Cytological identification of an Aegilops variabilis chromosome carrying stripe rust resistance in wheat

Development and characterization of small translocations between the Pm13 introgression from Aegilops longissima and wheat homoeologous A, B and D chromosomes

BACKGROUND

Wild relatives have substantial impacts on the resistance of wheat to biotic and abiotic stresses. The genetic diversity of these wild varieties can be employed to widen the wheat gene pool by introducing wild allele introgression and genome structure variations. The powdery mildew resistance gene Pm13 was derived from the wheat wild relative species Aegilops longissima (S1S1, 2n = 2x = 14) and was transferred into wheat chromosome 3BS over 30 years. Until recently, it has not been widely used in wheat breeding, possibly because of the linkage drag associated with Pm13 introgression or poor alien segment compensation to 3BS.

RESULTS

In this study, translocations between the Pm13 introgression and wheat homoeologous A, B and D chromosomes were developed by using a wheat ph1b mutant. The 3Sl (3B) substitution line was hybridized with the CS nullisomic-tetrasomic line N3AT3B, and then F1 was hybridized with the CSph1b mutant. Individuals homozygous for the ph1b mutant carrying the alien chromosome 3Sl were identified from the segregating populations via molecular markers and cytological analysis. Whole-arm recombinant translocations T3SlS.3AL and T3SlS.3BL and small recombinant translocations T3SlS-3AS.3AL, T3SlS-3BS.3BL and T3DS-3SlS-3DS.3DL carrying Pm13 introgression were subsequently identified via molecular cytological analysis. Furthermore, 4 disomic T3SlS-3BS.3BL recombinants carrying the homozygous Pm13 introgression were identified. All the translocations were nearly immune to powdery mildew.

CONCLUSIONS

Our results provide novel alien homoeologous Pm13 translocations for improving powdery mildew resistance in wheat and insights into the interactions between different wheat genomes and alien chromosome segments.

Chromosome stability of synthetic Triticum turgidum-Aegilops umbellulata hybrids

BACKGROUND

Unreduced gamete formation during meiosis plays a critical role in natural polyploidization. However, the unreduced gamete formation mechanisms in Triticum turgidum-Aegilops umbellulata triploid F1 hybrid crosses and the chromsome numbers and compostions in T. turgidum-Ae. umbellulata F2 still not known.

RESULTS

In this study, 11 T.turgidum-Ae. umbellulata triploid F1 hybrid crosses were produced by distant hybridization. All of the triploid F1 hybrids had 21 chromosomes and two basic pathways of meiotic restitution, namely first-division restitution (FDR) and single-division meiosis (SDM). Only FDR was found in six of the 11 crosses, while both FDR and SDM occurred in the remaining five crosses. The chromosome numbers in the 127 selfed F2 seeds from the triploid F1 hybrid plants of 10 crosses (no F2 seeds for STU 16) varied from 35 to 43, and the proportions of euploid and aneuploid F2 plants were 49.61% and 50.39%, respectively. In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes. The chromosome loss of the U genome was the highest (26.77%) among the three genomes, followed by that of the B (22.83%) and A (11.81%) genomes, and the chromosome gain for the A, B, and U genomes was 3.94%, 3.94%, and 1.57%, respectively. Of the 21 chromosomes, 7U (16.54%), 5 A (3.94%), and 1B (9.45%) had the highest loss frequency among the U, A, and B genomes. In addition to chromosome loss, seven chromosomes, namely 1 A, 3 A, 5 A, 6 A, 1B, 1U, and 6U, were gained in the aneuploids.

CONCLUSION

In the aneuploid F2 plants, the frequency of chromosome loss/gain varied among genomes, chromsomes, and crosses. In addition to variations in chromosome numbers, three types of chromosome translocations including 3UL·2AS, 6UL·1AL, and 4US·6AL were identified in the F2 plants. Furthermore, polymorphic fluorescence in situ hybridization karyotypes for all the U chromosomes were also identified in the F2 plants when compared with the Ae. umbellulata parents. These results provide useful information for our understanding the naturally occurred T. turgidum-Ae. umbellulata amphidiploids.

