

The longest available sequence of the H1 haplotype (T. monococcum DV92) (Wicker et al. 2001; Fig. 2A,B) was compared with the sequence of the H2 haplotype (T. aestivum) (Fig. 2B). The region where the two haplotypes differ dramatically is delimited by the two RGA2 fragments RGA2-b and RGA2-a in the T. aestivum sequence (50 kb), and by RGA2 and the foldback element Gorgon (G, Fig. 2B) upstream of the NLL1 gene in T. monococcum (170 kb). On the proximal (left) side of both sequences, RGA2-b is conserved in the same orientation (Fig. 2B). On the distal (right) side, conserved sequences including a fragmented LTR of a Sukkula-type retroelement (Sukkula_AF326781-1 and Sukkula_930H14-1), the NLL1 gene, three foldback elements (MITES Athos or A, Fortuna or F, and Gorgon or G), as well as RGA2-a are in reverse orientation (Fig. 2B). Such a complex pattern of conservation and divergence indicates extensive rearrangements at the origin of the two haplotypes. A model for these rearrangements is presented in Figure 5, starting with a common ancestor sequence containing RGA2, Lr10, NLL1, Sukkula, and the conserved foldback elements. In this ancestral “A” locus, insertions and deletions of repetitive sequences must have occurred between RGA2 and Lr10, resulting in an H1 haplotype progenitor, which was then further modified to give the modern Am and Au haplotype of T. monococcum DV92 and T. turgidum Langdon (Fig. 5).

Figure 5.
Model for the evolution of the H1 and H2 haplotypes at the Lr10 locus. Genes are indicated by black boxes. The short arrows located below the genes indicate the transcriptional orientation. Identified nested repetitive elements are shown by colored boxes. ...

In the evolution of the H2 haplotype, a first deletion event removed a sequence containing the beginning of RGA2 (corresponding to the first 2537 bp of RGA2 of T. monococcum) and the complete Lr10 gene (Fig. 5). Then, the second half of RGA2 (bases 2538–4769) was split into RGA2-a and RGA2-b at position 3272 and a large sequence including RGA2-a, the foldback elements, the LTR of the Sukkula-type element, and the NLL1 gene were inverted (Fig. 5). The two RGA2 fragments were disrupted without any sequence loss; at the disruption point, the fragment RGA2-a ends at the base 3272, and the fragment RGA2-b starts at the base 3273. The lack of TSDs or inverted repeats at the breakpoints did not allow the identification of a precise mechanism responsible for this sequence disruption and inversion. Although the same types of fragmented LTR retrotransposons (data not shown) are found in the vicinity of these breakpoints, they do not start exactly at the breakpoints (at least 20 bp after) and are highly degenerated. It is therefore not clear whether they were involved in the rearrangement. Sequence inversion usually requires inverted repeats that align next to each other and act as recombination sites. Upon cross-over, the DNA sequence between these sites is inverted. The only features that could have acted as inverted repeats are (TA) microsatellites of 56 and 59 bp found on the hexaploid sequence at the positions 34,333 and 85,957 bp. However, their position relative to RGA2-b and RGA2-a (90 bp and 5 kb downstream, respectively, Fig. 2B) does not allow to identify them as the origin of this rearrangement. Afterward, insertions and partial deletions involving Angela LTR retrotransposons occurred in the inverted sequence, leading to nested Angela retrotransposons (Fig. 2B).

Identical H2 haplotypes are found at three ploidy levels, and H2 subhaplotypes result from different types of rearrangements

In an earlier study, we did not find the H2 haplotype in tetraploid wheat lines (Scherrer et al. 2002), a finding which contrasted with the large number of H2 lines in hexaploid wheat that evolved from tetraploid wheat (Feldman 2001). Therefore, we have studied haplotypes at the Lr10 locus in an additional large set of 300 tetraploid lines, consisting of 67 accessions of T. turgidum subsp. dicoccoides, 27 T. turgidum subsp. carthlicum, 34 T. turgidum subsp. dicoccum,20 T. turgidum subsp. turgidum, and 152 accessions of T. timopheevi subsp. armeniacum. A total of 38 of these 300 tetraploid accessions showed the H2 haplotype by Southern hybridization with Lr10 and RGA2 probes (data not shown). The 38 lines consisted of eight T. turgidum subsp. dicoccoides accessions, 16 T. turgidum subsp. dicoccum, two T. turgidum subsp. durum, and 12 T. timopheevi subsp. armeniacum lines, demonstrating the presence of the H2 haplotype in a variety of tetraploid species.

