Cytogenetics and stripe rust resistance of wheat-Thinopyrum elongatum hybrid derivatives

Cytogenetic identification and molecular mapping for the wheat-Thinopyrum ponticum introgression line with resistance to Fusarium head blight

KEY MESSAGE

Xinong 511, a new wheat-Thinopyrum ponticum variety with excellent fusarium head blight resistance, the QTLs were mapped to the wheat chromosomes 5B and 7A with named QFhb.nwafu-5B and QFhb.nwafu-7A, respectively. Novel Fusarium head blight (FHB) resistance germplasms and genes are valuable for wheat improvement and breeding efforts. Thinopyrum ponticum, a wild relative of common wheat, is a valuable germplasm of disease resistance for wheat improvement and breeding. Xinong 511 (XN511) is a high-quality wheat variety widely cultivated in the Yellow and Huai Rivers Valley of China with stable FHB-resistance. Through analysis of pedigree materials of the wheat cultivar XN511, we found that the genetic material and FHB resistance from Th. ponticum were transmitted to the introgression line, indicating that the FHB resistance in XN511 likely originates from Th. ponticum. To further explore the genetic basis of FHB resistance in XN511, QTL mapping was conducted using the RILs population of XN511 and the susceptible line Aikang 58 (AK58). Survey with makers closely-linked to Fhb1, Fhb2, Fhb4, Fhb5, and Fhb7, indicated that both XN511 and the susceptible lines do not contain these QTL. Using bulked segregant analysis RNA-seq (BSR-Seq) and newly developed allele-specific PCR (AS-PCR) markers, QTLs in XN511 were successfully located on wheat chromosomes 5B and 7A. These findings are significant for further understanding and utilizing FHB resistance genes in wheat improvement.

Cytogenetic and Genomic Characterization of a Novel Wheat-Tetraploid Thinopyrum elongatum 1BS⋅1EL Translocation Line with Stripe Rust Resistance

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a destructive wheat disease pathogen. Thinopyrum elongatum is a valuable germplasm including diploid, tetraploid, and decaploid with plenty of biotic and abiotic resistance. In a previous study, we generated a stripe rust-resistant wheat-tetraploid Th. elongatum 1E/1D substitution line, K17-841-1. To further apply the wild germplasm for wheat breeding, we selected and obtained a new homozygous wheat-tetraploid Th. elongatum translocation line, T1BS⋅1EL, using genomic in situ hybridization, fluorescence in situ hybridization (FISH), oligo-FISH painting, and the wheat 55K single nucleotide polymorphism genotyping array. The T1BS⋅1EL is highly resistant to stripe rust at the seedling and adult stages. Pedigree and molecular marker analyses revealed that the resistance gene was located on the chromosome arm 1EL of tetraploid Th. elongatum, tentatively named Yr1EL. In addition, we developed and validated 32 simple sequence repeat markers and two kompetitive allele-specific PCR assays that were specific to the tetraploid Th. elongatum chromosome arm 1EL to facilitate marker-assisted selection for alien 1EL stripe rust resistance breeding. This will help us explore and locate the stripe rust resistance gene mapping on the 1E chromosome and deploy it in the wheat breeding program.

GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives

KEY MESSAGE

A total of 90,000 capture probes derived from wheat and Thinopyrum elongatum were integrated into one chip, which served as an economical genotype for explorating Thinopyrumspecies and their derivatives. Thinopyrum species play a crucial role as a source of new genetic variations for enhancing wheat traits, including resistance to both abiotic and biotic factors. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is essential following the introduction of alien genetic material into wheat, but this task remains challenging. This study aimed to develop a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information by genotyping using a target sequencing system. This GenoBaits®WheatplusEE array included 90,000 capture probes derived from two species and integrated into one chip, with 10,000 and 80,000 originating from wheat and Th. elongatum, respectively. The capture probes were strategically positioned in genes and evenly distributed across the genome, facilitating the development of a roadmap for identifying each alien gene. The array was applied to the high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species and their derivatives. Our results demonstrated that the GenoBaits®WheatplusEE array could be used for direct identification of the breakpoint of alien segments, determine copy number of alien chromosomes, and reveal variations in wheat chromosomes by a single round of target sequencing of the sample. Additionally, we could efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and polymorphisms in essential genes (e.g., Fhb7 gene) among Thinopyrum species and their derivatives. We hope that GenoBaits®WheatplusEE will become a widely adopted tool for exporting wild germplasm for wheat improvement in the future.