Mapping and characterization of rust resistance genes Lr53 and Yr35 introgressed from Aegilops species

KEY MESSAGE

The rust resistance genes Lr53 and Yr35 were introgressed into bread wheat from Aegilops longissima or Aegilops sharonensis or their S-genome containing species and mapped to the telomeric region of chromosome arm 6BS. Wheat leaf and stripe rusts are damaging fungal diseases of wheat worldwide. Breeding for resistance is a sustainable approach to control these two foliar diseases. In this study, we used SNP analysis, sequence comparisons, and cytogenetic assays to determine that the chromosomal segment carrying Lr53 and Yr35 was originated from Ae.longissima or Ae. sharonensis or their derived species. In seedling tests, Lr53 conferred strong resistance against all five Chinese Pt races tested, and Yr35 showed effectiveness against Pst race CYR34 but susceptibility to race CYR32. Using a large population (3892 recombinant gametes) derived from plants homozygous for the ph1b mutation obtained from the cross 98M71 × CSph1b, both Lr53 and Yr35 were successfully mapped to a 6.03-Mb telomeric region of chromosome arm 6BS in the Chinese Spring reference genome v1.1. Co-segregation between Lr53 and Yr35 was observed within this large mapping population. Within the candidate region, several nucleotide-binding leucine-rich repeat genes and protein kinases were identified as candidate genes. Marker pku6B3127 was completely linked to both genes and accurately predicted the absence or presence of alien segment harboring Lr53 and Yr35 in 87 tetraploid and 149 hexaploid wheat genotypes tested. We developed a line with a smaller alien segment (< 6.03 Mb) to reduce any potential linkage drag and demonstrated that it conferred resistance levels similar to those of the original donor parent 98M71. The newly developed introgression line and closely linked PCR markers will accelerate the deployment of Lr53 and Yr35 in wheat breeding programs.

Development and application of specific FISH probes for karyotyping Psathyrostachys huashanica chromosomes

Background

Psathyrostachys huashanica Keng has long been used as a genetic resource for improving wheat cultivar because of its genes mediating the resistance to various diseases (stripe rust, leaf rust, take-all, and powdery mildew) as well as its desirable agronomic traits. However, a high-resolution fluorescence in situ hybridization (FISH) karyotype of P. huashanica remains unavailable.

Results

To develop chromosome-specific FISH markers for P. huashanica, repetitive sequences, including pSc119.2, pTa535, pTa713, pAs1, (AAC)₅, (CTT)₁₂, pSc200, pTa71A-2, and Oligo-44 were used for a FISH analysis. The results indicated that the combination of pSc200, pTa71A-2 and Oligo-44 probes can clearly identify all Ns genomic chromosomes in the two P. huashanica germplasms. The homoeologous relationships between individual P. huashanica chromosomes and common wheat chromosomes were clarified by FISH painting. Marker validation analyses revealed that the combination of pSc200, pTa71A-2, and Oligo-44 for a FISH analysis can distinguish the P. huashanica Ns-genome chromosomes from wheat chromosomes, as well as all chromosomes (except 4Ns) from the chromosomes of diploid wheat relatives carrying St, E, V, I, P and R genomes. Additionally, the probes were applicable for discriminating between the P. huashanica Ns-genome chromosomes in all homologous groups and the corresponding chromosomes in Psathyrostachys juncea and most Leymus species containing the Ns genome. Furthermore, six wheat–P. huashanica chromosome addition lines (i.e., 2Ns, 3Ns, 4Ns, 7Ns chromosomes and chromosomal segments) were characterized using the newly developed FISH markers. Thus, these probes can rapidly and precisely detect P. huashanica alien chromosomes in the wheat background.