To assess conservation of the H2 haplotype in the wheat gene pool and to determine whether the same rearrangements are at the origin of diploid, tetraploid, and hexaploid lines with the H2 haplotype, we amplified short genomic fragments (fragments A, B, and C, Fig. 6A) spanning the deletion and disruption breakpoints of the RGA2-b and RGA2-a fragments from 56 lines of haplotype H2 (based on hybridization data) using primers derived from the hexaploid sequence (Table 1, Supplemental material). Six diploid T. monococcum lines, two diploid T. urartu lines (of 10 tested lines, of which eight had haplotype H1), 10 tetraploid wheat, and 38 hexaploid T. aestivum lines were analyzed. Based on successful PCR amplification, two groups of lines could be distinguished. The first group amplified all three fragments A, B, and C, like cv. Renan. It comprises all of the 38 European hexaploid lines, nine tetraploid lines, and four of the six T. monococcum lines (e.g., Fig. 6B, lanes 1,2,4,5,7–11). The B fragments amplified from the T. monococcum line TRI 17434, as well as from seven tetraploid wheat lines (see Supplemental Table 1) were sequenced. This 331-bp B fragment was identical to the sequence of T. aestivum cv. Renan for all lines, demonstrating that the deletion breakpoint is identical. The finding of such a conserved molecular structure strongly suggests that in most lines with the H2 haplotype, the deletion derives from the same evolutionary event that occurred in the gene pool of the ancestor species of the wheat A genomes.

Figure 6.
Analysis of H2 haplotype conservation in the wheat gene pool. (A.) Schematic representation of the amplified fragments spanning the RGA2 fragments of T. aestivum. (B.) PCR amplification of 331-bp fragment (B) and the positive control for amplification ...

A second group of H2 lines comprising two T. urartu, two T. monococcum, and one tetraploid line, did not amplify any of the fragments (Supplemental Table 1, lanes 3,6; Fig. 6B). Thus, whereas the sequence organization observed in Renan is conserved in all but one of the tetraploid and hexaploid lines of the H2 haplotype, this is not the case for all diploid lines of this haplotype. The presence of this second group of lines suggests either sequence divergence after the formation of the haplotype from a common ancestor or completely independent deletion events leading to similar haplotype structures.

To further investigate conservation among the 51 H2 lines that had the same PCR amplification pattern as Renan, we amplified a 3-kb fragment spanning the deletion breakpoint of the RGA2-a fragment with a primer common to the B fragment previously described and a primer located 3-kb upstream in the sequence (Fig. 6A). Successful PCR amplification was observed for 40 lines (three T. monococcum, seven tetraploid lines, and 30 T. aestivum lines), whereas no amplification was observed in 11 lines (one T. monococcum, two tetraploid, and eight T. aestivum lines, Supplemental Table 1) suggesting sequence divergence in these lines. In conclusion, we could classify 56 H2 lines into three sub-H2 haplotypes. The presence of a main haplotype, represented by Renan, including diploid T. monococcum, tetraploid, and hexaploid lines, indicates high conservation and stability of the H2 haplotype during evolution and throughout polyploidization events in the last 1–3 million years of A genome divergence.


