Conversion of a RAPD-generated PCR product,containing a novel dispersed repetitive element,into a fast and robust assay for the presence of rye chromatin in wheat

Bulk segregant analysis was used to obtain a random amplified polymorphic DNA (RAPD) marker specific for the rye chromosome arm of the 1BL.1RS translocation, which is common in many high-yielding bread wheat varieties. The RAPD-generated band was cloned and end-sequenced to allow the construction of a pair of oligonucleotide primers that PCR-amplify a DNA sequence only in the presence of rye chromatin. The amplified sequence shares a low level of homology to wheat and barley, as judged by the low strength of hybridization of the sequence to restriction digests of genomic DNA. Genetic analysis showed that the amplified sequence was present on every rye chromosome and not restricted to either the proximal or distal part of the 1RS arm. In situ hybridization studies using the amplified product as probe also showed that the sequence was dispersed throughout the rye genome, but that the copy number was greatly reduced, or the sequence was absent at both the centromere and the major sites of heterochromatin (telomere and nucleolar organizing region). The probe, using both Southern blot and in situ hybridization analyses, hybridized at a low level to wheat chromosomes, and no hybridizing restriction fragments could be located to individual wheat chromosomes from the restriction fragment length polymorphism (RFLP) profiles of wheat aneuploids. The disomic addition lines of rye chromosomes to wheat shared a similar RFLP profile to one another. The amplified sequence does not contain the RIS 1 sequence and therefore represents an as yet undescribed dispersed repetitive sequence. The specificity of the amplification primers is such that they will provide a useful tool for the rapid detection of rye chromatin in a wheat background. Additionally, the relatively low level of cross-hybridization to wheat chromatin should allow the sequence to be used to analyse the organization of rye euchromatin in interphase nuclei of wheat lines carrying chromosomes, chromosome segments or whole genomes derived from rye.     

Dosage response of rye genes in a wheat background

Summary A series of hexaploid wheat lines containing zero, two or four doses of rye chromosome arm 1RS was used to investigate the response to changes in dosage by the rye genes when in a wheat background. The quantity of protein produced by the secalin protein genes contained on 1RS was directly related to the number of copies of 1RS present in the line. No response could be detected by representative wheat proteins suggesting that the increase in secalin protein observed was due to an increase in mRNA produced when four copies of the secalin gene was present. These results suggest that increasing the dosage of alien genes introgressed into wheat may be a useful tool for enhancing their expression.Mention of a trade name or proprietary product does not constitute a guarantee, warranty or recommendation of the product by the U.S. Department of Agriculture or the University of Missouri and does not imply its approval to the exclusion of other products that may be suitable.Contribution from the Missouri Agricultural Experiment Station. Journal Series No. 11,413     

Homoeologous chromosomal location of the genes encoding thionins in wheat and rye

Summary Thionins are high sulphur basic polypeptides present in the endosperm of Gramineae. In wheat there are three thionins encoded by genes located in the long arms of chromosomes 1A, 1B and 1D. Rye has one thionin encoded by a gene which has been assigned to chromosome 1R after analysis of the Imperial-Chinese Spring rye-wheat disomic addition lines. Commercial varieties and experimental stocks with a 1B/1R substitution carry the thionin from rye ( _R) instead of the _B thionin from wheat. The _R thionin gene is not located in the large chromosomal segment representing most of the short arm of chromosome 1R.     

The use of random amplified polymorphic DNA markers in wheat

Summary An evaluation was made of the use of random amplified polymorphic DNA (RAPD) as a genetic marker system in wheat. Reproducible amplification products were obtained from varietal, homozygous single chromosome recombinant line and wheat/alien addition line genomic DNA with selected primers and rigorously optimized reaction conditions. Factors influencing the RAPD patterns are DNA concentration, Mg²⁺ concentration, polymerase concentration and denaturing temperature. In wheat, the non-homoeologous, non-dose responsive and dominant behaviour of RAPD products devalues their use as genetic markers for the construction of linkage maps, and the high probability that the amplified fragments derive from repetitive DNA limits their use as a source of conventional RFLP probes. However, RAPD markers will most certainly find many applications in the analysis of genotypes where single chromosomes or chromosome segments are to be manipulated.     

