Genomic rearrangement between wheat and Thinopyrum elongatum revealed by mapped functional molecular markers

Thinopyrum elongatum serves as an excellent gene pool for wheat improvement. Genes for resistance to many biotic and abiotic stresses have been transferred from Th. elongatum to wheat through chromosome manipulation. For breeding programs, molecular markers enable screening of a large number of genotypes for alien chromosome introgressions. The main objective of the present study was to develop and characterize EST (expressed sequence tags) and PLUG (PCR-based Landmark Unique Gene) markers that can distinguish Th. elongatum chromatin from the wheat genomes. A total of 258 mapped EST primer pairs and 46 PLUG primer pairs were tested on DNA from wheat Chinese Spring (CS) and CS-Th. elongatum addition lines. The results showed that 43 primer pairs could be effectively mapped to specific Th. elongatum chromosomes. Twenty-two of the 43 markers displayed similar homoeologous chromosome locations to hexaploid wheat. Nine markers mapped to different linkage groups between wheat and Th. elongatum, while 12 makers mapped on two or three different Th. elongatum chromosomes. A comparison of molecular marker locations indicated that Th. elongatum genome was closely related to the D genome of wheat, and chromosome rearrangements and duplication had occurred in Th. elongatum and the wheat genomes. The markers will be useful in comparative gene mapping, chromosome evolutionary analysis, and gene introgression for wheat improvement using Th. elongatum accessions as gene donors.     

Development and utilization of new sequenced characterized amplified region markers specific for E genome of Thinopyrum

Species containing E genome of Thinopyrum offered potential to increase the genetic variability and desirable characters for wheat improvement. However, E genome specific marker was rare. The objective of the present report was to develop and identify sequenced characterized amplified region (SCAR) markers that can be used in detecting E chromosome in wheat background for breeding purpose. Total 280 random amplified polymorphic DNA (RAPD) primers were amplified for seeking of E genome specific fragments by using the genomic DNA of Thinopyrum elongatum and wheat controls as templates. As a result, six RAPD fragments specific for E genome were found and cloned, and then were converted to SCAR markers. The usability of these markers was validated using a number of Egenome-containing species and wheat as controls. These markers were subsequently located on E chromosomes using specific PCR and fluorescence in situ hybridization (FISH). SCAR markers developed in this research could be used in molecular marker assisted selection of wheat breeding with Thinopyrum chromatin introgressions.     

Physical mapping of the blue-grained gene from <Emphasis Type="Italic">Thinopyrum ponticum</Emphasis> chromosome 4Ag and development of blue-grain-related molecular markers and a FISH probe based on SLAF-seq technology

Key message

A Thinopyrum ponticum chromosome 4Ag physical map was constructed, the blue-grained gene was localized, and related specific markers and a FISH probe were developed by SLAF-seq.

Abstract

Decaploid Thinopyrum ponticum (2n?=?10x?=?70) serves as an important gene pool for wheat improvement. The wheat-Th. ponticum 4Ag (4D) disomic substitution line Blue 58, derived from a distant hybridization between Th. ponticum and common wheat (Triticum aestivum L.), bears blue coloration in the aleurone layer. To map the blue-grained gene, eight wheat-Th. ponticum 4Ag translocation lines with different chromosomal segment sizes were obtained from Blue 58 using ⁶⁰Co-γ ray irradiation and were characterized using cytogenetic and molecular marker analysis. A small-segment blue-grained wheat translocation line L13, accounting for one-fifth of 4AgL, was obtained. A physical map of chromosome 4Ag was constructed containing 573 specific-locus amplified fragment sequencing (SLAF-seq) markers, including three bins with 223 markers on 4AgS and eight bins with 350 markers on 4AgL. The blue-grained gene in three blue-grained translocation lines L5, L9, and L13, was located on bin 4AgL-6 with FL 0.75–0.89. Moreover, 89 blue-grain-related molecular markers and one fluorescence in situ hybridization (FISH) probe, pThp12.19, were identified in this bin. The newly developed translocation lines and the molecular markers and FISH probe will facilitate the application of the Th. ponticum-origin blue-grained characteristic in wheat breeding.

