Molecular cytogenetic identification of a wheat–Aegilops geniculata Roth 7Mg disomic addition line with powdery mildew resistance

Genetic Mapping of a Novel Gene PmAege7M from Aegilops geniculata Conferring Resistance to Wheat Powdery Mildew

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most damaging foliage diseases of wheat across the world. Aegilops geniculata Roth is a valuable gene resource for enhancing wheat resistance to powdery mildew. This study identified Ae. geniculata accession PI 487224 as immune and PI 487228 as susceptible to powdery mildew. Genetic analysis of the F1, F2, and F2:3 progeny derived from PI 487224 × PI 487228 showed that powdery mildew resistance in PI 487224 was controlled by two independent dominant genes located on two different nonhomologous chromosomes. By combing bulked segregant RNA-Seq, genetic linkage analysis of a single resistance gene segregation population, and marker analysis of a set of 14 wheat-Ae. geniculata chromosome addition lines, one of the resistance genes, temperately designated PmAege7M, was mapped to a 4.9-cM interval flanked by markers STS7-55926 and SNP7-45792/STS7-65911 on the long arm of chromosome 7 Mg of PI 487224, spanning 604.73 to 622.82 Mb on the 7D long arm based on the Ae. tauschii reference genome (Aet_v4.0). The map and closely linked markers of PmAege7M from Ae. geniculata in this study will facilitate the transfer of PmAege7M into common wheat and fine mapping of the gene.

Genetic analysis of resistance to powdery mildew on 7Mg chromosome of wheat-Aegilops geniculata, development and utilization of specific molecular markers

BACKGROUND

Powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is prevalent in the main wheat-producing regions of China, resulting in severe yield losses in recent years. Mining and utilization of resistant genes from wild relatives of wheat is the most environmentally sound measure to control disease. Aegilops geniculata Roth (2n = 2x = 28, UgUgMgMg) is an essential and valuable disease-resistance gene donor for wheat improvement as a close relative species.

RESULTS

In this study, to validate powdery mildew resistance locus on chromosome 7Mg, two genetic populations were constructed and through crossing wheat - Ae. geniculata 7Mg disomic addition line NA0973-5-4-1-2-9-1 and 7Mg (7 A) alien disomic substitution line W16998 with susceptible Yuanfeng175 (YF175, authorized varieties from Shaanxi province in 2005), respectively. Cytological examination, in situ hybridization (ISH), and functional molecular markers analysis revealed that the plants carrying chromosome 7Mg showed high resistance to powdery mildew in both F1 and F2 generation at the seedling stage. Besides, 84 specific markers were developed to identify the plants carrying chromosome 7Mg resistance based on the specific-locus amplified fragment sequencing (SLAF-seq) technique. Among them, four markers were selected randomly to check the reliability in F2 segregating populations derived from YF175/NA0973-5-4-1-2-9-1 and YF175/W16998. In summary, the above analysis confirmed that a dominant high powdery mildew resistance gene was located on chromosome 7Mg of Ae. geniculata.

CONCLUSION

The results provide a basis for mapping the powdery mildew resistance gene mapping on chromosome 7Mg and specific markers for their utilization in the future.

Identification and Characterization of Wheat-Aegilops comosa 7M (7A) Disomic Substitution Lines with Stripe Rust and Powdery Mildew Resistance

Aegilops comosa (MM, 2n = 2x = 14), an important diploid species from the wheat tertiary gene pool, contains many unique genes/traits of potential use for wheat breeding, such as disease resistance. In this study, three sister lines, NAL-32, NAL-33, and NAL-34, were identified from a wheat-A. comosa distant cross using fluorescence in situ hybridization, simple sequence repeat markers, and PCR-based unique gene markers combined with single nucleotide polymorphism (SNP) array analysis. Genetically, NAL-32 contained neither an alien nor translocation chromosome, whereas NAL-33 and NAL-34 had disomic 7M (7A) substitution chromosomes but differed in the absence or presence of the 1BL/1RS translocation chromosomes, respectively. The absence of 7A in NAL-33 and NAL-34 and the unusual 1B in the latter were verified by wheat 55K SNP arrays. The two 7M (7A) substitution lines had similar levels of resistance to stripe rust and powdery mildew, but better than that of NAL-32 and their common wheat parents, suggesting that the stripe rust and powdery mildew resistance of NAL-33 and NAL-34 were derived from the 7M of A. comosa. This research provides important bridge materials that can potentially be used for transferring stripe rust and powdery mildew resistance.

