Molecular cytogenetic characterization of Dasypyrum breviaristatum chromosomes in wheat background revealing the genomic divergence between Dasypyrum species

Comparative Characterization of Pseudoroegneria libanotica and Pseudoroegneria tauri Based on Their Repeatome Peculiarities

Pseudoroegneria species play an important role among Triticeae grasses, as they are the putative donors of the St genome in many polyploid species. Satellite repeats are widely used as a reliable tool for tracking evolutionary changes because they are distributed throughout the genomes of plants. The aim of our work is to perform a comparative characterization of the repeatomes of the closely related species Ps. libanotica and Ps. tauri, and Ps. spicata was also included in the analysis. The overall repeatome structures of Ps. libanotica, Ps. tauri, and Ps. spicata were similar, with some individual peculiarities observed in the abundance of the SIRE (Ty1/Copia) retrotransposons, Mutator and Harbinger transposons, and satellites. Nine new satellite repeats that have been identified from the whole-genome sequences of Ps. spicata and Ps. tauri, as well as the CL244 repeat that was previously found in Aegilops crassa, were localized to the chromosomes of Ps. libanotica and Ps. tauri. Four satellite repeats (CL69, CL101, CL119, CL244) demonstrated terminal and/or distal localization, while six repeats (CL82, CL89, CL168, CL185, CL192, CL207) were pericentromeric. Based on the obtained results, it can be assumed that Ps. libanotica and Ps. tauri are closely related species, although they have individual peculiarities in their repeatome structures and patterns of satellite repeat localization on chromosomes. The evolutionary fate of the identified satellite repeats and their related sequences, as well as their distribution on the chromosomes of Triticeae species, are discussed. The newly developed St genome chromosome markers developed in the present research can be useful in population studies of Ps. libanotica and Ps. tauri; auto- and allopolyploids that contain the St genome, such as Thinopyrum, Elymus, Kengyilia, and Roegneria; and wide hybrids between wheat and related wild species.

Genome Analysis of Thinopyrum intermedium and Its Potential Progenitor Species Using Oligo-FISH

The genome composition of intermediate wheatgrass (IWG) is complex and continues to be a subject of investigation. In this study, molecular cytogenetics were used to investigate the karyotype composition of Th. intermedium and its relative diploid species. St2-80 developed from Pseudowroegneria strigose and pDb12H developed from Dasypyrum breviaristatum were used as probes in fluorescence in situ hybridization (FISH) to classify the chromosomes of Th. intermedium into three groups, expressed as JvsJvsJrJrStSt. A combined multiplex oligonucleotide probe, including pSc119.2-1, (GAA)10, AFA-3, AFA-4, pAs1-1, Pas1-3, pAs1-4, and pAs1-6, was used to establish the FISH karyotype of ten accessions of Th. intermedium. Variability among and within the studied accessions of intermediate wheatgrass was observed in their FISH patterns. Results of this study led to the conclusions that Jvs had largely been contributed from Da. breviaristatum, but not the present-day Da. villosum; IWG had only one J genome, Jr, which was related to either Th. elongatum or Th. bessarabicum; and St was contributed from the genus Pseudoroegneria by hybridization with Th. junceiforme or Th. sartorii.

Molecular and Cytogenetic Identification of Stem Rust Resistant Wheat-Thinopyrum intermedium Introgression Lines

Thinopyrum intermedium (JJJ^sJ^sStSt, 2n = 6x = 42), a wild relative of common wheat, possesses many desirable agronomic genes for wheat improvement. The production of wheat-Thinopyrum intermedium introgression lines is a key step for transferring these beneficial genes into wheat. In this study, we characterized three wheat-Thinopyrum intermedium introgression lines TA3681, TA5566, and TA5567 using non-denaturing fluorescence in situ hybridization, genomic in situ hybridization, PCR-based landmark unique gene, and intron targeting markers. Our results showed that TA3681 is a wheat-Thinopyrum intermedium 1St disomic addition line, TA5566 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying two pairs of 3A-7J^s translocation chromosomes, and that TA5567 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying a pair of 3A-7J^s translocation chromosomes. We developed 13, 36, and 15 Thinopyrum intermedium chromosome-specific markers for detecting the introgressed Thinopyrum chromosomes in TA3681, TA5566, and TA5567, respectively. Stem rust assessment revealed that TA3681 exhibited a high level of seedling resistance to Chinese-prevalent Puccinia graminis f. sp. tritici pathotypes, and both TA5566 and TA5567 were highly resistant to Australian P. graminis f. sp. tritici pathotypes, indicating that Thinopyrum intermedium chromosomes 1St and 7J^s might carry new stem rust resistance genes. Therefore, the new identified introgression lines may be useful for improving wheat stem rust resistance.

