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First published online November 16, 2007; 10.1104/pp.107.108852 Plant Physiology 146:200-212 (2008) © 2008 American Society of Plant Biologists OPEN ACCESS ARTICLE
Recurrent Deletions of Puroindoline Genes at the Grain Hardness Locus in Four Independent Lineages of Polyploid Wheat1,[W],[OA]Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506–5502
Polyploidy is known to induce numerous genetic and epigenetic changes but little is known about their physiological bases. In wheat, grain texture is mainly determined by the Hardness (Ha) locus consisting of genes Puroindoline a (Pina) and b (Pinb). These genes are conserved in diploid progenitors but were deleted from the A and B genomes of tetraploid Triticum turgidum (AB). We now report the recurrent deletions of Pina-Pinb in other lineages of polyploid wheat. We analyzed the Ha haplotype structure in 90 diploid and 300 polyploid accessions of Triticum and Aegilops spp. Pin genes were conserved in all diploid species and deletion haplotypes were detected in all polyploid Triticum and most of the polyploid Aegilops spp. Two Pina-Pinb deletion haplotypes were found in hexaploid wheat (Triticum aestivum; ABD). Pina and Pinb were eliminated from the G genome, but maintained in the A genome of tetraploid Triticum timopheevii (AG). Subsequently, Pina and Pinb were deleted from the A genome but retained in the Am genome of hexaploid Triticum zhukovskyi (AmAG). Comparison of deletion breakpoints demonstrated that the Pina-Pinb deletion occurred independently and recurrently in the four polyploid wheat species. The implications of Pina-Pinb deletions for polyploid-driven evolution of gene and genome and its possible physiological significance are discussed.
For over 100 years, wheat grain has been classified into hard and soft types. Grain hardness or texture is mainly determined by the Hardness (Ha) locus. This classification forms the fundamental basis for differentiating wheat grain worldwide (for review, see Morris, 2002  ). Wheat speciation has been molded by polyploidy. Diploid (Triticum monococcum), tetraploid (Triticum turgidum), and hexaploid (Triticum aestivum) wheat species have been known since the 1920s (for review, see Gill and Friebe, 2002). Of the 600 million metric tons of wheat produced in the world in 2005 (http://faostat.fao.org), over 90% comes from hexaploid wheat, also called common or bread wheat, and the remaining from tetraploid, also called macaroni or durum wheat (http://www.fas.usda.gov/pecad/highlights/2005/10/durum_27oct2005). Bread wheat grain is either soft and used for pastries or hard and used for bread and noodles. Durum wheat grain is classified as extrahard and used for pasta. Diploid wheat grain is soft and, although it was the first domesticated wheat, is now grown as a specialty crop in isolated areas. Recently, See et al. (2004) produced a supersoft hexaploid wheat genotype by introgressing softness genes from diploid species.
Because of the pivotal importance of grain texture in determining end use quality, this trait has been intensively studied by geneticists, cereal chemists, and, more recently, by molecular biologists. In the 1970s, Mattern et al. (1973)
Cloning of the Pin genes stimulated genomics research on the Ha locus. Gautier et al. (2000)
Sequencing the Ha loci of T. monococcum (Chantret et al., 2004
During routine mapping of the tetraploid T. timopheevii genome, we detected one copy of the Pin genes in its genome. This was a surprising result in view of the previous report of Gautier et al. (2000)
Phylogeny of Polyploid Wheat and Genetic Nomenclature of Loci
To interpret the Ha deletion haplotype survey results, it is important to briefly introduce understanding of the phylogeny of polyploid wheat. Two lineages of tetraploid wheat, emmer (T. turgidum, 2n = 4x = 28; AB) and Timopheevi (T. timopheevii Zhuk., 2n = 4x = 28; AG), originated less than 0.5 million years ago (Huang et al., 2002
Sequence Analysis of the Ha-S Genomic Region of A. speltoides
Of the three diploid ancestors of polyploid wheat, bacterial artificial chromosome (BAC) sequences of the Ha genomic region of A- and D-genome ancestors were reported previously (Chantret et al., 2004
Survey of the Haplotype Structure at the Ha Locus in Aegilops and Triticum We determined the haplotype structure at the Ha locus by Southern analysis of tester DNA digested with restriction enzymes EcoRI, HindIII, or BamHI using Pina and Pinb gene probes. We estimated the copy number of Pina or Pinb genes in tester species by counting the number of fragments detected by Southern hybridization. The data were tabulated to determine whether the haplotype structure was conserved or there were null haplotypes for either one or both the Pin genes at the Ha locus (Table I ; Supplemental Table S1). Null haplotypes were further characterized according to the size of the deletion, either by Southern analysis using additional gene probes that mark the Ha locus (see Fig. 1), or by sequencing as described below.
