Pyramiding of Adult-Plant Resistance Genes Enhances All-Stage Resistance to Wheat Stripe Rust

Rapid isolation of Yr9 via MutIsoSeq and QTL analysis of durable stripe rust resistance in wheat cultivar Xingzi 9104

The fungus Puccinia striiformis f. sp. tritici (Pst) is the causal agent of wheat stripe rust which constitutes a major limitation to wheat production. Cloning and applying disease-resistant genes are considered as an effective solution. Chinese wheat cultivar Xingzi 9104 (XZ9104) has exhibited durable resistance across multiple environments since its release. Through quantitative trait loci (QTL) analysis, eight QTL were found on chromosome arms 1BS, 1BL, 2AL, 2BL, 3BS, 4BL, 5BL and 7BL. YrXZ identified as 1RS.1BL translocation conferred race-specific all-stage resistance to Pst race CYR23. QYrxz.nwafu-1BL.6 and QYrxz.nwafu-3BS.7 were considered as the adult plant resistance genes Yr29 and Yr30, respectively. Notably, QYrxz.nwafu-2BL.5 accounted for 15.75-47.63% of the phenotypic variation across diverse environments and its pyramiding with Yr29 and Yr30 can confer high level of resistance. Other QTL were environment-dependent with minor effects. To clone the above resistance genes, we created a population of over 2,000 M5 mutants in XZ9104 using ethylmethane sulfonate (EMS) mutagenesis and screened various types of susceptible mutants. Using the MutIsoseq approach with five mutant lines susceptible to race CYR23, we rapid isolated a candidate gene for YrXZ encoding coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) protein. Integrating cytological analysis, gene-based association analysis, transcriptomic profiling and virus-induced gene silencing (VIGS), we confirmed that the causal gene for YrXZ was indeed Yr9. This study demonstrated that multiple QTL with different effects contributed to the durable resistance in XZ9104. Understanding the molecular mechanisms and pathways involved in plant defense can inform future strategies for deploying resistance gene and engineering of genetic resistance against evolving diseases.

A large-scale multi-environment study dissecting adult-plant resistance haplotypes for stripe rust resistance in Australian wheat breeding populations

KEY MESSAGE

Genetic variation in stripe rust resistance exists in Australian wheat breeding populations and is environmentally influenced. Stacking multiple resistance haplotypes or using whole-genome approaches will improve resistance stability and environmental specificity. Wheat stripe rust (Puccinia striiformis) is a fungal disease responsible for substantial yield losses globally. To maintain crop productivity in future climates, the identification of genetics offering durable resistance across diverse growing conditions is crucial. To stay one-step ahead of the pathogen, Australian wheat breeders are actively selecting for adult-plant resistance (APR), which is considered more durable than seedling resistance. However, deploying resistance that is stable or effective across environments and years is challenging as expression of underling APR loci often interacts with environmental conditions. To explore the underlying genetics and interactions with the environment for stripe rust resistance, we employ haplotype-based mapping using the local GEBV approach in elite wheat breeding populations. Our multi-environment trial analyses comprising 35,986 inbred lines evaluated across 10 environments revealed significant genotype-by-environment interactions for stripe rust. A total of 32 haploblocks associated with stripe rust resistance were identified, where 23 were unique to a specific environment and nine were associated with stable resistance across environments. Population structure analysis revealed commercial or advanced breeding lines carried desirable resistance haplotypes, highlighting the opportunity to continue to harness and optimise resistance haplotypes already present within elite backgrounds. Further, we demonstrate that in silico stacking of multiple resistance haplotypes through a whole-genome approach has the potential to substantially improve resistance levels. This represents the largest study to date exploring commercial wheat breeding populations for stripe rust resistance and highlights the breeding opportunities to improve stability of resistance across and within target environments.

Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding

High-quality genome information is essential for efficiently deciphering and improving crop traits. Here, we report a highly contiguous and accurate hexaploid genome assembly for the key wheat breeding parent Zhou8425B, an elite 1BL/1RS translocation line with durable adult plant resistance (APR) against yellow rust (YR) disease. By integrating HiFi and Hi-C sequencing reads, we have generated a 14.75-Gb genome assembly for Zhou8425B with a contig N50 of 70.94 and a scaffold N50 of 735.11 Mb. Comparisons with previously sequenced common wheat cultivars shed light on structural changes in the 1RS chromosome arm, which has been extensively used in wheat improvement. Interestingly, Zhou8425B 1RS carries more genes encoding AP2/ERF-ERF or B3 transcription factors than its counterparts in four previously sequenced wheat and rye genotypes. The Zhou8425B genome assembly aided in the fine mapping of a new APR locus (YrZH3BS) that confers resistance to YR disease and promotes grain yield under field conditions. Notably, pyramiding YrZH3BS with two previously characterized APR loci (YrZH22 and YrZH84) can further reduce YR severity and enhance grain yield, with the triple combination (YrZH3B + YrZH22 + YrZH84) having the greatest effect. Finally, the founder genotype effects of Zhou8425B were explored using publicly available genome resequencing data, which reveals the presence of important Zhou8425B genomic blocks in its derivative cultivars. Our data demonstrate the value of the Zhou8425B genome assembly for further study of the structural and functional characteristics of 1RS, the genetic basis of durable YR resistance, and founder genotype effects in wheat breeding. Our resources will facilitate the development of elite wheat cultivars through genomics-assisted breeding.

