Rye Chromosome 1R Research Articles

Development and Characterization of Two Wheat-Rye Introgression Lines with Resistance to Stripe Rust and Powdery Mildew.

Rye (Secale cereale L.) genes, which contribute to the tertiary gene pool of wheat, include multiple disease resistance genes useful for the genetic improvement of wheat. Introgression lines are the most valuable materials for wheat breeding because of their small alien segments and limited or lack of linkage drag. In the present study, wheat-rye derivative lines SN21627-2 and SN21627-6 were produced via distant hybridization. A genomic in situ hybridization analysis revealed that SN21627-2 and SN21627-6 lack alien segments, while a multi-color fluorescence in situ hybridization analysis detected structural changes in both introgression lines. At the seedling and adult plant stages, SN21627-2 and SN21627-6 were highly resistant to stripe rust and powdery mildew. Primers for 86 PCR-based landmark unique gene markers and 345 rye-specific SLAF markers were used to amplify SN21627-2 and SN21627-6 genomic DNA. Eight markers specific to rye chromosome 2R were detected in both introgression lines, implying these lines carry chromosome 2R segments with genes conferring stripe rust and powdery mildew resistance. Therefore, SN21627-2 and SN21627-6 are resistant to more than one major wheat disease, making them promising bridging parents for breeding disease-resistant wheat lines.

QTL Regions and Candidate Genes Associated with Selected Morphological Traits of Winter Triticale (× Triticosecale) Seedlings

The development and viability of seedlings are crucial in overwintering cereals, as it can affect not only an adult plant physiological condition, but also the size and quality of future grain. Recent studies on the genetic control of morphological and yield-related traits have been focused on adult plants of wheat, barley, maize, and rice. However, there is insufficient research describing the genetic control of cereals in the seedling stage. To fill that gap, the winter triticale ‘Hewo’ × ‘Magnat’-doubled haploid lines population was used to locate quantitative trait loci associated with selected traits measured at the seedling stage: the width and length of the first and second leaves, the leaf blade and leaf sheath lengths as well as the length-to-width ratio. Based on the genetic map for ‘Hewo’ × ‘Magnat’ DH population, main four loci, statistically significant (P < 0.05) and strongly associated with the second leaf length and width as well as their ratio were identified. Those regions were located on rye chromosomes 4R, 5R, and 6R with LOD value up to 20.35. In addition, candidate genes in localized regions were identified. The work also demonstrated correlations between the morphology of the second leaf, especially its length-to-width ratio, and the encoded proteins. As described in this paper, results are, to our knowledge, a first attempt to determine the genetic control of triticale seedlings and can provide a new insight on this field and become a reference for developing novel triticale varieties in breeding programmes.

The Genome Regions Associated with Abiotic and Biotic Stress Tolerance, as Well as Other Important Breeding Traits in Triticale.

This review article presents the greatest challenges in modern triticale breeding. Genetic maps that were developed and described thus far, together with the quantitative trait loci and candidate genes linked to important traits are also described. The most important part of this review is dedicated to a winter triticale mapping population based on doubled haploid lines obtained from a cross of the cultivars 'Hewo' and 'Magnat'. Many research studies on this population have focused on the analysis of quantitative trait loci regions associated with abiotic (drought and freezing) and biotic (pink snow mold and powdery mildew) stress tolerance as well as related to other important breeding traits such as stem length, plant height, spike length, number of the productive spikelets per spike, number of grains per spike, and thousand kernel weight. In addition, candidate genes located among these regions are described in detail. A comparison analysis of all of these results revealed the location of common quantitative trait loci regions on the rye chromosomes 4R, 5R, and 6R, with a particular emphasis on chromosome 5R. Described here are the candidate genes identified in the above genome regions that may potentially play an important role in the analysis of trait expression. Nevertheless, these results should guide further research using molecular methods of gene identification and it is worth extending the research to other mapping populations. The article is also a review of research led by other authors on the triticale tolerance to the most current stress factors appearing in the breeding.

Molecular cytogenetic identification of new wheat-rye 6R, 6RS, and 6RL addition lines with resistance to stripe rust and powdery mildew.