Diploid Species We randomly selected at least two accessions from each of the 12 diploid species of Aegilops and Triticum (a total of 90 accessions; Table I; Supplemental Table S1) for the haplotype survey. In all cases, Southern hybridization detected a single band or, rarely, multiple bands for Pina and Pinb gene probes, indicating that haplotype structure at the Ha locus is conserved in the diploid species. A single copy of Pina and Pinb was detected in A- and D-genome donor species of polyploid wheat (Table I). Five Aegilops species share the S genome and all except A. speltoides are self-pollinated. All self-pollinated S-genome species had one copy of Pina and Pinb. Most accessions of A. speltoides also carry one copy of the Pin genes and the observed multiple Southern hybridization fragments in some accessions (Supplemental Table S1) may be due to either heterozygosity, because it is a cross-pollinated species, or, rarely, the presence of intragenic restriction sites or gene duplication. All the C-, M-, U-, and N-genome species also had one copy of the Pin genes, except for one accession of Aegilops comosa, where Southern analysis indicated multiple gene copies.
Tetraploid Species
We screened 65 accessions of T. timopheevii, including two subspecies representing the range of wild and domesticated forms (Supplemental Table S1). All carried only one copy of the Pina and Pinb genes, indicating null haplotype at the Ha locus for one of its genomes (Supplemental Table S1). Gene5, which lies between Pina and Pinb, was, as expected, present in one copy. The Gsp probe detected two copies, indicating that one of the breakpoints that produced the null haplotype is located between Gsp and Pina (Fig. 3). Nine tetraploid Aegilops spp. are grouped into the U- and D-genome clusters. In the U-genome cluster, one accession each was analyzed for Aegilops columnaris Zhuk. (UcoMco) and Aegilops peregrina (Hack. in J. Fraser) Marie and Weiller (USs), two accessions for Aegilops biuncialis Vis. (UM), and nine accessions for Aegilops kotschyii Boiss. (USs); all showed conserved haplotype structure for the Pin genes in both of their genomes (Table I). The other three U-genome cluster species, Aegilops geniculata Roth (UgMg), Aegilops neglecta Req. ex Bertol. (UM), and Aegilops triuncialis L. (UtCt), where more than one accession was analyzed, were polymorphic in Pina copy number. One or more accessions in each species had a conserved haplotype structure for the Pin genes and the other accessions for the same species showed unique haplotypes in one of their genomes where the Pina gene was deleted, but the Pinb gene was retained. Therefore, it is possible that, if a larger survey of the U-genome cluster species is undertaken, all may turn out to be polymorphic for Ha haplotype structure. The D-genome cluster species Aegilops crassa Boiss. (DX), Aegilops cylindrica Host (DcCc), and Aegilops ventricosa Tausch (DvNv) showed a conserved haplotype structure for the Pin genes, except one of the 12 accessions of A. crassa was null for Pina in one of its genomes.