PCR-based detection of a tracheal mite of the honey bee Acarapis woodi

The effects of the tracheal mite Acarapis woodi on the health of honey bees have been neglected since the prevalence of Varroa mites to Apis mellifera colonies. However, tracheal mite infestation of honey bee colonies still occurs worldwide and could impose negative impact on apiculture. The detection of A. woodi requires the dissection of honey bees followed by microscopic observation of the tracheal sacs. We thus developed PCR methods to detect A. woodi. These methods facilitate rapid and sensitive detection of A. woodi in many honey bee samples for epidemiologic surveys.     

The effect of wheat cytoplasm on the synthesis of wheat x rye hybrids

Summary Four nuclear genotypes of Triticum aestivum L., each substituted into the cytoplasm of T. timococcum Kostoff, Aegilops ventricosa Tausch and T. timopheevi Zhuk., were crossed with four homozygous Secale cereale L. inbred lines to produce 48 alloplasmic octoploid primary triticales. Crossability, embryo differentiation, amphihaploid plantlet recovery in vitro, and response to colchicine treatment were investigated. It was found that in general the effects of the wheat cytoplasm on the characteristics studied were of equal importance as those of the wheat and the rye nuclear genotypes. Cytoplasm can be regarded as an additional source of variation in the synthesis of primary triticales. Cross-compatibility in wheat x rye hybrids appeared to be determined by specific parental genotypes and their nucleo-cytoplasmic interactions rather than by any general compatibility of particular nuclear genotypes and/or cytoplasms.     

Comparison of rates of natural senescence of the root cortex of wheat (with and without mildew infection), barley,oats and rye

Summary In comparative tests in a glasshouse, the cortex of oat and rye roots senesced more slowly than the cortex of wheat and barley roots. Of the cereals tested, wheat showed the most rapid rate of root cortical senescence, and the rate was unaffected by inoculation of leaves withErysiphe graminis. The results are discussed in relation to infection by root pathogens.     

Genetic analysis of a polyembryonic mutant in rye

We have obtained one plant regenerated from rye tissue culture which showed a high percentage of polyembryonic seeds in its progeny. The mutation inducing the development of extra embryos is also influencing erroneous cell division, mitosis and meiosis. The genetic analysis indicated that the aptitude for polyembryonic seed formation is a heritable trait controlled by a dominant gene. However, for expression of the phenotype the female parent should have a specific cytoplasm.     

Genetic and physical mapping of sequence-specific amplified polymorphic (SSAP) markers on the 1RS chromosome arm of rye in a wheat background

Three rye-specific repeated sequences, pSc10C, pSc20H and R173-1, were used to design sequence-specific anchored primers. These primers and 16 restriction site-specific adaptor primers were used in all possible combinations to establish sequence-specific amplified polymorphic (SSAP) markers for the 1RS chromosome arm of rye in a wheat background. Thirty 1RS-specific SSAP markers were detected in 19 primer combinations. Along with six markers localised previously on 1RS, 26 of the SSAP markers were mapped genetically in wheat genotypes carrying recombinant 1BL.1RS translocations. A clear decrease in recombination frequency from distal to proximal regions was observed. Wheat-rye addition lines for the 1R chromosome with different-sized deletions of the short arm were used to physically localise these markers. Physical mapping suggested an even distribution of the SSAP markers along the total length of the 1RS chromosome arm.Communicated by J.W. Snape     

Genetic control of 6-phosphogluconate dehydrogenase (6-PGD) isozymes in cultivated wheat and rye

Summary The 6-phosphogluconate dehydrogenase (6-PGD) zymogram phenotypes of wheat, rye and their aneuploid derivatives were determined. Two genes involved in the production of 6-PGD isozymes were located on chromosome arms CRL (4 RL) and FRL (6 RL) of Imperial rye. On the basis of differential interactions between wheat and rye chromosomes, evidence was obtained that genes located on chromosomes 6 A, 6 BL and 7 BL control 6-PGD isozyme activities in Chinese Spring wheat. The wheat and rye 6-PGD zymogram phenotypes were indicative of homoeologous relationships between rye chromosome 6 RL to wheat chromosomes of group 6, and rye chromosome 4 RL to wheat chromosomes of group 7.     

