Secale Research Articles

Morphological and agronomic characteristics of winter rye cultivars in connection with their resistance to lodging

Background. Lodging resistance of winter rye is associated with morphological features of the stem. Searching for source material to breed non-lodging high-yielding cultivars requires studying the varietal phenotypic diversity according to morphological characters of the stem that affect the resistance to lodging and the productivity of the ear.Materials and methods. Experiments were carried out in 2017–2020 at the Federal Agricultural Research Center of the North-East (FARC North-East), Kirov. Field resistance to lodging, morphological characteristics of the stem, yield, and ear productivity were evaluated in 16 winter rye cultivars. The study was based on the International COMECON List of Descriptors for the Genus Secale L., and Methodology for the State Variety Trials of Agricultural Crops. The weight of segments of the second lower internodes was measured in 10 plants of each cultivar under laboratory conditions.Results and conclusions. Negative correlations of lodging resistance with stem length (r= –0.55) and the weight of the second lower internode (r = –0.65) were revealed. Ear productivity of rye cultivars was significantly associated with the wall thickness (r = 0.52) and the length of the second lower internode (r = –0.52). According to the results of the path analysis, the main causes of a decrease in lodging resistance were the weight of the segment (P = –0.467) and the length of the second lower internode (P = –0.408), while an increase was connected with the wall thickness of the second lower internode (P = 0.424). The cultivars differed significantly in their resistance to lodging (LSD05 = 0.8). Cvs. ‘Moskovskaya 12’, ‘Tatyana’, ‘Bylina’ and ‘Yantarnaya’ were identified; they are recommended as source material for breeding for lodging resistance.

100 Years of Chromosome Research in Rye, Secale L.

Although microscopy and genetics were still in their infancy, there are cytological results produced a hundred years ago that are still relevant today. Since the 1920s, rye has been a subject of chromosome research. It started by plotting its mitotic and meiotic chromosomes to determine genome size. After controversial evidence, it became clear that the base number is n = 7. However, structural differences exist between species within the genus Secale. Some rye populations even carry accessory chromosomes evolutionary derived from the A genome. The development of tetraploid strains significantly promoted chromosome analysis. Various techniques have tried to stabilize the disturbed chromosome pairing of the induced tetraploids. Although slight improvements could be achieved, they did not lead to a breakthrough. However, the various aneuploid derivatives of the polyploids found major advances in the genetic analysis of rye. Trisomics, telo-trisomics, and reciprocal translocation have served as important tools for gene mapping. Since the 1970s, various chromosome banding techniques have stimulated scientific progress. The seven haploid chromosomes could be diagnosed unequivocally, not only in S. cereale but also in related species. These findings led to a clear homoeologous assignment to the genomes of related grass species such as wheat, barley, rice, etc. Current applications of in situ fluorescence staining methods, such as GISH and FISH, allow even more precise results, depending on the specificity of the DNA samples. Advanced preparation techniques are supplemented by the variety of innovations in the field of molecular genome analysis. They replace complex cytological examinations. In this way, introgressions can be safely detected by DNA markers and be much more detailed. In addition, CRISPR/CAS-mediated chromosome engineering will become an important method of the future.

Variations of subtelomeric tandem repeats and rDNA on chromosome 1RS arms in the genus Secale and 1BL.1RS translocations

BackgroundThe wheat-rye 1BL.1RS translocations have played an important role in common wheat breeding programs. Subtelomeric tandem repeats have been often used to investigate polymorphisms of 1RS arms, but further research about their organizations on the 1RS chromosome is needed.Results162 1RS arms from a wild rye species (Secale strictum) and six cultivated rye accessions (Secale cereale L.) (81 plants), 102 1BL.1RS and one 1AL.1RS translocations were investigated using oligo probes Oligo-TaiI, Oligo-pSc119.2–1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250, which were derived from tandem repeats TaiI, pSc119.2, pTa71, pSc200 and pSc250, respectively. The variations of 1RS arms were revealed by signal intensity of probes Oligo-pSc119.2–1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250. Proliferation of rDNA sequences on the 1RS chromosomes was observed. According to the presence of probe signals, 34, 127 and 144 of the 162 1RS arms contained TaiI, pSc200 and pSc250, respectively, and all of them contained pSc119.2 and pTa71. Most of the 1RS arms in rye contained three kinds of subtelomeric tandem repeats, the combination of pSc119.2, pSc200 and pSc250 was most common, and only eight of them contained TaiI, pSc119.2, pSc200 and pSc250. All of the 1RS arms in 1BL.1RS and 1AL.1RS translocations contained pSc119.2, pTa71, pSc200 and pSc250, but the presence of the TaiI family was not observed.ConclusionNew organizations of subtelomeric tandem repeats on 1RS were found, and they reflected new genetic variations of 1RS arms. These 1RS arms might contain abundant allelic diversity for agricultural traits. The narrow genetic base of 1RS arms in 1BL.1RS and 1AL.1RS translocations currently used in agriculture is seriously restricting their use in wheat breeding programs. This research has found new 1RS sources for the future restructuring of 1BL.1RS translocations. The allelic variations of these 1RS arms should be studied more intensely as they may enrich the genetic diversity of 1BL.1RS translocations.

