Molecular and Cytogenetic Characterization of a Wheat-Rye 7BS.7RL Translocation Line with Resistance to Stripe Rust, Powdery Mildew, and Fusarium Head Blight

Genome-wide simple sequence repeat analysis and specific molecular marker development of rye

BACKGROUND

Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics.

RESULTS

In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes.

CONCLUSION

These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.

Molecular Cytogenetic Characterization of Novel Wheat-Rye T1RS.1AL Translocation Lines with Resistance to Powdery Mildew and Stripe Rust Derived from the Chinese Rye Landrace Qinling

Stripe rust and powdery mildew are serious diseases that severely decrease the yield of wheat. Planting wheat cultivars with powdery mildew and stripe rust resistance genes is the most effective way to control these two diseases. Introducing disease resistance genes from related species into the wheat genome via chromosome translocation is an important way to improve wheat disease resistance. In this study, nine novel T1RS.1AL translocation lines were developed from the cross of wheat cultivar Chuannong25 (CN25) and a Chinese rye Qinling. The results of non-denaturing fluorescence in situ hybridization and PCR showed that all new lines were homozygous for the T1RS.1AL translocation. These new T1RS.1AL translocation lines exhibited strong resistance to stripe rust and powdery mildew. The cytogenetics results indicated that the resistance of the new lines was conferred by the 1RS chromosome arms, which came from Qinling rye. The genetic analysis indicated that there were new dominant resistance genes on the 1RS chromosome arm resistant to stripe rust and powdery mildew, and their resistance patterns were different from those of Yr9, Pm8, and Pm17 genes. In addition, the T1RS.1AL translocation lines generally exhibited better agronomic traits in the field relative to CN25. These T1RS.1AL translocations have great potential in wheat-breeding programs in the future.

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.

Phenotypic characterization of the wheat temperature-sensitive leaf color mutant and physical mapping of mutant gene by reduced-representation sequencing

Few available leaf color mutants in crops have greatly limited the understanding of photosynthesis mechanisms, leading to few accomplishments in crop yield improvement via enhanced photosynthetic efficiency. Here, a noticeable albino mutant, CN19M06, was identified. A comparison between CN19M06 and the wild type CN19 at different temperatures showed that the albino mutant was temperature-sensitive and produced leaves with a decreased chlorophyll content at temperatures below 10 °C. Genetic analysis suggested that the albinism was controlled by one recessive nuclear gene named TSCA1, which was putatively assigned to the region of 718.1-729.8 Mb on chromosome 2AL using bulked-segregant analysis and double-digest restriction site-associated DNA. Finally, molecular linkage analysis physically anchored TSCA1 to a narrowed region of 718.8-725.3 Mb with a 6.5 Mb length on 2AL flanked by InDel 18 and InDel 25 with 0.7 cM genetic interval. Among the 111 annotated functional genes in the corresponding chromosomal region, only TraesCS2A01G487900 of the PAP fibrillin family was both related to chlorophyll metabolism and temperature sensitivity; therefore, it was considered the putative candidate gene of TSCA1. Overall, CN19M06 has great potential for exploring the molecular mechanism of photosynthesis and monitoring temperature changes in wheat production.

Transferring a new Fusarium head blight resistance locus FhbRc1 from Roegneria ciliaris into wheat by developing alien translocation lines

A new FHB resistance locus FhbRc1 was identified from the R. ciliaris chromosome 7S^c and transferred into common wheat by developing alien translocation lines. Fusarium head blight (FHB) caused by multiple Fusarium species is a globally destructive disease of common wheat. Exploring and utilization of resources with FHB resistance are the most effective and environmentally beneficial approach for the disease control. Roegneria ciliaris (Trin.) Nevski (2n = 4x = 28, S^cS^cY^cY^c), a tetraploid wheat wild relative, possesses high resistance to FHB. In the previous study, a complete set of wheat-R. ciliaris disomic addition (DA) lines were evaluated for FHB resistance. DA7S^c had stable FHB resistance, which was confirmed to be derived from alien chromosome 7S^c. We tentatively designated the resistant locus as FhbRc1. For better utilization of the resistance in wheat breeding, we developed translocations by inducing chromosome structural aberrations using iron irradiation and the homologous pairing gene mutant ph1b. Totally, 26 plants having various 7S^c structural aberrations were identified. By marker analysis, a cytological map of 7S^c was constructed and 7S^c was dissected into 16 cytological bins. Seven alien chromosome aberration lines, which all had the bin 7S^c-1 on the long arm of 7S^c, showed enhanced FHB resistance. Thus, FhbRc1 was mapped to the distal region of 7S^cL. A homozygous translocation line T4BS·4BL-7S^cL (NAURC001) was developed. It showed improved FHB resistance, while had no obvious genetic linkage drag for the tested agronomic traits compared with the recurrent parent Alondra's. When transferring the FhbRc1 into three different wheat cultivars, the derived progenies having the translocated chromosome 4BS·4BL-7S^cL all showed improved FHB resistance. This revealed the potential value of the translocation line in wheat breeding for FHB resistance.

