Establishment of a set of wheat-rye addition lines with resistance to stem rust

Stable minichromosome and functional neocentromere derived from rye 7R chromosome arm

BACKGROUND

The study of newly formed centromere with stable transmission ability can provide theoretical guidance for the construction of artificial chromosomes. More neocentromeres are needed to study the mechanisms of their formation.

RESULTS

In this study, a minichromosome 7RLmini was derived from the progeny of wheat-rye 7R monosomic addition line. The minichromosome 7RLmini contained subtelomeric tandem repeats pSc119.2 and rye-specific pSc200, and it came from the distal region of the long arm of 7R chromosome. A neocentromere was formed in this minichromosome, and it did not contain centromeric repetitive sequences CCS1 and pAWRC.1. CENH3 ChIP-seq and ssDRIP-seq data confirmed that a 2.4 Mb segment from the rye 7R chromosome was involved in the neocentromere formation and enrichment of R-loops in this region. Within the 2.4 Mb segment, the GC content was higher that of AT, and a major binding position of CENH3 nucleosomes was identified on a 6 kb unknown LTR retrotransposon TE00002448. This unknown LTR retrotransposon was rye-specific and distributed through all the arms of rye chromosomes. The minichromosome exhibited stable generational transmission.

CONCLUSION

A minichromosome from rye 7R with neocentromere was obtained in this study and the neocentromere was formed at the position far away from its native equivalent. This minichromosome provides additional material for the research on the mechanism of neocentromere formation. We theorize that R-loops and transposable element might be involved in the positioning of CENH3 nucleosomes in a functional neocentromere.

Past innovations and future possibilities in plant chromosome engineering

Plant chromosome engineering has emerged as a pivotal tool in modern plant breeding, facilitating the transfer of desirable traits through the incorporation of alien chromosome fragments into plants. Here, we provide a comprehensive overview of the past achievements, current methodologies and future prospects of plant chromosome engineering. We begin by examining the successful integration of specific examples such as the incorporation of rye chromosome segments (e.g. the 1BL/1RS translocation), Dasypyrum villosum segments (e.g. the 6VS segment for powdery mildew resistance), Thinopyrum intermedium segments (e.g. rust resistance genes) and Thinopyrum elongatum segments (e.g. Fusarium head blight resistance genes). In addition to trait transfer, advancements in plant centromere engineering have opened new possibilities for chromosomal manipulation. This includes the development of plant minichromosomes via centromere-mediated techniques, the generation of haploids through CENH3 gene editing, and the induction of aneuploidy using KaryoCreate. The advent of CRISPR/Cas technology has further revolutionized chromosome engineering, enabling large-scale chromosomal rearrangements, such as inversions and translocations, as well as enabling targeted insertion of large DNA fragments and increasing genetic recombination frequency. These advancements have significantly expanded the toolkit for genetic improvement in plants, opening new horizons for the future of plant breeding.

Development and Characterization of Two Wheat-Rye Introgression Lines with Resistance to Stripe Rust and Powdery Mildew

Rye (Secale cereale L.) genes, which contribute to the tertiary gene pool of wheat, include multiple disease resistance genes useful for the genetic improvement of wheat. Introgression lines are the most valuable materials for wheat breeding because of their small alien segments and limited or lack of linkage drag. In the present study, wheat-rye derivative lines SN21627-2 and SN21627-6 were produced via distant hybridization. A genomic in situ hybridization analysis revealed that SN21627-2 and SN21627-6 lack alien segments, while a multi-color fluorescence in situ hybridization analysis detected structural changes in both introgression lines. At the seedling and adult plant stages, SN21627-2 and SN21627-6 were highly resistant to stripe rust and powdery mildew. Primers for 86 PCR-based landmark unique gene markers and 345 rye-specific SLAF markers were used to amplify SN21627-2 and SN21627-6 genomic DNA. Eight markers specific to rye chromosome 2R were detected in both introgression lines, implying these lines carry chromosome 2R segments with genes conferring stripe rust and powdery mildew resistance. Therefore, SN21627-2 and SN21627-6 are resistant to more than one major wheat disease, making them promising bridging parents for breeding disease-resistant wheat lines.

Unveiling the distinctive traits of functional rye centromeres: minisatellites, retrotransposons, and R-loop formation

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments. Despite their conserved functionality, centromeric DNA sequences exhibit rapid evolution, presenting diverse sizes and compositions across species. The functional significance of rye centromeric DNA sequences, particularly in centromere identity, remains unclear. In this study, we comprehensively characterized the sequence composition and organization of rye centromeres. Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons (LTR-RTs) and interspersed minisatellites. We systematically classified LTR-RTs into five categories, highlighting the prevalence of younger CRS1, CRS2, and CRS3 of CRSs (centromeric retrotransposons of Secale cereale) were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes. The minisatellites, mainly derived from retrotransposons, along with CRSs, played a pivotal role in establishing functional centromeres in rye. Additionally, we observed the formation of R-loops at specific regions of CRS1, CRS2, and CRS3, with both rye pericentromeres and centromeres exhibiting enrichment in R-loops. Notably, these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres, suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification. Our work provides insights into the DNA sequence composition, distribution, and potential function of R-loops in rye centromeres. This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres, offering implications for the development of synthetic centromeres in future plant modifications and beyond.