     

Whole genome development of intron targeting (IT) markers specific for <Emphasis Type="Italic">Dasypyrum villosum</Emphasis> chromosomes based on next-generation sequencing technology

Dasypyrum villosum (Dv), a wild relative of wheat, is an important and useful gene resource for wheat improvement. A large number of wheat-Dv aneuploid lines harboring whole or fragments of Dv chromosomes have been developed. However, the lack of sufficient molecular markers hindered accurate identification of Dv chromatin, especially when the introgressed fragments are small. Development of molecular markers covering the whole Dv genome and evenly distributed on different chromosome regions is not only useful for the detection of the introgressed alien chromatin in wheat background, but also provides evidence of the syntenic relationship between homoeologous chromosomes. In the present study, in order to develop high density and evenly distributed molecular markers on individual Dv chromosomes, genomic DNA of Dv leaves was sequenced and assembled. Sequence assemblies of all wheat chromosomes were first used to identify exon–exon junctions and localize introns in Dv. Intron length polymorphisms suitable for designing Dv primers flanking introns were evaluated, and a total of 1624 intron targeting (IT) markers was designed. By using the Chinese Spring, the Triticum durum-Dv amphiploid and the Dv sequenced DNA libraries, 841 IT molecular markers specific for Dv chromosomes were developed, with maximum efficiency up to 51.79%. We assigned the 841 IT markers to seven Dv chromosomes (1V–7V) using seven wheat–Dv chromosome addition and substitution lines: 135 to 1V, 175 to 2V, 120 to 3V, 89 to 4V, 140 to 5V, 71 to 6V, and 111 to 7V, respectively. Using T. aestivum-Dv telosomic and whole arm translocation lines, they were further located on the short or long chromosome arms. These specific markers for individual chromosomes of Dv provided efficient tools for the characterization of structural variation involving the individual chromosome of Dv, as well as for the selection of useful genes located on individual Dv chromosome in breeding programs.     

Thinopyrum 7Ai-1-derived small chromatin with Barley Yellow Dwarf Virus (BYDV) resistance gene integrated into the wheat genome with retrotransposon

Thinopyrum intermedium is a useful source of resistance genes for Barley Yellow Dwarf Virus (BYDV), one of the most damaging wheat diseases. In this study, wheat/Th. intermedium translocation lines with a BYDV resistance gene were developed using the Th. intermedium 7Ai-1 chromosome. Genomic in situ hybridization (GISH), using a Th. intermedium total genomic DNA probe, enabled detection of 7Ai-1-derived small chro-matins containing a BYDV resistance gene, which were translocated onto the end of wheat chromosomes in the lines Y95011 and Y960843. Random amplified polymorphic DNA (RAPD) analyses using 120 random 10-mer primers were conducted to compare the BYDV-resistant translocation lines with susceptible lines. Two primers amplified the DNA fragments specific to the resistant line that would be useful as molecular markers to identify 7Ai-1-derived BYDV resistance chromatin in the wheat genome. Additionally, the isolated Th. intermedium-specific retrotransposon-like sequence pTi28 can be used to identify Th. intermedium chromatin transferred to the wheat genome.     

Chromosomal control of the tolerance of gradually and suddenly imposed salt stress in the Lophopyrum elongatum and wheat,Triticum aestivum L. genomes

The facultatively halophytic Lophopyrum elongatum, closely related wheat, Triticum aestivum, and their amphiploid tolerate salt stress better if they are gradually exposed to it than if they are suddenly stressed. Lophopyrum elongatum has greater tolerance of both forms of salt stress than wheat, and its genome partially confers this tolerance on their amphiploid. Chromosomal control of the tolerance of both stress regimes in the L. elongatum and wheat genomes was investigated with disomic and ditelosomic addition lines and disomic substitution lines of L. elongatum chromosomes in wheat and with wheat tetrasomics. The tolerance of the sudden salt stress is principally controlled by L. elongatum chromosomes 3E and 5E and less by 1E, 2E, 6E, and 7E and the tolerance of gradually imposed salt stress principally by chromosomes 3E, 4E, and 5E, and less by chromosome 1E and 7E. Ditelosomic analysis indicated that genes conferring the tolerance of sudden stress are on chromosome arms 1EL, 5ES, 5EL, 6EL, 7ES and 7EL and those controlling the gradual stress regime are on 1ES, 1EL, 5ES, 5EL, 6ES, 7ES, and 7EL. In wheat, chromosomes in homoeologous groups 1, 3, and 7 and chromosomes in homoeologous groups 1, 4, and 6 were shown to enhance the tolerance of suddenly and gradually imposed stress, respectively. The arms of chromosome 3E individually conferred tolerance to neither stress regime. Chromosome 2E and wheat chromosomes 2B and 2D reduce the tolerance of both stress regimes in a hyperploid state. In 2E this effect was associated with arm 2EL. A potential relationship between the tolerance of these stress regimes and the expression of the early-salt induced genes is examined.     