Population genomic analysis reveals domestication of cultivated rye from weedy rye

Rye (Secale cereale) is an important crop with multiple uses and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. The geneticist N.I. Vavilov proposed that cultivated rye had been domesticated from weedy rye, rather than directly from wild species like other crops. Unraveling the domestication history of rye will extend our understanding of crop evolution and upend our inherent understanding of agricultural weeds. To this end, in this study we generated the 8.5 Tb of whole-genome resequencing data from 116 worldwide accessions of wild, weedy, and cultivated rye, and demonstrated that cultivated rye was domesticated directly from weedy relatives with a similar but enhanced genomic selection by humans. We found that a repertoire of genes that experienced artificial selection is associated with important agronomic traits, including shattering, grain yield, and disease resistance. Furthermore, we identified a composite introgression in cultivated rye from the wild perennial Secale strictum and detected a 2-Mb introgressed fragment containing a candidate ammonium transporter gene with potential effect on the grain yield and plant growth of rye. Taken together, our findings unravel the domestication history of cultivated rye, suggest that interspecific introgression serves as one of the likely causes of obscure species taxonomy of the genus Secale, and provide an important resource for future rye and wheat breeding.

Retracted: Modulation of Signal Proteins: A Plausible Mechanism to Explain How a Potentized Drug Secale Cor 30C Diluted beyond Avogadro’s Limit Combats Skin Papilloma in Mice

[This retracts the article DOI: 10.1093/ecam/nep084.].

Characterization of a new gene for resistance to wheat powdery mildew on chromosome 1RL of wild rye Secale sylvestre.

PmSESY, a new wheat powdery mildew resistance gene was characterized and genetically mapped to the terminal region of chromosome 1RL of wild rye Secale sylvestre. The genus Secale is an important resource for wheat improvement. The Secale species are usually considered as non-adapted hosts of Blumeria graminis f. sp. tritici (Bgt) that causes wheat powdery mildew. However, as a wild species of cultivated rye, S. sylvestre is rarely studied. Here, we reported that 25 S. sylvestre accessions were susceptible to isolate BgtYZ01, whereas the other five confer effective resistance to all the tested isolates of Bgt. A population was then constructed by crossing the resistant accession SESY-01 with the susceptible accession SESY-11. Genetic analysis showed that the resistance in SESY-01 was controlled by a single dominant gene, temporarily designated as PmSESY. Subsequently, combining bulked segregant RNA-Seq (BSR-Seq) analysis with molecular analysis, PmSESY was mapped into a 1.88 cM genetic interval in the terminus of the long arm of 1R, which was closely flanked by markers Xss06 and Xss09 with genetic distances of 0.87cM and 1.01cM, respectively. Comparative mapping demonstrated that the corresponding physical region of the PmSESY locus was about 3.81 Mb in rye cv. Lo7 genome, where 30 disease resistance-related genes were annotated, including five NLR-type disease resistance genes, three kinase family protein genes, three leucine-rich repeat receptor-like protein kinase genes and so on. This study gives a new insight into S. sylvestre that shows divergence in response to Bgt and reports a new powdery mildew resistance gene that has potential to be used for resistance improvement in wheat.

An efficient Oligo-FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae.

A chromosome-specific painting technique has been developed which combines the most recent approaches of the companion disciplines of molecular cytogenetics and genome research. We developed seven oligonucleotide (oligo) pools derivd from single-copy sequences on chromosomes 1 to 7 of barley (Hordeum vulgare L.) and corresponding collinear regions of wheat (Triticum aestivum L.). The seven groups of pooled oligos comprised between 10986 and 12496 45-bp monomers, and these then produced stable fluorescence in situ hybridization (FISH) signals on chromosomes of each linkage group of wheat and barley. The pooled oligo probes were applied to high-throughput karyotyping of the chromosomes of other Triticeae species in the genera Secale, Aegilops, Thinopyrum, and Dasypyrum, and the study also extended to some wheat-alien amphiploids and derived lines. We demonstrated that a complete set of whole-chromosome oligo painting probes facilitated the study of inter-species chromosome homologous relationships and visualized non-homologous chromosomal rearrangements in Triticeae species and some wheat-alien species derivatives. When combined with other non-denaturing FISH procedures using tandem-repeat oligos, the newly developed oligo painting techniques provide an efficient tool for the study of chromosome structure, organization, and evolution among any wild Triticeae species with non-sequenced genomes.