Hexaploid Species
We surveyed three accessions of T. zhukovskyi (AAmG), the second A-genome cluster hexaploid species. It is expected to have two copies of Pin genes, one from T. timopheevii and the second from T. monococcum. However, only one copy of the Pin genes was detected, indicating the presence of a second null haplotype at the Ha locus in one of its genomes (Fig. 4). Because T. zhukovskyi is autoallohexaploid, the loss of a Ha locus could be due to either recombination between A and Am genomes or a deletion event. This question can be resolved based on BGGP and Gsp hybridization patterns: (1) if each detects three bands, Pina and Pinb were deleted from one genome; (2) if two bands with similar intensity are observed, all BGGP, Gsp, Pina, and Pinb were deleted from the A or Am genome; and (3) if the two bands differ significantly in intensity, A-Am recombination, instead of deletion, occurred. Our results support the second scenario (Fig. 4); i.e. BGGP, Gsp, Pina, and Pinb were deleted from the A or Am genome, similar to the Ha-D haplotype in ‘Red Egyptian’. We surveyed three D-genome cluster and one U-genome cluster hexaploid Aegilops spp. and all are expected to have two to three copies of Pina and three copies of Pinb, depending upon the genotype of the tetraploid parent (see above). A. crassa (DDX) and Aegilops vavilovii (Zhuk.) Chennav. (DXSs) were polymorphic; three accessions of A. crassa and two accessions of A. vavilovii had two copies of Pina and three copies of Pinb, and the rest had two copies of both Pina and Pinb. Aegilops juvenalis (Thell.) Eig (DXU) had three copies of Pina and two copies of Pinb in their genomes. The U-genome cluster hexaploid A. neglecta (UnMnNn) was polymorphic; six accessions had two copies of Pina and three of Pinb, four accessions had one copy of Pina and three copies of Pinb, and the remaining three accessions had one copy of Pina and two copies of Pinb. Because tetraploid A. neglecta (UM) was polymorphic for Pina (one or two copies), the data suggest recurrent deletion of Pina at tetraploid and hexaploid levels in this species. Compared to Pina, Pinb deletion was only detected at the hexaploid level in the polyploid Aegilops spp.
A sequence analysis of deletion haplotypes detected in polyploid wheat species was used to further characterize and allocate their genomic origin. These results are summarized in Figure 1.
The Ha-A Haplotype of T. timopheevii The promoters and coding regions of Pina and Pinb are highly conserved among the timopheevii accessions and between timopheevii and urartu, except for a 1-bp insertion in the promoter region of Pina in one accession and an A-to-C transversion at position 181 of Pinb in another (Supplemental Figs. S1 and S2). In the 3' region of Pinb, an 88-bp fragment, spanning the stop codon and polyadenylation signal, was found in triplicate in Pinb-A of T. timopheevii compared to its ancestor T. urartu. The repeat members are identical, except for a single-nucleotide polymorphism (Supplemental Fig. S2). A PCR assay showed that the 88-bp triple repeat is fixed at the species level (Fig. 5 ). A 7-bp sequence (CAACATG) was found at the beginning of each repeat member and immediately after the triple repeat in T. timopheevii and flanking the 88-bp sequence in T. urartu, suggesting that it originated by replication slippage after polyploidization (Supplemental Fig. S2). The alignments of nucleotide sequences of the Pina and Pinb genes and amino acid sequences of the PINA and PINB proteins between T. timopheevii and T. urartu are shown in Supplemental Figures S1, S2, S3, and S4.
The Ha-G Haplotype of T. timopheevii To determine the fine structure of Ha-G, particularly the deletion breakpoints, we isolated Ha-G from a fosmid library constructed from accession Tim01 of T. timopheevii. The Gsp-containing fosmid clone, 1E05, was sequenced at 8 times coverage and assembled into five contigs after prefinishing, totaling 41,262 bp. The largest contig, 23,807 bp, contains three non-TE protein-coding genes within 10,919 bp, BGGP, Gsp, and ATPase (Fig. 2). In addition, a 311-bp sequence, corresponding to the 5' portion of Gene3 was found 1,806 bp downstream of Gsp and 2,749 bp upstream of ATPase, and a partial coding sequence of another copy of the ATPase gene was found 778 bp downstream of the intact ATPase at the 3' end of the fosmid clone. At the nucleotide sequence level, Gsp-G is highly homologous to Gsp-S of A. speltoides and Gsp-B of T. turgidum and T. aestivum. ATPase-G showed highest identity (98%) to ATPase-1 (Gene7-1, pseudogene) from chromosome 5B of T. turgidum and T. aestivum. BGGP-G has high homology to BGGP-D of A. tauschii and T. aestivum and to BGGP-B of T. turgidum and T. aestivum. As expected, GSP-G is encoded by the plus strand, and BGGP-G and ATPase-G are encoded by the minus strand. The Ha-G haplotype lost Gene8 along with Pina, Pinb, ATPase-4, and ATPase-5, and has a distal breakpoint between Gene3 and Pina and a proximal breakpoint between Gene8 and ATPase-1. Compared to the Ha-S locus, more than 200 kb of sequence was deleted from the Ha-G and Ha-B loci during polyploid wheat evolution (Fig. 2).
