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PubMed1993

Comparative analysis of a recombining-repeat-sequence family in the mitochondrial genomes of wheat (Triticum aestivum L.) and rye (Secale cereale L.).

The mitochondrial genomes of wheat and rye each contain a three-member family of recombining repeat sequences (the "18S/5S repeat") that encode genes for 18S and 5S rRNAs (rrn18 and rrn5) and tRNA(fMet) (trnfM). Here we present, for wheat and rye, the sequence and boundaries of the "common sequence unit" (CSU) that is shared between all three repeat copies in each species. The wheat CSU is 4,429 base-pairs long and contains (in addition to trnfM, rrn18 and rrn5) a putative promoter, three tRNA-like elements ("t-elements"), and part of a pseudogene ("psi atpAc") that is homologous to chloroplast atpA, which encodes the alpha subunit of chloroplast F1 ATPase. The rye CSU is somewhat smaller (2,855 base pairs) but contains much the same genic and other sequence elements as its wheat counterpart, except that two of the three t-elements as well as psi atpAc are found in only one of the three downstream flanks of the 18S/5S repeat, outside the CSU boundaries. In interpreting the sequence data in terms of the evolutionary history of the 18S/5S-repeat family of wheat and rye, we conclude that: (1) the wheat-rye form of the 18S/5S repeat most likely originated between 3 and 14 million years ago, in a lineage that gave rise to wheat and rye but not to barley, oats, rice or maize; (2) the close linkage (1-bp apart) between trnfM and rrn18 is similarly limited in its taxonomic distribution to the wheat/rye lineage; (3) the trnfM-rrn18 pair arose via a single mutation that inserted a sequence block containing trnfM immediately upstream of rrn18; and (4) the presence of a putative promoter upstream of rrn18 in all wheat and rye repeats is consistent with all three repeat copies being transcriptionally active. We discuss these conclusions in the light of the possible functional significance of recombining-repeats in plant mitochondrial genomes.

Base Sequence↗
PubMed1996

Molecular cytogenetic characterisation of the terminal heterochromatic segment of the B-chromosome of rye (Secale cereale).

The terminal heterochromatic segments of the long arms of 20 rye B-chromosomes were isolated by means of laser microdissection technology. Also the remaining portions of the long arms, along with the short arms of the same chromosomes were isolated. Each sample was used for degenerate oligonucleotide primer-polymerase chain reaction (DOP-PCR) amplification reactions. The resulting products were used as probes for chromosome in situ hybridisation experiments, and in Southern hybridisation to digests of 0B and +B DNA. Competition hybridisation of these probes with 0B DNA allowed the detection of B-specific sequences. The terminal heterochromatin of the rye B-chromosome contains both B-specific sequences and sequences also present on the A-chromosomes of rye. The B-specific D1100 family is the major repeat species located in the terminal heterochromatin. Primers designed to the cloned sequence (E1100) were used to search for related low copy sequences in 0B DNA. The sequences of the PCR products revealed no similarities to that of the clone E1100 except for the primer sequences. The possible origin of this sequence is discussed in the context of models for the evolution of the rye B-chromosome.

Base Sequence↗
PubMed2003

Leaf-rust resistance in rye (Secale cereale L.). 1. Genetic analysis and mapping of resistance genes Pr1 and Pr2.

Genetic analysis of resistance to leaf rust in rye (Puccinia recondita f. sp. secalis) led to the identification of two dominant resistance genes, Pr1 and Pr2. Both genes proved to be effective against a local leaf-rust population as well as a subset of single-pustule isolates (SPIs) the latter of which comprised SPIs with very high virulence complexity. Resistance conferred by Pr1 and Pr2 was expressed in detached-leaf tests of seedlings as well as in field tests of adult plants. Molecular marker analysis allowed us to map Pr1 in the proximal part of rye chromosome 6RL, whereas Pr2 was assigned to the distal part of chromosome 7RL. These results are discussed in view of homoeology relationships among Triticeae. A proposal is submitted for the designation of resistance genes to rye leaf rust which would avoid interference with existing gene-symboling in respect to wheat leaf-rust resistances introgressed from rye into wheat or triticale.

Basidiomycota↗
PubMed2003

Evaluation of rye (Secale cereale L.) inbred lines and their crosses for tissue culture response and stable genetic transformation of homozygous rye inbred line L22 by biolistic gene transfer.