Molecular Cytogenetic Identification of the Wheat–Dasypyrum villosum T3DL·3V#3S Translocation Line with Resistance against Stripe Rust

The annual species Dasypyrum villosum possesses several potentially valuable genes for the improvement of common wheat. Previously, we identified a new stripe rust-resistant line, the Chinese Spring (CS)–D. villosum 3V#3 (3D) substitution line (named CD-3), and mapped its potential rust resistance gene (designated as YrCD-3) on the 3V#3 chromosome originating from D. villosum. The objective of the present study was to further narrow down the YrCD-3 locus to a physical region and develop wheat-3V#3 introgression lines with strong stripe rust resistance. By treating CD-3 seeds with 60Co γ-irradiation, two CS-3V#3 translocation lines, T3V#3S.3DL and T3DS.3V#3L (termed 22-12 and 24-20, respectively), were identified from the M4 generation through a combination of non-denaturing fluorescence in situ hybridization (ND-FISH) and functional molecular markers. Stripe rust resistance tests showed that the line 22-12 exhibited strong stripe rust resistance similarly to CD-3, whereas 24-20 was susceptible to stripe rust similarly to CS, indicating that YrCD-3 is located on the short arm of 3V#3. The line 22-12 can potentially be used for further wheat improvement. Additionally, to trace 3V#3 in the wheat genetic background, we produced 30 3V#3-specific sequence tag (EST) markers, among which, 11 markers could identify 3V#3S. These markers could be valuable in fine-mapping YrCD-3.

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 10 986 and 12 496 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.

Karyotyping Dasypyrum breviaristatum chromosomes with multiple oligonucleotide probes reveals the genomic divergence in Dasypyrum

The perennial species Dasypyrum breviaristatum (genome V^b) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of D. breviaristatum chromosomes will be useful for the detection of Dasypyrum chromatin in wheat background. We established the standard karyotype of 1V^b-7V^b chromosomes through nondenaturing fluorescence in situ hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat - D. breviaristatum partial amphiploid TDH-2 (AABBV^bV^b) and newly identified wheat - D. breviaristatum disomic translocation and addition lines D2138 (6V^bS.2V^bL), D2547 (4V^b), and D2532 (3V^bS.6V^bL) by comparative molecular marker analysis. The ND-FISH with multiple oligo probes was conducted on the durum wheat - D. villosum amphiploid TDV-1 and large karyotype differences between D. breviaristatum and D. villosum was revealed. These ND-FISH probes will be valuable for screening the wheat - Dasypyrum derivative lines for chromosome identification, and the newly developed wheat - D. breviaristatum addition lines may broaden the gene pool of wheat breeding. The differences between D. villosum and D. breviaristatum chromosomes revealed by ND-FISH will help us understand evolutionary divergence of repetitive sequences within the genus Dasypyrum.

Preferential Subgenome Elimination and Chromosomal Structural Changes Occurring in Newly Formed Tetraploid Wheat-Aegilops ventricosa Amphiploid (AABBDvDvNvNv)