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species.

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

Молекулярные основы пищевых и кормовых качеств зерна ржи (Secale sereale)

Молекулярные основы пищевых и кормовых качеств зерна ржи (Secale sereale)

Taxonomic Relationships and Genetic Variability of Wild Secale L. Species as a Source for Valued Traits in Rye, Wheat and Triticale Breeding

Rye (Secale L.) is a member of family Poaceae (tribe Triticeae) and includes perennial or annual, self-incompatible or self-compatible, and cultivated, weedy or wild species. Classification of the genus Secale is inconsistent, and comprises 3–4 to 8 species from the phylogenetic studies in the last ten years. Progress in rye breeding has been significantly reduced due to involving a small number of cultivars and landraces in crosses. The wild rye species and subspecies possess many valuable breeding traits for research aimed at expanding the variability in Secale cereale subsp. cereale. They are, due to their genetic diversity and high breeding trait expression, useful sources of genes for tetraploid and hexaploid wheat, and triticale improvement, too. One of the species, S. vavilovii, is attractive for rye breeding due to its high self-fertility, resistance to fusarium ear blight, septoria leaf blotch, high protein content, sprouting and sterilising cytoplasm, and genetic similarity with S. cereale subsp. dighoricum. Chromosomes of S. strictum are sources for resistance to yellow rust, Russian wheat aphid, grain hardness, increased protein and arabinoxylan content.

Patterns of nucleotide diversity for different domains of centromeric histone H3 (CENH3) gene in Secale L.

Rye (Secale) is among staple cereals along with other members of the Triticeae tribe: wheat and barley. The genus Secale includes perennial and annual, cross-pollinating and self-pollinating species, and they can be donors of valuable genes in wheat and rye breeding programs. Studies of the structure of the gene for centromeric histone H3 (CENH3), essential for centromere functions, are relevant to the breeding of agronomically important crops. We have investigated the nucleotide diversity of sequences of two variants of the rye CENH3 gene inside the N-terminal tail (NTT) and the conservative HFD (histone fold domain) domain in the genus Secale. The mean values of nucleotide diversity in the NTT and HFD of wild cross- and self-pollinating taxa are close in αCENH3: πtot = 0.0176–0.0090 and 0.0136–0. 0052, respectively. In the case of βCENH3, the mean values for NTT (πtot = 0.0168–0.0062) are lower than for HFD (πtot = 0.0259–0.084). The estimates of nucleotide and haplotype diversity per site for the CENH3 domains are considerably lower in taxa with narrow geographic ranges: S. cereale subsp. dighoricum and S. strictum subsp. kuprijanovii. Commercial breeding reduces the nucleotide sequence variability in αCENH3 and βCENH3. Cultivated rye varieties have π values within 0.0122–0.0014. The nucleotide and haplotype diversity values in αCENH3 and βCENH3 are close in S. sylvestre, which is believed to be the oldest rye species. The results of this study prove that the frequency of single nucleotide polymorphisms and nucleotide diversity of sequences in genes for CENH3 in Secale species are influenced by numerous factors, including reproduction habits, the geographic isolation of taxa, breeding, and the evolutionary age of species.

Verification of taxonomic relationships within the genus Secale (Poaceae: Pooideae: Triticeae) based on multiple molecular methods

This study aimed to verify the taxonomic relationships within the genus Secale. The plant material included 16 wild rye accessions from four species. Two approaches were applied: 1) whole genome scanning using three molecular marker systems: diversity arrays technology sequencing, simple sequence repeats and sequence-specific amplification polymorphism; and 2) characterisation based on polymorphisms within the sequences of two genes involved in benzoxazinoid biosynthesis: ScBx1 and ScBx5. Bayesian and neighbour-joining clustering and principal coordinate analysis were applied to illustrate relationships among species and accessions of Secale based on genetic distance (GD) matrices. Pearson’s correlation analysis between GD matrices was conducted. Clustering of Secale accessions revealed that S. sylvestre samples were the most divergent. The remaining accessions formed two clusters. One of them comprised S. strictum accessions while the second cluster consisted of subspecies of S. cereale, the species S. vavilovii and S. strictum subsp. ciliatoglume.

