Evolutionary trends of microsatellites during the speciation process and phylogenetic relationships within the genus Secale

Eleven weedy or wild species or subspecies of the genus Secale L. were compared with a set of cultivated rye accessions, based on inter-simple sequence repeat (ISSR) markers to analyze their phylogenetic relationships. A total of 846 bands were amplified from reactions using 12 screening primers, including 79 loci with a mean of 10.1 alleles per locus. The number of amplified bands for each primer ranged from 12 to 134, with a mean of 70.5 amplified bands per primer. The presence and distribution of amplified bands in different accessions demonstrate that a rapid evolutionary trend of microsatellite repeats occurred during the speciation process from the perennial wild form to annual cultivated rye. In addition, variation, amplification, and deletion of microsatellites in genomes revealed phylogenetic relationships in the genus Secale. Analysis of the presence, number, and distribution of amplified bands in genomes, as well as the comparison with genetic similarity (GS) indices based on ISSR, indicate that Secale strictum subsp. africanum (Stapf) Hammer, Secale strictum anatolicum (Boiss.) Hammer, Secale sylvestre Host, and Secale strictum subsp. strictum (C. Presl) Hammer emerged in succession from a common ancestor of Secale following geographic separation and genetic differentiation. The annual weedy rye evolved from S. strictum subsp. strictum, which was domesticated as present-day cultivated rye. Data from ISSR analyses separated all investigated accessions of the genus Secale into three distinct groups. These results support the division of the genus Secale into three species: the annual wild species S. sylvestre; the perennial wild species S. strictum, including several differential subspecies forms such as strictum, africanum, and anatolicum; and S. cereale, including cultivated and weedy rye as subspecies forms.     

Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms.

Amplified fragment length polymorphism (AFLP) data were utilized to analyze the phylogenetic relationships among 29 accessions representing 14 of the most commonly recognized ranked species or subspecies in the genus Secale. We observed 789 AFLP markers of 1130 fragments utilizing 18 P-/M- and E-/M- primer combinations. All polymorphic fragments were used to construct phenetic and phylogenetic trees. The resulting phenogram and cladogram had similar tree topologies. Cluster analysis showed that Secale sylvestre was the most distantly related to all other ryes. Annual forms were grouped together, and the perennial forms appeared more closely related to each other. This suggested that life cycle could have played an important role in determining the relationships among Secale species. Secale sylvestre was considered to be the most ancient species, whereas Secale cereale was the most recently evolved species. Amplified fragment length polymorphism analysis clearly separated all Secale species into only 3 major species groups, within the genus Secale: S. sylvestre, Secale montanum (syn. Secale strictum) for perennial forms, and S. cereale for annual forms. This study demonstrated that the AFLP approach is a useful tool for discriminating species differences, and also gave a much better resolution in discerning genetic relationships among Secale species as compared with previous studies using other approaches.     

Physical mapping of the 5S rRNA multigene family in 6x triticale and rye: identification of a new rye locus.

In situ hybridization was used to physically map the 5S rRNA multigene family in three selected lines of hexaploid triticale and five lines of diploid rye. Using this technique, evidence for a new locus on the 3RS arm of the three triticale lines was first obtained, as well as confirmation of the presence of 5S rRNA loci on wheat and rye chromosomes of homoeologous groups 1 and 5. The new locus on the 3RS arm was confirmed in two lines of rye, Secale cereale L., although it was not present in the other rye varieties studied. We propose that the new 5S rRNA locus be referred to as 5SDna-R3.     

Discrimination of Repetitive Sequences Polymorphism in Secale cereale by Genomic In Situ Hybridization-Banding

Genomic in situ hybridization banding (GISH-banding), a technique slightly modified from conventional GISH, was used to probe the Chinese native rye (Secale cereale L.) DNA, and enabled us to visualize the Individual rye chromosomes and create a universal reference karyotype of the S. cereale chromosome 1R to 7R. The GISH-banding approach used in the present study was able to discriminate S. cereale chromosomes or segments in the wheat (Triticum aeativum L.) background, including the Triticale, wheat-rye addition and translocation lines. Moreover, the GISH-banding pattern of S.cereale subsp. Afghanicum chromosomes was consistent with that of Chinese native rye cv. Jingzhou rye; whereas the GISH-banding pattem of Secale vavilovli was different from that of S. cereale, indicating that GISH-banding can be used to study evolutionary polymorphism in species or subspecies of Secale. In addition, the production and application of GISH-banding to the study of adenine-thymine-riched heterochromatin is discussed.     