Stripe rust and powdery mildew are devastating diseases that have severe effects on wheat production. Introducing resistant genes/loci from wheat-related species into the wheat genome is an important method to improve wheat resistance. Rye (Secale cereale L.) is a cross-pollinating plant and is the most important related species for wheat genetic improvement. In this study, we developed three 6RS ditelosomic addition lines, three 6RL ditelosomic addition lines, and two 6R disomic addition lines by crossing common wheat cultivar Chuannong 25 and rye inbred line QL2. The chromosome composition of all new lines was confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH) and molecular marker analyses. Disease responses to different Puccinia striiformis f. sp. tritici (Pst) races and Blumeria graminis f. sp. tritici (Bgt) isolates and cytogenetic analysis showed that the resistance of the new lines was derived from the rye chromosome 6R of QL2, and both arms (6RS and 6RL) may harbor resistance genes against Pst and Bgt. These new lines could be used as a promising bridging parent and valuable genetic resource for wheat disease resistance improvement.

Bouquet Formation Failure in Meiosis of F1 Wheat-Rye Hybrids with Mitotic-Like Division.

Bouquet formation is believed to be involved in initiating homologous chromosome pairings in meiosis. A bouquet is also formed in the absence of chromosome pairing, such as in F1 wheat–rye hybrids. In some hybrids, meiosis is characterized by a single, mitotic-like division that leads to the formation of unreduced gametes. In this study, FISH with the telomere and centromere-specific probe, and immunoFISH with ASY1, CENH3 and rye subtelomere repeat pSc200 were employed to perform a comparative analysis of early meiotic prophase nuclei in four combinations of wheat–rye hybrids. One of these, with disomic rye chromosome 2R, is known to undergo normal meiosis, and here, 78.9% of the meiocytes formed a normal-appearing telomere bouquet and rye subtelomeres clustered in 83.2% of the meiocytes. In three combinations with disomic rye chromosomes 1R, 5R and 6R, known to undergo a single division of meiosis, telomeres clustered in 11.4%, 44.8% and 27.6% of the meiocytes, respectively. In hybrids with chromosome 1R, rye subtelomeres clustered in 12.19% of the meiocytes. In the remaining meiocytes, telomeres and subtelomeres were scattered along the nucleus circumference, forming large and small groups. We conclude that in wheat–rye hybrids with mitotic-like meiosis, chromosome behavior is altered already in the early prophase.

Molecular Cytogenetic Identification of a New Wheat-Rye 6R Addition Line and Physical Localization of Its Powdery Mildew Resistance Gene

Rye (Secale cereale L.), a naturally cross-pollinating relative of wheat, is a tertiary gene donor and of substantial value in wheat improvement. Wheat powdery mildew is caused by Blumeria graminis f. sp. tritici (Bgt), which seriously affects yield and quality worldwide. Identifying and transferring new, effective resistance genes against powdery mildew from rye is important for wheat breeding. The current study developed a wheat-rye line YT2 resistant to powdery mildew by crossing, backcrossing, and self-pollination for multiple generations between octoploid triticale 09R2-100 and common wheat cultivar Shixin 616. YT2 was confirmed to be a 6R disomic addition and T1RS⋅1BL translocation line by genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), multicolor-GISH (mc-GISH), and molecular marker analyses. Disease responses to different Bgt isolates and genetic analysis showed that the powdery mildew resistance gene of YT2 was derived from the rye chromosome 6R of 09R2-100, which differed from the previously reported Pm genes from rye including Pm20 on 6RL. Resistance phenotype of different translocation lines and deletion lines derived from YT2 combined with newly developed 6RL-specific markers analysis suggested that the powdery mildew resistance gene of YT2 was localized to the region in chromosome 6RL: 890.09–967.51 Mb and flanked by markers XM189 and X4M19, corresponding to the reference genome of Weining rye. Therefore, YT2 could be used as a promising bridging parent for wheat disease resistance improvement.

Genetic mapping of adult-plant resistance genes to powdery mildew in triticale

Triticale is a cereal of high economic importance; however, along with the increase in the area of this cereal, it is more often infected by the fungal pathogen Blumeria graminis, which causes powdery mildew. The rapid development of molecular biology techniques, in particular methods based on molecular markers may be an important tool used in modern plant breeding. Development of genetic maps, location of the QTLs defining the region of the genome associated with resistance and selection of markers linked to particular trait can be used to select resistant genotypes as well as to pyramidize several resistance genes in one variety. In this paper, we present a new, high-density genetic map of triticale doubled haploids (DH) population “Grenado” × “Zorro” composed of DArT, silicoDArT, and SNP markers. Composite interval mapping method was used to detect eight QTL regions associated with the area under disease progress curve (AUDPC) and 15 regions with the average value of powdery mildew infection (avPM) based on observation conducted in 3-year period in three different locations across the Poland. Two regions on rye chromosome 4R, and single loci on 5R and 6R were reported for the first time as regions associated with powdery mildew resistance. Among all QTLs, 14 candidate genes were identified coded cyclin-dependent kinase, serine/threonine-protein kinase-like protein as well as AMEIOTIC 1 homolog DYAD-like protein, DETOXIFICATION 16-like protein, and putative disease resistance protein RGA3. Three of identified candidate genes were found among newly described QTL regions associated with powdery mildew resistance in triticale.