Development, identification, and utilization of wheat-tetraploid Thinopyrum elongatum 4EL translocation lines resistant to stripe rust

KEY MESSAGE

The new stripe rust resistance gene Yr4EL in tetraploid Th. elongatum was identified and transferred into common wheat via 4EL translocation lines. Tetraploid Thinopyrum elongatum is a valuable genetic resource for improving the resistance of wheat to diseases such as stripe rust, powdery mildew, and Fusarium head blight. We previously reported that chromosome 4E of the 4E (4D) substitution line carries all-stage stripe rust resistance genes. To optimize the utility of these genes in wheat breeding programs, we developed translocation lines by inducing chromosomal structural changes through 60Co-γ irradiation and developing monosomic substitution lines. In total, 53 plants with different 4E chromosomal structural changes were identified. Three homozygous translocation lines (T4DS·4EL, T5AL·4EL, and T3BL·4EL) and an addition translocation line (T5DS·4EL) were confirmed by the genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), FISH-painting, and wheat 55 K SNP array analyses. These four translocation lines, which contained chromosome arm 4EL, exhibited high stripe rust resistance. Thus, a resistance gene (tentatively named Yr4EL) was localized to the chromosome arm 4EL of tetraploid Th. elongatum. For the application of marker-assisted selection (MAS), 32 simple sequence repeat (SSR) markers were developed, showing specific amplification on the chromosome arm 4EL and co-segregation with Yr4EL. Furthermore, the 4DS·4EL line could be selected as a good pre-breeding line that better agronomic traits than other translocation lines. We transferred Yr4EL into three wheat cultivars SM482, CM42, and SM51, and their progenies were all resistant to stripe rust, which can be used in future wheat resistance breeding programs.

Development and Characterization of a Novel Wheat-Tetraploid Thinopyrum elongatum 6E (6D) Disomic Substitution Line with Stripe Rust Resistance at the Adult Stage

Stripe rust, which is caused by Puccinia striiformis f. sp. tritici, is one of the most devastating foliar diseases of common wheat worldwide. Breeding new wheat varieties with durable resistance is the most effective way of controlling the disease. Tetraploid Thinopyrum elongatum (2n = 4x = 28, EEEE) carries a variety of genes conferring resistance to multiple diseases, including stripe rust, Fusarium head blight, and powdery mildew, which makes it a valuable tertiary genetic resource for enhancing wheat cultivar improvement. Here, a novel wheat-tetraploid Th. elongatum 6E (6D) disomic substitution line (K17-1065-4) was characterized using genomic in situ hybridization and fluorescence in situ hybridization chromosome painting analyses. The evaluation of disease responses revealed that K17-1065-4 is highly resistant to stripe rust at the adult stage. By analyzing the whole-genome sequence of diploid Th. elongatum, we detected 3382 specific SSR sequences on chromosome 6E. Sixty SSR markers were developed, and thirty-three of them can accurately trace chromosome 6E of tetraploid Th. elongatum, which were linked to the disease resistance gene(s) in the wheat genetic background. The molecular marker analysis indicated that 10 markers may be used to distinguish Th. elongatum from other wheat-related species. Thus, K17-1065-4 carrying the stripe rust resistance gene(s) is a novel germplasm useful for breeding disease-resistant wheat cultivars. The molecular markers developed in this study may facilitate the mapping of the stripe rust resistance gene on chromosome 6E of tetraploid Th. elongatum.

