Wheat-rye Translocation Lines Research Articles

Young retrotransposons and non-B DNA structures promote theestablishment of dominant rye centromere in the 1RS.1BL fused centromere.

The fine centromere structure in Robertsonian wheat-rye translocation chromosomes exhibits variation among different translocation genotypes. Within extensively employed wheat-rye 1RS.1BL translocation lines in wheat breeding, their translocated chromosomes frequently display fused centromere. Nevertheless, the mechanism governing the functionality of the fused centromere in 1RS.1BL translocated chromosomes remains to be clarified. In this study, we investigated the fine centromere structure of the 1RS.1BL translocated chromosome through a combination of cytological and genomics methods. We found that only the rye-derived centromere exhibits functional activity, whether in breeding applications or artificially synthesized translocation chromosomes. The active rye-derived centromere had higher proportion of young full-length long terminal repeat retrotransposons (flLTR-RTs) and more stable non-B DNA structures, which may be beneficial toward transcription of centromeric repeats and CENH3 loading to maintain the activity of rye centromeres. High levels of DNA methylation and H3K9me2 were found in the inactive wheat-derived centromeres, suggesting that it may play a crucial role in maintaining the inactive status of the wheat centromere. Our works elucidate the fine structure of 1RS.1BL translocations and the potential mechanism of centromere inactivation in the fused centromere, contributing knowledge to the application of fused centromere in wheat breeding formation of new wheat-rye translocation lines.

Discovery of a novel powdery mildew (Blumeria graminis) resistance locus in rye (Secale cereale L.)

Powdery mildew is one of the most destructive diseases in the world, causing substantial grain yield losses and quality reduction in cereal crops. At present 23 powdery mildew resistance genes have been identified in rye, of which the majority are in wheat-rye translocation lines developed for wheat improvement. Here, we investigated the genetics underlying powdery mildew resistance in the Gülzow-type elite hybrid rye (Secale cereale L.) breeding germplasm. In total, 180 inbred breeding lines were genotyped using the state-of-the-art 600 K SNP array and phenotyped for infection type against three distinct field populations of B. graminis f. sp. secalis from Northern Germany (2013 and 2018) and Denmark (2020). We observed a moderate level of powdery mildew resistance in the non-restorer germplasm population, and by performing a genome-wide association study using 261,406 informative SNP markers, we identified a powdery mildew resistance locus, provisionally denoted PmNOS1, on the distal tip of chromosome arm 7RL. Using recent advances in rye genomic resources, we investigated whether nucleotide-binding leucine-rich repeat genes residing in the identified 17 Mbp block associated with PmNOS1 on recent reference genomes resembled known Pm genes.

Molecular cytogenetic analysis of novel wheat-rye translocation lines and their characterization for drought tolerance and yellow rust resistance

Molecular cytogenetic analysis of novel wheat-rye translocation lines and their characterization for drought tolerance and yellow rust resistance

The consensus rye microsatellite map with EST-SSRs transferred from wheat.

Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped. The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R. With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.

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.

Molecular mapping and genetic analysis of a QTL controlling spike formation rate and tiller number in wheat

Spike formation rate (SR), which is based on maximum tiller number per unit area and spike number per unit area, is an important yield-related trait in wheat. Increasing the spike formation rate reduces growth competition and wastage of photosynthate from ineffective tillers. Unfortunately, research studies involving quantitative trait locus (QTL) mapping for wheat spike formation rate are limited. In the present study, a set of 371 recombinant inbreed line (RIL) population, which were derived from 1BL/LRS wheat-rye translocation lines CN18 and T1208, was analysed by simple sequence repeat (SSR) markers. Genetic analysis showed that a stable and major QTL (QSR.sicau-4D) for spike formation rate was localized to chromosome 4D and explained 18.24% and 24.48% of the observed phenotypic variance in 2015 and 2016, respectively. This QTL was closely linked to SSR marker Xcfd23, and the genetic distance between the flank markers was 3.28cM. Furthermore, QSR.sicau-4D might be a novel pleiotropic QTL, which also controlled maximum tiller number per unit area (QMTN.sicau-4D) and tiller number during pre-winter per unit area (QTNW.sicau-4D). The marker Xcfd23 associated with SR may be utilized in marker-assisted selection in wheat breeding.

