Quantitative trait loci on chromosome 4B for coleoptile length and early vigour in wheat (Triticum aestivum L.)

The Norin-10 dwarfing genes, Rht-B1b (Rht1) and Rht-D1b (Rht2), are commonly used to reduce plant height and increase grain yield in wheat breeding programs. These dwarfing genes lower sensitivity of vegetative tissue to endogenous gibberellin to reduce cell and subsequent stem elongation. This reduction in cell elongation capacity reportedly results in a concomitant reduction in coleoptile length and early vigour (leaf area) thereby affecting seedling establishment and growth. A detailed genetic map from a cross between tall Halberd (Rht-B1a) and semidwarf Cranbrook (Rht-B1b) wheat cultivars was used to assess genetic factors affecting seedling growth. Parental and 150 doubled haploid progeny lines were characterised for seedling and height-related traits in controlled and field environments. Genotypic variation was large and predominantly under additive genetic control with evidence for transgressive segregation for some traits. Narrow-sense heritabilities were moderate to high (h2 = 0.31–0.91) indicating a strong genetic basis for differences between progeny. Molecular marker analyses identified a number of significant (P < 0.05) quantitative trait loci (QTL) for each trait. A major QTL, mapping directly to the Rht-B1 locus on chromosome arm 4BS, accounted for up to 49% of the genotypic variance in peduncle length and plant height, and 27–45% of the genotypic variance in coleoptile length across different temperatures. Another QTL, located close to the RFLP marker XksuC2 on the long arm of chromosome 4B, accounted for 15–27% of the genotypic variance in coleoptile length. The influence of the XksuC2-linked QTL on coleoptile length was greatest at 19˚C and decreased with cooler temperatures. The same QTL affected reductions in leaf size, and both coleoptile tiller size and presence to affect overall seedling vigour. There was also some evidence for epistatic interactions influencing coleoptile tiller growth. Reductions in plant size at the Rht-B1b and XksuC2 loci were associated with presence of the Cranbrook 4B allele. The negative genetic effect of the Rht-B1b dwarfing gene on early growth of wheat confirms phenotypic evidence of a pleiotropic effect of Rht-B1b on establishment and early vigour. Genetic increases in coleoptile length and early leaf area development are likely to be limited in wheat populations containing the Rht-B1b dwarfing gene.

Targetting AFLP-DNA markers to specific traits and chromosome regions

The amplified fragment length polymorphism (AFLP) technique is widely used in mapping of wheat as high polymorphism rates are obtained and the procedure is relatively simple. In this study the AFLP markers were targetted to wheat chromosome regions of interest, especially those in which random mapping approaches located relatively few markers. Results showed that the combination of bulk segregant analysis and AFLP markers could target new markers to regions of interest in wheat, and as a result, additional markers were identified for the dough mixing time and noodle colour traits. The new markers for noodle colour were closer to this trait than the markers previously identified by random procedures. As a result, their association with the trait was more significant, an aspect that is important for selection efficiency. In order to improve genome coverage, it was found that regions of chromosomes containing telomere sequences could be targetted using AFLPs combined with a telomere sequence anchor primer.