Pairing and recombination between individual chromosomes of wheat and rye in hybrids carrying the ph1b mutation

Wheat-rye chromosome associations at metaphase I studied by Naranjo and Fernández-Rueda (1991) in ph1b ABDR hybrids have been reanalysed to establish the frequency of pairing between individual chromosomes of wheat and rye. Wheat chromosomes, except for 2A and 2D, and their arms were identified by C-banding. Diagnostic C-bands and other cytological markers such as telocentrics or translocations were used to identify each one of the rye chromosomes and their arms. Both the amount of telomeric C-heterochromatin and the structure of the rye chromosomes relative to wheat affected the level of wheatrye pairing. The degree to which rye chromosomes paired with their wheat homoeologues varied with each of the three wheat genomes; in most groups, the B-R association was more frequent than the A-R or D-R associations. Recombination between arms 1RL and 2RL and their homoeologues of wheat possessing a different telomeric C-banding pattern was detected and quantified at anaphase I. The frequency of recombinant chromosomes obtained supports the premise that recombination between wheat and rye chromosomes may be estimated from wheat-rye pairing.     

Rye chromosome translocations in hexaploid wheat: a re-evaluation of the loss of heterochromatin from rye chromosomes

Summary Using in situ hybridization techniques, we have been able to identify the translocated chromosomes resulting from whole arm interchanges between homoeologous chromosomes of wheat and rye. This was possible because radioactive probes are available which recognize specific sites of highly repeated sequence DNA in either rye or wheat chromosomes. The translocated chromosomes analysed in detail were found in plants from a breeding programme designed to substitute chromosome 2R of rye into commercial wheat cultivars. The distribution of rye highly repeated DNA sequences showed modified chromosomes in which (a) most of the telomeric heterochromatin of the short arm and (b) all of the telomeric heterochromatin of the long arm, had disappeared. Subsequent analyses of these chromosomes assaying for wheat highly repeated DNA sequences showed that in type (a), the entire short arm of 2R had been replaced by the short arm of wheat chromosome 2B and in (b), the long arm of 2R had been replaced by the long arm of 2B. The use of these probes has also allowed us to show that rye heterochromatin has little effect on the pairing of the translocated wheat arm to its wheat homologue during meiosis. We have also characterized the chromosomes resulting from a 1B-1R translocation event.From these results, we suggest that the observed loss of telomeric heterochromatin from rye chromosomes in wheat is commonly due to wheat-rye chromosome translocations.     

Induction of recombination between rye chromosome 1RL and wheat chromosomes

Summary The ph1b mutant in bread wheat has been used to induce homoeologous pairing and recombination between chromosome arm 1RL of cereal rye and wheat chromosome/s. A figure of 2.87% was estimated for the maximal frequency of recombination between a rye glutelin locus tightly linked to the centromere and the heterochromatic telomere on the long arm of rye chromosome 1R in the progeny of ph1b homozygotes. This equates to a gametic recombination frequency of 1.44%. This is the first substantiated genetic evidence for homoeologous recombination between wheat and rye chromosomes. No recombinants were confirmed in control populations heterozygous for ph1b. The ph1b mutant was also observed to generate recombination between wheat homoeologues.     

