Rye Chromosome Research Articles

SSR Marker TsM106 Is a Convenient Tool for Identifying Wheat-Rye 1AL.1RS Translocation

Wheat continues to be one of the most cultivated cereals in the world. The research undertaken to find new genetic resources and new favourable alleles are a priority in wheat breeding programs. Increasing genetic diversity is necessary to cope with the social, natural and economic challenges. Rye (Secale cereale L.) represents an important genetic resource for wheat breeding. The short arm of the rye chromosome 1 (1RS) contains several genes inducing resistance to biotic and abiotic stresses, increase yield and better adaptation to various environments. Therefore, identification of new tools for detection/selection of favourable alleles can help obtaining fast and reliable results. Molecular markers-SSRs are such convenient tools. In our study, conducted on 17 genotypes (rye cultivar - Harkovskaya; five Romanian wheat cultivars; four 1AL.1RS translocation genotypes, including “Amigo” derived from “Insave” rye, and seven 1BL.1RS translocation), we used SSR markers to detect the presence of 1RS translocation. We found that the SSR-TSM 106(~170bp) marker clearly distinguished the wheat-rye 1AL.1RS translocation, coming from “Insave” or related rye chromatin, from the wheat-rye 1BL.1RS translocation, coming from other rye sources. Therefore, SSR-TSM marker could be used in MAS (Marker-Assisted Selection) for 1AL.1RS translocation.

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.

Evaluation of triticale accessions for resistance to wheat bacterial leaf streak caused by Xanthomonas translucens pv. undulosa

The bacterium Xanthomonas translucens pv. undulosa (Xtu) causes bacterial leaf streak (BLS) on wheat and other small grains. Several triticale accessions were reported to possess high levels of resistance to wheat Xtu strains. In this study, a worldwide collection of triticale accessions as well as the major North Dakota hard red spring and durum wheat cultivars were evaluated for reaction to two local Xtu strains. All wheat cultivars showed a susceptible reaction but a wide range of reactions was observed among triticale accessions. Out of the 502 accessions tested, 45 and 10 accessions were resistant to the two virulent strains BLS‐LB10 and BLS‐P3, respectively, with five accessions, PI 428736, PI 428854, PI 428913, PI 542545 and PI 587229, being highly resistant to both strains. Statistical analysis showed significant difference among the accessions, strains, and the accession by strain interaction (P < 0.001). Bacterial population growth in resistant triticale was significantly slower than that in susceptible triticale. Molecular cytogenetic characterization in four representative triticale accessions confirmed the hexaploid level of the species and the presence of 12 or 14 rye chromosomes. The triticale accessions identified are valuable materials for developing wheat germplasm with high levels of BLS resistance.

Physical Location of New PCR-Based Markers and Powdery Mildew Resistance Gene(s) on Rye (Secale cereale L.) Chromosome 4 Using 4R Dissection Lines.

Rye (Secale cereale L.) 4R chromosome contains elite genes that are applicable for wheat (Triticum aestivum L.) cultivar improvement. PCR-based 4R-specific markers can benefit the detection of elite genes on 4R in wheat backgrounds. In this study, a new fluorescence in situ hybridization (FISH) map of the 4RKu chromosome of rye Kustro has been constructed. A set of 4RKu dissection lines was obtained and 301 new 4RKu-specific markers were developed using specific length amplified fragment sequencing (SLAF-seq) technology. These markers were combined with the 99 4RKu-specific markers previously developed, and were physically mapped to 4RKu chromosome using the new FISH map and the 4RKu dissection lines. A total of 338 of the 400 markers have been successfully mapped to six regions of 4RKu chromosome. Additionally, the powdery mildew resistance gene(s) on the 4RLKu arm was located to the segment between L.4 and L.8, the same region where 115 4RLKu-specific markers were mapped. The markers developed in this study can be used to identify a specific segment of 4R chromatin in wheat backgrounds, help construct a high-density physical map of 4R chromosome, and facilitate the utilization of elite genes on 4R chromosome in wheat breeding programs.

High photosynthetic capability observed in the wheat germplasm with rye chromosomes