Origin and genetic structure of feral rye in the western United States

Feral rye (Secale cereale) is a serious, introduced weed of dry land agricultural regions of the western United States. It closely resembles cultivated cereal rye (Secale cereale cereale L.) with the exception of having a shattering seed head. Feral rye may have originated from hybridization of cultivated rye with mountain rye, Secale strictum, as past studies of northern Californian populations suggest, or directly from volunteer cultivated rye. We characterized the genetic structure of feral rye populations across a broad geographical range and reexamined evidence for hybrid origin versus direct evolution from domesticated cultivars. Eighteen feral populations were examined from three climatically distinct regions in the western United States. Seven cultivars, four mountain rye accessions, and one wild annual relative (Secale cereale ancestrale) were included in our analysis as possible progenitors of feral rye. Individual plants were scored for 14 allozyme and three microsatellite loci. Estimates of genetic diversity in feral populations were relatively high compared to those of the possible progenitors, suggesting that the weed had not undergone a genetic bottleneck. Weed populations had no geographical structure at either a broad or a local scale, suggesting idiosyncratic colonization and gene-flow histories at each site. Feral rye populations were no more closely related to mountain rye than cultivars were. They were, however, weakly clustered as a distinct lineage relative to cultivars. Our results do not support an interspecific hybrid origin for feral rye, but do suggest that the sampled populations of feral rye share a common ancestry that may explain its weedy nature.     

Investigation of the site of synthesis of chIcoroplastic enzymes of nitrogen metabolism by the use of heat-treated 70S ribosomedeficient rye leaves

The activities of the enzymes nitrate reductase (EC 1.6.6.1), nitrite reductase (EC 1.6.6.4), glutamine synthetase (EC 6.3.1.2), glutamate synthase (GOGAT; EC 1.4.7.1), glutamate-oxaloacetate aminotransferase (EC 2.6.1.1), and glutamate dehydrogenase (EC 1.4.1.2) were compared in light-grown green or etiolated leaves of rye seedlings ( Secale cereale L. cv. Halo) raised at 22°C, and in the bleached 70S ribosome-deficient leaves of rye seedlings grown at a non-permissive high temperature of 32°C. Under normal permissive growth conditions the activities of most of the enzymes were higher in light-grown, than in dark-grown, leaves. All enzyme activities assayed were also observed in the heat-treated 70S ribosome-deficient leaves. Glutamine synthetase, glutamate synthase, and glutamate-oxaloacetate aminotransferase occurred in purified ribosome-deficient plastids separated on sucrose gradients. For glutamate-oxaloacetate aminotransferase four multiple forms were separated by polyacrylamide gel electrophoresis from leaf extracts. The chloroplastic form of this enzyme was also present in 70S ribosome-deficient leaves. It is concluded that the chloroplast-localized enzymes nitrite reductase, glutamine synthetase, glutamate synthase and glutamate-oxaloacetate aminotransferase, or their chloroplast-specific isoenzyme forms, are synthesized on cytoplasmic 80S ribosomes.     

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.     

A taxonomic revision of Secale (Triticeae, Poaceae)

Several taxa have previously been recognized within Secale , but most of them are difficult or even impossible to distinguish morphologically. We recognize only three species: S. sylvestre, S. strictum , and S. cereale. Secale strictum has priority over S. montanum and has two subspecies, ssp. strictum and ssp. africanum , and two varieties within ssp. strictum , van strictum and var. ciliatoglume comb. nov. Secale cereale is also treated as having two subspecies. The cultivated taxa, marked by their tough rachises, are placed in ssp. cereale and the wild or weedy taxa that have more or less fragile rachis, in ssp. ancestrale. A complete synonymy is given for S. cereale , but typification has been omitted because, in many instances, type material does not exist or has been impossible to trace.     