Disomic Substitution of 3D Chromosome with Its Homoeologue 3E in Tetraploid Thinopyrum elongatum Enhances Wheat Seedlings Tolerance to Salt Stress

The halophytic wild relatives within Triticeae might provide valuable sources of salt tolerance for wheat breeding, and attempts to use these sources of tolerance have been made for improving salt tolerance in wheat by distant hybridization. A novel wheat substitution line of K17-1078-3 was developed using common wheat varieties of Chuannong16 (CN16), Zhengmai9023 (ZM9023), and partial amphidiploid Trititrigia8801 (8801) as parents, and identified as the 3E(3D) substitution line. The substitution line was compared with their parents for salt tolerance in hydroponic culture to assess their growth. The results showed that less Na⁺ accumulation and lower Na⁺/K⁺ ratio in both shoots and roots were achieved in K17-1078-3 under salinity compared to its wheat parents. The root growth and development of K17-1078-3 was less responsive to salinity. When exposed to high salt treatment, K17-1078-3 had a higher photosynthesis rate, more efficient water use efficiency, and greater antioxidant capacity and stronger osmotic adjustment ability than its wheat parents. In conclusion, a variety of physiological responses and root system adaptations were involved in enhancing salt tolerance in K17-1078-3, which indicated that chromosome 3E possessed the salt tolerance locus. It is possible to increase substantially the salt tolerance of wheat by the introduction of chromosome 3E into wheat genetic background.

Development and Identification of a Novel Wheat-Thinopyrum scirpeum 4E (4D) Chromosomal Substitution Line with Stripe Rust and Powdery Mildew Resistance

Stripe rust caused by Puccinia striiformis f. sp. tritici and powdery mildew caused by Blumeria graminis f. sp. tritici are devastating diseases of wheat worldwide. Exploration of new disease-resistant genes from cultivated wheat and wild relatives are the most effective means of reducing the amounts of fungicides applied to combat these diseases. Thinopyrum scirpeum (2n = 4x = 28, EEEE) is an important promising reservoir of useful genes, including stripe rust and powdery mildew resistance, and may be useful for increasing wheat disease resistance. Here, we characterize a novel wheat-Th. scirpeum disomic substitution line, K16-730-3, and chromosome-specific markers were developed that can be used to trace the Th. scirpeum chromosome or chromosome segments transferred into wheat. Genomic in situ hybridization and fluorescence in situ hybridization analyses indicated that K16-730-3 is a new 4E (4D) chromosomal substitution line. Evaluation of seedling and adult disease responses revealed that K16-730-3 is resistant to stripe rust and powdery mildew. In addition, no obvious difference in grain yield was observed between K16-730-3 and its wheat parents. Genotyping-by-sequencing analyses indicated that 74 PCR-based markers can accurately trace chromosome 4E, which were linked to the disease resistance genes in the wheat background. Further marker validation analyses revealed that 13 specific markers can distinguish between the E-genome chromosomes of Th. scirpeum and the chromosomes of other wheat-related species. The new substitution line K16-730-3 carrying the stripe rust and powdery mildew resistance genes will be useful as novel germplasm in breeding for disease resistance. The markers developed in this study can be used in marker-assisted selection for increasing disease resistance in wheat.

Raise and characterization of a bread wheat hybrid line (Tulaykovskaya 10 × Saratovskaya 29) with chromosome 6Agi2 introgressed from Thinopyrum intermedium