Development and characterization of wheat lines carrying stem rust resistance gene Sr43 derived from Thinopyrum ponticum

Key message

Wheat lines carrying Ug99-effective stem rust resistance gene Sr43 on shortened alien chromosome segments were produced using chromosome engineering, and molecular markers linked to Sr43 were identified for marker-assisted selection.

Abstract

Stem rust resistance gene Sr43, transferred into common wheat (Triticum aestivum) from Thinopyrum ponticum, is an effective gene against stem rust Ug99 races. However, this gene has not been used in wheat breeding because it is located on a large Th. ponticum 7el₂ chromosome segment, which also harbors genes for undesirable traits. The objective of this study was to eliminate excessive Th. ponticum chromatin surrounding Sr43 to make it usable in wheat breeding. The two original translocation lines KS10-2 and KS24-1 carrying Sr43 were first analyzed using simple sequence repeat (SSR) markers and florescent genomic in situ hybridization. Six SSR markers located on wheat chromosome arm 7DL were identified to be associated with the Th. ponticum chromatin in KS10-2 and KS24-1. The results confirmed that KS24-1 is a 7DS·7el₂L Robertsonian translocation as previously reported. However, KS10-2, which was previously designated as a 7el₂S·7el₂L-7DL translocation, was identified as a 7DS-7el₂S·7el₂L translocation. To reduce the Th. ponticum chromatin carrying Sr43, a BC₂F₁ population (Chinese Spring//Chinese Spring ph1bph1b*2/KS10-2) containing ph1b-induced homoeologous recombinants was developed, tested with stem rust, and genotyped with the six SSR markers identified above. Two new wheat lines (RWG33 and RWG34) carrying Sr43 on shortened alien chromosome segments (about 17.5 and 13.7 % of the translocation chromosomes, respectively) were obtained, and two molecular markers linked to Sr43 in these lines were identified. The new wheat lines with Sr43 and the closely linked markers provide new resources for improving resistance to Ug99 and other races of stem rust in wheat.     

Chromosomal Localization of Genes Conferring Desirable Agronomic Traits from Wheat-Agropyron cristatum Disomic Addition Line 5113

Creation of wheat-alien disomic addition lines and localization of desirable genes on alien chromosomes are important for utilization of these genes in genetic improvement of common wheat. In this study, wheat-Agropyron cristatum derivative line 5113 was characterized by genomic in situ hybridization (GISH) and specific-locus amplified fragment sequencing (SLAF-seq), and was demonstrated to be a novel wheat-A. cristatum disomic 6P addition line. Compared with its parent Fukuhokomugi (Fukuho), 5113 displayed multiple elite agronomic traits, including higher uppermost internode/plant height ratio, larger flag leaf, longer spike length, elevated grain number per spike and spikelet number per spike, more kernel number in the middle spikelet, more fertile tiller number per plant, and enhanced resistance to powdery mildew and leaf rust. Genes conferring these elite traits were localized on the A. cristatum 6P chromosome by using SLAF-seq markers and biparental populations (F₁, BC₁F₁ and BC₁F₂ populations) produced from the crosses between Fukuho and 5113. Taken together, chromosomal localization of these desirable genes will facilitate transferring of high-yield and high-resistance genes from A. cristatum into common wheat, and serve as the foundation for the utilization of 5113 in wheat breeding.     

Identification and Physical Mapping of New PCR-Based Markers Specific for the Long Arm of Rye(Secale cereale L.) Chromosome 6

To effectively use elite genes on the long arm of rye chromosome 6(the 6RL arm) in wheat breeding programs,precise and fast identification of 6RL chromatin in wheat backgrounds is necessary.PCR-based 6RL-specific markers can facilitate the detection of elite genes on 6RL in wheat breeding.However,only a limited number of 6RL-specific markers have been developed.In the present study.300 new PCR-based 6RL-specific markers were identified using specific length amplified fragment sequencing(SLAF-seq) technology,and were further physically mapped to four regions on the 6RL arm using 6R and 6RL deletion lines.Interestingly,127 of the 300 markers were physically localized to a region from the site between 2.3 and 2.5 to the telomere,the same region where the powdery mildew resistance gene was mapped.In addition,95 of the 300 markers exhibit polymorphisms,which can be used to investigate the diversity of rye 6RL arms.The markers developed in this study can be used to identify given segments of 6RL in wheat backgrounds and accelerate the utilization of elite genes on 6RL in wheat breeding.     