Conclusions

The FISH karyotype established in this study lays a solid foundation for the efficient identification of P. huashanica chromosomes in wheat genetic improvement programs.

Chromosome karyotype and stability of new synthetic hexaploid wheat

Synthetic hexaploid wheat offers breeders ready access to potentially novel genetic variation in wild ancestral species. In this study, we crossed MY3478 (2n = 4x = 28, AABB) as the maternal parent with the stripe rust-resistant SY41 (2n = 2x = 14, DD) as the paternal parent to construct the new hexaploid wheat line NA0928 through natural allopolyploidization. Agronomic traits and the cytology of the S8-S9 generations of NA0928 were analyzed. Abundant variation in agronomic traits was observed among each strain of NA0928 in the S8 generation. Agronomic traits were superior in strains resistant to stripe rust compared with those of highly susceptible strains. The rank order of the coefficients of variation were tiller number (55.3%) > spike length (15.3%) > number of spikelets (13.9%) > plant height (8.7). Number of tillers and spike length are important traits in wheat breeding to improve yield. Cytological observation and fluorescence in situ hybridization showed that the chromosome number and configuration showed rich variation among NA0928 strains in the S9 generation. Chromosome number ranged from 36 to 44. Variation in chromosome karyotype was detected in the A and B subgenomes. Meiotic chromosome behavior in pollen mother cells and multicolor genomic in situ hybridization revealed that two new synthetic hexaploid wheat strains showed genetic stability; one strain was resistant to stripe rust and developed multiple tillers, and the other strain was susceptible to stripe rust, but both showed improved thousand-kernel weight (TKW) weight and produced multiple tillers. The two strains will be valuable germplasm resources for use in wheat breeding.

PAL-mediated SA biosynthesis pathway contributes to nematode resistance in wheat

The pathogen cereal cyst nematode (CCN) is deleterious to Triticeae crops and is a threat to the global crop yield. Accession no. 1 of Aegilops variabilis, a relative of Triticum aestivum (bread wheat), is highly resistant to CCN. Our previous study demonstrated that the expression of the phenylalanine ammonia lyase (PAL) gene AevPAL1 in Ae. variabilis is strongly induced by CCN. PAL, the first enzyme of phenylpropanoid metabolism, is involved in abiotic and biotic stress responses. However, its role in plant-CCN interaction remains unknown. In the present study, we proved that AevPAL1 helps to confer CCN resistance through affecting the synthesis of salicylic acid (SA) and downstream secondary metabolites. The silencing of AevPAL1 increased the incidence of CCN infection in roots and decreased the accumulation of SA and phenylalanine (Phe)-derived specialized metabolites. The exogenous pre-application of SA also improved CCN resistance. Additionally, the functions of PAL in phenylpropanoid metabolism correlated with tryptophan decarboxylase (TDC) functioning in tryptophan metabolism pathways. The silencing of either AevPAL1 or AevTDC1 exhibited a concomitant reduction in the expression of both genes and the contents of metabolites downstream of PAL and TDC. These results suggested that AevPAL1, possibly in coordination with AevTDC1, positively contributes to CCN resistance by altering the downstream secondary metabolites and SA content in Ae. variabilis. Moreover, AevPAL1 overexpression significantly enhanced CCN resistance in bread wheat and did not exhibit significant negative effects on yield-related traits, suggesting that AevPAL1 is valuable for the genetic improvement of CCN resistance in bread wheat.