CRISPR-mediated genome editing of wheat for enhancing disease resistance

Wheat is cultivated across diverse global environments, and its productivity is significantly impacted by various biotic stresses, most importantly but not limited to rust diseases, Fusarium head blight, wheat blast, and powdery mildew. The genetic diversity of modern cultivars has been eroded by domestication and selection, increasing their vulnerability to biotic stress due to uniformity. The rapid spread of new highly virulent and aggressive pathogen strains has exacerbated this situation. Three strategies can be used for enhancing disease resistance through genome editing: introducing resistance (R) gene-mediated resistance, engineering nucleotide-binding leucine-rich repeat receptors (NLRs), and manipulating susceptibility (S) genes to stop pathogens from exploiting these factors to support infection. Utilizing R gene-mediated resistance is the most common strategy for traditional breeding approaches, but the continuous evolution of pathogen effectors can eventually overcome this resistance. Moreover, modifying S genes can confer pleiotropic effects that hinder their use in agriculture. Enhancing disease resistance is paramount for sustainable wheat production and food security, and new tools and strategies are of great importance to the research community. The application of CRISPR-based genome editing provides promise to improve disease resistance, allowing access to a broader range of solutions beyond random mutagenesis or intraspecific variation, unlocking new ways to improve crops, and speeding up resistance breeding. Here, we first summarize the major disease resistance strategies in the context of important wheat diseases and their limitations. Next, we turn our attention to the powerful applications of genome editing technology in creating new wheat varieties against important wheat diseases.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

Evaluation of stripe rust resistance and analysis of resistance genes in wheat genotypes from Pakistan and Southwest China

Introduction

Stripe rust, caused by Puccinia striiformis f. sp. tritici, poses a significant threat to wheat quality and production worldwide. The rapid evolution of Pst races caused several resistance genes to be ineffective.

Methods

This study evaluated stripe rust resistance genes in 349 Pakistan and Southwest China genotypes. We utilized previously published functional and linked molecular markers to detect 13 major stripe rust resistance genes: Yr5, Yr9, Yr10, Yr15, Yr17, Yr18, Yr26, Yr29, Yr30, Yr36, Yr48, Yr65, and YrSp. Field evaluations assessed IT and resistance levels, while the impact of gene combinations on resistance was also analyzed.

Results

Field evaluations showed that over 60% of Chuanyu wheat, 50% of recent Pakistani cultivars, and 20% of historic Pakistani lines were resistant to current stripe rust races. In Chuanyu wheat, the dominant genes were Yr17, YrSp, and Yr48; however, Yr17, Yr26, and YrSp were overused, while Yr36 was absent, and Yr18 was rare. In historic lines, Yr5, Yr17, Yr18, and Yr26 were prevalent, with Yr15, Yr26, and YrSp demonstrating effective resistance against current stripe rust races. Furthermore, the study identified specific combinations of Yr genes (Yr26+Yr48, Yr29+Yr5, Yr26+Yr30, and Yr30+Yr17) that enhanced resistance to Pst.

Discussion

This research highlights effective resistance genes and gene combinations for stripe rust in wheat and emphasizes the deployment of durable resistance. The findings guide the strategic use of these genes in breeding programs aimed at developing durable resistance in wheat genotypes in Pakistan and Southwest China.

Gene editing of the E3 ligase PIRE1 fine-tunes ROS production for enhanced bacterial disease resistance in tomato