Development and Molecular Cytogenetic Identification of Two Wheat-Aegilops geniculata Roth 7Mg Chromosome Substitution Lines with Resistance to Fusarium Head Blight, Powdery Mildew and Stripe Rust

Fusarium head blight (Fhb), powdery mildew, and stripe rust are major wheat diseases globally. Aegilops geniculata Roth (U^gU^gM^gM^g, 2n = 4x = 28), a wild relative of common wheat, is valuable germplasm of disease resistance for wheat improvement and breeding. Here, we report the development and characterization of two substitution accessions with high resistance to powdery mildew, stripe rust and Fhb (W623 and W637) derived from hybrid progenies between Ae. geniculata and hexaploid wheat Chinese Spring (CS). Fluorescence in situ hybridization (FISH), Genomic in situ hybridizations (GISH), and sequential FISH-GISH studies indicated that the two substitution lines possess 40 wheat chromosomes and 2 Ae. geniculata chromosomes. Furthermore, compared that the wheat addition line parent W166, the 2 alien chromosomes from W623 and W637 belong to the 7M^g chromosomes of Ae. geniculata via sequential FISH-GISH and molecular marker analysis. Nullisomic-tetrasomic analysis for homoeologous group-7 of wheat and FISH revealed that the common wheat chromosomes 7A and 7B were replaced in W623 and W637, respectively. Consequently, lines W623, in which wheat chromosomes 7A were replaced by a pair of Ae. geniculata 7M^g chromosomes, and W637, which chromosomes 7B were substituted by chromosomes 7M^g, with resistance to Fhb, powdery mildew, and stripe rust. This study has determined that the chromosome 7M^g from Ae. geniculata exists genes resistant to Fhb and powdery mildew.

Fine mapping and distribution analysis of hybrid necrosis genes Ne1 and Ne2 in wheat in China

Flanking markers useful for identifying hybrid necrosis alleles were identified by fine mapping Ne1 and Ne2 and the distribution of the two necrosis genes was investigated in Chinese elite wheat varieties. Hybrid necrosis of wheat is caused by the interaction of two dominant complementary genes Ne1 and Ne2 present separately in normal parents and is regarded as a barrier to gene transfer in wheat breeding. However, the necrosis alleles still occur at a high frequency in modern wheat varieties. In this study, we constructed two high-density genetic maps of Ne1 and Ne2 in winter wheat. In these cultivars, Ne1 was found to be located in a span interval of 0.50 centimorgan (cM) on chromosome 5BL delimited by markers Nwu_5B_4137 and Nwu_5B_5114, while Ne2 co-segregated with markers Lseq102 and TC67744 on 2BS. Statistical analysis confirmed that the dosage effect of Ne1 and Ne2 also existed in moderate and severe hybrid necrosis systems, and the symptoms of necrosis can also be affected by the genetic background. Furthermore, we clarified the discrete distribution and proportion of the Ne1 and Ne2 in the 10 China's agro-ecological production zones. We concluded that 26.2% and 33.2% of the 1364 cultivars (lines) were genotyped with Ne1Ne1ne2ne2 and ne1ne1Ne2Ne2, respectively and introduced modern cultivars should directly affect the frequencies of necrosis genes in modern Chinese cultivars (lines), especially that of Ne2. Taking investigations in spring wheat together, we proposed that hybrid necrosis alleles could positively affect breeding owing to their linked excellent genes such as Lr13. Additionally, based on the pedigrees and hybridization tests, we speculated that the Ne1 and Ne2 in winter wheat may directly originate from wild emmer and introduced cultivars or hexaploid triticale, respectively.