Preliminary tests indicate the absence of polymorphism among 1RS.1BL translocations in wheat for root biomass enhancement

The introduction of the short arm of rye chromosome 1R (1RS) into wheat significantly increased grain yields. Studies have shown that 1RS carries a locus controlling root biomass and improves canopy water status under water-stressed conditions. The general genetic map location of the locus is known but allelic variation would facilitate precise mapping and identification of the responsible gene(s). To this end, six 1RS.1BL translocations from various sources in three wheat backgrounds were tested for root biomass and response to drought but no significant differences among different 1RS arms were observed. The behavior of the standard 1RS.1BL translocation in cv. Pavon 76 in various experiments suggested that wheat chromosome arm 1BS of Pavon 76 may carry a locus for root system plasticity. A set of single substitutions of chromosome 1B from 15 different sources, in the same genetic background of cv. Pavon 76, were tested for root biomass in various experiments. Again, no significant variation among the 1B substitution lines was observed. These results suggest that either no allelic variation at the targeted loci exists, or the sets of lines were biased. While various 1B chromosomes originated from a random sample of wheats, all 1RS arms were imported into wheat from various triticales, perhaps preselecting certain allelic combinations.

Winter hardiness analysis of wheat-rye 5R(5A)-substituted lines in Western Siberia

Homoeologous group 5 chromosomes of wheat possess genes that have a significant influence on the time of earing, growth habit (Vrn), frost resistance (Fr) and winter hardiness. The Vrn-A1/Fr-A1, Vrn-B1/Fr-B1 and Vrn-D1/Fr-D1 genes are assigned to the long arm of the 5A, 5B and 5D chromosomes, respectively. In rye (Secale cereale L.), Vrn-R1/Fr-R1 genes, which determine the growth habit and cold/frost resistance, are localized on chromosome 5RL. To investigate the effect of individual chromosomes on winter hardiness, as well as their interactions with the background, wheat-rye 5R(5A)-substituted lines based on winter and spring wheats were used in this study. We created the wheat-rye 5R(5A) substitution lines based on the winter wheats cvs. ‘Filatovka’ and ‘Ulʼynovka’ and based on the spring wheats cvs. ‘Rang’ and ‘Mironovskaya krupnozernaya’ to identify the role of rye chromosome 5R in controlling the growth habit and winter hardiness. Two cultivars of rye—‘Onokhoiskaya’ (spring habit) and ‘Vietnamskaya Mestnaya’—are the source of chromosome 5R. We do not know the growth habit of rye ‘Vietnamskaya Mestnaya’. Field experiments were carried out over three years during the winters of 2015/2016, 2016/2017 and 2017/2018 in the Novosibirsk Region. It was found that 5R(5A) substitution lines for spring cvs. ‘Rang’ and ‘Mironovskaya krupnozernaya’, with the participation of the spring rye ‘Onokhoiskaya’, have a winter habit. The wheat-rye 5R(5A) lines for winter cvs. ‘Ul'yanovka’ and ‘Filatovka’, with the participation of rye ‘Vietnamskaya Mestnaya’, have a facultative habit. These substituted lines can grow in both spring and autumn sowing. The evaluation of winter hardiness conducted was carried out by means of visual scoring on a 1–9 score basis. All wheat-rye-substituted lines survived in the conditions of the Novosibirsk Region. Winter hardiness scores ranged from 5 to 6 after the 2015/2016 and 2016/2017 winters, whereas winter hardiness scores varied from 8 to 9 after the 2017/2018 winter.

Diverse Wheat-Alien Introgression Lines as a Basis for Durable Resistance and Quality Characteristics in Bread Wheat.