The efficient and reproducible production of stably expressing transgenic rye plants is described. Analysis of the genotype-specific callus culture-response of 21 rye inbred lines, single crosses and a population variety resulted in the identification of the highly responsive inbred line L22. Biolistic transformation experiments were performed using line L22 and the impact of different selection agents on the regeneration capacity was analyzed. Using the selectable marker gene nptII and corresponding paromomycin selection resulted in transformation efficiencies of up to 4.0% of the bombarded explants. A total of 17 independent transgenic rye plants were produced, and their stability and level of transgene expression was analyzed. The majority of these lines showed stable transgene expression. In contrast a few transgenic lines with multiple transgene inserts, provided evidence of transcriptional and post-transcriptional gene silencing.

Biolistics↗
PubMed2004

Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags.

The genetic map of rye contains predominantly restriction fragment length polymorphism (RFLP) markers but also a limited number of microsatellite markers, which are known to be more reliable and easier to apply. We report here the saturation of the genomic map of rye with additional microsatellite-derived markers that we obtained from the rye expressed sequence tag (EST) databases and the Gatersleben collection of wheat microsatellite markers (WMS). A total of 99 loci (39 EST and 60 WMS) were mapped into the RFLP frameworks of four rye mapping populations consisting of 139, 64, 58 and 60 RFLPs, respectively. For another ten WMS loci, which amplified PCR products not polymorphic in any of the mapping populations, chromosome and chromosome arm locations were determined using wheat-rye addition lines. Chromosomes 1R, 2R, 3R, 4R, 5R, 6R and 7R were enriched with 9, 19, 9, 13, 27, 16 and 16 microsatellite loci, respectively. The microsatellite loci mapped were evenly distributed along the chromosomes, which is important for the further application of these markers for gene mapping or diversity studies in rye. Forty-four of the WMS loci mapped in rye were found to be homologous to those mapped in bread wheat ( Triticum aestivum L.).

Chromosome Mapping↗
PubMed2004

Leaf-rust resistance in rye (Secale cereale L.). 2. Genetic analysis and mapping of resistance genes Pr3, Pr4, and Pr5.

Three dominant resistance genes, Pr3, Pr4, and Pr5, were identified by genetic analysis of resistance to leaf rust in rye (Puccinia recondita f. sp. secalis). Each of the three genes confers resistance to a broad scale of single-pustule isolates (SPIs), but differences could be observed for specific Pr gene/SPI combinations. Resistance conferred by the three genes was effective in both detached-leaf tests carried out on seedlings and in field tests of adult plants. Molecular marker analysis mapped Pr3 to the centromeric region of rye chromosome arm 1RS, whereas Pr4 and Pr5 were assigned to the centromeric region of 1RL. Chromosomal localization and reaction patterns to specific SPIs provide evidence that the three Pr genes represent distinct and novel leaf-rust resistance genes in rye. The contributions of these genes to resistance breeding in rye and wheat are discussed.

Base Sequence↗
PubMed2005

Approaching the self-incompatibility locus Z in rye (Secale cereale L.) via comparative genetics.

Using barley and wheat expressed sequence tags as well as rice genomic sequence and mapping information, we revisited the genomic region encompassing the self-incompatibility (SI) locus Z on rye chromosome 2RL applying a comparative approach. We were able to arrange 12 novel sequence-tagged site (STS) markers around Z, spanning a genetic distance of 32.3 cM, with the closest flanking markers mapping at a distance of 0.5 cM and 1.0 cM from Z, respectively, and one marker cosegregating with Z, in a testcross population of 204 progeny. Two overlapping rice bacterial artifical chromosomes (BACs), OSJNBa0070O11 and OSJNBa0010D21, were found to carry rice orthologs of the three rye STS markers from the 1.5-cM interval encompassing Z. The STS-marker orthologs on these rice BACs span less than 125,000 bp of the rice genome. The STS marker TC116908 cosegregated with Z in a mapping population and revealed a high degree of polymorphism among a random sample of rye plants of various origin. TC116908 was shown via Southern hybridization to correspond to gene no. 10 (OSJNBa0070O11.10) on rice BAC OSJNBa0070O11. Reverse transcription-PCR with a TC116908-specific primer pair resulted in the amplification of a fragment of the expected size from the rye pistil but not from leaf cDNA. OSJNBa0070O11.10 was found to show a highly significant sequence similarity to AtUBP22, a ubiquitin-specific protease (UBP). TC116908 likely represents a putative UBP gene that is specifically expressed in rye pistils and cosegregates with Z. Given that the ubiquitination of proteins is emerging as a general mechanism involved in different SI systems of plants, TC116908 appears to be a promising target for further investigation with respect to its relation to the SI system of the grasses.