De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

Chromosome Stability of Synthetic-Natural Wheat Hybrids

Primary allopolyploids are not only ideal materials to study species evolution, but also important bridges in incorporating genetic diversity of wild species into crops. Primary allopolyploids typically exhibit chromosome instability that a disadvantage trait in crop breeding. Newly synthesized hexaploid wheat has been widely used in wheat genetics and breeding studies. To better understand the cytological and genetic basis of chromosome instability, this study investigated the chromosomes of a large number of seeds derived from the synthetic wheat SHW-L1 and its hybrids with natural wheat. SHW-L1 exhibited persistent chromosome instability since we observed a high frequent chromosome variation de novo generated from euploid SHW-L1 plants at the 14th generation of selfing (F₁₄). High frequent chromosome variations were also observed in the F₂ hybrids and most of the analyzed recombinant inbred lines (RILs) at F₁₄, derived from the cross of SHW-L1 with common wheat variety Chuanmai 32. Chromosome instability was associated with frequent univalency during meiotic metaphase I. The experiment on reciprocal crosses between SHW-L1 and Chuanmai 32 indicated that cytoplasm has not obvious effects on chromosome instability. An analysis on 48 F₁₄ RILs revealed chromosome variation frequency was not associated with the Ph1 alleles from either SHW-L1 or Chuanmai 32, rejecting the hypothesis that chromosome instability was due to the Ph1 role of synthetic wheat. In the analyzed RILs, chromosome instability influences the phenotype uniformity, showing as obvious trait differences among plants within a RIL. However, the analyzed commercial varieties only containing ∼12.5% genomic components of synthetic wheat were chromosomally stable, indicating that chromosome instability caused by synthetic wheat can be effectively overcome by increasing the genetic background of common wheat.

Multiple wheat genomes reveal global variation in modern breeding

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome¹, and the lack of genome-assembly data for multiple wheat lines^2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses^4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1⁶, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.

Analysis of Structural Genomic Diversity in Aegilops umbellulata, Ae. markgrafii, Ae. comosa, and Ae. uniaristata by Fluorescence In Situ Hybridization Karyotyping

Fluorescence in situ hybridization karyotypes have been widely used for evolutionary analysis on chromosome organization and genetic/genomic diversity in the wheat alliance (tribe Triticeae of Poaceae). The karyotpic diversity of Aegilops umbellulata, Ae. markgrafii, Ae. comosa subsp. comosa and subsp. subventricosa, and Ae. uniaristata was evaluated by the fluorescence in situ hybridization (FISH) probes oligo-pSc119.2 and pTa71 in combination with (AAC)5, (ACT)7, and (CTT)12, respectively. Abundant intra- and interspecific genetic variation was discovered in Ae. umbellulata, Ae. markgrafii, and Ae. comosa, but not Ae. uniaristata. Chromosome 7 of Ae. umbellulata had more variants (six variants) than the other six U chromosomes (2-3 variants) as revealed by probes oligo-pSc119.2 and (AAC)5. Intraspecific variation in Ae. markgrafii and Ae. comosa was revealed by oligo-pSc119.2 in combination with (ACT)7 and (CTT)12, respectively. At least five variants were found in every chromosome of Ae. markgrafii and Ae. comosa, and up to 18, 10, and 15 variants were identified for chromosomes 2 of Ae. markgrafii, 4 of Ae. comosa subsp. comosa, and 6 of Ae. comosa subsp. subventricosa. The six Ae. uniaristata accessions showed identical FISH signal patterns. A large number of intra-specific polymorphic FISH signals were observed between the homologous chromosomes of Ae. markgrafii and Ae. comosa, especially chromosomes 1, 2, 4, and 7 of Ae. markgrafii, chromosome 4 of Ae. comosa subsp. comosa, and chromosome 6 of Ae. comosa subsp. subventricosa. Twelve Ae. comosa and 24 Ae. markgrafii accessions showed heteromorphism between homologous chromosomes. Additionally, a translocation between the short arms of chromosomes 1 and 7 of Ae. comosa PI 551038 was identified. The FISH karyotypes can be used to clearly identify the chromosome variations of each chromosome in these Aegilops species and also provide valuable information for understanding the evolutionary relationships and structural genomic variation among Aegilops species.

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.