A PCR-based tool for cultivation-independent detection and quantification of Metarhizium clade 1

The entomopathogenic fungus Metarhizium anisopliae and sister species are some of the most widely used biological control agents for insects. Availability of specific monitoring and quantification tools are essential for the investigation of environmental factors influencing their environmental distribution. Naturally occurring as well as released Metarhizium strains in the environment traditionally are monitored with cultivation-dependent techniques. However, specific detection and quantification may be limited due to the lack of a defined and reliable detection range of such methods. Cultivation-independent PCR-based detection and quantification tools offer high throughput analyses of target taxa in various environments. In this study a cultivation-independent PCR-based method was developed, which allows for specific detection and quantification of the defined Metarhizium clade 1, which is formed by the species Metarhizium majus, Metarhizium guizhouense, Metarhizium pingshaense, Metarhizium anisopliae, Metarhizium robertsii and Metarhiziumbrunneum, formerly included in the M. anisopliae cryptic species complex. This method is based on the use of clade-specific primers, i.e. Ma 1763 and Ma 2097, that are positioned within the internal transcribed spacer regions 1 and 2 of the nuclear ribosomal RNA gene cluster, respectively. BLAST similarity searches and empirical specificity tests performed on target and non-target species, as well as on bulk soil DNA samples, demonstrated specificity of this diagnostic tool for the targeted Metarhizium clade 1. Testing of the primer pair in qPCR assays validated the diagnostic method for specific quantification of Metarhizium clade 1 in complex bulk soil DNA samples that significantly correlated with cultivation-dependent quantification. The new tool will allow for highly specific and rapid detection and quantification of the targeted Metarhizium clade 1 in the environment. Habitat with high Metarhizium clade 1 densities can then be analyzed for habitat preferences in greater detail using cultivation-dependent techniques and genetic typing of isolates.     

Molecular cytogenetic analysis of Agropyron elongatum chromatin in wheat germplasm specifying resistance to wheat streak mosaic virus

Summary Three lines derived from wheat (6x) x Agropyron elongatum (10x) that are resistant to wheat streak mosaic virus (WSMV) were analyzed by chromosome pairing, banding, and in situ hybridization. Line CI15321 was identified as a disomic substitution line where wheat chromosome 1D is replaced by Ag. elongatum chromosome 1Ae-1. Line 87-94-1 is a wheat-Ag. elongatum ditelosomic addition 1Ae-1L. Line CI15322 contains an Ag. elongatum chromosome, 1Ae-2, that substitutes for chromosome 1D. The short arm of 1Ae-2 paired with the short arm of 1Ae-1 at metaphase I (MI) in 82% of the pollen mother cells (PMCs). However, the long arms of these two chromosomes did not pair with each other. In CI15322, the long arm of chromosome 4D has an Agropyron chromosome segment which was derived from the distal part of 1Ae-1L. This translocation chromosome is designated as T4DS·4DL-1L. T4DS·4DL-1Ae-1L has a 0.73 m distal part of the long arm of 4D replaced by a 1.31 m distal segment from 1Ae-1L. The major WSMV resistance gene(s) in these lines is located on the distal part of 1Ae-1L.Contribution No. 92-599-J from the Kansas Agricutural Experiment Station, Kansas State University, Manhattan, Kansas, USA     

Genomic characterization of self-incompatibility ribonucleases (S-RNases) in European pear cultivars and development of PCR detection for 20 alleles

Sexual self-incompatibility in European pear (Pyrus communis L.) is controlled by a single locus (S-locus) encoding a polymorphic stylar ribonuclease (S-RNase) that is responsible for the female function in pollen–pistil recognition. In this study, genomic DNA sequences corresponding to five new S-RNase alleles (named S ₂₀ , S ₂₁ , S ₂₂ , S ₂₃ , and S ₂₄ ) and to S _m were characterized in European pear cultivars. Re-sequencing S _q from ‘General Le Clerc’ showed this S-RNase to encode the same protein as S ₁₂ . Based on these findings, a polymerase chain reaction (PCR)-based method was developed for the molecular typing of cultivars bearing 20 S-RNases (S ₁ –S ₁₄ , S _m , and S ₂₀ –S ₂₄ ) using consensus and allele-specific primers. Genomic PCR with consensus primers amplified product sizes characteristic of the S-RNases S ₁ , S ₂ , S ₄ , S ₁₀ , S ₁₃ , and S ₂₀ . However, the allele groups S ₃ /S ₁₂ , S ₆ /S ₈ /S ₁₁ /S ₂₂ and S ₅ /S ₇ /S ₉ /S ₁₄ /S _m /S ₂₁ /S ₂₃ /S ₂₄ amplified PCR products of similar size. To discriminate between alleles within these groups, primers to specifically amplify each S-RNase were developed. Application of this approach in 19 cultivars with published S-alleles allowed re-evaluation of one of the alleles of ‘Passe Crassane,’ ‘Conference,’ and ‘Condo.’ Finally, this method was used to assign S-genotypes to 37 cultivars. Test crosses confirmed molecular results. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Intrachromosomal mapping of crossability genes in wheat (Triticum aestivum)