Artificial allopolyploids derived from the genera Triticum and Aegilops have been used as genetic resources for wheat improvement and are a classic example of evolution via allopolyploidization. In this study, we investigated chromosomes and subgenome transmission behavior in the newly formed allopolyploid of wheat group via multicolor Fluorescence in situ hybridization (mc-FISH), using pSc119.2, pTa535, and (GAA)₇ as probe combinations, to enabled us to precisely identify individual chromosomes in 381 S₃ and S₄ generations plants derived from reciprocal crosses between Ae. ventricosa (D^vD^vN^vN^v) and T. turgidum (AABB). A higher rate of aneuploidy, constituting 66.04–86.41% individuals, was observed in these two early generations. Of the four constituent subgenomes, D^v showed the highest frequency of elimination, followed by N^v and B, while A was the most stable. In addition, structural chromosomal changes occurred ubiquitously in the selfed progenies of allopolyploids. Among the constituent subgenomes, B showed the highest number of aberrations. In terms of chromosomal dynamics, there was no significant association between the chromosomal behavior model and the cytoplasm, with the exception of chromosomal loss in the D^v subgenome. The chromosome loss frequency in the D^v subgenome was significantly higher in the T. turgidum × Ae. ventricosa cross than in the Ae. ventricosa × T. turgidum cross. This result indicates that, although the D subgenome showed great instability, allopolyploids containing D subgenome could probably be maintained after a certain hybridization in which the D subgenome donor was used as the maternal parent at its onset stage. Our findings provide valuable information pertaining to the behavior patterns of subgenomes during allopolyploidization. Moreover, the allopolyploids developed here could be used as potential resources for the genetic improvement of wheat.

FISH karyotype comparison between Ab- and A-genome chromosomes using oligonucleotide probes

Triticum boeoticum (2n = 2x = 14, A^bA^b) contains beneficial traits for common wheat improvement. The discrimination of A^b-genome chromosomes from A-genome chromosomes is an important step in gene transfer from T. boeoticum to common wheat. In this study, fluorescence in situ hybridization (FISH) analysis using nine oligonucleotide probes revealed high divergence between chromosomes of the common wheat germplasm Crocus and T. boeoticum accession G52. The combination of Oligo-pTa535-HM and Oligo-pSc119.2-HM can differentiate A^b and A chromosomes within homologous groups 2, 4, 5, and 6; chromosomes 2A^b and 6A^b can be identified by using (ACT)₇, (CTT)₇, and (GAA)₇. The probes Oligo-pTa713 and (ACT)₇ can be utilized for the identification of chromosomes 1A^b and 3A^b, respectively. Probes (CAG)₇ and (CAC)₇ can be applied in the identification of 7A^b. Moreover, probe combinations consisting of Oligo-pTa535-HM and (AAC)₇ with (ACT)₇ or (CTT)₇ and of Oligo-pTa535-HM and Oligo-pTa713 with (CAC)₇ or (CTT)₇ will help discriminate the A^b-genome chromosomes of T. boeoticum. These probes are being used as potential markers to select common wheat Crocus-T. boeoticum G52 alien chromosome lines. Moreover, FISH patterns are highly divergent between A^b- and A-genome chromosomes, indicating that obvious chromosome structural variations arose during wheat evolution.

Molecular-cytogenetic analysis of diploid wheatgrass Thinopyrum bessarabicum (Savul. and Rayss) A. Löve

Thinopyrum bessarabicum (T. Săvulescu & T. Rayss, 1923) A. Löve, 1980 is diploid (2n=2x=14, JJ or E^bE^b), perennial self-fertilizing rhizomatous maritime beach grass, which is phylogenetically close to another diploid wheatgrass species, Agropyron elongatum (N. Host, 1797) P. de Beauvois, 1812. The detailed karyotype of Th. bessarabicum was constructed based on FISH with six DNA probes representing 5S and 45S rRNA gene families and four tandem repeats. We found that the combination of pAesp_SAT86 (= pTa-713) probe with pSc119.2 or pAs1/ pTa-535 allows the precise identification of all J-genome chromosomes. Comparison of our data with the results of other authors showed that karyotypically Th. bessarabicum is distinct from A. elongatum. On the other hand, differences between the J-genome chromosomes of Th. bessarabicum and the chromosomes of hexaploid Th. intermedium (N. Host, 1797) M. Barkworth & D.R. Dewey, 1985 and decaploid Th. ponticum (J. Podpěra, 1902) Z.-W. Liu & R.-C. Wang, 1993 in the distribution of rDNA loci and hybridization patterns of pSc119.2 and pAs1 probes could be an indicative of (1) this diploid species was probably not involved in the origin of these polyploids or (2) it could has contributed the J-genome to Th. intermedium and Th. ponticum, but it was substantially modified over the course of speciation.