Wheatgrass Thinopyrum intermedium is a source of agronomically valuable traits for common wheat. Partial wheat–wheatgrass amphidiploids and lines with wheatgrass chromosome substitutions are extensively used as intermediates in breeding programs. Line Agis 1 (6Agi2/6D) is present in the cultivar Tulaykovskaya 10 pedigree. Wheatgrass chromosome 6Agi2 carries multiple resistance to fungal diseases in various ecogeographical zones. In this work, we studied the transfer of chromosome 6Agi2 in hybrid populations Saratovskaya 29 × skaya 10 (S29 × T10) and Tulaykovskaya 10 × Saratovskaya 29 (T10 × S29). Chromosome 6Agi2 was identif ied by PCR with chromosome-specif ic primers and by genomic in situ hybridization (GISH). According to molecular data, 6Agi2 was transmitted to nearly half of the plants tested in the F2 and F3 generations. A new breeding line 49-14 (2n = 42) with chromosome pair 6Agi2 was isolated and characterized in T10 × S29 F5 by GISH. According to the results of our f ield experiment in 2020, the line had high productivity traits. The grain weights per plant (10.04 ± 0.93 g) and the number of grains per plant (259.36 ± 22.49) did not differ signif icantly from the parent varieties. The number of grains per spikelet in the main spike was signif icantly higher than in S29 ( p ≤ 0.001) or T10 ( p ≤ 0.05). Plants were characterized by the ability to set 3.77 ± 0.1 grains per spikelet, and this trait varied among individuals from 2.93 to 4.62. The grain protein content was 17.91 %, and the gluten content, 40.55 %. According to the screening for fungal disease resistance carried out in the f ield in 2018 and 2020, chromosome 6Agi2 makes plants retain immunity to the West Siberian population of brown rust and to dominant races of stem rust. It also provides medium resistant and medium susceptible types of response to yellow rust. The possibility of using lines/varieties of bread wheat with wheatgrass chromosomes 6Agi2 in breeding in order to increase protein content in the grain, to confer resistance to leaf diseases on plants and to create multif lowered forms is discussed.

Characterization of a wheat-tetraploid Thinopyrum elongatum 1E(1D) substitution line K17-841-1 by cytological and phenotypic analysis and developed molecular markers

Background

Tetraploid Thinopyrum elongatum (2n = 4x = 28) is a promising source of useful genes, including those related to adaptability and resistance to diverse biotic (Fusarium head blight, rust, powdery mildew, and yellow dwarf virus) and abiotic (cold, drought, and salt) stresses. However, gene transfer rates are low for this species and relatively few species-specific molecular markers are available.

Results

The wheat-tetraploid Th. elongatum line K17–841-1 derived from a cross between a hexaploid Trititrigia and Sichuan wheat cultivars was characterized based on sequential genomic and fluorescence in situ hybridizations and simple sequence repeat markers. We revealed that K17–841-1 is a 1E (1D) chromosomal substitution line that is highly resistant to stripe rust pathogen strains prevalent in China. By comparing the sequences generated during genotyping-by-sequencing (GBS), we obtained 597 specific fragments on the 1E chromosome of tetraploid Th. elongatum. A total of 235 primers were designed and 165 new Th. elongatum-specific markers were developed, with an efficiency of up to 70%. Marker validation analyses indicated that 25 specific markers can discriminate between the tetraploid Th. elongatum chromosomes and the chromosomes of other wheat-related species. An evaluation of the utility of these markers in a F₂ breeding population suggested these markers are linked to the stripe rust resistance gene on chromosome 1E. Furthermore, 28 markers are unique to diploid Th. elongatum, tetraploid Th. elongatum, or decaploid Thinopyrum ponticum, which carry the E genome. Finally, 48 and 74 markers revealed polymorphisms between Thinopyrum E-genome- containing species and Thinopyrum bessarabicum (E^b) and Pseudoroegneria libanotica (St), respectively.

Conclusions

This new substitution line provide appropriate bridge–breeding–materials for alien gene introgression to improve wheat stripe rust resistance. The markers developed using GBS technology in this study may be useful for the high-throughput and accurate detection of tetraploid Th. elongatum DNA in diverse materials. They may also be relevant for investigating the genetic differences and phylogenetic relationships among E, E^b, St, and other closely-related genomes and for further characterizing these complex species.