Transfer of the Resistance to Multiple Diseases from a Triticum-Secale-Thinopyrum Trigeneric Hybrid to Ningmai 13 and Yangmai 23 Wheat Using Specific Molecular Markers and GISH

The middle to lower reaches of the Yangtze River are China's second largest area for wheat production; wheat disease is more serious there than in other areas because of the high humidity and warm weather. However, most cultivated varieties are susceptible to Fusarium head blight (FHB), powdery mildew, and stripe rust, and the lack of disease-resistant germplasm is an obstacle in wheat breeding. Rye and Thinopyrum elongatum, related species of wheat, carry many genes involved in disease resistance. In this study, a trigeneric hybrid, YZU21, with resistance to FHB, powdery mildew, and stripe rust was used to improve two major wheat cultivars, Ningmai 13 (NM13) and Yangmai 23 (YM23). Specific molecular markers and GISH were used to identify hybrid progenies. Five addition or substitution lines and one translocation line of the Triticum-Secale-Thinopyrum trigeneric hybrid were obtained and evaluated for agronomic traits and the resistance to multiple diseases. The results showed that the six trigeneric hybrid lines had desirable agronomic traits and improved resistance to FHB, powdery mildew, and stripe rust; they might be used as parents in wheat breeding for the resistance to multiple disease.

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.

Molecular cytogenetic identification of new wheat-rye 6R, 6RS, and 6RL addition lines with resistance to stripe rust and powdery mildew

Stripe rust and powdery mildew are devastating diseases that have severe effects on wheat production. Introducing resistant genes/loci from wheat-related species into the wheat genome is an important method to improve wheat resistance. Rye (Secale cereale L.) is a cross-pollinating plant and is the most important related species for wheat genetic improvement. In this study, we developed three 6RS ditelosomic addition lines, three 6RL ditelosomic addition lines, and two 6R disomic addition lines by crossing common wheat cultivar Chuannong 25 and rye inbred line QL2. The chromosome composition of all new lines was confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH) and molecular marker analyses. Disease responses to different Puccinia striiformis f. sp. tritici (Pst) races and Blumeria graminis f. sp. tritici (Bgt) isolates and cytogenetic analysis showed that the resistance of the new lines was derived from the rye chromosome 6R of QL2, and both arms (6RS and 6RL) may harbor resistance genes against Pst and Bgt. These new lines could be used as a promising bridging parent and valuable genetic resource for wheat disease resistance improvement.

Development and Molecular Cytogenetic Characterization of Novel Primary Wheat-Rye 1RS.1BL Translocation Lines from Multiple Rye Sources with Resistance to Stripe Rust