Identification of P genome chromosomes in Agropyron cristatum and wheat-A. cristatum derivative lines by FISH

Agropyron cristatum (L.) Gaertn. (P genome) is cultivated as pasture fodder and can provide many desirable genes for wheat improvement. With the development of genomics and fluorescence in situ hybridization (FISH) technology, probes for identifying plant chromosomes were also developed. However, there are few reports on A. cristatum chromosomes. Here, FISH with the repeated sequences pAcTRT1 and pAcpCR2 enabled the identification of all diploid A. cristatum chromosomes. An integrated idiogram of A. cristatum chromosomes was constructed based on the FISH patterns of five diploid A. cristatum individuals. Structural polymorphisms of homologous chromosomes were observed not only among different individuals but also within individuals. Moreover, seventeen wheat-A. cristatum introgression lines containing different P genome chromosomes were identified with pAcTRT1 and pAcpCR2 probes. The arrangement of chromosomes in diploid A. cristatum was determined by identifying correspondence between the P chromosomes in these genetically identified introgression lines and diploid A. cristatum chromosomes. The two probes were also effective for discriminating all chromosomes of tetraploid A. cristatum, and the differences between two tetraploid A. cristatum accessions were similar to the polymorphisms among individuals of diploid A. cristatum. Collectively, the results provide an effective means for chromosome identification and phylogenetic studies of P genome chromosomes.

Diversified Chromosome Rearrangements Detected in a Wheat‒Dasypyrum breviaristatum Substitution Line Induced by Gamma-Ray Irradiation

To determine the composition of chromosome aberrations in a wheat‒Dasypyrum breviaristatum substitution line with seeds treated by a dose of gamma-rays (200 Gy), sequential non-denaturing fluorescence in situ hybridization (ND-FISH) with multiple oligonucleotide probes was used to screen individual plants of the mutagenized progenies. We identified 122 types of chromosome rearrangements, including centromeric, telomeric, and intercalary chromosome translocations from a total of 772 M1 and 872 M2 plants. The frequency of reciprocal translocations between B- and D-chromosomes was higher than that between A- and D-chromosomes. Eight translocations between D. breviaristatum and wheat chromosomes were also detected. The 13 stable plants with multiple chromosome translocations displayed novel agronomic traits. The newly developed materials will enhance wheat breeding programs through wheat‒Dasypyrum introgression and also facilitate future studies on the genetic and epigenetic effects of translocations in wheat genomics.

Physical location of tandem repeats in the wheat genome and application for chromosome identification

A general distribution of tandem repeats (TRs) in the wheat genome was predicted and a new web page combined with fluorescence in situ hybridization experiments, and the newly developed Oligo probes will improve the resolution for wheat chromosome identification. Comprehensive sequence analysis of tandem repeats (TR) in the wheat reference genome permits discovery and application of TRs for chromosome identification. Genome-wide localization of TRs was identified in the reference sequences of Chinese Spring using Tandem Repeat Finder (TRF). A database of repeats unit size, array number, and physical coverage length of TRs in the wheat genome was built. The distribution of TRs occupied 3-5% of the wheat chromosomes, with non-random dispersal across the A, B, and D genomes. Three classes of TRs surrounding the predicted genes were compared. An optimized computer-assisted website page B2DSC was constructed for the general distribution and chromosomally enriched zones of TR sequences to be displayed graphically. The physical distribution of predicted TRs in the wheat genome by B2DSC matched well with the corresponding hybridization signals obtained with fluorescence in situ hybridization (FISH). We developed 20 oligonucleotide probes representing 20-60 bp lengths of high copy number of TRs and verified by FISH. An integrated physical map of TR-Oligo probes for wheat chromosome identification was constructed. Our results suggest that the combination of both molecular cytogenetics and genomic research will significantly benefit wheat breeding through chromosome manipulation and engineering.

Characterization of New Wheat-Dasypyrum breviaristatum Introgression Lines with Superior Gene(s) for Spike Length and Stripe Rust Resistance

Dasypyrum breviaristatum (genome VbVb) contains potentially important traits for commercial wheat production. Chromosome 2Vb of D. breviaristatum carries several desirable agronomic characters, including long spike length as well as enhanced resistance to stripe rust, which are expressed in a common wheat background. In this study, wheat-D. breviaristatum 2Vb deletion lines were produced and identified by fluorescence in situ hybridization (FISH), and 74 molecular markers specific to D. breviaristatum chromosome 2Vb were physically localized in 4 distinct chromosomal regions. New wheat-D. breviaristatum 2Vb translocation lines were also characterized by FISH. The breakpoint of the translocation T3AS.3AL-2VbS was determined by physically mapped molecular markers. Field evaluation revealed that genes affecting plant height and spike length are located on fraction length (FL) 0.65-1.00 of 2VbS, while the stripe rust resistance gene(s) are located on FL 0.40-1.00 of D. breviaristatum chromosome 2VbL. The newly characterized wheat-Dasypyrum chromosomal introgressions are of potential value for the improvement of the yield and disease resistance of wheat.