Chromosomal location of wheat genes of the carotenoid biosynthetic pathway and evidence for a catalase gene on chromosome 7A functionally associated with flour b* colour variation

Knowledge of molecular and genetic mechanisms controlling wheat grain quality characteristics is significant for improving flour for end-product functionality. Flour b* colour is an important quality trait for breeding wheat varieties to produce grain for specific market requirements. The degree of flour yellowness is due to the accumulation of carotenoids in grain, particularly lutein. Flour b* is under polygenic control and quantitative trait loci (QTL) have frequently been reported on chromosome 7AL. Analysis of carotenoid genes showed that phytoene synthase (PSY) co-located to the QTL on 7AL but other genes at this locus are also thought to contribute flour b* colour variation. This study used the wheat genome survey sequence and identified the chromosomal location of all wheat carotenoid genes, but none other than PSY were located on 7AL and, therefore, other genes may control flour b* colour variation including oxidative genes that degrade carotenoids. An investigation of EST bin mapped to 7AL identified a gene encoding a catalase enzyme (Cat3-A1) that was phylogenetically related to other plant class III enzymes, co-located to the QTL for flour b* colour variation on 7AL in three mapping populations and expressed during seed development. Therefore, Cat3-A1 was functionally associated with flour b* colour variation. Catalase acts upon hydrogen peroxide as a substrate and it was postulated that Cat3-A1 alleles control varying degrees of bleaching action on lutein in developing wheat grain. Markers for Cat3-A1 developed in this study can be used in conjunction with other candidate gene markers including phytoene synthase and lycopene-ε-cylase to develop a molecular signature for selecting lines with specific flour b* colour values in wheat breeding.     

Analysis of nucleolar activity in Agropyron elongatum,its amphiploid with Triticum aestivum and the chromosome addition lines

Summary The nucleolar organizer activity of the Agropyron elongatum, its amphiploid with hexaploid wheat (Triticum aestivum) and the chromosome addition lines is analyzed by the silver-staining procedure. Four Ag-NORs are observed in A. elongatum corresponding to the chromosomes 6E and 7E. In the amphiploid T. aestivum — A. elongatum, eight Ag-NORs are observed which corresponds the wheat chromosomes 1B and 6B and to the elongatum chromosomes 6E and 7E. Thus, there is codominance in the nucleolar organizer activity of the chromosomes of the two species. However, a partial amphiplasty is detected since less than 8 Ag-NORs (7 up to 4) are observed in some metaphase cells; the chromosomes 6E and 7E are occasionally suppressed by wheat chromosomes. This conclusion is confirmed by the behaviour of the addition lines since only in those corresponding to the chromosomes 6E and 7E are the elongatum chromosomes nucleolar active although occasionally they can be suppressed by wheat chromosomes.     

Physical localization of a novel blue-grained gene derived from Thinopyrum bessarabicum

Blue wheat grain contains different groups of pigments that can be used for making specialty foods or as food colorants. Thinopyrum bessarabicum, a wild relative of wheat, carries a blue-grained gene on chromosome 4J. In this study, we analyzed the mitotic chromosomes of 159 F7 lines derived from the cross between Triticum aestivum cv. Chinese Spring (CS) and a CS–Th. bessarabicum amphiploid by using multi-color fluorescence in situ hybridization, genomic in situ hybridization, and newly developed chromosome 4J-specific DNA markers. Intact chromosome 4J and various 4J chromosomal segments were identified in the 159 lines. The blue-grained gene of Th. bessarabicum was physically localized to the region between the centromere and FL0.52 on chromosome arm 4JL. The chromosomal location of this gene differed from the location of previously reported blue-grained genes. In addition, a strong dosage effect was observed with this gene. These results suggest that the blue-grained gene in Th. bessarabicum represents a novel gene locus for blue aleurone, designated BaThb. The wheat lines and 4J chromosome-specific molecular markers developed in this study will facilitate the introgression and utilization of BaThb for wheat nutritional quality improvement.     