Wheat productivity has been significantly improved worldwide through the incorporation of novel genes from various gene pools, not least from wild relatives of wheat, into the commonly cultivated bread and durum wheat. Here, we present and summarize results obtained from a diverse set of wheat-alien introgression lines with mainly introgressions of rye, but also of Leymus spp. and Thinopyrum junceiforme into bread-wheat (Triticum aestivum L.). From this material, lines carrying 2RL were found with good agronomic performance and multiple resistance not least towards several races of powdery mildew. A novel resistance gene, one of few showing resistance towards all today identified stem rust races, designated Sr59, was also found originating from 2RL. Lines with multiple introgressions from 4R, 5R, and 6R were found resistant towards the majority of the stripe rust races known today. Due to lack of agricultural adaptation in these lines, transfer of useful genes into more adapted wheat material is a necessity, work which is also in progress through crosses with the CSph1b mutant, to be able to only transfer small chromosome segments that carry the target gene. Furthermore, resistance towards Russian wheat aphid was found in lines having a substitution of 1R (1D) and translocations of 3DL.3RS and 5AL.5RS. The rye chromosomes 1R, 2R, and 6R were found responsible for resistance towards the Syrian Hessian fly. High levels of especially zinc was found in several lines obtained from crosses with Leymus racemosus and Leymus mollis, while also some lines with 1R, 2R, or 5R showed increased levels of minerals and in particular of iron and zinc. Moreover, lines with 1R, 2R, 3R, and Leymus spp. introgressions were also found to have a combination of high iron and zinc and low cadmium concentrations. High variation was found both in grain protein concentration and gluten strength, measured as %UPP, within the lines, indicating large variation in bread-making quality. Thus, our study emphasizes the impact that wheat-alien introgression lines can contribute to current wheat lines and shows large opportunities both to improve production, resistance, and quality. To obtain such improvements, novel plant breeding tools, as discussed in this paper, opens unique opportunities, to transfer suitable genes into the modern and adapted wheat cultivars.

Isolation and characterization of a new MATE gene located in the same chromosome arm of the aluminium tolerance (Alt1) rye locus

Aluminium (Al) toxicity is the major constraint for crop productivity in acid soils. Wild rye species (Secale spp.) exhibit high Al tolerance, being a good source of genes related to this trait. The Alt1 locus located on the 6RS chromosome arm is one of the four main loci controlling Al tolerance in rye and is known to harbour major genes but, so far, none have been found. Through synteny among the short arm of the rye chromosome 6R and the main grass species, we found a candidate MATE gene for the Atl1 locus, later named ScMATE3, which was isolated and characterized in different Secale species. The sequence comparisons revealed both intraspecific and interspecific variability, with high sequence conservation in the Secale genus. SNP with replacement substitution that changed the structure of the protein and can be involved in the Al tolerance trait were found in ScMATE3 gene. The predicted subcellular localization of ScMATE3 is the vacuolar membrane which, together with the phylogenetic relationships performed with other MATE genes of the Poaceae related to Al detoxification, suggest involvement of ScMATE3 in an internal tolerance mechanism. Moreover, expression studies of this gene in rye corroborate its contribution in some Al resistance mechanisms. The ScMATE3 gene is located on the 6RS chromosome arm between the same markers in which the Alt1 locus is involved in Al resistance mechanisms in rye, thus being a good candidate gene for this function.

Identification and characterization of a new stripe rust resistance gene Yr83 on rye chromosome 6R in wheat.

A physical map of Secale cereale chromosome 6R was constructed using deletion mapping, and a new stripe rust resistance gene Yr83 was mapped to the deletion bin of FL 0.73-1.00 of 6RL. Rye (Secale cereale L., RR) possesses valuable genes for wheat improvement. In the current study, we report a resistance gene conferring stripe rust resistance effective from seedling to adult plant stages located on chromosome 6R. This chromosome was derived from triticale line T-701 and also carries highly effective resistance to the cereal cyst nematode species Heterodera avenae Woll. A wheat-rye 6R(6D) disomic substitution line exhibited high levels of seedling resistance to Australian pathotypes of the stripe rust (Puccinia striiformis f. sp. tritici; Pst) pathogen and showed an even greater resistance to the Chinese Pst pathotypes in the field. Ten chromosome 6R deletion lines and five wheat-rye 6R translocation lines were developed earlier in the attempt to transfer the nematode resistance gene to wheat and used herein to map the stripe rust resistance gene. These lines were subsequently characterized by sequential multicolor fluorescence in situ hybridization (mc-FISH), genomic in situ hybridization (GISH), mc-GISH, PCR-based landmark unique gene (PLUG), and chromosome 6R-specific length amplified fragment sequencing (SLAF-Seq) marker analyses to physically map the stripe rust resistance gene. The new stripe rust resistance locus was located in a chromosomal bin with fraction length (FL) 0.73-1.00 on 6RL and was named Yr83. A wheat-rye translocation line T6RL (#5) carrying the stripe rust resistance gene will be useful as a new germplasm in breeding for resistance.