On the origin of cultivated rye

The origin of cultivated rye has been studied, taking into consideration evidence from various fields. Based on morphological resemblances and cytogenetic affinities, cultivated rye is included in Secale cereale L. emend. Sencer, which also includes annual wild and weedy ryes. Wild populations of 5. cereale , which have evolved from Secale montanum Guss. emend. Sencer, invaded wheat and barley fields during the early days of cultivation and gave rise to weedy ryes with varying degrees of rachis brittleness. Cultivated rye was selected from weedy ryes for non-brittle rachis and bigger caryopsis both unconsciously and consciously by man. The geographic origin of cultivated rye is postulated for the Büyük Ari Dai (Mt. Ararat) and Lake Van area in eastern Turkey. It spread from this area as a weed in wheat and barley fields towards the north, east and west and imposed itself as a secondary crop under conditions unfavourable for wheat and barley. It thus became a crop in its own right in several places independently, in addition to it being known by the people living in the Caucasus and Transcaucasus from very early agricultural times.     

Self-incompatibility in ryegrass 12. Genotyping and mapping the S and Z loci of Lolium perenne L

Perennial ryegrass (Lolium perenne L.) is an outcrossing, wind-pollinated species exhibiting a gametophytic two-locus system of self-incompatibility (S and Z). The two incompatibility loci were genotyped in a cross between a doubled-haploid plant crossed as the female parent with a normal heterozygous plant. The S and Z loci were found to segregate in the expected 1:1 ratio and also segregated independently. The two loci were mapped to linkage groups one and two respectively, in accordance with the Triticeae consensus map. In addition, there were notable associations between the segregation of particular alleles mapping to the S locus region of linkage group 1 and those mapping to the WG889/CDO920 loci region of linkage group 3 which resulted in significant segregation distortions. No such associations were found between the Z locus and this region or any other region of the genome. The L. perenne S and Z loci showed conserved synteny with the equivalent loci in rye (Secale cereale L.).     

Ultrastructural Changes in Chloroplasts of Cucumis sativus L. and Secale cereale L. during Low-Temperature Hardening

Russian Journal of Plant Physiology - Chloroplast ultrastructural changes were investigated in chilling-sensitive (cucumber, Cucumis sativus L.) and cold-tolerant (winter rye, Secale cereale L.)...     

Respiration and Involvement of an Alternative Pathway as Related to Age and Phenological Strategy of the Leaf

Russian Journal of Plant Physiology - Plants of spring wheat (Triticum aestivum L.) and winter rye (Secale cereale L.) pursuing different phenological strategies were studied. Respiratory activity,...     

Resistance genes for rye stem rust (SrR) and barley powdery mildew (Mla) are located in syntenic regions on short arm of chromosome.

Genetic stocks were developed for the localization and eventual cloning of the stem rust resistance gene SrR that occurs in wheat lines carrying the 1RS translocation from Secale cereale 'Imperial' rye. We have used a mutation-based approach for molecular analysis of the SrR region in rye. Forty-one independent mutants resulting in loss of SrR resistance were isolated: many of these were deletions of various sizes that were used to locate SrR with respect to chromosome group 1S markers. The analysis of the mutants showed that markers about 1 Mb apart flanking the barley Mla locus also flank SrR. Additionally, three of the approximately 20 closely related sequences of Mla in rye are deleted in each of six interstitial deletion mutants of SrR. The results indicate that the SrR region in rye is syntenic to the Mla region in barley or that SrR is possibly orthologous to the Mla locus.     

Linkage mapping of powdery mildew and greenbug resistance genes on recombinant 1RS from 'Amigo' and 'Kavkaz' wheat-rye translocations of chromosome 1RS.1AL.