Reactive oxygen species (ROS) accumulation is required for effective plant defense. Accumulation of the Arabidopsis NADPH oxidase RBOHD is regulated by phosphorylation of a conserved C-terminal residue (T912) leading to ubiquitination by the RING E3 ligase PIRE. Arabidopsis PIRE knockouts exhibit enhanced ROS production and resistance to the foliar pathogen Pseudomonas syringae. Here, we identified 170 PIRE homologs, which emerged in Tracheophytes and expanded in Angiosperms. We investigated the role of Solanum lycopersicum (tomato) PIRE homologs in regulating ROS production, RBOH stability, and disease resistance. Mutational analyses of residues corresponding to T912 in the tomato RBOHD ortholog, SlRBOHB, affected protein accumulation and ROS production in a PIRE-dependent manner. Using CRISPR-cas9, we generated mutants in two S. lycopersicum PIRE homologs (SlPIRE). SlPIRE1 edited lines (Slpire1) in the tomato cultivar M82 displayed enhanced ROS production upon treatment with flg22, an immunogenic epitope of flagellin. Furthermore, Slpire1 exhibited decreased disease symptoms and bacterial accumulation when inoculated with foliar bacterial pathogens Pseudomonas syringae and Xanthomonas campestris. However, Slpire1 exhibited similar levels of colonization as wild type upon inoculation with diverse soilborne pathogens. These results indicate that phosphorylation and ubiquitination crosstalk regulate RBOHs in multiple plant species, and PIRE is a promising target for foliar disease control. This study also highlights the pathogen-specific role of PIRE, indicating its potential for targeted manipulation to enhance foliar disease resistance without affecting root-associated interactions, positioning PIRE as a promising target for improving overall plant health.

Transferring an Adult-Plant Stripe-Rust Resistance Gene Yr7VS from Chromosome 7V of Dasypyrum villosum (L.) to Bread Wheat

Stripe rust (Puccinia striiformis West. f.sp. tritici, Pst) is a destructive disease that seriously threatens wheat production globally. Exploring novel resistance genes for use in wheat breeding is an urgent need, as continuous Pst evolution frequently leads to a breakdown of host resistance. Here, we identified a set of wheat-Dasypyrum villosum 01I139 (V#6) disomic introgression lines for the purpose of determining their responses to a mixture of Pst isolates CYR32, CYR33 and CYR34 at both seedling and adult-plant stages. The results showed that all introgression lines exhibited high susceptibility at the seedling stage, with infection-type (IT) scores in the range of 6-8, whereas, for chromosomes 5V#6 and 7V#6, disomic addition lines NAU5V#6-1 and NAU7V#6-1 displayed high resistance at the adult-plant stage, indicating that adult-plant resistance (APR) genes were located on them. Further, in order to transfer the stripe-rust resistance on chromosome 7V#6, four new wheat-D. villosum introgression lines were identified, by the use of molecular cytogenetic approaches, from the self-pollinated seeds of 7D and 7V#6, in double monosomic line NAU7V#6-2. Among them, NAU7V#6-3 and NAU7V#6-4 were t7V#6L and t7V#6S monosomic addition lines, and NAU7V#6-5 and NAU7V#6-6 were homozygous T7DS·7V#6L and T7DL·7V#6S whole-arm translocation lines. Stripe-rust tests and genetic analyses of chromosome 7V#6 introgression lines revealed a dominant APR gene designated as Yr7VS on the chromosome arm 7V#6S. Comparison with the homozygous T7DL·7V#6S translocation line and the recurrent parent NAU0686 showed no significant differences in yield-related traits. Thus, T7DL·7V#6S whole-arm translocation with the APR gene Yr7VS provided a valuable germplasm for breeding for resistance.

Gene pyramiding of ZmGLK36 and ZmGDIα-hel for rough dwarf disease resistance in maize

Maize rough dwarf disease (MRDD) caused by pathogenic viruses in the genus Fijivirus in the family Reoviridae is one of the most destructive diseases in maize. The pyramiding of effective resistance genes into maize varieties is a potential approach to reduce the damage resulting from the disease. Two major quantitative trait loci (QTLs) (qMrdd2 and qMrdd8) have been previously identified. The resistance genes ZmGLK36 and ZmGDIα-hel have also been cloned with the functional markers Indel-26 and IDP25K, respectively. In this study, ZmGLK36 and ZmGDIα-hel were introgressed to improve MRDD resistance of maize lines (Zheng58, Chang7-2, B73, Mo17, and their derived hybrids Zhengdan958 and B73 × Mo17) via marker-assisted selection (MAS). The converted lines and their derived hybrids, carrying one or two genes, were evaluated for MRDD resistance using artificial inoculation methods. The double-gene pyramiding lines and their derived hybrids exhibited increased resistance to MRDD compared to the monogenic lines and the respective hybrids. The genetic backgrounds of the converted lines were highly similar (90.85-98.58%) to the recurrent parents. In addition, agronomic trait evaluation demonstrated that pyramiding lines with one or two genes and their derived hybrids were not significantly different from the recurrent parents and their hybrids under nonpathogenic stress, including period traits (tasseling, pollen shedding, and silking), yield traits (ear length, grain weight per ear and 100-kernel weight) and quality traits (protein and starch content). There were differences in plant architecture traits between the improved lines and their hybrids. This study illustrated the successful development of gene pyramiding for improving MRDD resistance by advancing the breeding process.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01466-9.