Improving photosynthetic capability is one of the most important factors for increasing wheat yield potential. The photosynthetic capability of wheat germplasm with different alien chromosomes was investigated and compared with bread wheat cultivars (BC) in this study, including wheat addition lines (CA), hexaploid triticale (HT), octoploid triticale (OT), and synthetic hexaploid wheat lines (SHW). Results indicated that HT, OT, and SHW produced significantly higher biomass plant−1(BMPP), with HT displaying the highest grain yield plant−1 (GYPP). Distinct superiority of net photosynthetic rate (Pn) and carboxylation activities of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was observed in HT and OT. Meanwhile, OT showed the highest expression of the Rubisco large subunit gene (rbcL) in the flag leaves at heading and grain-filling stages, though the coding region of rbcL was highly conserved in all investigated materials. Further analysis indicated that OT and Chinese Spring-rye disomic addition lines displayed higher expression of Rubisco small subunit gene (rbcS). Correlation analysis revealed significant and positive correlations between Pn and the expressions of rbcL (at both heading and grain-filling stages), the expression of rbcS (at heading stage), and the carboxylation activity of Rubisco (at grain-filling stage). Anatomical structure analysis of the chloroplasts showed SHW with longer chloroplasts and more chloroplast grana and grana lamella. In the present study, HT, OT, and Chinese Spring-rye disomic addition lines with rye chromosomes displayed greater photosynthetic capability than BC and SHW, and could be applied in breeding programs to improve the photosynthetic efficiency of wheat.

Tracking of intercalary DNA sequences integrated into tandem repeat arrays in rye Secale vavilovii

The structure of repetitive sequences of the JNK block present in the pericentromeric region of the 2RL chromosome was studied in <em>Secale vavilovii</em>. Amplification of sequences present between the JNK sequences led to the identification of seven abnormal DNA fragments. Two of these fragments showed high similarity to the glutamate 5-kinase gene and putative alcohol dehydrogenase gene of trypanosomatid from the genus <em>Leishmania</em>, whose presence can be explained by horizontal gene transfer (HGT). Other fragments were similar to mitochondrial gene for ribosomal protein S4 in plants and to the glycoprotein (G) gene of the IHNV virus. Presumably, they are pseudogenes inserted into the JNK heterochromatin region. Within this region, also fragments similar to the rye repetitive sequence and chromosome 3B in wheat were found. There is no known mechanism that would explain how foreign sequences were inserted into the block region of tandem repetitive sequences of the JNK family.

Chromosome identification by new molecular markers and genomic in situ hybridization in the Triticum-Secale-Thinopyrum trigeneric hybrids.

It is very important to use chromosome-specific markers for identifying alien chromosomes in advanced generations of distant hybridization. The chromosome-specific markers of rye and Thinopyrum elongatum, as well as genomic in situ hybridization, were used to identify the alien chromosomes in eight lines that were derived from the crossing between Triticum trititrigia (AABBEE) and triticale (AABBRR). The results showed that four lines contained all rye chromosomes but no Th. elongatum chromosomes. The line RE36-1 contained all of the rye chromosomes except for chromosome 2R. The lines RE33-2 and RE62-1 contained all rye chromosomes and 1E and 5E translocated chromosome, respectively. The line RE24-4 contained 12 rye chromosomes plus a 7E chromosome or 12 rye chromosomes plus one R-E translocated chromosome. Chromosome identification in the above lines was consistent using chromosome-specific markers and genomic in situ hybridization. These chromosome-specific markers provide useful tools for detecting alien chromosomes in trigeneric hybrids, and these lines could be utilized as valuable germplasm in wheat improvement.

Comparative analysis of genetic architectures for nine developmental traits of rye

Genetic architectures of plant height, stem thickness, spike length, awn length, heading date, thousand-kernel weight, kernel length, leaf area and chlorophyll content were aligned on the DArT-based high-density map of the 541 × Ot1–3 RILs population of rye using the genes interaction assorting by divergent selection (GIABDS) method. Complex sets of QTL for particular traits contained 1–5 loci of the epistatic D class and 10–28 loci of the hypostatic, mostly R and E classes controlling traits variation through D–E or D–R types of two-loci interactions. QTL were distributed on each of the seven rye chromosomes in unique positions or as a coinciding loci for 2–8 traits. Detection of considerable numbers of the reversed (D′, E′ and R′) classes of QTL might be attributed to the transgression effects observed for most of the studied traits. First examples of E* and F QTL classes, defined in the model, are reported for awn length, leaf area, thousand-kernel weight and kernel length. The results of this study extend experimental data to 11 quantitative traits (together with pre-harvest sprouting and alpha-amylase activity) for which genetic architectures fit the model of mechanism underlying alleles distribution within tails of bi-parental populations. They are also a valuable starting point for map-based search of genes underlying detected QTL and for planning advanced marker-assisted multi-trait breeding strategies.

Identification of rye chromosomes by flow cytogenetics

Identification of rye chromosomes by flow cytogenetics

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.

Introduction of Thinopyrum intermedium ssp. trichophorum chromosomes to wheat by trigeneric hybridization involving Triticum, Secale and Thinopyrum genera.