The hardness locus in Australian wheat lines

The genetic factors that determine grain hardness in Australian wheat (Triticum aestivum L.) germplasm were investigated by studying the grain from 4 crosses (160–180 lines per cross). Although not all the crosses were between hard and soft wheats, the doubled haploid lines derived from the crosses showed significant variation in hardness as assessed either by the Single-Kernel Characterisation System (SKCS 4100) or the scanning electron microscopy appearance of cut surfaces. The wheat cultivars used in the study were Cranbrook, Halberd, CD87, Katepwa, Sunco, Tasman, Egret, and Sunstar and of these only Egret is normally regarded as soft. The quantitative information from the SKCS 4100 was integrated into the genetic map information established for the Cranbrook Halberd, CD87 Katepwa, and Sunco Tasman crosses. For the Egret Sunstar cross, the limited information available from the positioning of genetic markers was used to specifically examine the linkage between the hardness trait and the Pina-D1 (puroindoline) genetic locus on 5DS, and very close linkage was established. The Egret Sunstar cross was also used to develop a more rigorous rheologically based analysis of the raw SKCS crush response data. In addition, the cut surface of the lines was analysed and most (98%) of the samples showed a genetic linkage between the appearance of the cut surface (related to vitreousness) and the SKCS hardness index. Among the other crosses only Cranbrook Halberd showed linkage of the hardness trait to the previously identified hardness locus (ha) located on 5DS as defined by DNA markers for the Pina-D1 locus, and the microsatellite wmc233. The statistical association was shown to be highly significant, with approximately 30% of the variation accounted for by the 5DS region. Another region on chromosome 4D showed a significant association in the Cranbrook Halberd cross. The CD87 Katepwa cross did not show any consistent associations between the SKCS measures and chromosome region, whereas in the Sunco Tasman cross a highly significant association only on chromosome 4B (accounting for 20% of the variation) was suggested. The Sunco Tasman cross showed an overlap of the chromosome region that accounted for variation in both grain weight and hardness and this influence of grain weight on hardness was independently confirmed by a detailed qualitative rheological analysis of the crush response profiles for the Egret Sunstar lines. It is evident from the study that, in Australian wheat lines, there are some major effects on grain hardness that are not associated with the classical ha locus located on 5DS.

Development of robust PCR-based DNA markers for each homoeo-allele of granule-bound starch synthase and their application in wheat breeding programs

The absence of expression of the granule-bound starch synthase I (GBSSI) allele from chromosome 4A of wheat is associated with improved starch quality for making Udon noodles. Several PCR-based methods for the analysis of GBSS alleles have been developed for application in wheat. A widely applied approach has involved a simple PCR followed by electrophoretic separation of DNA products on agarose gels. The PCR amplifies one band from each of the loci on chromosomes 4A (Wx-B1), 7A (Wx-A1), and 7D (Wx-D1), and the band from the Wx-B1 locus is diagnostic for the occurrence of the null Wx-B1 allele that is associated with improved starch quality. The reliable detection of the null Wx-B1 allele has been important in identifying wheat breeding lines. Allele-specific PCR has also been used to successfully detect the occurrence of the null Wx-B1 allele. In the present paper the various protocols were evaluated by testing a segregating double haploid population from a cross between Cranbrook and Halberd and the tests gave good agreement in different laboratories. The application of the DNAbased tests applied in wheat breeding programs provides one of the first examples of a molecular marker selection for a grain quality trait being successfully applied in an Australian wheat breeding program.

Application of a high-throughput antibody-based assay for identification of the granule-bound starch synthase Wx-B1b allele in Australian wheat lines

An enzyme-linked immunosorbent assay (ELISA) for the discrimination of Wx-B1a and Wx-B1b genotypes at the granule-bound starch synthase I (GBSSI) or waxy locus of hexaploid wheat (Triticum aestivum L.) was adapted to a high-throughput, 96-well microtitre plate format. This test is applicable to the direct analysis of starch, flour, or crushed grain and requires less than 1 grain to perform. Several hundred samples may be routinely analysed in one day. The assay was validated using quantitative trait locus (QTL) analysis of a doubled haploid mapping population of the cross Cranbrook (Wx-B1a)/Halberd (Wx-B1b). This demonstrated that the assay unambiguously identified 153 of 161 lines analysed, with a highly significant QTL (LRS value 270) accounting for 83% of ELISA variation, at the Wx-B1 locus on chromosome 4AL. In addition, measurement of total GBSSI variation using a non-isoform-specific GBSSI detection monoclonal antibody also gave a significant QTL (LRS of 84, accounting for 42% of ELISA variation) at the Wx-B1 locus. Application of the assay to crude flour extracts of 8 grains for each of 1093 progeny from 4 crosses segregating at the Wx-B1 locus permitted the unambiguous scoring of lines as pure Wx-B1a or pure Wx-B1b. The scoring by ELISA was strongly related to the flour swelling volume of the lines, thus demonstrating the utility of this high-throughput screening method for the faster, more efficient development of Australian noodle wheats.