Blotting, Southern↗
PubMed2006

Candidate gene identification of an aluminum-activated organic acid transporter gene at the Alt4 locus for aluminum tolerance in rye (Secale cereale L.).

Among cereal crops, rye is one of the most tolerant species to aluminum. A candidate gene approach was used to determine the likely molecular identity of an Al tolerance locus (Alt4). Using PCR primers designed from a wheat aluminum tolerance gene encoding an aluminum-activated malate transporter (TaALMT1), a rye gene (ScALMT1) was amplified, cloned and sequenced. Subsequently, the ScALMT1 gene of rye was found to be located on 7RS by PCR amplification using the wheat-rye addition lines. SNP polymorphisms for this gene were detected among the parents of three F(2) populations that segregate for the Alt4 locus. A map of the rye chromosome 7R, including the Alt4 locus ScALMT1 and several molecular markers, was constructed showing a complete co-segregation between Alt4 and ScALMT1. Furthermore, expression experiments were carried out to clarify the function of this candidate gene. Briefly, the ScALMT1 gene was found to be primarily expressed in the root apex and upregulated when aluminum was present in the medium. Five-fold differences in the expression were found between the Al tolerant and the Al non-tolerant genotypes. Additionally, much higher expression was detected in the rye genotypes than the moderately tolerant "Chinese Spring" wheat cultivar. These results suggest that the Alt4 locus encodes an aluminum-activated organic acid transporter gene that could be utilized to increase Al tolerance in Al sensitive plant species. Finally, TaALMT1 homologous sequences were identified in different grasses and in the dicotyledonous plant Phaseolus vulgaris. Our data support the hypothesis of the existence of a common mechanism of Al tolerance encoded by a gene located in the homoeologous group four of cereals.

Aluminum↗
PubMed2005

Changes over time in the allelochemical content of ten cultivars of rye (Secale cereale L.).

Published studies focused on characterizing the allelopathy-based weed suppression by rye cover crop mulch have provided varying and inconsistent estimates of weed suppression. Studies were initiated to examine several factors that could influence the weed suppressiveness of rye: kill date, cultivar, and soil fertility. Ten cultivars of rye were planted with four rates of nitrogen fertilization, and tissue from each of these treatment combinations was harvested three times during the growing season. Concentrations of a known rye allelochemical DIBOA (2,4-dihydroxy-1,4-(2H)benzoxazine-3-one) were quantified from the harvested rye tissue using high performance liquid chromatography (HPLC). Phytotoxicity observed from aqueous extracts of the harvested rye tissue correlated with the levels of DIBOA recovered in harvested tissue. The amount of DIBOA in rye tissue varied depending on harvest date and rye cultivar, but was generally lower with all cultivars when rye was harvested later in the season. However, the late maturing variety 'Wheeler' retained greater concentrations of DIBOA in comparison to other rye cultivars when harvested later in the season. The decline in DIBOA concentrations as rye matures, and the fact that many rye cultivars mature at different rates may help explain why estimates of weed suppression from allelopathic agents in rye have varied so widely in the literature.

Amaranthus↗
PubMed1991

High mutability in rye (Secale cereale L.).

Analysis of the rye cultivar Ailés of several descents derived from crosses between plants carrying specific genotypes and/or chromosome constitutions resulted in the detection of high chromosome (2.05 x 10(-2)) and gene (9.3 x 10(-3)) mutation frequencies. The existence of a transposon system responsible for this instability is suggested.

Chromosomes↗
PubMed1993

Identification of the nuclear-encoded chloroplast ribosomal protein L12 of the monocotyledonous plant Secale cereale and sequencing of two different cDNAs with strong codon bias.

Two different cDNA clones (SCL12-1 and SCL12-2) encoding precursors of a chloroplast ribosomal protein with homology to L12 from Escherichia coli were isolated from rye leaf cDNA libraries and sequenced. The corresponding polypeptide of rye chloroplast ribosomes was identified. The sequences for the mature proteins of M(r) 13,447 and 13,609 share 85% amino acid identity. The mature polypeptide of clone SCL12-1 has an amino acid identity of 71%, 72% or 44%, respectively, relative to L12 proteins from spinach, tobacco, or E. coli. Codon usage of the rye L12 cDNAs shows a high preference (97% and 82%) for G or C in the third base position.