Identification and fine-mapping of QYrAS286-2BL conferring adult-plant resistance to stripe rust in cultivated emmer wheat

KEY MESSAGE

A novel major adult-plant stripe rust resistance QTL derived from cultivated emmer wheat was mapped to a 123.6-kb region on wheat chromosome 2BL. Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat. Identification of new sources of resistance and their utilization in breeding programs is the effectively control strategy. The objective of this study was to identify and genetically characterize the stripe rust resistance derived from the cultivated emmer accession AS286. A recombinant inbred line population, developed from a cross between the susceptible durum wheat line langdon and AS286, was genotyped using the Wheat55K single nucleotide polymorphism array and evaluated in field conditions with a mixture of the prevalent Chinese Pst races (CYR32, CYR33, CYR34, Zhong4, and HY46) and in growth chamber with race CYR34. Three QTLs conferring resistance were mapped on chromosomes 1BS, 2BL, and 5BL, respectively. The QYrAS286-1BS and QYrAS286-2BL were stable with major effects, explaining 12.91% to 18.82% and 11.31% to 31.43% of phenotypic variation, respectively. QYrAS286-5BL was only detected based on growth chamber seedling data. RILs harboring both QYrAS286-1BS and QYrAS286-2BL showed high levels of stripe rust resistance equal to the parent AS286. The QYrAS286-2BL was only detected at the adult-plant stage, which is different from previously named Yr genes and inherited as a single gene. It was further mapped to a 123.6-kb region using KASP markers derived from SNPs identified by bulked segregant RNA sequencing (BSR-Seq). The identified loci enrich our stripe rust resistance gene pool, and the flanking markers developed here could be useful in marker-assisted selection for incorporating QYrAS286-2BL into wheat cultivars.

A major yellow rust resistance QTL on chromosome 6A shows increased frequency in recent Norwegian spring wheat cultivars and breeding lines

KEY MESSAGE

A major yellow rust resistance QTL, QYr.nmbu.6A, contributed consistent adult plant resistance in field trials across Europe, China, Kenya and Mexico. Puccinia striiformis f. sp. tritici, causing wheat yellow rust (YR), is one of the most devastating biotrophic pathogens affecting global wheat yields. Owing to the recent epidemic of the PstS10 race group in Europe, yellow rust has become a reoccurring disease in Norway since 2014. As all stage resistances (ASR) (or seedling resistances) are usually easily overcome by pathogen evolution, deployment of durable adult plant resistance (APR) is crucial for yellow rust resistance breeding. In this study, we assessed a Nordic spring wheat association mapping panel (n = 301) for yellow rust field resistance in seventeen field trials from 2015 to 2021, including nine locations in six countries across four different continents. Nine consistent QTL were identified across continents by genome-wide association studies (GWAS). One robust QTL on the long arm of chromosome 6A, QYr.nmbu.6A, was consistently detected in nine out of the seventeen trials. Haplotype analysis of QYr.nmbu.6A confirmed significant QTL effects in all tested environments and the effect was also validated using an independent panel of new Norwegian breeding lines. Increased frequency of the resistant haplotype was found in new varieties and breeding lines in comparison to older varieties and landraces, implying that the resistance might have been selected for due to the recent changes in the yellow rust pathogen population in Europe.

Haplotype Analysis Sheds Light on the Genetic Evolution of the Powdery Mildew Resistance Locus Pm60 in Triticum Species

Wheat powdery mildew (Blumeria graminis f. sp. tritici, Bgt, recently clarified as B. graminis s. str.), is one of the most destructive diseases of wheat. Pm60 is a nucleotide-binding leucine-rich repeat (NLR) gene that confers race-specific resistance to Bgt. Allelic variants (Pm60, Pm60a, and Pm60b) were found in Triticum urartu and T. dicoccoides, the wild progenitors of wheat. In the present study, we studied the diversity of the Pm60 locus in a large set of wheat germplasm and found 20 tetraploid wheats harboring the Pm60 alleles, which correspond to three novel haplotypes (HapI-HapIII). HapI (Pm60 allele) and HapII (Pm60a allele) were present in domesticated tetraploid wheats, whereas HapIII (Pm60a allele) was identified in wild tetraploid T. araraticum. A sequence comparison of HapII and HapIII revealed that they differed by three SNPs and a GCC deletion. Results of the phylogenetic analysis revealed that HapII was more closely related to the functional haplotype MlIW172. Infection tests showed that HapII-carrying lines display a partial resistance response to Bgt#GH, while HapI was susceptible. Our results provide insights into the genetic evolution of the Pm60 locus and potential valuable alleles for powdery mildew resistance breeding.