DNA Barcoding in Selected Species and Subspecies of Rye (Secale) Using Three Chloroplast Loci (matK, rbcL, trnH-psbA)

DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Secale. In this study the plant material consisted of 10 cultivated and non-cultivated species and subspecies of rye genus. Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions. Universal primers were used, and sequenced products were analyzed using Neighbor Joining and the Maximum Likelihood in the MEGA 7.1 program. We did not observe high variability in nucleotide sequences within the matK and rbcL regions. Only 2.2% of the sequences showed polymorphism in the rbcL region, while 6.5% in the matK region. The most variable trnH-psbA (15.6%) intergenic region was the most useful for rye barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of rye species and subspecies according to the adopted classification of the genus Secale. The results confirm that the use of matK and rbcL is insufficient for DNA barcoding in rye species, and better discrimination within the genus Secale can be obtained only in combination with the non-coding trnH-psbA sequence. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in Genbank.

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing.

Rye (Secale cereale L.) is a cereal grass that is an important food crop in Central and Eastern Europe. In contrast to its close relatives wheat and barley, it was not a founder crop of Neolithic agriculture, but is considered a secondary domesticate that may have become a crop plant only after a transitory phase as a weed. As a minor crop of only local importance, genomic resources in rye are underdeveloped, and few population genetic studies using genomewide markers have been published to date. We collected genotyping‐by‐sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale. Variant detection in the context of a recently published draft sequence assembly of cultivated rye yielded 55,744 single nucleotide polymorphisms with present genotype calls in 90% of samples. Analysis of population structure recapitulated the taxonomy of the genus Secale. We found only weak genetic differentiation between wild and domesticated rye with likely gene flow between the two groups. Moreover, incomplete lineage sorting was frequent between Secale species because of either ongoing gene flow or recent speciation. Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in‐depth analysis of the interplay between sequence divergence and reproductive isolation in the genus Secale.

Identification of Barley Yellow Dwarf Viruses in Poland

Barley yellow dwarf (BYD) is the most important and widespread viral disease of cereal crops, and is caused by a group of related spherical viruses belonging to the family Luteoviridae. In the spring of 2015, BYD symptoms were observed on several winter barley (Hordeum vulgare L.), triticale (Triticosecale Wittm. ex A. Camus), rye (Secale cereale L.), and wheat (Triticum aestivum L.) plants throughout Poland. Infections were confirmed with an enzyme-linked immunosorbent assay involving polyclonal antibodies raised against Barley yellow dwarf virus (BYDV)-MAV and BYDV-PAV. Reverse transcription polymerase chain reaction diagnostic assays were conducted on a subset of 35 samples collected from 11 provinces of Poland. The primer sets targeted the open reading frame-3 fragments of BYDV-GAV, -MAV, -PAV, -PAS, -RMV, and -SGV as well as Cereal yellow dwarf virusRPV species. The specificity of obtained products were verified by sequencing. Molecular analyses revealed the predominance of co-infections with BYDV-MAV and BYDV-PAV, and the presence of other viral species that induced BYD symptoms. A comparative analysis of coat protein gene sequences indicated that some Polish isolates were highly similar (i.e., 99% identity) to Chinese BYDV-GAV, Czech BYDV-PAS, and Jordanian and Turkish BYDV-SGV isolates, thus confirming that these isolates are BYDV-GAV, -PAS, or -SGV species. To the best of my knowledge, this is the first report describing BYDV-GAV, BYDVPAS, and BYDV-SGV infections in Poland.

Evolutionary relationships in the genus Secale revealed by DArTseq DNA polymorphism

Till this day, there is not much known about the phylogeny of the Secale genus; therefore, in our research, we tried to shed some lights on the issue of rye (Secale genus) taxonomy. The genetic diversity and phylogenetic relationships were evaluated using 13,842 DArTseq™ polymorphic markers. The model-based clustering (STRUCTURE software) separated our 84 samples into three main clusters: perennial cluster, annual cluster, and S. sylvestre cluster. The same result was obtained using Neighbour Joining tree and self-organizing maps. Secale sylvestre, S. strictum, and S. cereale are the three main species of the Secale genus. Three samples of rye are in basal positions in phylogenetic trees. These accessions share ancient morphological characters and are probably the ancestors of different lineages within Secale. Annual Secale taxa, with the exception of S. sylvestre, create one mutual taxon. We have found out that the semi-perennial taxa of S. cereale var. multicaule and S. strictum subsp. ciliatoglume are genetically closest to the annual species of S. cereale. Phylogenetic signals for semi-perennial and annual taxa are also present in S. strictum subsp. africanum. SNP-based analysis revealed that evolution of annual S. cereale has already begun in S. strictum subsp. africanum. The results showed that S. vavilovii cannot be considered as a separate species but a subspecies of S. cereale Secale cereale subsp. dighoricum is a hybrid. It is still not clear whether we can consider S. strictum subsp. strictum and S. strictum subsp. kuprijanovii as two separate species.