Development of a Set of Wheat-Rye Derivative Lines from Hexaploid Triticale with Complex Chromosomal Rearrangements to Improve Disease Resistance, Agronomic and Quality Traits of Wheat

An elite hexaploid triticale Yukuri from Australia was used as a bridge for transferring valuable genes from Secale cereale L. into common wheat for enriching the genetic variability of cultivated wheat. Non-denaturing-fluorescence in situ hybridization (ND-FISH) identified that Yukuri was a secondary triticale with a complete set of rye chromosomes and a 6D(6A) substitution. Seed protein electrophoresis showed that Yukuri had a unique composition of glutenin subunits. A set of Yukuri-derived wheat-rye introgression lines were created from a Yukuri x wheat population, and all lines were identified by ND-FISH with multiple probes and validated by diagnostic molecular marker analysis. A total of 59 wheat-rye introgression lines including modified chromosome structural variations of wheat, and new complex recombinant chromosomes of rye were detected through ND-FISH and Oligo-FISH painting based on oligonucleotide pools derived from wheat-barley genome collinear regions. Wheat lines carrying the 1R chromosome from Yukuri displayed resistance to both stripe rust and powdery mildew, while the lines carrying the 3RL and 7RL chromosome arms showed stripe rust resistance. The chromosome 1R-derived lines were found to exhibit a significant effect on most of the dough-related parameters, and chromosome 5R was clearly associated with increased grain weight. The development of the wheat-rye cytogenetic stocks carrying disease resistances and superior agronomic traits, as well as the molecular markers and FISH probes will promote the introgression of abundant variation from rye into wheat improvement programs.

Development of novel wheat-rye 6RS small fragment translocation lines with powdery mildew resistance and physical mapping of the resistance gene PmW6RS

KEY MESSAGE

Novel wheat-rye 6RS small fragment translocation lines with powdery mildew resistance were developed, and the resistance gene PmW6RS was physically mapped onto 6RS-0.58-0.66-bin corresponding to 18.38 Mb in Weining rye. Rye (Secale cereale L., RR) contains valuable genes for wheat improvement. However, most of the rye resistance genes have not been successfully used in wheat cultivars. Identification of new rye resistance genes and transfer of these genes to wheat by developing small fragment translocation lines will make these genes more usable for wheat breeding. In this study, a broad-spectrum powdery mildew resistance gene PmW6RS was localized on rye chromosome arm 6RS using a new set of wheat-rye disomic and telosomic addition lines. To further study and use PmW6RS, 164 wheat-rye 6RS translocation lines were developed by 60Coγ-ray irradiation. Seedling and adult stage powdery mildew resistance analysis showed that 106 of the translocation lines were resistant. A physical map of 6RS was constructed using the 6RS translocation and deletion lines, and PmW6RS was localized in the 6RS-0.58-0.66-bin, flanked by markers X6RS-3 and X6RS-10 corresponding to the physical interval of 50.23-68.61 Mb in Weining rye genome. A total of 23 resistance-related genes were annotated. Nine markers co-segregate with the 6RS-0.58-0.66-bin, which can be used to rapidly trace the 6RS fragment carrying PmW6RS. Small fragment translocation lines with powdery mildew resistance were backcrossed with wheat cultivars, and 39 agronomically acceptable homozygous 6RS small fragment translocation lines were obtained. In conclusion, this study not only provides novel gene source and germplasms for wheat resistance breeding, but also laid a solid foundation for cloning of PmW6RS.

Development and Molecular Cytogenetic Characterization of a Novel Wheat-Rye T6RS.6AL Translocation Line from Secale cereale L. Qinling with Resistance to Stripe Rust and Powdery Mildew

In this study, a novel T6RS.6AL translocation line, 117-6, was selected from a cross between common Chuannong25 (CN25) wheat and Qinling rye. The results of nondenaturing fluorescence in situ hybridization (ND-FISH) and PCR showed that 117-6 contained two T6RS.6AL translocation chromosomes. The distal region of the 6RS chromosome in 117-6 was mutant and showed different FISH signal patterns. When inoculated with different stripe rust races and powdery mildew races in seedlings, 117-6 expressed high resistance to them. The 117-6 line also exhibited high resistance to stripe rust and powdery mildew in the field under natural Puccinia striiformis f. sp. tritici (Pst) and Blumeria graminis f. sp. tritici (Bgt) infection. The cytogenetic analysis indicated that the introduction of 6RS conferred resistance ability. Compared with wheat parent CN25, 117-6 exhibited excellent agronomic traits in the field. The present study indicated that Qinling rye may carry favorite genes as a potential source for wheat genetic improvement, and 117-6 could be a useful germplasm for wheat breeding programs in the future.