Cultivated rye (Secale cereale L., 2n = 2x = 14, RR) is an important source of genes for insect and disease resistance in wheat (Triticum aestivum L., 2n = 6x = 42). Rye chromosome arm 1RS of S. cereale 'Kavkaz' originally found as a 1BL.1RS translocation, carries genes for disease resistance (e.g., Lr26, Sr31, Yr9, and Pm8), while 1RS of the S. cereale 'Amigo' translocation (1RSA) carries a single resistance gene for greenbug (Schizaphis graminum Rondani) biotypes B and C and also carries additional disease-resistance genes. The purpose of this research was to identify individual plants that were recombinant in the homologous region of.1AL.1RSV and 1AL.1RSA using both molecular and phenotypic markers. Secale cereale 'Nekota' (1AL.1RSA) and S. cereale 'Pavon 76' (1AL.1RSV) were mated and the F1 was backcrossed to 'Nekota' (1AL.1AS) to generate eighty BC1F2:3 families (i.e., ('Nekota' 1AL.1RSA x 'Pavon 76' 1AL.1RSV) x 'Nekota' 1AL.1AS). These families were genotyped using the secalin-gliadin grain storage protein banding pattern generated with polyacrylamide gel electrophoresis to discriminate 1AL.1AS/1AL.1RS heterozygotes from the 1AL.1RSA+V and 1AL.1AS homozygotes. Segregation of the secalin locus and PCR markers based on the R173 family of rye specific repeated DNA sequences demonstrated the presence of recombinant 1AL.1RSA+V families. Powdery mildew (Blumeria graminis) and greenbug resistance genes on the recombinant 1RSA+V arm were mapped in relation to the Sec-1 locus, 2 additional protein bands, 3 SSRs, and 13 RFLP markers. The resultant linkage map of 1RS spanned 82.4 cM with marker order and spacing showing reasonable agreement with previous maps of 1RS. Fifteen markers lie within a region of 29.7 cM next to the centromere, yet corresponded to just 36% of the overall map length. The map position of the RFLP marker probe mwg68 was 10.9 cM distal to the Sec-1 locus and 7.8 cM proximal to the powdery mildew resistance locus. The greenbug resistance gene was located 2.7 cM proximal to the Sec-1 locus.     

Genetic determination of stem-rust resistance in rye

The harmful effect of stem rust on the crops of short-stem diploid winter rye was studied. If stem rust affected the plants by 70-100%, this decreased the mass of 1000 grains by about 35.8%. The genes that control the stemrust resistance of rye might originate from the following cultivars and forms: Ilmen, Orlovskii Gibrid, Kharkovskaya 55, Kharkovskaya 60, Kustovka, Kombaininyai, Kazanskaya, Krupnozernaya, Novozybkovskaya 4, Alfa, Derzhavinskaya 29, Chulpan, and Rossul, as well as wild populations of the perennial rye Secale montanum. This study was first to demonstrate that the resistance of the Kharkovskaya 55 and Rossul rye cultivars to the population of stem rust was controlled by a single dominant gene, which was designated Sr1.     

Genetics of rye phosphatases: evidence of a duplication

Summary Genetic analyses were conducted on alkaline phosphatases of the endosperm of dry kernels and leaf acid phosphatases in four open pollinated and one inbred line of cultivated rye (Secale cereale L.). A total of seven alkaline phosphatase isozymes were observed occurring at variable frequencies in the different cultivars analyzed. We propose that at least five loci control the alkaline phosphatases of rye endosperm — Alph-1, Alph-2, Alph-3, Alph-4 and Alph-5 — all of which have monomeric behaviour. The leaf acid phosphatases are controlled by one locus and have a dimeric quaternary structure. All loci coding for alkaline phosphatase isozymes showed one active, dominant allele and one null, recessive allele, except for the locus Alph-3 which showed two active, dominant alleles and one null, recessive one. The linkage analyses suggest the existence of two linkage groups for alkaline phosphatases: one of them would contain Alph-2, Alph-4, Alph-5 and the locus/loci coding isozymes 6 and 7. This linkage group is located in the 7RS chromosome arm. The other group would include Alph-1 and Alph-3 loci, being located in the 1RL chromosome arm. Leaf acid phosphatases have been previously located in the 7RL chromosome arm. Our data also support an independent relationship between loci controlling the endosperm alkaline phosphatases and leaf acid phosphatases.     