Genetic mapping of commercially significant starch characteristics in wheat crosses

Starch properties were measured on the doubled haploid progeny of 2 crosses, one between Cranbrook and Halberd and the other between CD87 and Katepwa. Properties studied included starch peak and final viscosity measured by Rapid Visco Analyser, starch granule size distribution measured by laser light scattering, starch gelatinisation temperature by differential scanning calorimetry, and flour swelling volume. In the Cranbrook Halberd cross (samples from 2 environments), a highly significant quantitative trait locus (QTL) was located on chromosome 4A for both starch peak viscosity and starch/flour swelling volume, centred around the Wx-B1 locus. In previous studies, this locus has been found to be linked to Japanese noodle quality. The increases in starch peak viscosity and flour swelling volume are derived from the Halberd parent, consistent with the fact that Halberd is null for the Wx-B1 locus on chromosome 4A and is missing the respective granule-bound starch synthase protein, whereas Cranbrook is a wheat line carrying the normal 3 Wx loci. The final starch viscosity also showed an association with the Wx-B1 locus. In the CD87 Katepwa cross, the progeny showed an association between peak viscosity and a marker on chromosome 7A. This appeared to be near the Wx-A1 locus. In some experiments, flour viscosity showed a highly significant QTL on chromosome 7B, apparently at the same locus as the late maturity - amylase derived from the Cranbrook parent. Starch gelatinisation onset temperature indicated a significant QTL on chromosomes 2B and 7A (LOD = 2.58 and 3.66, respectively, in interval analyses). Starch gelatinisation peak temperatures indicated a QTL on chromosome 7A, which, although not in the significant (P = 0.05) class based on regression analyses, indicated a LOD score of 3.06 in interval analyses. Heat of gelatinisation (H) indicated a suggestive QTL (LRS = 14.5 with a threshold of 14.7 for P < 0.05, LOD = 2.65 for interval analysis), on chromosome 4A, at the Wx-B1 locus with an increased effect coming from the Halberd parent. The A:B granule ratio analysis indicated a significant QTL on chromosome 4B, but this was not observed in all environments and may be due to the fact that the QTL corresponded to the position of a major QTL controlling plant growth.

The structure and expression of the wheat starch synthase III gene. Motifs in the expressed gene define the lineage of the starch synthase III gene family

The endosperm of hexaploid wheat (Triticum aestivum [L.]) was shown to contain a high molecular weight starch synthase (SS) analogous to the product of the maize du1 gene, starch synthase III (SSIII; DU1). cDNA and genomic DNA sequences encoding wheat SSIII were isolated and characterized. The wheat SSIII cDNA is 5,346 bp long and contains an open reading frame that encodes a 1,628-amino acid polypeptide. A putative N-terminal transit peptide, a 436-amino acid C-terminal catalytic domain, and a central 470-amino acid SSIII-specific domain containing three regions of repeated amino acid similarity were identified in the wheat gene. A fourth region between the transit peptide and the SSIII-specific domain contains repeat motifs that are variable with respect to motif sequence and repeat number between wheat and maize. In dicots, this N-terminal region does not contain repeat motifs and is truncated. The gene encoding wheat SSIII, designated ss3, consists of 16 exons extending over 10 kb, and is located on wheat chromosome I. Expression of ss3 mRNA in wheat was detected in leaves, pre-anthesis florets, and from very early to middle stage of endosperm development. The entire N-terminal variable repeat region and the majority of the SSIII-specific domain are encoded on a single 2,703-bp exon. A gene encoding a class III SS from the Arabidopsis genome sequencing project shows a strongly conserved exon structure to the wheat ss3 gene, with the exception of the N-terminal region. The evolutionary relationships of the genes encoding monocot and dicot class III SSs are discussed.

Genes active in developing wheat endosperm

This paper describes the construction and characterisation of a cDNA library from wheat endosperm tissue during the early stages of grain filling. Developing wheat endosperm tissue was characterised with respect to standard measures including dry weight, cytological appearance and timing of expression of major sources of mRNA such as the seed storage protein genes. In addition, the full complement of proteins present at mid-endosperm development was examined using 2D-electrophoretic techniques. Based on this characterisation, endosperm from the developing grain 8-12 days post-anthesis was chosen for isolating mRNA and preparing cDNA. At this stage in development the mRNA population is not yet dominated by the accumulation of mRNA from seed storage protein genes. A cDNA library, not normalised, containing a high percentage of full length cDNA clones was constructed and 4,319 clones sequenced ("single-pass"). Partitioning of the cDNA sequences into gene families and singletons provided the basis for quantifying the accumulation of sequence classes relative to the total number of sequences determined. The accumulation of gene families/singletons was not linear. However, mathematical modeling of the data suggested that the maximum number of different genes expressed is within the range of 4,500-8,000 (detailed in the Appendix). If an average is taken of these extremes, approximately 27% of the gene products were visible as proteins in the 2D-electrophoretic analysis. Analysis of a functional class of genes relevant to wheat grain end-use, namely the glutenin/gliadin seed storage protein class of genes, revealed a new category of gene characterised by a distinctive N-terminal domain and a reduced central repetitive domain.