Introgression of Powdery Mildew Resistance Gene Pm56 on Rye Chromosome Arm 6RS Into Wheat.

Powdery mildew, caused by the fungus Blumeria graminis f. sp. tritici, represents a yield constraint in many parts of the world. Here, the introduction of a resistance gene carried by the cereal rye cv. Qinling chromosome 6R was transferred into wheat in the form of spontaneous balanced translocation induced in plants doubly monosomic for chromosomes 6R and 6A. The translocation, along with other structural variants, was detected using in situ hybridization and genetic markers. The differential disease response of plants harboring various fragments of 6R indicated that a powdery mildew resistance gene(s) was present on both arms of rye chromosome 6R. Based on karyotyping, the short arm gene, designated Pm56, was mapped to the subtelomere region of the arm. The Robertsonian translocation 6AL⋅6RS can be exploited by wheat breeders as a novel resistance resource.

Two Rye Genes Responsible for Abnormal Development of Wheat⁻Rye Hybrids Are Linked in the Vicinity of an Evolutionary Translocation on Chromosome 6R.

The post-zygotic reproductive isolation (RI) in plants is frequently based on the negative interaction of the parental genes involved in plant development. Of special interest is the study of such types of interactions in crop plants, because of the importance of distant hybridization in plant breeding. This study is devoted to map rye genes that are incompatible with wheat, determining the development of the shoot apical meristem in wheat–rye hybrids. Linkage analysis of microsatellite loci, as well as genes of embryo lethality (Eml-R1) and hybrid dwarfness (Hdw-R1) was carried out in hybrids of Chinese Spring wheat with recombinant inbred lines as well as interline rye hybrids. Eml-R1 and Hdw-R1 could be mapped proximal and distal of two closely linked EST-SSR markers, Xgrm902 and Xgrm959, on rye chromosome 6R. Both rye genes are located on a segment of chromosome 6R that contains a breakpoint of evolutionary translocation between the ancestral chromosomes of homeologous groups 6 and 3. The obtained results are discussed in relation to genes interacting in developmental pathways as a class of causal genes of RI.

Populations of doubled haploids for genetic mapping in hexaploid winter triticale

To create a framework for genetic dissection of hexaploid triticale, six populations of doubled haploid (DH) lines were developed from pairwise hybrids of high-yielding winter triticale cultivars. The six populations comprise between 97 and 231 genotyped DH lines each, totaling 957 DH lines. A consensus genetic map spans 4593.9 cM is composed of 1576 unique DArT markers. The maps reveal several structural rearrangements in triticale genomes. In preliminary tests of the populations and maps, markers specific to wheat segments of the engineered rye chromosome 1R (RM1B) were identified. Example QTL mapping of days to heading in cv. Krakowiak revealed loci on chromosomes 2BL and 2R responsible for extended vernalization requirement, and candidate genes were identified. The material is available to all parties interested in triticale genetics.

Chromosomal assignment of centromere-specific histone CENH3 genes in rye (Secale cereale L.) and their phylogeny.

Centromeres are essential for correct chromosome segregation during cell division and are determined by the presence of centromere-specific histone 3 (CENH3). Most of the diploid plant species, in which the structure and copy number of CENH3 genes have been determined, have this gene as a singleton; however, some cereal species in the tribe Triticeae have been found to have CENH3 in two variants. In this work, using the set of the wheat-rye addition lines we wanted to establish the chromosomal assignment of the CENH3 genes in the cultivated rye, Secale cereale (Linnaeus, 1753), in order to expand our knowledge about synteny conservation in the most important cereal species and about their chromosome evolution. To this end, we have also analyzed data in available genome sequencing databases. As a result, the αCENH3 and βCENH3 forms have been assigned to rye chromosomes 1R and 6R: specifically, the commonest variants αCENH3v1 and βCENH3v1 to chromosome 1R, and the rare variants, αCENH3v2 and probably βCENH3v2, to chromosome 6R. No other CENH3 variants have been found by analysis of the rye genome sequencing databases. Our chromosomal assignment of CENH3 in rye has been found to be the same as that in barley, suggesting that both main forms of CENH3 appeared in a Triticeae species before the barley and wheatrye lineages split.