We have compared at the molecular level, the organization and evolution of two haplotypes at the Lr10 locus on the wheat A genomes of three different ploidy levels. The recent construction of two BAC libraries from hexaploid wheat lines belonging to the H2 haplotype (cv. Chinese Spring and Renan) (Allouis et al. 2003; B. Chalhoub, unpubl.) allowed the molecular comparison of the two haplotypes, including, for the first time, a sequence from hexaploid wheat. Conservation between the two haplotypes was limited to the genes located on both sides of a large 150-kb region, including the Lr10 and RGA2 genes, whereas extensive rearrangements occurred within this region.

Sequence comparison between H1 haplotypes derived from two different species revealed complete conservation of the structure and orientation of all of the genes, whereas the composition of the intergenic regions, which mainly consist of blocks of repetitive elements, is very different. Strikingly, despite these differences, the length of the large intergenic region of about 130 kb between the RGA2 and Lr10 genes is very similar. Conservation of the distances between blocks of genes has also been observed at the Glu-3A locus (Wicker et al. 2003a), as well as in two maize cultivars at the orthologous bz1 loci (Fu and Dooner 2002), although the intergenic regions were extensively rearranged. This suggests that the specific length (and not necessarily content) of an LTR retrotransposon cluster is conserved during evolution of orthologous loci, possibly acting as a determinant of chromatin and chromosome structure (Bennetzen and Ramakrishna 2002a).

A large deletion/inversion event is at the origin of the H2 haplotype

In the grass genomes, gene loss plays an important role in genome evolution and is the basis of the mosaic conservation of orthologous sequences (e.g., Song et al. 2002; Illic et al. 2003). The Lr10 haplotype evolution provides an interesting example, where the molecular events leading to such a gene loss could be studied in detail. The extensive rearrangements found at the origin of haplotype H2 are due to a large deletion that includes the disease resistance gene Lr10 and part of RGA2. The molecular basis of this deletion is possibly an illegitimate recombination event, a mechanism that is at the origin of other rearrangements in wheat (Wicker et al. 2003a; Ma et al. 2004). So far, the only mechanism responsible for gene disruption that has been described in wheat was the insertion of retroelements into genes (Gu et al. 2004). In the H2 haplotype, the deletion was followed by a large inversion that led to the disruption of the remaining RGA2 gene fragment. The molecular mechanism of this sequence inversion could not be determined, but the TA repeats found on both sides of the inverted fragment might be relevant. It is likely that during the estimated 4 million years since the deletion/inversion events, all tracks of the original sequences have been covered by other elements. Sequence inversions have already been described in other comparative studies in grasses, but they specifically concerned complete genes in the distantly related barley and rice species (Dubcovsky et al. 2001) or groups of genes in rice compared with sorghum and maize (Bennetzen and Ramakrishna 2002b). Interestingly, Dubcovsky et al. (2001) have also identified two sequences of inverted homology in the vicinity of gene 2, which was found inverted in barley compared with rice. In this case, the inversion did not cause disruption of the gene.

The deletion/inversion events in the H2 haplotype had several consequences for the further evolution of the Lr10-RGA2 region in the wheat gene pool. In fact, it may have effectively inhibited recombination between the different haplotypes. If recombination occurs within the inverted sequence (e.g., in or near the NLL1 gene), the recombinant gametes will carry chromosomes that are partially deleted or duplicated. Such gametes probably have a greatly reduced fitness, and recombination between the haplotypes in the Lr10-RGA2 interval is effectively suppressed. This provides a molecular explanation for two earlier observations; first, there are no recombinant haplotypes between H1 and H2 in the gene pool, and the Lr10 gene was always found together with an intact RGA2 (Scherrer et al. 2002). Second, there was no recombination between the two genes in a segregating population of more than 6000 gametes originating from a cross between the cultivars Frisal and ThatcherLr10 (Stein et al. 2000), which belong to the H2 and H1 haplotypes, respectively. Thus, our data indicate that recombination in hexaploid wheat cannot only be blocked by chromosomal segments derived from recent introgressions from wild relatives, but also by inversions that originate from ancient haplotypes.