Molecular cytogenetics for a wheat-Aegilops geniculata 3Mg alien addition line with resistance to stripe rust and powdery mildew

BACKGROUND

Aegilops geniculata Roth is closely related to common wheat (Triticum aestivum L.) and is a valuable genetic resource for improvement of wheat.

RESULTS

In this study, the W19513 line was derived from the BC₁F₁₀ progeny of a cross between wheat 'Chinese Spring' and Ae. geniculata SY159. Cytological examination showed that W19513 contained 44 chromosomes. Twenty-two bivalents were formed at the first meiotic metaphase I in the pollen mother cellsand the chromosomes were evenly distributed to opposite poles at meiotic anaphase I. Genomic in situ hybridization demonstrated that W19513 carried a pair of alien chromosomes from the M genome. Fluorescence in situ hybridization confirmed detection of variation in chromosomes 4A and 6B. Functional molecular marker analysis using expressed sequence tag-sequence-tagged site and PCR-based landmark unique gene primers revealed that the alien gene belonged to the third homologous group. The marker analysis confirmed that the alien chromosome pair was 3M^g. In addition, to further explore the molecular marker specificity of chromosome 3M^g, based on the specific locus amplified fragment sequencing technique, molecular markers specific for W19513 were developed with efficiencies of up to 47.66%. The W19513 line was inoculated with the physiological race E09 of powdery mildew (Blumeria graminis f. sp. tritici) at the seedling stage and showed moderate resistance. Field inoculation with a mixture of the races CYR31, CYR32, CYR33, and CYR34 of the stripe rust fungus (Puccinia striiformis f. sp. triticii) revealed that the line W19513 showed strong resistance.

CONCLUSIONS

This study provides a foundation for use of the line W19513 in future genetic research and wheat improvement.

Molecular Cytogenetic Identification of a Novel Wheat-Thinopyrum ponticum 1JS (1B) Substitution Line Resistant to Powdery Mildew and Leaf Rust

Thinopyrum ponticum (2n = 10x = 70) is a wild relative of wheat with high tolerance to both biotic and abiotic stresses; it has been wildly used in wheat genetic improvement. A disomic substitution line named SN19647 was derived from a cross between Triticum aestivum and the wheat-Th. ponticum partial amphiploid SNTE20 (2n = 8x = 56). It was evaluated for disease resistance and characterized via sequential fluorescence in situ hybridization (FISH)-genomic in situ hybridization (GISH) and molecular markers. The results showed that SN19647 carried resistance to both powdery mildew and leaf rust. It contained 42 chromosomes with a pair of wheat chromosome 1B replaced by a pair of J^S chromosomes from Th. ponticum. In addition to chromosomal substitution events, structural variation also occurred on wheat chromosomes 2A, 5A, 6B, and 7B. Based on marker analysis, 19 markers specific to the J^S chromosome were obtained, of which seventeen markers belonged to homoeologous group one. These results indicated that SN19647 was a 1J^S (1B) substitution line. Compared with the known 1J^S (1D) substitution line CH10A5, it was found that 17 markers generated different specific bands to Th. ponticum, confirming the novelty of the 1J^S chromosome in SN19647. Therefore, SN19647, resistant to powdery mildew and leaf rust, was a novel 1J^S (1B) substitution line that can be used in wheat genetic improvement.

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.