Fluorescence in situ hybridization and molecular markers have confirmed that several chromosomes from Thinopyrum intermedium ssp. trichophorum have been added to a wheat background, which originated from a cross between a wheat- Thinopyrum partial amphiploid and triticale. The lines displayed blue grains and resistance to wheat stripe rust. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. With the aim to transfer novel genetic variation from Th. intermedium species for sustainable wheat breeding, a new trigeneric hybrid was produced by crossing an octoploid wheat-Th. intermedium ssp. trichophorum partial amphiploid with hexaploid triticale. Fluorescence in situ hybridization (FISH) revealed that Thinopyrum chromosomes were transmitted preferably and the number of rye chromosomes tended to decrease gradually in the selfed derivatives of the trigeneric hybrids. Four stable wheat-Th. intermedium chromosome substitution, addition and translocation lines were selected, and a 2JS addition line, two substitution lines of 4JS(4B) and 4J(4B), and a small 4J.4B translocation line were identified by FISH and molecular markers. It was revealed that the gene(s) responsible for blue grains may located on the FL0.60-1.00 of long arm of Th. intermedium-derived 4J chromosome. Disease resistance screenings indicated that chromosomes 4JS and 2JS appear to enhance the resistance to stripe rust in the adult plant stage. The new germplasm with Th. intermedium introgression shows promise for utilization of Thinopyrum chromosome segments in future wheat improvement.

B Chromosomes - A Matter of Chromosome Drive.

B chromosomes are supernumerary chromosomes which are often preferentially inherited, deviating from usual Mendelian segregation. The balance between the so-called chromosome drive and the negative effects that the presence of Bs applies on the fitness of their host determines the frequency of Bs in a particular population. Drive is the key for understanding most B chromosomes. Drive occurs in many ways at pre-meiotic, meiotic or post-meiotic divisions, but the molecular mechanism remains unclear. The cellular mechanism of drive is reviewed based on the findings obtained for the B chromosomes of rye, maize and other species. How novel analytical tools will expand our ability to uncover the biology of B chromosome drive is discussed.

Rye chromosome composition and seed characters in hexaploid triticale (X Triticosecale WITTMACK)

The individual characteristic features of chromosomes in Petkus rye (diploid) and 82 hexaploid triticale accessions were assessed to identify the replaced rye chromosome pair(s) in triticale and its effect on kernel characters. GiemsaC-banding technique was used for the study. Results revealed that 24 hexaploid triticales showed full complement of rye chromosome, 34 had replacement of one pair and 24 had replacement of two pairs of rye chromosomes. Triticale strains with 2R/2D and 4R/4D substitutions had higher and medium seed set, respectively. Seed set was considerably high when both with 2R/2D and 4R/4D substitution occured together.

Manifestation of frost-resistance in hybrid generation of winter wheat Triticum aestivum

Purpose. To produce new source material of winter wheat Triticum aestivum with high frost-resistance and using it to produce varieties resistant to adverse conditions of overwintering.Methods. Field, laboratory, analytical, and statistical.Results. In winter wheat T. aestivum hybrids, heterosis on frost-resistance appeared in the combination that involved female line ‘Ivanivska 16’, in which, apparently, had chromosomes of rye. In the resulting combinations, a part of rye chromosomes was transferred to genome of winter wheat T. aestivum. The involvement of winter wheat T. aestivum progeny containing genome of ‘AD 206’ (‘Odeska 66’ / ‘AD 206’) into hybridisation makes it possible to obtain new varieties with a set of agronomic features and transgression of frost-resistance. In the combination ‘Donskyi semi-dwarf’ / ‘Odeska semi-dwarf’, where parent lines were less frost-resistant, a depression was observed in both the first and second generations (hp 1.09–0.55). In other hybrid combinations, frost-resistance was inherited through the female line, i.e. more frost-resistant variety.Conclusions. It was found that heterosis of frost-resistance appeared in the combinations that involved female line ‘Ivanivska 16’, in which, apparently, chromosomes of rye were present.

CDNA-AFLP analysis of 1BL.1RS under water-deficit stress and development of wheat-rye translocation-specific markers

ABSTRACTDrought is a major stressor that severely hampers the production of many important crops. The short arm of rye (Secale cereale) chromosome 1 contains favourable stress-resistance alleles and is thus widely used in wheat (Triticum aestivum) breeding to generate 1BL.1RS translocation lines. In this study, 1BL.1RS-specific drought-responsive genes were identified using cDNA-amplified fragment length polymorphism (AFLP) analysis. Among the 144 transcript-derived fragments (TDF) differentially expressed in the 1BL.1RS line, we identified the function and chromosomal position of 84 TDF using public databases. Real-time PCR was performed to validate the results of cDNA-AFLP, and four TDF were significantly up-regulated. Furthermore, we developed two wheat-rye translocation-specific markers by comparing the TDF from the short arms of wheat and rye chromosome 1. One is specific to 1BL.1RS and the other is specific to 1AL.1RS and 1BL.1RS. Combinational use of both markers will be helpful to breed wheat possessing 1RS.