Karyotype mosaicism in early generation synthetic hexaploid wheats

It is known that both the number and the structure of somatic chromosomes can vary in early generation hexaploid wheats. The phenomenon is generally assumed to arise as a result of the meiotic instability characteristic of freshly created allopolyploids. Here, an analysis of the somatic karyotype of a set of 33 early generation synthetic hexaploid wheats has revealed that variation, taking the form of sub-chromosomal fragments and inter-chromosomal translocations, can also arise in somatic tissue. A possible explanation for the observations was that karyotypic instability in early generation hexaploid wheat probably occurs not just during sporogenesis, but also in somatic tissue. However, other factors such as the use of nitrous oxide during the experiments could also cause the chromosome variations, and additional experimentation would be required to determine the most likely.

Genetic mapping of a major QTL promoting homoeologous chromosome pairing in a wheat landrace

Common wheat landrace Kaixian-luohanmai carries a gene(s) that promotes homoeologous chromosome pairing. A major QTL responsible for this effect was mapped to chromosome arm 3AL. Polyhaploid hybrids of a Chinese common wheat landrace Kaixian-luohanmai (KL) and related species show increased levels of chromosome pairing. Over 90% of that pairing is between homoeologous arms of wheat chromosomes, with a very strong preference for pairing between homoeologs from genomes A and D. Wheat-rye pairing was also observed at low frequency. Two mapping populations were created from the hybrids of KL with two wheat genotypes top crossed to rye. Mean chiasmata numbers per plant were used as phenotypic data. Wheat 660 K and 15 K SNP arrays, DArT markers and SSR markers were used for genotyping of the top-cross ABDR hybrids. One major QTL, named QPh.sicau-3A, for increased homoeologous pairing was detected on chromosome arm 3AL, and it was responsible for ca. 16% of the total variation. This QTL was located in the interval 696-725 Mb in the Chinese Spring reference genome. SNP markers closely linked with QPh.sicau-3A were converted to KASP markers and validated for marker-assisted selection.

The karyotype of Aegilops geniculata and its use to identify both addition and substitution lines of wheat

BACKGROUND

The annual allotetraploid species Aegilops geniculata harbors a number of traits relevant for wheat improvement. An effective cytogenetic method has yet to be developed to distinguish between each of its 14 chromosomes.

RESULTS

A fluorescence in situ hybridization (FISH) approach was adopted to describe the karyotype of Ae. geniculata. Each of its 14 chromosomes was unequivocally recognized using a cocktail of three probes, namely pTa-713, (AAC)5 and pTa71. FISH karyotyping was then used to detect and characterize selections from an Ae. geniculata × bread wheat wide cross of a chromosome 1Mg disomic addition line and three 4Mg(4B) substitution lines. The identity of the addition line was confirmed by the presence of Glu-M1, detected both using an SDS-PAGE separation of endosperm proteins and by applying a PCR assay directed at the Glu-M1 locus. The status of the substitution lines was validated by genotyping using a wheat single nucleotide polymorphism chip.

CONCLUSION

FISH karyotyping based on pTa-713, (AAC)5 and pTa71 will be useful for determining the contribution of Ae. geniculata to derivatives of an Ae. geniculata × wheat wide cross. SNP chip-based genotyping is effective for confirming the status of whole chromosome wheat/alien substitution lines.

Cytological markers used for identification and transfer of Aegilops spp. chromatin carrying valuable genes into cultivated forms of Triticum

There are many reports describing chromosome structure, organization and evolution within goatgrasses (Aegilops spp.). Chromosome banding and fluorescence in situ hybridization techniques are main methods used to identify Aegilops Linnaeus, 1753 chromosomes. These data have essential value considering the close genetic and genomic relationship of goatgrasses with wheat (Triticumaestivum Linnaeus, 1753) and triticale (× Triticosecale Wittmack, 1899). A key question is whether those protocols are useful and effective for tracking Aegilops chromosomes or chromosome segments in genetic background of cultivated cereals. This article is a review of scientific reports describing chromosome identification methods, which were applied for development of prebreeding plant material and for transfer of desirable traits into Triticum Linnaeus, 1753 cultivated species. Moreover, this paper is a resume of the most efficient cytomolecular markers, which can be used to follow the introgression of Aegilops chromatin during the breeding process.