Common themes of evolution in both haplotypes

Insertions of retroelements followed by deletions, most likely through illegitimate or unequal recombination, played a prominent role in the evolution of both haplotypes, similar to observations in other wheat comparative studies (Wicker et al. 2003a; Gu et al. 2004). These two mechanisms were also found to be responsible for LTR retrotransposon removal in the Arabidopsis and rice genomes (Devos et al. 2002; Ma et al. 2004) and seem to play a key role in plant genome evolution in general. Dating of intact elements in T. monococcum and T. turgidum revealed two distinct groups of insertion times for LTR retrotransposons. It is possible that different types of retroelements evolve at different rates, and that dates of retroelement insertions may, in general, be overestimated (San Miguel et al. 1998; Ma et al. 2004). However, “old” and “recent” Angela retroelements, which are likely to evolve at the same rate, are found at the same locus, supporting the idea that two series of insertions of repetitive elements have occurred at the Lr10 locus in both diploid and tetraploid species. This suggests that at least two waves of retrotransposon insertions have occurred during the evolution of the A ancestral wheat genome.

It is very rare to find conserved sequences of transposable elements in colinear regions of cereal species, and so far, only partial sequences of conserved elements have been reported (Wicker et al. 2003a; Gu et al. 2004; Kong et al. 2004). The half-life of LTR retrotransposons was recently estimated to be ∼6 million years in rice (Ma et al. 2004). Therefore, the conservation of nine complete elements (including one CACTA transposon, one LTR retrotransposon, one LITE, and six MITES) at the Lr10 locus is exceptional and might be due to a lower tolerance of random rearrangements in this region of the genome. These 25 kb of conserved sequences from repetitive elements allowed us to estimate a divergence date between the wheat A genomes that had previously been estimated to 0.5–3 Mya (Huang et al. 2002; Wicker et al. 2003a). Our estimate (2.4 Mya) confirms, at a larger scale, what had previously been published by Wicker et al. (2003a) based on 8 kb of conserved sequence. However, it differs from the results of Huang at al. (2002). This is probably due to variations in rates of sequence divergence (e.g., study of genes vs. repetitive elements). Such variations in substitution rates have been found at different levels. Repetitive elements may diverge more rapidly than genes, as shown in rice (Ma and Bennetzen 2004). Ma and Bennetzen (2004) have also shown that the two rice subspecies indica and japonica have diverged at different rates, and they suggest that, even within a genome, separate regions may evolve at different rates. Finally, genes have very different divergence rates (Ma and Bennetzen 2004). All of these variations in rates of sequence divergence between subspecies, within a genome at different loci, or even among genes of the same locus, are very intriguing and seem to be common in grasses. Further sequence comparisons between and within grass species, or even wheat varieties, are needed at a larger scale to deepen our understanding of these variations.

The conservation of two ancient haplotypes in the wheat species of three ploidy levels suggests that no significant rearrangements have affected the Lr10 locus during the polyploidization events that are at the origin of tetraploid and hexaploid wheat. Thus, there is no evidence in this region for rapid genomic changes following polyploidization, as observed for a substantial proportion of noncoding regions in newly synthetized allopolyploids (Liu et al. 1998; Ozkan et al. 2001). The stability of the two haplotypes at the Lr10 locus throughout evolution and polyploidization is striking and contrasts with the assumption that disease resistance loci are generally more variable than other loci. This might only be true for some R gene clusters, but not for loci under balancing selection (see below).