The genes encoding granule-bound starch synthases at the waxy loci of the A, B, and D progenitors of common wheat

Three genes encoding granule-bound starch synthase (wx-TmA, wx-TsB, and wx-TtD) have been isolated from Triticum monococcum (AA), and Triticum speltoides (BB), by the polymerase chain reaction (PCR) approach, and from Triticum tauschii (DD), by screening a genomic DNA library. Multiple sequence alignment indicated that the wx-TmA, wx-TsB, and wx-TtD genes had the same extron and (or) intron structure as the previously reported waxy gene from barley. The lengths of the three wx-TmA, wx-TsB, and wx-TtD genes were 2834 bp, 2826 bp, and 2893 bp, respectively, each covering 31 bp in the untranslated leader and the entire coding region consisting of 11 exons and 10 introns. The three genes had identical lengths of exons, except exonl, and shared over 95% identity with each other within the exon regions. The majority of introns were significantly variable in length and sequence, differing mainly in length (1-57 bp) as a result of insertion and (or) deletion events. The deduced amino acid sequence from these three genes indicated that the mature WX-TMA, -TSB, and -TTD proteins contained the same number of amino acids, but differed in predicted molecular weight and isoelectric point (pI) due to amino acid substitutions (13-18). The predicted physical characteristics of the WX proteins matched the respective proteins in wheat very closely, but the match was not perfect. Furthermore the exon5 sequences of the wx-TmA, wx-TsB, and wx-TtD genes were different from a cDNA encoding a waxy gene of common wheat previously reported. The striking difference was that an insertion of 11 amino acids occurred in the cDNA sequence that could not be observed in the exons of the A, B, and D genes. It was noted, however, that the 3' end of intron4 of these genes could account for the additional 11 amino acids. The sequence information from the available waxy genes identified the intron4-exon5-intron5 region as being diagnostic for sequence variation in waxy. The sequence variation in the waxy genes provides the basis for primer design to distinguish the respective genes in common wheat, and its progenitors, using PCR.

Genetic variability in a collection of Stagonospora nodorum isolates from Western Australia

Stagonospora nodorum isolates were collected from the Western Australian grain-belt during 1993. These isolates and a subset of isolates taken from a single location were used to assay the level of variation within the pathogen population. The isolates were compared using anonymous nuclear DNA markers. Three low copy-number and a single high copy-number RFLP probe were used to generate polymorphisms. The collection exhibited a high genotypic diversity for the high copy-number probe, a result consistent with the high level of sexual reproduction previously found in the fungal population. The high level of genotypic diversity was consistent with previous international studies. There was no evidence of differentiation between the total collection of isolates and the subset of isolates taken from the single location. Further work needs to be undertaken to determine if the aggressiveness of the pathogen is influenced by the host genotype.

The Ha locus of wheat: identification of a polymorphic region for tracing grain hardness in crosses