Molecular markers and cytogenetics to characterize a wheat-Dasypyrum villosum 3V (3D) substitution line conferring resistance to stripe rust

Dasypyrum villosum has been used as a valuable gene resource for disease resistances, yield increase and quality improvement in wheat. A novel wheat-D. villosum alien introgression line CD-3 was generated through hybridization between the common wheat Chinese Spring (CS) and a CS- D. villosum 3V addition line having considerably high stripe rust resistance, which enable the characterization of a potential new stripe rust resistance gene (s) derived from D. villosum. The results of non-denaturing fluorescent in situ hybridization (ND-FISH) showed that CD-3 contained 42 chromosomes, including a 3V chromosome pair, and the absence of both of the 3D chromosomes. PCR-based Landmark Unique Gene (PLUG) molecular marker analysis supported results from the FISH analysis, revealing CD-3 was a wheat-D. villosum 3V (3D) disomic substitution line. Resistant test of stripe rust on 52 plants of F2 generation (CD-3/CS), CD-3, CS and D.villosum have been conducted at seedling stage. 7 plants of F2 generation possessing two 3V chromosomes exhibited high resistance to stripe rust as CD-3 and D.villosum, 10 plants carrying one 3V chromosome and 35 plants without 3V chromosome were susceptive to stripe rust as CS. The result implied the high stripe rust resistance of CD-3 should be controlled by recessive gene(s) originating from D.villosum. To rapidly detect chromosome 3V in the genetic background of wheat, we developed a novel Sequence Characterized Amplified Region (SCAR) marker specific for 3V chromosome based on the sequence of a grain size-related gene DvGS5 in D. villosum, an orthologue of TaGS5 from wheat. The SCAR marker was designated DvGS5-1443, which could successfully amplify a unique 3V-specific fragment in CD-3 and D. villosum, suggesting that this SCAR marker could facilitate targeting the chromosome 3V in the genetic background of wheat for wheat improvement.

Developing New Oligo Probes to Distinguish Specific Chromosomal Segments and the A, B, D Genomes of Wheat (Triticum aestivum L.) Using ND-FISH

Non-denaturing FISH (ND-FISH) technology has been widely used to study the chromosomes of Triticeae species because of its convenience. The oligo probes for ND-FISH analysis of wheat (Triticum aestivum L.) chromosomes are still limited. In this study, the whole genome shotgun assembly sequences (IWGSC WGA v0.4) and the first version of the reference sequences (IWGSC RefSeq v1.0) of Chinese Spring (T. aestivum L.) were used to find new tandem repeats. One hundred and twenty oligo probes were designed according to the new tandem repeats and used for ND-FISH analysis of chromosomes of wheat Chinese Spring. Twenty nine of the 120 oligo probes produce clear or strong signals on wheat chromosomes. Two of the 29 oligo probes can be used to conveniently distinguish wheat A-, B-, and D-genome chromosomes. Sixteen of the 29 oligo probes only produce clear or strong signals on the subtelomeric regions of 1AS, 5AS, 7AL, 4BS, 5BS, and 3DS arms, on the telomeric regions of 1AL, 5AL, 2BS, 3BL, 6DS, and 7DL arms, on the intercalary regions of 4AL and 2DL arms, and on the pericentromeric regions of 3DL and 6DS arms. Eleven of the 29 oligo probes generate distinct signal bands on several chromosomes and they are different from those previously reported. In addition, the short and long arms of 6D chromosome have been confirmed. The new oligo probes developed in this study are useful and convenient for distinguishing wheat chromosomes or specific segments of wheat chromosomes.