Old and stable haplotypes at the Lr10 resistance locus

The arms-race model for host-pathogen interactions predicts resistance loci to be young and monomorphic. Neither is true for the Lr10 locus, making this wheat resistance locus a new member of a group of resistance loci described in Arabidopsis and tomato that existed before speciation and are also old and polymorphic (Grant et al. 1998; Stahl et al. 1999; Bergelson et al. 2001; Riely et al. 2001). Similar to Arabidopsis RPM1, which confers resistance to Pseudomonas syringae, there is a presence/absence polymorphism for Lr10 in the wheat gene pool. This H2 haplotype caused by the deletion event is identical in lines of all three ploidy levels, as determined by sequencing the deletion breakpoint in the RGA2 gene. Thus, the polymorphism represented by the two haplotypes is evolutionarily stable, and the two haplotypes have coexisted for 4 million years, suggesting a balanced polymorphism. The Lr10–RGA2 complex might confer a fitness advantage under certain environmental conditions, whereas fitness costs are associated with it under other conditions, resulting in natural selection for both haplotypes and their maintenance in the wheat gene pool. In the absence of the pathogen, fitness costs associated with a resistance gene have been shown for the RPM1 gene (Tian et al. 2003). Evidence for balancing selection at a resistance locus was described for the Arabidopsis RPS5 gene (Tian et al. 2002). There, an island of enhanced sequence variability could be detected around the gene, indicative of an old polymorphism under selection.

Our study of the Lr10 locus demonstrates the power of comparative studies between the A genomes of different ploidy levels in wheat to unravel molecular mechanisms involved in genome evolution. It has also provided a molecular explanation for previous observations at the genetic and phenotypic levels. The detailed molecular understanding of polymorphism at this resistance locus, including its consequence on recombination, provides a solid basis for further evolutionary studies. The presence of both haplotypes in the large collection of accessions of wild diploid and tetraploid wheat in the gene banks will allow future studies correlating ecogeographical and molecular data for a better understanding of the environmental factors underlying balancing selection and haplotype stability.


Genomic DNA isolation and PCR

The plant material used in this study is listed in Supplemental Table 1A. Genomic DNA isolation was performed as described by Graner et al. (1990). The primers used for PCR amplification are listed in Supplemental Table 1B and PCR amplifications were performed according to standard procedures (Sambrook et al. 1989), and using the annealing temperatures specific for the different primer pairs.

BAC clone isolation and sequencing

The T. turgidum subsp. durum Langdon BAC library (Cenci et al. 2003) was screened by hybridization as described by Stein et al. (2000) using probes derived from the T. monococcum DV92 sequence (Wicker et al. 2001). The T. aestivum Renan BAC library was screened by PCR with the primer pair specifically amplifying the RGA2 copy on chromosome 1D (primers DF: 5′-GT GGTGTTGTGTTGCCAG-3′ and DR: 5′-GCAAGCTGGGTCCG GAAC-3′) and with a primer pair amplifying RGA2 from the 1A and 1D chromosomes (primers ADF: 5′-GAAGCCGGATTATAGT GTC-3′ and ADR: 5′-CTGCCCAGCTAAGTTCTCT-3′) according to standard procedures (Sambrook et al. 1989). BAC DNA preparation for fingerprint analysis and BAC end sequencing were performed as previously described (Stein et al. 2000). Resulting BAC clones from both BAC libraries were assembled into individual contigs based on HindIII, NotI, and SalI restriction patterns and hybridization with BAC end probes as well as probes derived from the T. monoccoccum DV92 orthologous sequence (Fig. 1) (Stein et al. 2000; Scherrer et al. 2002).

Shotgun library construction of the BAC clones 1156G16 and 930H14 and sequencing of shotgun clones for each BAC were performed as follows: The BAC DNA was isolated using the large construct kit (Qiagen). A total of 20 μg of BAC DNA were sonicated, and the resulting fragments were purified by agarose gel electrophoresis. The fractions of 1200–1800 bp and 2500–3000 bp were eluted from the gel, and the fragments were subcloned into a SmaI-digested pUC19 sequencing vector. The subclones were sequenced using Big-Dye terminator chemistry (Applied Biosystems). Data were collected using ABI 3730 automated sequencers (Applied Biosystems). A total of 700–1200 clones were sequenced for each BAC clone for seven- to ninefold coverage. Gaps between subcontigs were filled by primer walking on the spanning shotgun clones or direct sequencing of BAC DNA. The assembled BAC sequences were finally checked by comparison of BamHI, EcoRI, HindIII, NotI, and PacI BAC fingerprints with theoretical restriction digests of the assembled sequences.