Centromere structure and function analysis in wheat-rye translocation lines.

1RS.1BL translocations are centric translocations formed by misdivision and have been used extensively in wheat breeding. However, the role that the centromere plays in the formation of 1RS.1BL translocations is still unclear. Fluorescence insitu hybridization (FISH) was applied to detect the fine structures of the centromeres in 130 1RS.1BL translocation cultivars. Immuno-FISH, chromatin immunoprecipitation (ChIP)-qPCR and RT-PCR were used to investigate the functions of the hybrid centromeres in 1RS.1BL translocations. New 1R translocations with different centromere structures were created by misdivision and pollen irradiation to elucidate the role that the centromere plays in the formation of 1RS.1BL translocations. We found that all of the 1RS.1BL translocations detected contained hybrid centromeres and that wheat-derived CENH3 bound to both the wheat and rye centromeres in the 1RS.1BL translocation chromosomes. Moreover, a rye centromere-specific retrotransposon was actively transcribed in 1RS.1BL translocations. The frequencies of new 1RS hybrid centromere translocations and group-1 chromosome translocations were higher during 1R misdivision. Our study demonstrates the hybrid nature of the centromere in 1RS.1BL translocations. New 1R translocations with different centromere structures were created to help understand the fusion centromere used for wheat breeding and for use as breeding material for the improvement of wheat.

Distribution of Wheat-Rye Translocation Line T1BL·1RS in Wheat and Its Association with Fusarium Head Blight Resistance

The short arm of 1R chromosome (1RS) of rye carries resistant genes to stripe rust, leaf rust, stem rust, powdery mil- dew and aphids. To understand if 1RS also mediates resistance to wheat Fusarium head blight (FHB), we genotyped a panel of 192 wheat accessions from diverse geographic regions and a population of recombinant inbred lines (RIL) consisting of 184 lines developed from the cross of Ning 7840 and Chokwang by 1RS-specific molecular marker Xscm9 and evaluated FHB severities in three consecutive seasons in greenhouses using single floret inoculation method. The results demonstrated that 22 of 192 acces- sions carried a T1BL1RS translocation, and the mean FHB severity (PSS) of varieties carrying T1BL1RS translocation was sig- nificantly lower than that of lines without the translocation across the three experiments (P < 0.05), indicating 1RS may have a positive effect on reducing FHB severity. 1RS-specific marker Xscm9 and Genome in situ hybridization (GISH) showed Ning 7840 carries T1BL1RS translocation. In the population of RILs, irrespective of Fhb1 locus, the mean PSS of lines with T1BL1RS translocation was significantly lower than that of those lines without T1BL1RS. The effects of Fhb1 and 1RS on FHB resistance were additive and the interactions between them were not significant (P = 0.48). The results of this study suggested that 1RS of rye most likely carries the genes resistant to FHB.

Stem rust resistance in 1BL.1RS and 2RL.2BS double wheat-rye translocation lines

Stem rust resistance in 1BL.1RS and 2RL.2BS double wheat-rye translocation lines

Identification of genome-specific transcripts in wheat-rye translocation lines.

Studying gene expression in wheat–rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [1]; Devos et al., 1995 [2]; Lee et al., 2010 [3]; Lee et al., 2013 [4]). To overcome limitations of current gene expression studies on wheat–rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat–rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.