The Ha-Am Haplotype of T. zhukovskyi
The fixation of Ha deletion patterns in tetraploid wheat suggested that Pin genes may have been eliminated immediately upon polyploidization similar to the low-copy sequences demonstrated by Feldman et al. (1997)
The most remarkable observation on the structure and evolution of the Ha locus in wheat and the Triticeae is the absolute conservation of the locus in diploid species reported here and in previous articles (Gautier et al., 2000 ; Lillemo et al., 2002; Massa et al., 2004; Chen et al., 2005; Simeone et al., 2006) and recurrent and independent deletions in the polyploid Triticum and Aegilops spp. To date, more than 200 accessions from the two diploid Triticum and 10 diploid Aegilops spp. have been analyzed and not a single case of deletion polymorphism at the Ha locus has been reported. Especially, no deletion polymorphisms have been detected in a diverse sample of more than 130 accessions of the A-, B-, and D-genome donor species of polyploid wheat. This is in contrast to frequent deletion haplotype polymorphisms for a defense-gene cluster in the D-genome diploid, A. tauschii (Brooks et al., 2006). Against this high rate of deletion polymorphism in polyploid species, not a single case of insertion-deletion polymorphism was documented in a sample of Pina and Pinb sequences from 50 accessions of diploid A. tauschii, representing its geographical diversity (Massa et al., 2004). All polyploid wheat and most polyploid Aegilops spp. harbored deletion haplotypes of independent origin at the Ha locus. So how does a gene that is essential in a diploid suddenly become deleterious so that it must be deleted in a polyploid? To begin to answer this question, some discussion about the nature of Pin genes, their function, the nature of gene action in polyploids and the mechanisms of polyploid genome evolution and speciation that promote expression and evolution of novel traits is needed.
Amino acid sequence analysis has shown that numerous storage proteins, including low-molecular-weight glutenin,
One of the consequences of polyploidy is doubling and tripling of gene copy number and, thus, the amount of proteins may be doubled or tripled for some of these genes. This dosage response has been demonstrated for the Pin genes and a supersoft hexaploid wheat genotype has been created (See et al., 2004
To test our hypothesis of the deleterious effect of a high dose of Pin genes on seed physiology, a preliminary germination experiment was performed using seeds from hexaploid ‘Chinese Spring’ wheat plants with two (background control), four, and six doses of the Pina-Pinb genes (See et al., 2004
Because at least one copy of the Pin genes is maintained in the vast majority of polyploid species, the loss and fixation of null haplotype copies of both Pin genes in tetraploid T. turgidum require explanation. As mentioned earlier, a number of proteins have AAI activity and higher doses of their expression may partially compensate for the loss of function of the Pin genes. Gsp was not involved in most deletion haplotype polymorphisms and may have some compensatory functional role in defending against microbe attacks. Because extensive resetting of gene expression patterns follows polyploidy, it is possible that other genes may have been recruited for the same role. In fact, quantitative trait loci for hardness phenotype have been mapped in other regions of the genome besides the 5DS locus (Breseghello et al., 2005
Accumulating evidence suggests that polyploidization is accompanied by significant genome restructuring and resetting of gene expression patterns (for review, see Chen and Ni, 2006
Polyploidization leads to both additive and nonadditive gene expression patterns (for review, see Chen, 2007
Plant Materials
Plant materials are summarized in Table I regarding the species, ploidy levels, genome formula, and number of accessions. The details of individual accessions are listed in Supplemental Table S1 with their Pina and Pinb scores. Accessions prefixed with TA are maintained by the Wheat Genetic and Genomic Resources Center, Kansas State University (Manhattan, KS); accessions prefixed with CItr, PI, and PVP were obtained from Dr. Harold Bockelman at the U.S. Department of Agriculture Small Grains Collection (Aberdeen, ID). Triticum timopheevii accession Tim01, the TH02/TMB02 amphiploid (AmAmSS), the Aegilops sharonensis (TH02), and Triticum monococcum (TMB02) were provided by Dr. Moshe Feldman, Weizmann Institute of Science (Rehovot, Israel). The amphiploid (TA3438, AASS) was derived from a cross made at the Wheat Genetic and Genomic Resources Center between Aegilops speltoides accession TA1785 and Triticum urartu accession TA831. All lines were grown in the greenhouse. The ploidy levels of Aegilops crassa and Aegilops neglecta accessions were determined by Badaeva et al. (1998
Wheat (Triticum aestivum) cDNA clones TMA9 (Pina) and TMA10 (Pinb) were provided by Dr. Marie-Françoise Gautier (Unité de Biochimie et Biologie Moléculaire des Céréales, Institut National de la Recherche Agronomique, France). EST BU100707 homologous to Gene1 was obtained from the Arizona Genomics Institute (Tucson, AZ). The BAC clone 197O23 of A. speltoides was provided by Dr. Jan Dvorak (University of California, Davis, CA). All PCR primers for amplification of Gsp, Pina, Gene5, and Pinb and annealing temperatures are given in Supplemental Table S2.