Summary Intrachromosomal mapping studies were used to locate the positions of the genes Kr1 and Kr2, which control the crossability of wheat with Hordeum bulbosum, on chromosomes 5B and 5A, respectively. The location of Kr1 was established using the telocentric mapping technique and found to be on the long arm of chromosome 5B, distal to the centromere with a mean recombination frequency of 44.8±3.28%. Kr2 was located on the long arm of chromosome 5A by linkage with the major gene markers Vrn1, controlling vernalization requirement, and q, controlling ear morphology. Kr2 is closely linked to Vrn1, with a mean recombination frequency of 4.8±4.66%, and is distal to q with a mean recombination frequency of 38.1±10.60%. The similar locations of Kr1 and Kr2 on homoeologous chromosomes suggest that these two loci are homoeoallelic. Significant correlations between Hordeum bulbosum and rye crossability confirmed that Kr1 and Kr2 control the crossability of wheat with both species.     

Mapping of a BYDV resistance gene from Thinopyrum intermedium in wheat background by molecular markers

The wheat line H960642 is a homozygous wheat-Thinopyrum intermedium translocation line with resistance to BYDV by genomicin situ hybridization (GISH) and RFLP analysis. The genomic DNA ofTh. intermedium was used as a probe, and common wheat genomic DNA as a blocking in GISH experiment. The results showed that the chromosome segments ofTh. intermedium were transferred to the distal end of a pair of wheat chromosomes. RFLP analysis indicated that the translocation line H960642 is a T7DS-7DL-7XL translocation by using 8 probes mapped on the homoeologous group 7 in wheat. The translocation breakpoint is located between Xpsr680 and Xpsr965 about 90–99 cM from the centromere. The RFLP markers psr680 and psr687 were closely linked with the BYDV resistance gene. The gene is located on the distal end of 7XL around Xpsr680 and Xpsr687. Project supported by the 863 program and the National Natural Science Foundation of China (Grant No. 39680027).     

The inheritance of rye seed peroxidases

Summary Genetic analyses were conducted on peroxidase of the embryo and endosperm of seeds of one open pollinated and six inbred lines of cultivated rye (Secale cereale L.), and one line of Secale vavilovii Grossh. The analyses of the individual parts of the S. cereale seed yield a total of 14 peroxidase isozymes. Isozymes m, a, b, c, d, e, f and g (in order from faster to slower migration) were found in the embryo plus scutellum, while isozymes 1, 2, 3, 4, 5 and 6 (also from faster to slower migration) were peculiar of the endosperm. S. vavilovii has isozymes m, c₁, d, e, f and g in its embryo plus scutellum, and isozyme 2 in the endosperm. Segregation data indicated that at least 13 different loci would be controlling the peroxidase of S. cereale. Isozymes a and b are controlled by alleles of the same locus, all the other loci have one active and dominant allele coding for one isozyme, and other null and recessive allele. The estimation of linkage relationships shows that five endosperm loci are linked, and tentative maps are shown. A possible dosage effect and the existence of controlling gene(s) for endosperm isozyme 4 is reported. All these data and the high frequency of null alleles found are discussed in relation to recent reports.