RNA-seq facilitates development of chromosome-specific markers and transfer of rye chromatin to wheat

Transcriptome shotgun sequencing (RNA-seq) provides an abundant resource for developing molecular markers specifically related to functional genes. In this study, transcriptomes of Chinese rye cultivar Jingzhouheimai (JZHM) challenged with powdery mildew pathogen Bgt (Blumeria graminis f. sp. tritici) were obtained and used to develop expressed sequence tag (EST)-based simple sequence repeat (SSR) and sequence-tagged site (STS) markers. A total of 866 primer sets for EST-SSRs and STSs were designed, from which we developed 401 rye-specific markers. The highest level of polymorphism was observed in EST-SSRs (56.73%) followed by STS2 (49.07%) designed via rye-specific contigs and STS1 (35.90%) primers designed from upregulated contigs. Genotyping with newly developed markers along with cytogenetic techniques allowed us to identify nine wheat alien chromosome lines from the cross of Zhoumai 18/Jinghui 1 (Jinghui 1 is an amphiploid of wheat landrace Huixianhong and JZHM) carrying rye chromosome 6R or 6R segments of different length, which permitted preliminary location of the powdery mildew resistance gene PmJZHM6RL and 12 specific markers to 6RL FL 0.51–1.0. 5R-specific markers and genomic in situ hybridization/fluorescence in situ hybridization detected MtA5RL and T5AS·5AL-5RL chromosomes among 41 F5 plants from the cross CS ph1bph1b/MA5R, and aberrations permitted the location of the hairy peduncle gene (Hp) and marker XLFZ3473 to the region 5RL FL 0.78–1.0 with another nine markers locating to 5RL 0.0–0.78. The chromosome-specific markers and chromosome aberrations developed in this study will facilitate the introgression of rye chromatin into wheat.

Reorganization of wheat and rye genomes in octoploid triticale (\xd7\xa0Triticosecale)

Main conclusionThe analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations. This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes. Wheat chromosomes were eliminated to a higher extent. The lower content of telomeric heterochromatin was also found in rye chromosomes in comparison with parental rye. Studying the location of selected retrotransposons from Ty1-copia and Ty3-gypsy families using fluorescence in situ hybridization revealed additional locations of these retrotransposons that were not present in chromosomes of parental species. ISSR, IRAP and REMAP analyses showed significant changes at the level of specific DNA nucleotide sequences. In most cases, the disappearance of certain types of bands was observed, less frequently new types of bands appeared, not present in parental species. This demonstrates the scale of genome rearrangement and, above all, the elimination of wheat and rye sequences, largely due to the reduction of chromosome number. With regard to the proportion of wheat to rye genome, the rye genome was more affected by the changes, thus this study was focused more on the rye genome. Observations suggest that genome reorganization is not finished in the F5 generation but is still ongoing in the F8 generation.

Targeted Segment Transfer from Rye Chromosome 2R to Wheat Chromosomes 2A, 2B, and 7B

Increased chromosome instability was induced by a rye (Secale cereale L.) monosomic 2R chromosome into wheat (Triticum aestivum L.). Centromere breakage and telomere dysfunction result in high rates of chromosome aberrations, including breakages, fissions, fusions, deletions, and translocations. Plants with target traits were sequentially selected to produce a breeding population, from which 3 translocation lines with target traits have been selected. In these lines, wheat chromosomes 2A, 2B, and 7B recombined with segments of the rye chromosome arm 2RL. This was detected by FISH analysis using repeat sequences pSc119.2, pAs1 and genomic DNA of rye together as probes. The translocation chromosomes in these lines were named as 2A^SMR, 2B^SMR, and 7B^SMR. The small segments that were transferred into wheat consisted of pSc119.2 repeats and other chromatin regions that conferred resistance to stripe rust and expressed target traits. These translocation lines were highly resistant to stripe rust, and expressed several typical traits that were associated with chromosome arm 2RL, which are better than those of its wheat parent, disomic addition, and substitution lines that show agronomic characteristics. The integration of molecular methods and conventional techniques to improve wheat breeding schemes are discussed.

The expansion of heterochromatin blocks in rye reflects the co-amplification of tandem repeats and adjacent transposable elements.

BackgroundA prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained.ResultsUsing a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences.ConclusionThe large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2667-5) contains supplementary material, which is available to authorized users.