Amino Acid Sequence↗
PubMed2000

cDNA cloning of cytoplasmic ribosomal protein S7 of winter rye (Secale cereale) and its expression in low-temperature-treated leaves.

A cDNA clone (ScRPS7) encoding the cytoplasmic ribosomal protein S7 was isolated from a rye leaf cDNA library and sequenced. The deduced protein of 192 amino acids with M(r) 22189 shows identity of 52% or 47%, respectively, relative to S7 proteins of human or yeast. A RPS7 mRNA accumulation is higher in the meristematic zone at the leaf base than in the non-meristematic middle and upper section of leaves. Short periods of cold stress sharply reduce the mRNA level while leaves of cold hardened plants contain normal levels of ScRPS7 transcripts.

Amino Acid Sequence↗
PubMedDate not supplied

Purification, biochemical characterisation and partial primary structure of a new alpha-amylase inhibitor from Secale cereale (rye).

Plant alpha-amylase inhibitors show great potential as tools to engineer resistance of crop plants against pests. Their possible use is, however, complicated by the observed variations in specificity of enzyme inhibition, even within closely related families of inhibitors. Better understanding of this specificity depends on modelling studies based on ample structural and biochemical information. A new member of the alpha-amylase inhibitor family of cereal endosperm has been purified from rye using two ionic exchange chromatography steps. It has been characterised by mass spectrometry, inhibition assays and N-terminal protein sequencing. The results show that the inhibitor has a monomer molecular mass of 13,756 Da, is capable of dimerisation and is probably glycosylated. The inhibitor has high homology with the bifunctional alpha-amylase/trypsin inhibitors from barley and wheat, but much poorer homology with other known inhibitors from rye. Despite the homology with bifunctional inhibitors, this inhibitor does not show activity against mammalian or insect trypsin, although activity against porcine pancreatic, human salivary, Acanthoscelides obtectus and Zabrotes subfasciatus alpha-amylases was observed. The inhibitor is more effective against insect alpha-amylases than against mammalian enzymes. It is concluded that rye contains a homologue of the bifunctional alpha-amylase/trypsin inhibitor family without activity against trypsins. The necessity of exercising caution in assigning function based on sequence comparison is emphasised.

Animals↗
PubMed2001

Studies on rye (Secale cereale L.) lines exhibiting a range of extract viscosities. 1. Composition, molecular weight distribution of water extracts, and biochemical characteristics of purified water-extractable arabinoxylan.

Five rye lines exhibiting a wide range of extract viscosities, along with commercial cultivars of rye and wheat, were compared with respect to their physical and chemical properties. Rye wholemeals contained significantly higher concentrations of total and soluble dietary fiber (TDF and SDF, respectively), total and water-extractable arabinoxylan (TAX and WEAX, respectively), and beta-glucan than did wheat. Significant positive correlations were obtained between rye wholemeal extract viscosity and SDF content (r = 0.90, p < 0.05) and WEAX content (r = 0.89, p < 0.05). Gel permeation chromatography (GPC) of water extracts of rye wholemeals revealed the presence of a high molecular weight fraction (HMWF), which was found in higher concentration in the ryes than in wheat. A significant positive correlation (r = 0.84, p < 0.05) was observed between HMWF content (expressed as a proportion of the total carbohydrate in water extracts) and extract viscosity of rye wholemeals. Treatment of a rye wholemeal extract with xylanase, followed by GPC, indicated that the HMWF consisted primarily of WEAX. Successive treatment of a rye wholemeal extract with alpha-amylase, lichenase, protease, and xylanase confirmed that the viscosity of the extract was primarily related to its content of WEAX. WEAX was isolated from high, intermediate, and low extract viscosity ryes. Structural differences were observed among the three arabinoxylans using H NMR and high-pressure size exclusion chromatography with triple detection. The WEAX from high extract viscosity rye was a higher molecular weight macromolecule exhibiting a higher intrinsic viscosity, a larger radius of gyration, a larger hydrodynamic radius, and a lower degree of branching compared to WEAX from low and intermediate extract viscosity ryes.

Chromatography, High Pressure Liquid↗