Meiotic homoeologous recombination-based mapping of wheat chromosome 2B and its homoeologues in <Emphasis Type="Italic">Aegilops speltoides</Emphasis> and <Emphasis Type="Italic">Thinopyrum elongatum</Emphasis>

Key message

We physically dissected and mapped wheat chromosome 2B and its homoeologues in Aegilops speltoides and Thinopyrum elongatum based on meiotic homoeologous recombination, providing a unique physical framework for genome studies.

Abstract

Common wheat has a large and complex genome with narrow genetic diversity and various degrees of recombination between the A, B, and D subgenomes. This has limited the homologous recombination-based genome studies in wheat. Here, we exploited meiotic homoeologous recombination for molecular mapping of wheat chromosome 2B and its homoeologue 2S from Aegilops speltoides and 2E from Thinopyrum elongatum. The 2B–2S and 2B–2E recombination was induced by the ph1b mutant, and recovered using molecular markers and fluorescent genomic in situ hybridization (FGISH). A total of 112 2B–2S and 87 2B–2E recombinants involving different chromosome regions were developed and physically delineated by FGISH. The 2B–2S and 2B–2E recombination hotspots mapped to the subterminal regions on both arms. Recombination hotspots with the highest recombination rates mapped to the short arms. Eighty-three 2B–2S and 67 2B–2E recombinants were genotyped using the wheat 90 K SNP arrays. Based on the genotyping results and FGISH patterns of the recombinants, chromosomes 2B, 2S, and 2E were partitioned into 93, 66, and 46 bins, respectively. In total, 1037 SNPs physically mapped onto distinct bins of these three homoeologous chromosomes. A homoeologous recombination-based bin map was constructed for chromosome 2B, providing a unique physical framework for genome studies in wheat and its relatives. Meiotic homoeologous recombination also facilitates gene introgression to diversify the wheat genome for germplasm development. Therefore, homoeologous recombination-based studies enhance understanding of the wheat genome and its homoeologous counterparts from wild grasses, and expand the genetic variability of the wheat genome.

     

Induction of 4VS chromosome recombinants using the CS ph1b mutant and mapping of the wheat yellow mosaic virus resistance gene from Haynaldia villosa

The wheat spindle streak mosaic virus (WSSMV) or wheat yellow mosaic virus (WYMV) resistance gene, Wss1, from Haynaldia villosa, was previously mapped to the chromosome arm 4VS by the development of 4V (4D) substitution and T4DL·4VS translocation lines. For better utilization and more accurate mapping of the Wss1, in this research, the CS ph1b mutant was used to induce new translocations with shortened 4VS chromosome fragments. Thirty-five homozygous translocations with different alien fragment sizes and breakpoints of 4VS were identified by GISH and molecular marker analysis. By field test, it was found that all the identified terminal translocations characterized as having smaller 4VS chromosome segments in the chromosome 4DS were highly resistant to WYMV, while all the interstitial translocations with 4VS inserted into the 4DS were WYMV susceptible. Marker analysis using 32 4VS-specific markers showed that both the terminal and interstitial translocations had different alien fragment sizes. Five specific markers could be detected in the WYMV-resistant terminal translocation line NAU421 with the shortest introduced 4VS fragment, indicating they can be used for marker-assisted selection in wheat breeding. Based on the resistance evaluation, GISH and molecular marker analysis of the available translocations, the gene(s) conferring the WYMV resistance on 4VS could be further cytologically mapped to the distal region of 4VS, immersed in the bin of FL 0.78–1.00. The newly developed small fragment translocations with WYMV resistance and 4VS specific markers have laid solid groundwork for the utilization in wheat breeding for WYMV resistance as well as further cloning of Wss1.     

A cytogenetic study of the blue-grain line of the common wheat cultivar Saratovskaya 29

The chromosome composition of the blue-grain line i:S29Ba of the cultivar Saratovskaya 29 was identified by cytological, GISH, and microsatellite analyses and C-banding. It was found that common wheat chromosome 4B of the cultivar Saratovskaya 29 was substituted with the Agropyron elongatum Host. chromosome carrying the gene for blue grain (s:S294Ag(4B)) during the construction of this nearly isogenic line. The blue-grain line was tested for productivity. The substitution of total chromosome 4B of the cultivar Saratovskaya 29 by Ag. elongatum chromosome 4 did not significantly affect the spike productivity parameters and grain quality with the exception of spike length (plus effect), spike density, and vitreousness (minus effects). The blue-grain line with s:S294Ag(4B) can be used in further studies associated with chromosome engineering in cereals and wheat breeding.     