Molecular Cytogenetic Characterization of New Wheat-Dasypyrum breviaristatum Introgression Lines for Improving Grain Quality of Wheat

As an important relative of wheat (Triticum aestivum L), Dasypyrum breviaristatum contains novel high molecular weight glutenin subunits (HMW-GSs) encoded by Glu-1Vb genes. We identified new wheat-D. breviaristatum chromosome introgression lines including chromosomes 1V^b and 1V^bL.5V^bL by fluorescence in situ hybridization (FISH) combined with molecular markers. We found that chromosome changes occurred in the wheat-D. breviaristatum introgression lines and particularly induced the deletion of 5BS terminal repeats and formation of a new type of 5B-7B reciprocal translocation. The results imply that the D. breviaristatum chromosome 1V^b may contain genes which induce chromosomal recombination in wheat background. Ten putative high molecular weight glutenin subunit (HMW-GS) genes from D. breviaristatum and wheat-D. breviaristatum introgression lines were isolated. The lengths of the HMW-GS genes in Dasypyrum were significantly shorter than typical HMW-GS of common wheat. A new y-type HMW-GS gene, named Glu-Vb1y, was characterized in wheat-D. breviaristatum 1V^b introgression lines. The new wheat-D. breviaristatum germplasm displayed reduced plant height, increased tillers and superior grain protein and gluten contents, improved gluten performance index. The results showed considerable potential for utilization of D. breviaristatum chromosome 1V^b segments in future wheat improvement.

Isolation of two new retrotransposon sequences and development of molecular and cytological markers for Dasypyrum villosum (L.)

Dasypyrum villosum is a valuable genetic resource for wheat improvement. With the aim to efficiently monitor the D. villosum chromatin introduced into common wheat, two novel retrotransposon sequences were isolated by RAPD, and were successfully converted to D. villosum-specific SCAR markers. In addition, we constructed a chromosomal karyotype of D. villosum. Our results revealed that different accessions of D. villosum showed slightly different signal patterns, indicating that distribution of repeats did not diverge significantly among D. villosum accessions. The two SCAR markers and FISH karyotype of D. villosum could be used for efficient and precise identification of D. villosum chromatin in wheat breeding.

Oligonucleotides and ND-FISH Displaying Different Arrangements of Tandem Repeats and Identification of Dasypyrum villosum Chromosomes in Wheat Backgrounds

Oligonucleotide probes and the non-denaturing fluorescence in situ hybridization (ND-FISH) technique are widely used to analyze plant chromosomes because they are convenient tools. New oligonucleotide probes, Oligo-Ku, Oligo-3B117.1, Oligo-3B117.2, Oligo-3B117.2.1, Oligo-3B117.3, Oligo-3B117.4, Oligo-3B117.5, Oligo-3B117.6, Oligo-pTa71A-1, Oligo-pTa71A-2, Oligo-pTa71B-1, Oligo-pTa71B-2, Oligo-pTa71C-1, Oligo-pTa71C-2, Oligo-pTa71C-3 and Oligo-pTa71D were designed based on the repetitive sequences KU.D15.15, pSc119.2-like sequence 3B117 and pTa71. Oligonucleotide probe (GT)₇ was also used. Oligo-Ku and (GT)₇ can be together used to identify Dasypyrum villosum from wheat chromosomes and to distinguish individual D. villosum chromosomes. The oligonucleotide probes that were derived from the same repeat sequence displayed different signal intensity and hybridization sites on the same chromosomes. Both the length and the nucleotide composition of oligonucleotide probes determined their signal intensity. For example, Oligo-3B117.2 (25 bp) and Oligo-pTa71A-2 (46 bp) produced the strongest signals on chromosomes of wheat (Triticum aestivum L.), rye (Secale cereale L.), barley (Hordeum vulgare ssp. vulgare) or D. villosum, the signal of Oligo-3B117.4 (18 bp) on the short arm of 7B chromosome was weaker than that of Oligo-3B117.2.1 (15 bp) and Oligo-3B117.3 (16 bp), and Oligo-pTa71A-1 (38 bp) produced the same strong signals as Oligo-pTa71A-2 did on 1B and 6B chromosomes, but its signals on 1R and 1V chromosomes were weaker than the ones of Oligo-pTa71A-2. Oligonucleotide probes and ND-FISH analysis can reflect the distribution and structural statues of different segments of tandem repeats on chromosomes. The possible reasons why different segments derived from the same repeat sequence produced different signal patterns are discussed.

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents

New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.