The copy numbers of Pina and Pinb were determined based on the number of fragments detected in Southern blots. Approximately 100 mg of leaf tissue were collected from each accession, lyophilized in a 2-mL microcentrifuge tube, and disrupted by shaking with metal beads. The procedures for DNA extraction, digestion, electrophoresis, and Southern hybridization generally followed those of Faris et al. (2000)
PCR products of genes Gsp, Pina, Gene5, and Pinb were separated by agarose gel electrophoresis, eluted from gel, ligated to T-easy vector (Promega), and transformed into Escherichia coli strain DH10B.
To clone the Ha locus from T. timopheevii, we constructed a fosmid library of accession Tim01. Briefly, total genomic DNA of Tim01 was sheared by 120 cycles of freezing in liquid nitrogen and thawing in a 65°C water bath, and separated by CHEF gel electrophoresis. Fragments of 30 to 50 kb were excised, eluted, end repaired with an End-It kit (Epicentre Biotech), and ligated to the CopyControl pCC1FOS. The ligation was packaged with MaxPlax Lambda Packaging Extracts (Epicentre Biotech), diluted 100-fold, and used to infect E. coli strain PE1300 following the manufacturer's instructions. An aliquot of 70 µL infected bacteria (approximately 70 clones) was distributed and maintained in 384-well plates. The library first was pooled by plate and screened by PCR using Gsp-S-specific primers. Positive plates were pooled by rows and columns. Once a positive well was identified, the culture from that well was spread onto Luria-Bertani agar plates containing chlorophenicol (12.5 µg/mL) and colonies were picked, arrayed in 96-well plates, and screened individually by PCR. To isolate the Ha locus from the G-genome donor species, we hybridized the Pina and Gsp to the macroarray filters of an A. speltoides BAC library (Akhunov et al., 2005
To design genome-specific primers, nucleotide sequences for Gsp, Pina, and Pinb of diploid species of Triticum and Aegilops were retrieved from NCBI (http://www.ncbi.nlm.nih.gov) and subjected to multiple sequence alignment with ClustalW software at Baylor College of Medicine (http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and formatted by BOXSHADE 3.21 (http://www.ch.embnet.org/software/BOX_form.html). For the Pina and Pinb genes cloned from T. timopheevii, Triticum zhukovskyi, amphiploids, and their parents, eight clones from a ligation were sequenced, and the sequences were assembled with CAP3 program (Huang and Medan, 1999
Gene designations followed the rules of nomenclature as listed in the Wheat Gene Symbol Catalogue (McIntosh et al., 1998 Sequence data for this article can be found in the GenBank/EMBL data libraries under accession numbers EU267678, EU267679, and EU268462 to EU268495.
The following materials are available in the online version of this article.
We thank Dr. Harold Bockelman and Dr. Moshe Feldman for providing seeds, Dr. Jan Dvorak and Dr. Marie-Françoise Gautier for providing cDNA clones, Dr. Bernd Friebe for C-banding identification of wheat accessions, and Jon Raupp and Duane Wilson for technical assistance. Received September 10, 2007; accepted November 2, 2007; published November 16, 2007.
1 This work is contributed from the Kansas Agricultural Experiment Station (contribution no. 07–255–J) and was partially supported by grants from the U.S. Department of Agriculture and the Kansas Wheat Commission.  The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Bikram S. Gill (bsgill{at}ksu.edu).
[W] The online version of this article contains Web-only data.
[OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.107.108852 * Corresponding author; e-mail wli{at}ksu.edu.
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ABSTRACT
RESULTS
/β gliadins, lipid transfer proteins, trypsin inhibitor,