Hybrid breeding boosted molecular genetics in rye

History of rye (Secale cereale L.) breeding began from the first targeted selections made in Germany by the Probsteier Seed Cooperative around 1850, and over 150 years breeding yielded a tremendous amount of results. Rye has also long been used as cytological subject due to its low number of chromosomes and their size. However, genetic findings in rye up to the early 1980s were rather scant. About 120 genes could be assigned to seven linkage groups. Only through the development of new methods such as C-banding, in situ DNA hybridization, enzymology and molecular marker techniques achieved an enormous progress. Particularly, the latter was driven by agronomic success of hybrid breeding in rye. The basic genetic knowledge resulted from intra- and interspecies genetic diversity assay and phylogenetic studies in the genus Secale using nuclear and cytoplasmic molecular markers facilitated successful selection of parents for hybrid breeding and hence contributed to improvement of heterosis effects. Main achievements in rye hybrid breeding and genetic mechanisms exploited for different hybrid breeding strategies are discussed. The utilsation of landraces and wild relatives via advanced backcross procedures, combined by QTL analysis and introgression libraries, contributed to increase of heterotic effects. Those marker-assisted approaches became the basis of recent hybrid breeding of rye. Prediction of hybrid performance can also be improved significantly by marker-assisted selection and genomic selection based on genomewide marker data. The findings in rye genetics (including phylogenetic, mapping and population studies) are reviewed in their relation with the hybrid breeding purposes and demands. Overall, about 450 morphological and biochemical traits are mapped throughout the genome plus about 5,000 DNA markers. They are not only associated with individual chromosome or segments but also efficiently used for comparative mapping (evolutionary studies) introgression monitoring, QTL tagging, and marker-assisted selection.

Crop Yield Responses to Temperature Fluctuations in 19th Century Finland: Provincial Variation in Relation to Climate and Tree Rings

Past agricultural responses to climate variability can helps us to better understand the current and future impacts of climate change on agricultural production. We studied rye (Secale cereale) and barley (Hordeum vulgare) yield responses to temperature fluctuations in Finland during the period 1861–1913. Our analyses demonstrate the high sensitivity of non-industrialised northern agriculture to temperature anomalies. We found evidence of a strong relationship between monthly and seasonal mean temperatures and crop yields. In particular, high spring temperatures were associated with higher yields. Additionally, we tested temperature-sensitive tree-ring series for their value in indicating previous agricultural outputs. The results imply that tree-ring proxies (in particular, maximum latewood density) can provide novel material for studies of historical periods and locations where instrumentally measured climate and harvest data are not available.

Intergenic Spacer Length Variability in Cultivated, Weedy and Wild Rye Species

Abstract Non-coding rDNA spacers (IGS) can vary substantially in size due to differences in the number of repetitive elements among closely related species. Three pairs of universal primers were used in this study for the amplification of non-coding regions of ribosomal (rRNA) IGS. The amplified IGS products obtained from 19 Secale accessions, which included both cultivated and noncultivated rye and which represented three species and four subspecies of the genus Secale, showed a high level of polymorphism. The PCR results were characterized by multiple bands (1-6), different sizes (750bp-3250bp) and 100% polymorphism. Cluster analysis using the neighborjoining method based on the Dice’s coefficient of genetic similarity showed a division of the studied species into two similarity groups. All the studied Secale cereale ssp. cereale were found to belong to the same similarity group. The variation in the size of the IGS among the species which was detected in this study could be due to dissimilarity between the sequences of their respective repetitive elements or between their tandem repeat numbers. The highly interspecific polymorphisms for the rDNA IGS regions suggested that IGS might be a useful molecular marker in studies of Secale species.

Evolution and genetic diversity of the wheat species of T. turanicum Jakubz. and their selection value

It has been comparatively studied the forms of Turan type of wheat with different ecological origins and turanoid forms formed as a result of hybridization and gathered into gene pool from Azerbaijan area, Devedishi, the ancient people selection species of Azerbaijan, which is related to the type of T.turanicum Jakubz., Turanicum-186 gained by I.D.Mustafayev based on electrophoreogram of gliadine fraction of protein. The Devedishi in Azerbaijan and the selection of popular species Turatish in other Turkic states has been proved to be of the same origin. The Turan wheat is a donor for the formation of big grained, high-quality wheat. This species has been proven to be one of the parental forms in the evolution of the Secale L.