Genome-wide identification, evolution, and expression of the SNARE gene family in wheat resistance to powdery mildew

SNARE proteins mediate eukaryotic cell membrane/transport vesicle fusion and act in plant resistance to fungi. Herein, 173 SNARE proteins were identified in wheat and divided into 5 subfamilies and 21 classes. The number of the SYP1 class type was largest in TaSNAREs. Phylogenetic tree analysis revealed that most of the SNAREs were distributed in 21 classes. Analysis of the genetic structure revealed large differences among the 21 classes, and the structures in the same group were similar, except across individual genes. Excluding the first homoeologous group, the number in the other homoeologous groups was similar. The 2,000 bp promoter region of the TaSNARE genes were analyzed, and many W-box, MYB and disease-related cis-acting elements were identified. The qRT-PCR-based analysis of the SNARE genes revealed similar expression patterns of the same subfamily in one wheat variety. The expression patterns of the same gene in resistant/sensitive varieties largely differed at 6 h after infection, suggesting that SNARE proteins play an important role in early pathogen infection. Here, the identification and expression analysis of SNARE proteins provide a theoretical basis for studies of SNARE protein function and wheat resistance to powdery mildew.

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.

Molecular cytogenetic characterization of a novel wheat-Psathyrostachys huashanica Keng T3DS-5NsL•5NsS and T5DL-3DS•3DL dual translocation line with powdery mildew resistance

BACKGROUND

Psathyrostachys huashanica Keng (2n = 2x = 14, NsNs) carries many outstanding agronomic traits, therefore is a valuable resource for wheat genetic improvement. Wheat-P. huashanica translocation lines are important intermediate materials for wheat breeding and studying the functions of alien chromosomes. However, powdery mildew resistance in these translocation lines has not been reported previously.

RESULTS

This study developed a novel wheat-P. huashanica translocation line TR77 by selecting a F₇ progeny from the cross between heptaploid hybrid H8911 (2n = 7x = 49, AABBDDNs) and durum wheat line Trs-372. Chromosome karyotype of 2n = 42 = 21II was observed in both mitotic and meiotic stages of TR77. Genomic in situ hybridization analysis identified two translocated chromosomes that paired normally at meiosis stage in TR77. Molecular marker analysis showed that part of chromosome 5D was replaced by part of alien chromosome fragment 5Ns. It meant replacement made part 5DL and part 5NsL·5NsS existed in wheat background, and then translocation happened between these chromosomes and wheat 3D chromosome. Fluorescence in situ hybridization demonstrated that TR77 carries dual translocations: T3DS-5NsL·5NsS and T5DL-3DS·3DL. Analysis using a 15 K-wheat-SNP chip confirmed that SNP genotypes on the 5D chromosome of TR77 matched well with these of P. huashanica, but poorly with common wheat line 7182. The translocation was physically located between 202.3 and 213.1 Mb in 5D. TR77 showed longer spikes, more kernels per spike, and much better powdery mildew resistance than its wheat parents: common wheat line 7182 and durum wheat line Trs-372.

CONCLUSIONS

TR77 is a novel stable wheat-P. huashanica T3DS-5NsL·5NsS and T5DL-3DS·3DL dual translocation line and showed significant improved spike traits and resistance to powdery mildew compared to its parents, thus, it can be an useful germplasm for breeding disease resistance and studying the genetic mechanism of dual translocations.

Characterization and Evaluation of Resistance to Powdery Mildew of Wheat-Aegilops geniculata Roth 7Mg (7A) Alien Disomic Substitution Line W16998