Employment of wheat-rye translocation in wheat improvement and broadening its genetic basis

Hexaploid common wheat (2n = 6x = 42, Triticum aestivum L.) is one of the most widely cultivated crops and numerous attempts to improve the genetic constituent for superior traits have been conducted. Some of the rye (Secale cereale L.) chromosomes, especially the short arm of rye chromosome 1 (1RS) contain several disease resistance genes and have been introgressed into the wheat genome to improve wheat yield. Among them, 1RS from ‘Petkus’ rye has been widely used throughout nations as a form of 1BL/1RS translocation. A number of methods to identify rye chromatin in the wheat chromosome such as PAGE, monoclonal antibody, and HPLC have been developed and directly applied in wheat breeding programs. Although disease resistance genes of wheatrye translocation lines are beneficial, some genes residing on 1RS provide deleterious end-use quality in some genetic backgrounds. This problem might be solved using molecular biology. Development of numerous markers closely linked to the genes allows for the introgression of the desirable genes. However, the lack of sequence information owing to the genome structure of rye has limited marker development. With the advent of NGS technology in the 2000s, enormous sequence data are available, especially for 1RS. The combination of NGS and chromosome-based analysis will help positional cloning of useful genes and marker development in 1RS, which results in further employment of rye chromatin in wheat breeding.

Cytogenetic and molecular identification of small-segment chromosome translocation lines from wheat-rye substitution lines to create wheat germplasm with beneficial traits

ABSTRACTIntergeneric crop plant hybrid lines with small-segment chromosome translocations are very useful in plant genetic research and breeding. In this study, to create small-segment chromosome translocations with beneficial agronomic characters, the progeny of wheat-rye substitution lines 5R/5A and 6R/6A were selected from generations F2 to F5 for rye-specific characteristics. A PCR primer and specific simple sequence repeat marker for rye were used in F5 populations to detect rye chromatin and to amplify a specific chromosome band in six translocation lines (06-6-5, 06-6-6, 06-6-9, 6-26-1, 7-23, and 7-33). Fragment pSc119.1 cloned from 7-33 had 99% homology with the big ear gene sequence (GenBank AF512607.1) in wheat. The six lines were further characterized via pollen mother cell meiosis analysis for genetic stability, and chromosome C-banding and genomic in situ hybridization for rye chromatin. The results show that line 7-33 was still within the 5R/5A substitution lines and possessed the big ear gene. The other lines all contained small-segment rye chromosome translocations. The results indicated that substitution line hybridization is an effective method for creating small-segment chromosome translocations with useful agronomic traits. Trials for these six wheat-rye translocation lines are justified because they possess many important stably-inherited agronomic characters, including disease resistance and improved yield.

RETRACTED ARTICLE: Analysis of DNA methylation polymorphism in a set of stable chromosome translocation lines

Interspecific hybridization is associated with the origin of novel traits and confers increased vigor compared with the parent lines, although its molecular basis is poorly understood. We report here the identification of genetic and epigenetic changes in a set of wheat–rye translocation lines (R59, R57, and R25) which exhibited novel heritable morphological characteristics compared with the parent lines (MY11 and L155). Genome in situ hybridization and amplified fragment length polymorphism analyses revealed no obvious variations in the primary structure of the genome in different translocation lines, with the exception of the same 1RS chromosome translocation. Global assessment of the extent and pattern of cytosine methylation alterations by methylation-sensitive amplified polymorphism (MSAP) analyses revealed differences in the extent of genomic DNA methylation between the rye and wheat parent lines. Fully-methylated sites were significantly increased and hemi-methylated sites were markedly decreased in the genome of translocation lines compared with the wheat parental cultivar MY11. Comparisons of different MSAP patterns revealed both monomorphic and polymorphic sites between translocation lines and wheat parents. Sequencing of 44 isolated fragments that showed methylation alterations indicated that cellular genes and especially transposable elements were targets for methylation alterations in translocation lines. The present study provides further understanding of the rules governing the distribution and existence of DNA methylation variations induced in the wheat genome during alien germplasm introduction. Furthermore, our study provides insights into the relationship between DNA methylation and hybrid vigor as well as a theoretical basis for further fundamental research and breeding application.

Allelopathy—A Tool to Improve the Weed Competitive Ability of Wheat with Herbicide-Resistant Black-Grass (Alopecurus myosuroides Huds.)