A second locus for the 5S multigene family in Secale L.: sequence divergence in two lineages of the family

The 5S RNA genes in Secale sp. are arranged as tandem arrays of a 460- and 480-bp repeating sequence. These size classes were initially discovered by restriction endonuclease analysis using BamHI and subsequently by DNA sequencing of cloned units. The length variation between short and long units originated from major deletion-insertion events in the noncoding spacer region of the 5S DNA repeat units. In situ hybridization with [3H]cRNA and biotin-labelled probes synthesized from both the short and long 5S DNA units of S. cereale localized the sites on chromosome 1R and a new site on a chromosome identified as 5R. We propose that the chromosome 1R locus, which has been mapped previously, be named 5SDna-R1 and the second locus, reported in the present paper, be referred to as 5SDna-R2. A preferential hybridization of a probe from the long unit to the 5SDna-R2 locus and of a probe from the short unit to the 5SDna-R1 locus is reported. The clustering of long units in the 5SDna-R2 locus was confirmed by restriction endonuclease digestion of DNA from rye chromosome 5R additions to wheat. Nucleotide sequence alignment of 5S DNA repeat units from a number of Secale species, using both phenetic and cladistic computer programmes, demonstrated that two clear lineages corresponding to the long and short units existed in this genus. The different Secale species could not be unambiguously differentiated using the 5S DNA sequences.     

Aspartate aminotransferase allozyme variation in a germplasm collection of the domesticated lentil (Lens culinaris)

Summary Variation at a polymorphic Aspartate aminotransferase locus was assayed in a sample of 298 accessions from the ICARDA germplasm collection of the domesticated lentil (Lens culinaris). Two alleles Aat-1 ^F and Aat-1 ^S were detected with global frequencies of 0.51 and 0.49, respectively. Fifty-nine percent of accessions were polymorphic for both alleles. The frequency of outcrossing was estimated from the observed heterozygosity to be about 1%. This is higher than direct estimates of outcrossing and implicates selection in favour of heterozygous gene combinations. Significant variation in allele frequency and in the occurrence of polymorphic accessions was observed between countries or geographic areas. Significant associations were observed between the allozymes and agronomic characters. In particular high frequency of Aat-1 ^F appeared to be associated with late flowering and maturity and low yield.     

黑麦基因组特异DNA片段的分离与SCAR标记的建立

以2个栽培黑麦、2个野生黑麦和4个普通小麦为材料,从200条10碱基RAPD随机引物中筛选出1条引物H11。H11在小麦中有1条低拷贝扩增,而在黑麦中却有极高拷贝的扩增。对H11在黑麦中的高拷贝片段进行克隆、测序,得其全长679 bp,记作OPH11679。根据OPH11679设计特异PCR引物H11-F和H11-R,对小麦族其它物种和含黑麦染色质的物种进行验证,结果发现仅含黑麦染色质的物种能扩增出长为643 bp的片段(命名为pScH643),这表明该片段为黑麦所特有。用H11-F和H11-R对1套中国春-Imperial黑麦附加系等进行扩增,结果显示pScH643片段分布在黑麦整套染色体上,这一结果在小麦-黑麦异源材料的分析中得到进一步验证。即表明pScH643片段可作为SCAR标记用于含黑麦染色质材料的检测。     

Molecular studies on genetic integrity of open-pollinating species rye (<Emphasis Type="Italic">Secale cereale</Emphasis> L.) after long-term genebank maintenance

The genetic integrity of six accessions represented by 14 sub-populations of the open-pollinating species rye (Secale cereale L.) was investigated. Seeds available from a herbarium collection (first regeneration) and from the cold store (most recent regeneration) were multiplied two to fourteen times and fingerprinted using microsatellite markers. Four accessions had significantly different allele frequencies. These were multiplied seven to thirteen times. Nearly 50% of the alleles discovered in the original samples were not found in the material present in the cold store. However alleles were detected in the most recently propagated sub-populations, that were not observed in the investigated plants of the original one. The change in allele frequencies is a continuous process. Reasons for the occurrence of genetic changes and consequences for managing open pollinating species maintained in ex situ genebanks are discussed.Communicated by G. Wenzel