The grain softness proteins or friabilins are known to be composed of three main components: puroindoline a, puroindoline b, and GSP-1. cDNAs for GSP-1 have previously been mapped to group-5 chromosomes and their location on chromosome 5D is closely linked to the grain hardness (Ha) locus of hexaploid wheat. A genomic DNA clone containing the GSP-1 gene (wGSP1-A1) from hexaploid wheat has been identified by fluorescent in situ hybridization as having originated from the distal end of the short arm of chromosome 5A. A genomic clone containing the gene (wGSP1-D1) was also isolated from Aegilops tauschii, the donor of the D genome to bread wheat. There are no introns in the GSP-1 genes, and there is high sequence identity between wGSP1-A1 and wGSP1-D1 up to 1 kb 5' and 300 bp 3' to wGSP1-D1. However, regions further upstream and downstream of wGSP1-D1 share no significant sequence identity to corresponding sequences in wGSP1-A1. These regions therefore identified potentially valuable sequences for tracing the Ha locus through assaying polymorphic DNA sequences. The sequence from 300 to 500 bp 3' to wGSP1-D1 (wGSP1-D13) was mapped to the Ha locus in a mapping population. wGSP1-D13 was also tightly linked to genes for puroindoline a and puroindoline b which have been previously mapped to be at the Ha locus. In addition wGSP1-D13 was used to detect RFLPs between near isogenic soft and hard Falcon lines and in a random selection of soft and hard wheats.

The Ha locus of wheat: Identification of a polymorphic region for tracing grain hardness in crosses

The grain softness proteins or friabilins are known to be composed of three main components: puroindoline a, puroindoline b, and GSP-1. cDNAs for GSP-1 have previously been mapped to group-5 chromosomes and their location on chromosome 5D is closely linked to the grain hardness (Ha) locus of hexaploid wheat. A genomic DNA clone containing the GSP-1 gene (wGSP1-A1) from hexaploid wheat has been identified by fluorescent in situ hybridization as having originated from the distal end of the short arm of chromosome 5A. A genomic clone containing the gene (wGSP1-D1) was also isolated from Aegilops tauschii, the donor of the D genome to bread wheat. There are no introns in the GSP-1 genes, and there is high sequence identity between wGSP1-A1 and wGSP1-D1 up to 1 kb 5' and 300 bp 3' to wGSP1-D1. However, regions further upstream and downstream of wGSP1-D1 share no significant sequence identity to corresponding sequences in wGSP1-A1. These regions therefore identified potentially valuable sequences for tracing the Ha locus through assaying polymorphic DNA sequences. The sequence from 300 to 500 bp 3' to wGSP1-D1 (wGSP1-D13) was mapped to the Ha locus in a mapping population. wGSP1-D13 was also tightly linked to genes for puroindoline a and puroindoline b which have been previously mapped to be at the Ha locus. In addition wGSP1-D13 was used to detect RFLPs between near isogenic soft and hard Falcon lines and in a random selection of soft and hard wheats.Key words: wheat, grain hardness, chromosome 5, puroindoline, GSP-1.

The localization and expression of the class II starch synthases of wheat

The starch granules of hexaploid wheat (Triticum aestivum) contain a group of three proteins known as SGP-1 (starch granule protein-1) proteins, which have apparent molecular masses of 100, 108, and 115 kD. The nature and role of these proteins has not been defined previously. We demonstrate that these polypeptides are starch synthases that are present in both the starch granule and the soluble fraction at the early stages of wheat endosperm development, but that are exclusively granule bound at mid and late endosperm development. A partial cDNA clone encoding a fragment of the 100-kD protein was obtained by screening a wheat endosperm cDNA expression library using monoclonal antibodies. Three classes of cDNA were subsequently isolated from a wheat endosperm cDNA library by nucleic acid hybridization and were shown to encode the 100-, 108-, and 115-kD proteins. The cDNA sequences are highly homologous to class II starch synthases and have the highest homology with the maize SSIIa (starch synthase IIa) gene. mRNA for the SGP-1 proteins was detected in the leaf, pre-anthesis florets, and endosperm of wheat and is highly expressed in the leaf and in the grain during the early to mid stages of development. We discuss the roles of the SGP-1 proteins in starch biosynthesis in wheat.

Stable, high-level expression of a type I antifreeze protein in Escherichia coli

The type I antifreeze proteins are simple amphipathic helical proteins found in abundance in polar fish species, where they act to prevent freezing of internal fluids by a mechanism of noncolligative freezing point depression. Large-scale production of these proteins for research and biotechnological purposes has been hampered by their apparent instability when expressed in heterologous host systems. This has necessitated their production as fusion proteins, in polymeric form, or as proproteins for secretion, with the concomitant necessity for postpurification processing to generate the mature form of the protein. We have successfully expressed a recombinant variant of type I antifreeze protein (rAFP) in Escherichia coli using the inducible T7 polymerase transcription expression system. The rAFP contains five copies of the 11 amino acid ice-binding repeat motif found in all type I antifreeze proteins. The protein accumulates to high levels intracellularly in the form of inclusion bodies, with no apparent degradation by the cellular proteolytic machinery. We have devised a simple and rapid purification protocol for this recombinant type I antifreeze protein which does not require cellular fractionation, purification of the inclusion bodies, or chromatographic steps. This protocol may be of general use for this class of protein. The protein displays all three activities common to these proteins: recrystallization inhibition, noncolligative freezing point depression, and modification of the morphology of single ice crystals in solution.