Development of V chromosome alterations and physical mapping of molecular markers specific to <Emphasis Type="Italic">Dasypyrum villosum</Emphasis>

Wheat-Dasypyrum villosum translocations were induced in the progeny of the amphiploid Triticum durum-D. villosum (AABBVV) by pollen irradiation. The rearranged V genome chromosomes were characterized by genomic/fluorescence in situ hybridization (GISH/FISH) and molecular markers. Twenty wheat-D. villosum translocation chromosomes were selected, including four centric, seven large segments, and nine small segments in a Chinese Spring (CS) background. The four centric translocations were subsequently identified by GISH/FISH and by molecular markers specific to chromosome arms of the Triticeae linkage groups. They were T5DL.4VL, T4BL.7VS, and T4BS.7VL as well as the compensating translocation T7AL.7VS. Using a combination of previously developed V chromosome alterations, 52 translocations or deletions that divided V chromosomes into 42 bins were employed for deletion mapping of molecular markers specific to D. villosum in a wheat background. Ninety-five expressed sequence tag (EST)-sequence-tagged site (STS) and seven SSR markers that were previously reported, as well as 72 STS markers screened in the present study, were physically allocated into 37 of 42 chromosome bins of D. villosum. Multiple loci of EST-STS markers were also mapped using CS nullisomic tetrasomic (NT) and ditelosomic (DT) genetic stocks. Most EST-STS homoeoloci were located on homoeologous chromosomes, suggesting a high degree of homology between the genomes of D. villosum and wheat. Four 4VL-specific markers detected homoeoloci on group 7 chromosomes of wheat, indicating that chromosome 4V of D. villosum shows some affinity to both wheat homoeologous groups 4 and 7. This is the first physical map of D. villosum, which will provide insight into the V genome for molecular breeding.     

Molecular cytogenetic identification of a novel dwarf wheat line with introgressed <Emphasis Type="Italic">Thinopyrum ponticum</Emphasis> chromatin

Novel dwarfing germplasms and dwarfing genes are valuable for the wheat breeding. A novel semi-dwarf line, 31505-1, with reduced height compared with its common wheat parent, was derived from a cross between common wheat and Thinopyrum ponticum. Cytological studies demonstrated that 31505-1 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genomic in situ hybridization (GISH) analysis showed that 31505-1 had no large Th. ponticum chromosome fragments. Fluorescence in situ hybridization (FISH) results revealed the absence of a pAs1 hybridization band on 2DL chromosome of 31505-1. Two SSR markers (Xwmc41 and Xcfd168) and two STS markers (Xmag4059 and Xmag3596), which were located on 2D chromosome, amplified unique bands of Th. Ponticum in 31505-1. These revealed presence of an introgressed Th. ponticum segment in 2DL chromosome of dwarf line 31505-1, although the alien segment could not be detected by GISH.     

Fusarium head blight resistance in hexaploid wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis>)-<Emphasis Type="Italic">Lophopyrum</Emphasis> genetic lines and tagging of the alien chromatin by PCR markers

The objective of this research was to identify Fusarium head blight (FHB) resistance in wheat (Triticum aestivum)-Lophopyrum genetic lines that might complement FHB resistance in common wheat; and to identify DNA markers that can be used to tag the resistance gene in the alien chromatin (E or el₂ genome) for the development of improved wheat cultivars. FHB resistance was evaluated in 19 Chinese Spring-Lophopyrum elongatum (EE) substitution lines, two Thatcher-L. ponticum (el₁ and el₂) substitution lines, and four Thatcher-L. ponticum translocation lines. Significant resistance was identified in the substitution lines 7E(7A), 7E(7B), and 7E(7D). The homoeologous chromosome, 7el₂,also showed resistance in the Thatcher genetic background. Both the Thatcher-7el₁ substitution and translocation lines were susceptible, like Thatcher, indicating that there is no resistance gene on the 7el₁ chromosome. Simple sequence repeat (SSR) and cleaved amplified polymorphic sequences (CAPS) in homoeologous group 7 chromosomes were used to identify DNA markers located on 7E and 7el₂. As expected, the transferability of wheat SSR markers to Lophopyrum is low. Of the 52 SSR markers that we tested, only five were found to be co-dominant on 7E of L. elongatum versus 7A, 7B, and 7D, one of which is also positive on 7el₂. A CAPS marker, derived from the RFLP probe PSR129, can serve as a dominant marker for 7el₂ chromatin.Communicated by J. Dvorak