Controlling black-grass in winter wheat production in northern Europe is an increasing problem because of more frequent winter crops and development of herbicide resistance in weeds. Alternative weed management strategies are needed, e.g., use of more competitive cultivars. Factors that increase cultivar competitiveness include early vigor and straw length, but also allelopathy. Therefore, the allelopathic properties of wheat cultivars included in the Swedish national list or in the release pipeline were investigated using a bioassay with herbicide-resistant and herbicide-sensitive black-grass as receiver plants. Wheat-rye translocation lines were also included in this screening to identify possible sources of high allelopathic activity. The bioassay results were followed up in two-year field trials. The results revealed large variations in allelopathic activity between cultivars. Most cultivars showed interference with both herbicide-sensitive and herbicide-resistant black-grass, although the allelopathic effect was lower on the herbicide-resistant biotype. Cultivars with high allelopathic activity gave only half the black-grass biomass of low allelopathic cultivars. Dinaro, a triticale (wheat-rye hybrid) cultivar and the new wheat cultivar Nimbus showed the highest allelopathy and inhibition of black-grass growth. Only a few wheat lines with rye chromatin, all or part of a rye chromosome, showed high allelopathy. Use of cultivars with high allelopathic activity can thus be important in integrated weed management of black-grass.

Root system plasticity to drought influences grain yield in bread wheat

Crop productivity in semiarid regions is mainly limited by water availability. Root characteristics and plasticity to drought may reduce the negative impact of drought on crop yield. A set of near-isogenic wheat-rye translocation lines was used to test the hypothesis that root system plasticity to drought influences grain yield in wheat. Bread wheat Pavon 76 and 1RS translocation lines, namely Pavon 1RS.1AL, Pavon 1RS.1BL, and Pavon 1RS.1DL were evaluated for root allocation and plasticity in sand-tube experiments under well-watered and droughted conditions across 2 years using factorial treatments in a randomized complete block design with four replicates. The 1RS translocation lines had greater root biomass per plant ranging from 7.37 to 8.6 compared to 5.81 g for Pavon 76. Only Pavon 76 showed a positive response to drought by producing more shallow roots (roots developed between 0 and 30 cm) and deep roots (roots developed below 30 cm) in droughted conditions than in well-watered conditions. Thus at drought intensity of 19% (measured as overall reduction in grain yield), grain yield in Pavon 76 was reduced only by 11% compared to the other genotypes with yield reductions ranging from 18 to 24%. However, at drought intensity of 36%, grain yield in Pavon 76 showed maximum reduction indicating that greater root production under drought is advantageous only when plant-available water is enough to support grain production. Grain yield was positively correlated with shallow and deep root weight and root biomass under terminal drought. Correlation coefficients between root system components (shallow and deep root weight and root biomass) and phenological periods were not significant. Our study indicated that genes influencing adaptive phenotypic plasticity of the root system to drought in Pavon 76 are located on chromosome 1BS.

New PCR based markers allowed to identify Secale chromatin in wheat-Secale africanum introgression lines

The genus of Secale has many agronomically important characters. In order to use the best of this species, markers tracking the rye chromatin incorporated into wheat must be developed. In this study, one rye genome-specific random amplified polymorphic DNA (RAPD) marker was isolated from Secale africanum (Ra genome). Two cloned markers, named OPP131165 and OPP13662, were 1165 bp and 662 bp, respectively. Sequence analysis revealed that OPP131165 was highly homologous to a part of a new class of transposon-like gene called the Revolver family, and OPP13662 was partially similar to LTR gypsy-like retrotransposon. Fluorescence in situ hybridization (FISH) showed only OPP131165 localized within the whole arms of rye except their terminal regions and no signal was detected on wheat chromosomes, while OPP13662 had no hybridization signal detected on wheat and rye genomes. Based on these sequences, two pairs of sequence-characterized amplified region (SCAR) primers were designed, and the resulted SCAR markers were able to target both cultivated and wild Secale species. The FISH patterns and the two SCAR markers should be able to identify and track all wheat-rye translocation lines, especially the S. africanum chromatin.