For the Langdon BAC 1156G16, a total of 2040 shotgun sequences resulted in 10 contigs with nine gaps. The preassembly procedures could not close those gaps due to the presence of G- and C-rich regions or aberrant assemblies caused by multiple Long Terminal Repeats (LTRs) of similar retroelements nested into each other. Despite the presence of these GC-rich regions, all of the gaps could be closed by primer walking. Finally, a total of 187,054 bp of sequence was assembled with a 9.18-fold redundancy for the Langdon 1156G16 BAC clone. For the cv. Renan BAC 930H14, a total of 1235 shotgun sequences resulted in 12 contigs with 11 gaps caused by similar features to the ones found in the cv. Langdon BAC. A total of 10 of the 11 gaps could be closed by primer walking, leaving one gap of 1 kb as determined from the sizes of the spanning shotgun clones. This 1 kb of missing sequence was located at base 121,554 of the BAC sequence, which is between the AH5Y and NLL2 genes and downsteam of the sequence used for the comparative study. We therefore filled it artificially with 1000 Ns, indicating in the annotation that 1 kb of sequence are missing at the position 121,554 bp of this BAC clone. Finally, a total of 154,778 bp of sequence was assembled. The final error rate for the two BAC sequences was <1 base per 10 kb, and all finished sequences were of high quality (PHRED scores >25).

Sequence analysis

Base calling and quality of the shotgun sequences were processed using Phred (Ewing and Green 1998) and initial assembly of each BAC clone was performed using the Phrap assembly engine (version 0.990319; provided by P. Green and available at http://www.phrap.org). Subcontigs and singlet DNA sequences were analyzed using BLAST (Basic Local Alignment Search Tool) algorithms (Altschul et al. 1997) against public DNA and protein databases. Shotgun clones overlapping between subcontigs were identified using the Staden Package program GAP4 version 2003.0b (Bonfield et al. 1995). Annotation of the genes was performed using a mixture of BLASTX, BLASTN, and RiceGAAS annotation system (Sakata et al. 2002). Known repetitive elements were identified by BLAST against TREP (http://www.wheat.pw.usda.gov/ITMI/Repeats; Wicker et al. 2002) database (nucleotide and protein) and dot plot analysis (DOTTER) (Sonnhammer and Durbin 1995). New repetitive elements were identified by dot plot analysis and BLAST against public protein databases. Comparisons of the assembled sequences were performed using dot plot and GCG sequence Analysis Software. Rates of nonsynonymous (Ka) vs. synonymous (Ks) nucleotide substitutions (Ka/Ks) per 100 sites were calculated for the exon 3 of RGA2 in T. monococcum DV92, cv. Langdon, and cv. Renan with MEGA2 (Kumar et al. 2001) based on the algorithm of Li (1993). The same method was applied to calculate the synonymous substitution rates of the other genes. Dating of retrotransposon insertions was performed as described by SanMiguel et al. (1998) using the MEGA2 software (Kumar et al. 2001). The average substitution rate of repetitive sequences was calculated using the complete conserved repetitive elements between T. monococcum and T. turgidum and the divergence time of the two loci was estimated as described in SanMiguel et al. (1998).


We thank Romain Guyot, Thomas Wicker, and Edith Schlagenhauf for their help and advice in bioinformatic analysis. We also thank Genoplante (French Plant Genome consortium, http://www.genoplante.com) for access to the hexaploid Renan wheat BAC clones and Jorge Dubcovsky for providing the tetraploid Langdon BAC library. We are very thankful to Jacques David, Moshe Feldman, and Jon Raupp for sharing with us the accessions of tetraploid wheat used in this study. This work was supported by grant 3100-065114 of the Swiss National Science Foundation.


Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3131005.


[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos. AY663391 and AY663392 for the BACs 1156G16 (T. turgidum subsp. durum, cv. Langdon) and 930H14 (T. aestivum cv. Renan), respectively.]


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