Similarities and differences in the nuclear genome organization within Pooideae species revealed by comparative genomic in situ hybridization (GISH)

In this paper, we highlight the affinity between the genomes of key representatives of the Pooideae subfamily, revealed at the chromosomal level by genomic in situ hybridization (GISH). The analyses were conducted using labeled probes from each species to hybridize with chromosomes of every species used in this study based on a “round robin” rule. As a result, the whole chromosomes or chromosome regions were distinguished or variable types of signals were visualized to prove the different levels of the relationships between genomes used in this study. We observed the unexpected lack of signals in secondary constrictions of rye (RR) chromosomes probed by triticale (AABBRR) genomic DNA. We have also identified unlabeled chromosome regions, which point to species-specific sequences connected with disparate pathways of chromosome differentiation. Our results revealed a conservative character of coding sequence of 35S rDNA among selected species of the genera Aegilops, Brachypodium, Festuca, Hordeum, Lolium, Secale, and Triticum. In summary, we showed strong relationships in genomic DNA sequences between species which have been previously reported to be phylogenetically distant.

Addition of chromosome 4R from Hungarian rye cultivar Lovászpatonai confers resistance to stripe rust and outstanding end-use quality in wheat

The Hungarian rye (Secale cereale L., 2n = 2x = 14, RR) cultivar Lovászpatonai possesses numerous agronomically useful traits that can be exploited in wheat breeding. This study reports on the production, molecular cytogenetic identification, and evaluation of resistance to wheat stripe (or yellow) rust (Puccinia striiformis f. sp. tritici) under field conditions of a newly developed wheat-rye (Mv9kr1-‘Lovászpatonai’) disomic 4R addition line. Analysis of grain quality properties showed that the transfer of ‘Lovászpatonai’ chromosome 4R into wheat significantly increased the total arabinoxylan and protein content. This genetic material proved to be resistant to stripe rust in 2014 and 2015 when epidemics broke out in Hungary. It is assumed that this addition line carries an effective, new resistance gene different from that on rye chromosome arm 1RS of the 1RS.1BL translocation. The Mv9kr1-‘Lovászpatonai’ 4R addition line is a promising pre-breeding material being the first step towards creating translocation lines in order to transfer stripe rust resistance as well as high protein and dietary fibre content into cultivated wheat without deleterious effects on yield and grain quality.

Similar Sister Chromatid Arrangement in Mono- and Holocentric Plant Chromosomes

Due to the X-shape formation at somatic metaphase, the arrangement of the sister chromatids is obvious in monocentric chromosomes. In contrast, the sister chromatids of holocentric chromosomes cannot be distinguished even at mitotic metaphase. To clarify their organization, we differentially labelled the sister chromatids of holocentric Luzula and monocentric rye chromosomes by incorporating the base analogue EdU during replication. Using super-resolution structured illumination microscopy (SIM) and 3D rendering, we found that holocentric sister chromatids attach to each other at their contact surfaces similar to those of monocentrics in prometaphase. We found that sister chromatid exchanges (SCEs) are distributed homogeneously along the whole holocentric chromosomes of Luzula, and that their occurrence is increased compared to monocentric rye chromosomes. The SCE frequency of supernumerary B chromosomes, present additionally to the essential A chromosome complement of rye, does not differ from that of A chromosomes. Based on these results, models of the sister chromatid arrangement in mono- and holocentric plant chromosomes are presented.

1BL/1RS translocation in durum wheat and its effect on end use quality traits

The gluten proteins document the genotypic identity of a wheat variety, in addition to providing valuable clues about its ancestry and technological properties. In this study, an Indian durum wheat genotype B662 was identified to carry 1BL/1RS translocation and characterized further for its effect on end use quality traits. Comparison of the end use quality traits of B662 with five other durum cultivars without 1BL/1RS, showed decreased gluten content, lower swelling index of glutenins and low MSDS-SV indicating that, B662 with 1BL/1RS is not good for pasta making. In F2:3 seeds from a durum wheat cross between the 1BL/1RS cultivar B662 and HI8498 without the translocation, the secalin Sec-1 loci segregated in theoretically expected 3:1 proportion and were inherited as a block of the rye chromosome arm. The analysis of F2:3 harvests for the two most important durum wheat quality tests showed that the presence of 1BL/1RS translocation did not alter the grain protein content values, but was associated with significant reduction of micro SDS-sedimentation volume indicating inferior quality, thus limiting the commercial exploitation of durum wheat genotypes with 1BL/1RS translocation. The cautious use of rye translocation in Indian durum wheat breeding is suggested.