Aegilops geniculata Roth has been used as a donor of disease-resistance genes, to enrich the gene pool for wheat (Triticum aestivum) improvement through distant hybridization. In this study, the wheat–Ae. geniculata alien disomic substitution line W16998 was obtained from the BC₁F₈ progeny of a cross between the common wheat ‘Chinese Spring’ (CS) and Ae. geniculata Roth (serial number: SY159//CS). This line was identified using cytogenetic techniques, analysis of genomic in situ hybridization (GISH), functional molecular markers (Expressed sequence tag-sequence-tagged site (EST–STS) and PCR-based landmark unique gene (PLUG), fluorescence in situ hybridization (FISH), sequential fluorescence in situ hybridization–genomic in situ hybridization (sequential FISH–GISH), and assessment of agronomic traits and powdery mildew resistance. During the anaphase of meiosis, these were evenly distributed on both sides of the equatorial plate, and they exhibited high cytological stability during the meiotic metaphase and anaphase. GISH analysis indicated that W16998 contained a pair of Ae. geniculata alien chromosomes and 40 common wheat chromosomes. One EST–STS marker and seven PLUG marker results showed that the introduced chromosomes of Ae. geniculata belonged to homoeologous group 7. Nullisomic–tetrasomic analyses suggested that the common wheat chromosome, 7A, was absent in W16998. FISH and sequential FISH–GISH analyses confirmed that the introduced Ae. geniculata chromosome was 7M^g. Therefore, W16998 was a wheat–Ae. geniculata 7M^g (7A) alien disomic substitution line. Inoculation of isolate E09 (Blumeria graminis f. sp. tritici) in the seedling stage showed that SY159 and W16998 were resistant to powdery mildew, indeed nearly immune, whereas CS was highly susceptible. Compared to CS, W16998 exhibited increased grain weight and more spikelets, and a greater number of superior agronomic traits. Consequently, W16998 was potentially useful. Germplasms transfer new disease-resistance genes and prominent agronomic traits into common wheat, giving the latter some fine properties for breeding.

Cytogenetic Analysis and Molecular Marker Development for a New Wheat-Thinopyrum ponticum 1Js (1D) Disomic Substitution Line With Resistance to Stripe Rust and Powdery Mildew

Thinopyrum ponticum (2n = 10x = 70), a member of the tertiary gene pool of wheat (Triticum aestivum L.), harbors many biotic and abiotic stress resistance genes. CH10A5, a novel disomic substitution line from a cross of T. aestivum cv. 7182 and Th. ponticum, was characterized by cytogenetic identification, in situ hybridization, molecular marker analysis, and morphological investigation of agronomic traits and disease resistance. Cytological observations showed that CH10A5 contained 42 chromosomes and formed 21 bivalents at meiotic metaphase I. Genome in situ hybridization (GISH) analysis indicated that two of its chromosomes came from the J^s genome of Th. ponticum, and wheat 15K array mapping and fluorescence in situ hybridization (FISH) revealed that chromosome 1D was absent from CH10A5. Polymorphic analysis of molecular markers indicated that the pair of alien chromosomes belonged to homoeologous group one, designated as 1J^s. Thus, CH10A5 was a wheat-Th. ponticum 1J^s (1D) disomic substitution line. Field disease resistance trials demonstrated that the introduced Th. ponticum chromosome 1J^s was probably responsible for resistance to both stripe rust and powdery mildew at the adult stage. Based on specific-locus amplified fragment sequencing (SLAF-seq), 507 STS molecular markers were developed to distinguish chromosome 1J^s genetic material from that of wheat. Of these, 49 STS markers could be used to specifically identify the genetic material of Th. ponticum. CH10A5 will increase the resistance gene diversity of wheat breeding materials, and the markers developed here will permit further tracing of heterosomal chromosome fragments in the future.

A wheat-Aegilops umbellulata addition line improves wheat agronomic traits and processing quality

Wheat processing quality is mainly correlated with high-molecular-weight glutenin subunits (HMW-GS) of grain endosperm. In bread wheat, the number of HMW-GS alleles are limited. However, wheat relative species possess numerous HMW-GS genes. In our previous study, a pair of novel HMW-GS 1Ux3.5+1Uy1.9 was characterized in Aegilops umbellulata. In this work, a novel wheat-Ae. umbellulata addition line, GN05, carrying a pair of 1U chromosome was developed and identified via cytogenetic analysis. Protein composition analysis indicated that GN05 carried HMW-GS of Ae. umbellulata. Accumulation of glutenin macropolymer (GMP) showed that GN05 had a much higher GMP content than the recurrent parent Chinese Spring. Rheological characteristics were analyzed by mixing test and the dough quality of GN05 was significantly improved compared to Chinese Spring. The results presented here may provide a valuable resource for the improvement of bread wheat quality.