A transient assay for evaluating promoters in wheat endosperm tissue

A transient assay was developed for the evaluation of promoter sequences in wheat endosperm tissue. A deletion series from an omega-secalin gene promoter, located on chromosome 1RS.1DL of specific wheat lines, were translationally fused to a uidA reporter gene. These promoters were evaluated for expression in wheat endosperm tissue after integration of the DNA into the cell using microprojectile bombardment. The results were compared with those obtained using other transient assay systems.

A transient assay for evaluating promoters in wheat endosperm tissue

A transient assay was developed for the evaluation of promoter sequences in wheat endosperm tissue. A deletion series from an omega-secalin gene promoter, located on chromosome 1RS.1DL of specific wheat lines, were translationally fused to a uidA reporter gene. These promoters were evaluated for expression in wheat endosperm tissue after integration of the DNA into the cell using microprojectile bombardment. The results were compared with those obtained using other transient assay systems.Key words: particle bombardment, transient assay, omega-secalin gene, wheat endosperm.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS-leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.

Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat

The Cre3 gene confers a high level of resistance to the root endoparasitic nematode Heterodera avenae in wheat. A DNA marker cosegregating with H. avenae resistance was used as an entry point for map-based cloning of a disease resistance gene family at the Cre3 locus. Two related gene sequences have been analysed at the Cre3 locus. One, identified as a cDNA clone, encodes a polypeptide with a nucleotide binding site (NBS) and a leucine-rich region; this member of the disease resistance gene family is expressed in roots. A second Cre3 gene sequence, cloned as genomic DNA, appears to be a pseudogene, with a frame shift caused by a deletion event. These two genes, related to members of the cytoplasmic NBS-leucine rich repeat class of plant disease resistance genes were physically mapped to the distal 0.06 fragment of the long arm of wheat chromosome 2D and cosegregated with nematode resistance.

A complex arrangement of genes at a starch branching enzyme I locus in the D-genome donor of wheat

Genomic DNA fragments from Triticum tauschii (D-genome donor to wheat) carrying starch branching enzyme I (SBE I) type genes have been characterized. One fragment contains one complete gene and two partial genes in 16 kb of DNA. One of the partial genes is oriented in the opposite strand to the other two. The gene that is complete was sequenced. Its structure corresponds closely to that of rice in that exons 3-8 are retained at similar sizes and spacings. A cDNA closely corresponding to the complete gene was isolated and characterized; it codes for a putative protein that represents a novel type of SBE I, as it is shorter at the 3' end than the forms reported so far in other plants. A second genomic fragment contains a different SBE I gene. There appear to be approximately 10 copies of SBE I type genes in wheat (approximately 5 in T. tauschii) and most of them have been assigned to group 7 chromosomes. In situ hybridization indicates that a major locus for the genes is located at the distal end of the short arm of chromosome 7D.

The Sec-1 locus on the short arm of chromosome 1R of rye (Secale cereale)

This paper describes a detailed sequence analysis of the omega-secalin gene array at the Sec-1 locus on the short arm of chromosome 1 of rye. The analysis shows that the genes are separated by 8 kb of spacer sequence and that the gene/spacer units are arranged in a head to tail fashion. The boundaries of the array are identified, and a fragment containing the majority of the genes in the array is separated by PFG analysis. The sequence data of one 9.2 kb gene unit have been determined, and because of the similarity of the gene units within the array these data provide a detailed sequence analysis of 140 kb of the Sec-1 locus. Fluorescence in situ hybridization, using lambda clones isolated for the structural analysis, identifies the position of the array on the rye chromosomes relative to the 5S rRNA genes.