FISH-Based Markers Enable Identification of Chromosomes Derived From Tetraploid Thinopyrum elongatum in Hybrid Lines

Tetraploid Thinopyrum elongatum, which has superior abiotic stress tolerance characteristics, and exhibits resistance to stripe rust, powdery mildew, and Fusarium head blight, is a wild relative of wheat and a promising source of novel genes for wheat improvement. Currently, a high-resolution Fluorescence in situ hybridization (FISH) karyotype of tetraploid Th. elongatum is not available. To develop chromosome-specific FISH-based markers, the hexaploid Trititrigia 8801 and two accessions of tetraploid Th. elongatum were characterized by different repetitive sequences probes. We found that all E-genome chromosomes could be unambiguously identified using a combination of pSc119.2, pTa535, pTa71, and pTa713 repeats, and the E-genome chromosomes of the wild accessions and the partial amphiploid failed to exhibit any significant variation in the probe hybridization patterns. To verify the validation of these markers, the chromosome constitution of eight wheat- Th. elongatum hybrid derivatives were analyzed. We revealed that these probes could quickly detect wheat and tetraploid Th. elongatum chromosomes in hybrid lines. K16-712-1-2 was a 1E (1D) chromosome substitution line, K16-681-4 was a 2E disomic chromosome addition line, K16-562-3 was a 3E, 4E (3D, 4D) chromosome substitution line, K15-1033-8-2 contained one 4E, two 5E, and one 4ES⋅1DL Robertsonian translocation chromosome, and four other lines carried monosomic 4E, 5E, 6E, and 7E chromosome, respectively. Furthermore, the E-genome specific molecular markers analysis corresponded perfectly with the FISH results. The developed FISH markers will facilitate rapid identification of tetraploid Th. elongatum chromosomes in wheat improvement programs and allow appropriate alien chromosome transfer.

Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii

Background

Aegilops tauschii is the donor of the bread wheat D genome. Based on spike morphology, the taxon has conventionally been subdivided into ssp. tauschii and ssp. strangulata. The present study was intended to address the poor match between this whole plant morphology-based subdivision and genetic relationships inferred from genotyping by fluorescence in situ hybridization karyotyping a set of 31 Ae. tauschii accessions.

Results

The distribution of sites hybridizing to the two probes oligo-pTa-535 and (CTT)₁₀ split the Ae. tauschii accessions into two clades, designated D^t and D^s, which corresponded perfectly with a previously assembled phylogeny based on marker genotype. The D^t cluster was populated exclusively by ssp. tauschii accessions, while the D^s cluster harbored both ssp. strangulata and morphologically intermediate accessions. As a result, it is proposed that Ae. tauschii ssp. tauschii is restricted to carriers of the D^t karyotype: their spikelets are regularly spaced along the rachis, at least in the central portion of their spike. Accessions classified as Ae. tauschii ssp. strangulata carry the D^s karyotype; their spikelets are irregularly spaced. Based on this criterion, forms formerly classified as ssp. tauschii var. meyeri have been re-designated ssp. strangulata var. meyeri.

Conclusions

According to the reworking of the taxon, the bread wheat D genome was most probably donated by ssp. strangulata var. meyeri. Chromosomal differentiation reveals intra-species taxon of Ae. tauschii. Ae. tauschii ssp. tauschii has more distant relationship with breed wheat than ssp. strangulata and can be used for breeding improving effectively.

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

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

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.

Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis

Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)₁₀ and (GTT)₉, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides _. The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)₁₀-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S^*-genomes. However, partial elimination of 45S rDNA repeats from 5S^* and 6S^* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the S^v-genome of Ae. vavilovii with the S^s genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.