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases for wheat production. An important method to improve the stripe rust resistance of wheat is to introduce resistance genes from related species into the wheat genome. The 1RS.1BL wheat-rye translocation from Petkus rye has contributed substantially to wheat resistance breeding worldwide. However, given the breakdown of the stripe rust resistance gene Yr9 in 1RS, its importance for wheat improvement has decreased. In this study, we developed 166 new primary 1RS.1BL translocation lines by crossing rye varieties Weining, Baili, and Aigan with several wheat cultivars. Cytogenetic and molecular analyses indicated that all of these lines contained a pair of intact 1RS.1BL translocation chromosomes. The stripe rust resistance of these translocation lines and their wheat parents was evaluated in southwestern China during the severe stripe rust epidemics in 2015 and 2021. The results showed diverse effects of the 1RS.1BL translocations from different rye cultivars on resistance to stripe rust. The highest genetic diversity was observed in 1RS.1BL translocations derived from diverse rye varieties but in the same wheat background. The development of diverse 1RS.1BL translocation lines offers ample opportunities to introduce new variations into wheat for improving stripe rust resistance. Finally, 71 new translocation lines, including nine developed from the cross of MY11 × Aigan, four from MY11 × Baili, 40 from MY11 × Weining, 14 from A42912 × Baili, and four from A42912 × Weining. These lines showed consistent resistance to stripe rust in fields under frequent changes of the pathogen races and could be useful genetic stocks for breeding wheat cultivars with resistance to stripe rust.

The Physical Location of Stripe Rust Resistance Genes on Chromosome 6 of Rye (Secale cereale L.) AR106BONE

It was reported that the chromosome 6R of rye (Secale cereale L.) carries stripe rust resistance gene Yr83, and the region with the candidate resistance gene(s) still needs to be narrowed down. This study confirmed that the chromosome 6RL^Ar derived from rye AR106BONE contains stripe rust resistance gene(s). A wheat-rye T6BS.6RL^Ar translocation chromosome, a wheat-rye small-segment translocation T6RL^Ar-6AS.6AL, and three kinds of deleted T6BS.6RL^Ar translocations, T6BS.6RL^Ar-1, T6BS.6RL^Ar-2, and T6BS.6RL^Ar-3, were identified. Translocations T6BS.6RL^Ar, T6BS.6RL^Ar-2, and T6RL^Ar-6AS.6AL were highly resistant to stripe rust and T6BS.6RL^Ar-1 and T6BS.6RL^Ar-3 were highly susceptible. The molecular markers specific to 6RL determined that the three regions of the 6RL^Ar arm from 732,999,830 bp to the telomere, from 735,010,030 to 848,010,414 bp, and from 848,011,262 bp to the telomere were deleted from T6BS.6RL^Ar-1, T6BS.6RL^Ar-2, and T6BS.6RL^Ar-3, respectively. T6BS.6RL^Ar-2 and T6RL^Ar-6AS.6AL contained the segment that was deleted in T6BS.6RL^Ar-3. Therefore, it can be concluded that about 37 Mb segment from 848,011,262 bp to the telomere carried stripe rust resistance gene(s), and it was smaller than that with the Yr83 gene. Gene annotation indicated that about 37 Mb region contains 43 potential resistance genes, and 42 of them are nucleotide-binding site and leucine-rich repeat (NBS-LRR)-like resistance protein genes. The results in this study narrowed down the size of the region with candidate stripe rust resistance gene(s) on the 6RL arm, and the T6RL^Ar-6AS.6AL is a promising small-segment translocation for improvement of wheat cultivars.

Development and Characterization of Novel Wheat-Rye 1RS·1BL Translocation Lines with High Resistance to Puccinia striiformis f. sp. tritici

Wheat-rye 1RS·1BL translocations from 'Petkus' rye have contributed substantially to wheat production worldwide with their great disease resistance and yield traits. However, the resistance genes on the 1RS chromosomes have completely lost their resistance to newly emerged pathogens. Rye could widen the variation of 1RS as a naturally cross-pollinated related species of wheat. In this study, we developed three new 1RS·1BL translocation lines by crossing rye inbred line BL1, selected from Chinese landrace rye Baili, with wheat cultivar Mianyang11. These three new translocation lines exhibited high resistance to the most virulent and frequently occurring stripe rust pathotypes and showed high resistance in the field, where stripe rust outbreaks have been most severe in China. One new gene for stripe rust resistance, located on 1RS of the new translocation lines, is tentatively named YrRt1054. YrRt1054 confers resistance to Puccinia striiformis f. sp. tritici pathotypes that are virulent toward Yr9 and YrCn17. This new resistance gene, YrRt1054, is available for wheat improvement programs. The present study indicated that rye cultivars may carry additional untapped variation as potential sources of resistance.