Study on Wheat-Rye Translocation Lines

In order to creat wheat-rye translocations which have very important value in wheat breeding and production,we selected the lines with common wheat rye's characters in the crossing between wheat-rye substitution line 5R/5A and 6R/6A.Now we have obtained 9 lines of F6,6-26,06-60-11,06-6-24,06-6-15,06-6-35,6-34,6-28,06-6-17,06-6-14.These lines are useful for the genetic stability and fertility and dry and disease resistance and they have multispikelets with more number of grains per ear,higher grain weight,more ears per plant as well as other good characters.Twenty primer pairs located on chromosomes 5R and 6R were used for SSR amplification in these lines and their parents.The results showed that the molecular marker SCM268 was singled out from 20 primers,which could amplify the specific molecular marker SCM268150 of rye in 8 of 9 lines,6-26,06-60-11,06-6-15,06-6-35,6-34,6-28,06-6-17 and 06-6-14.It can be deduced from the result that the 8 lines are wheat-rye translocation lines which have very important value in production and wheat breeding.

Notes on the origin of 4BL-5RL rye translocations in common wheat (Triticum aestivumL.)

In order to investigate the origin of two 4B-5R wheat-rye translocations a number of microsatellite markers were considered, (a) which were specific for the rye chromosome arm 5RL and (b) which should enable precise characterisation for the gene pool of a ‘Cornell’ wheat derivative. Seven out of eight markers revealed amplification fragments with the rye control, while the marker WMS0186 amplified only a PCR product with the appropriate chromosome arm of the wheat control. The heterogeneity of the DNA fragment patterns among five wheat-rye translocation lines confirms different wheat backgrounds of the American, Danish/UK, Hungarian, and Swedish sources of the 4B-5R translocations. The homogeneous DNA marker patterns of ‘Viking-hairy neck’ and ‘Cornell Sel. 82a1-2-4-7’ are particularly clear. The corresponding molecular markers together with the cytological data, genomic in situ hybridisation, the physiological investigations, and the historical review support the hypothesis of a common origin of ‘Viking-hairy neck’ and ‘Cornell Sel. 82a1-2-4-7’. The importance of the results for practical breeding and for introgression experiments is discussed.

Analysis of DNA methylation variation in wheat genetic background after alien chromatin introduction based on methylation-sensitive amplification polymorphism

During the process of alien germplasm introduced into wheat genome by chromosome engineering, extensive genetic variations of genome structure and gene expression in recipient could be induced. In this study, we performed GISH (genome in situ hybridization) and AFLP (amplified fragment length polymorphism) on wheat-rye chromosome translocation lines and their parents to detect the identity in genomic structure of different translocation lines. The results showed that the genome primary structure variations were not obviously detected in different translocation lines except the same 1RS chromosome translocation. Methylation sensitive amplification polymorphism (MSAP) analyses on genomic DNA showed that the ratios of fully-methylated sites were significantly increased in translocation lines (CN12, 20.15%; CN17, 20.91%; CN18, 22.42%), but the ratios of hemimethylated sites were significantly lowered (CN12, 21.41%; CN17, 23.43%; CN18, 22.42%), whereas 16.37% were fully-methylated and 25.44% were hemimethylated in case of their wheat parent. Twenty-nine classes of methylation patterns were identified in a comparative assay of cytosine methylation patterns between wheat-rye translocation lines and their wheat parent, including 13 hypermethylation patterns (33.74%), 9 demethylation patterns (22.76%) and 7 uncertain patterns (4.07%). In further sequence analysis, the alterations of methylation pattern affected both repetitive DNA sequences, such as retrotransposons and tandem repetitive sequences, and low-copy DNA.

The application of chromosome C--banding to identification on wheat--rye translocation line and substitution line

10 hybrids progeny which showed obvious rye characteristics were examinated by C-banding. 1 wheat-rye translocation line and 2 wheat-rye substitution lines were identified. Proper factors which influenced C-banding results were revised according to seasons （in winter and summer）, the results showed that C-banding was a rapid, economical and feasible method.