Molecular Cytogenetic and Physiological Characterization of a Novel Wheat-Rye T1RS.1BL Translocation Line from Secale cereal L. Weining with Resistance to Stripe Rust and Functional "Stay Green" Trait

In this study, a novel T1RS.1BL translocation line RT843-5 was selected from a cross between wheat Mianyang11 (MY11) and Weining rye. The results of MC-FISH, PCR, and A-PAGE showed that RT843-5 contained two intact T1RS.1BL translocation chromosomes. RT843-5 showed resistance to the most virulent and frequently occurring stripe rust races/isolates. Additionally, RT843-5 showed resistance in the field in locations where stripe rust outbreaks have been the most severe in China. Genetic analysis indicated one new gene for stripe rust resistance, located on 1RS of RT843-5, which was tentatively named YrRt843. Furthermore, the chlorophyll content, the activities of catalase (CAT), and superoxide dismutase (SOD), and the net photosynthetic rate (Pn) of RT843-5 were significantly higher than those in its wheat parent MY11, whereas malondialdehyde (MDA) accumulation was significantly lower after anthesis in RT843-5 compared to in MY11. RT843-5 had a significantly higher 1000-kernel weight and yield than MY11. The results indicated that RT843-5 exhibited functional stay-green traits after anthesis, that delayed the senescence process in wheat leaves during the filling stage and had positive effects on grain yield. The present study indicated that Weining rye may carry untapped variations as a potential source of resistance, and that RT843-5 could be an important material for wheat breeding programs in the future.

Molecular Cytogenetic Characterization of Novel 1RS.1BL Translocation and Complex Chromosome Translocation Lines with Stripe Rust Resistance

Rye is the most important source for the genetic improvement of wheat. In this study, two stable wheat-rye primary 1RS.1BL translocation lines, RT855-13 and RT855-14, were selected and identified by acid polyacrylamide gel electrophoresis (A-PAGE), co-dominant PCR, and multi-color fluorescence in situ hybridization (MC-FISH) from the progeny of the crossing of the wheat cultivar Mianyang11 and a Chinese rye Weining. When more than two independent, simple reciprocal translocations are involved in a carrier, they are defined as complex chromosome translocations (CCT). The MC-FISH results also indicated that CCT occurred in RT855-13; namely that, besides 1RS.1BL translocation chromosomes, there are other two pairs of balanced reciprocal translocations. It was demonstrated that the interchange between a distal segment of 4B and long arm of 3D occurred in the RT855-13. The novel translocation chromosomes in wheat were recorded as 3DS.4BS^DS and 3DL-4BS^PS.4BL. Reports about CCT as a genetic resource in plant breeding programs are scarce. Both lines expressed high resistance to Puccinia striiformis f. sp. tritici, which are prevalent in China and are virulent on Yr9, and the CCT line RT855-13 retained better resistance as adult plants compared with RT855-14 in the field. Both lines, especially the CCT line RT855-13, exhibited better agronomic traits than their wheat parent, Mianyang11, indicating that both translocation lines could potentially be used for wheat improvement. The results also indicated that the position effects of CCT can lead to beneficial variations in agronomic and resistant traits, making them a valuable genetic resource to wheat breeding programs.

Discovery of a novel powdery mildew (Blumeria graminis) resistance locus in rye (Secale cereale L.)

Powdery mildew is one of the most destructive diseases in the world, causing substantial grain yield losses and quality reduction in cereal crops. At present 23 powdery mildew resistance genes have been identified in rye, of which the majority are in wheat-rye translocation lines developed for wheat improvement. Here, we investigated the genetics underlying powdery mildew resistance in the Gülzow-type elite hybrid rye (Secale cereale L.) breeding germplasm. In total, 180 inbred breeding lines were genotyped using the state-of-the-art 600 K SNP array and phenotyped for infection type against three distinct field populations of B. graminis f. sp. secalis from Northern Germany (2013 and 2018) and Denmark (2020). We observed a moderate level of powdery mildew resistance in the non-restorer germplasm population, and by performing a genome-wide association study using 261,406 informative SNP markers, we identified a powdery mildew resistance locus, provisionally denoted PmNOS1, on the distal tip of chromosome arm 7RL. Using recent advances in rye genomic resources, we investigated whether nucleotide-binding leucine-rich repeat genes residing in the identified 17 Mbp block associated with PmNOS1 on recent reference genomes resembled known Pm genes.