ABSTRACT
Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum resistance genes could impart durable stem rust resistance. This study attempted transfer of Sr59 resistance gene from line TA5094 (developed through CSph1bM-induced T2DS·2RL Robertsonian translocation conferring broad-spectrum resistance). Poor agronomic performance of line TA5094 necessitates Sr59 transfer to adapted genetic backgrounds and utility evaluations for wheat improvement. Based on combined stem rust seedling and molecular analyses, 2070 BC1F1 and 1230 BC2F1 plants were derived from backcrossing BAJ#1, KACHU#1, and REEDLING#1 with TA5094. Genotyping-by-sequencing (GBS) results revealed the physical positions of 15,116 SNPs on chromosome 2R. The adapted genotypes used for backcrossing were found not to possess broad-spectrum resistance to selected stem rust races, whereas Sr59-containing line TA5094 showed resistance to all races tested. Stem rust seedling assays combined with kompetitive allele-specific PCR (KASP) marker analysis successfully selected and generated the BC2F2 population, which contained the Sr59 gene, as confirmed by GBS. Early-generation data from backcrossing suggested deviations from the 3:1 segregation, suggesting that multiple genes may contribute to Sr59 resistance reactions. Using GBS marker data (40,584 SNPs in wheat chromosomes) to transfer the recurrent parent background to later-generation populations resulted in average genome recovery of 71.2% in BAJ#1*2/TA5094, 69.8% in KACHU#1*2/TA5094, and 70.5% in REEDLING#1*2/TA5094 populations. GBS data verified stable Sr59 introgression in BC2F2 populations, as evidenced by presence of the Ph1 locus and absence of the 50,936,209 bp deletion in CSph1bM. Combining phenotypic selections, stem rust seedling assays, KASP markers, and GBS data substantially accelerated transfer of broad-spectrum resistance into adapted genotypes. Thus, this study demonstrated that the Sr59 resistance gene can be introduced into elite genetic backgrounds to mitigate stem rust-related yield losses.
Subject(s)
Basidiomycota , Triticum , Triticum/genetics , Triticum/microbiology , Genotype , Chromosome Mapping , Disease Resistance/genetics , Alleles , Basidiomycota/genetics , Plant Diseases/genetics , Plant Diseases/microbiologyABSTRACT
INTRODUCTION: Members of the family Geminiviridae have been reported to infect either a monocot plant or a dicot plant, but not both. This study reports a geminivirus, Wheat Dwarf India Virus (WDIV), first identified in wheat, that is capable of infecting both monocot and dicot plants and acting as a viral vector. OBJECTIVES: This study was aimed at developing a broad host range viral vector system for reverse genetics and genome editing. METHODS: Here we used a wheat isolate of WDIV and Ageratum yellow leaf curl betasatellite (AYLCB) for infectivity assays and vector development. We performed Agrobacterium-mediated inoculation of WDIV and AYLCB in wheat, oat, barley, corn, soybean, and tobacco. To examine the potential of WDIV to act as a viral vector, we modified the WDIV genome and cloned DNA fragments of the phytoene desaturase (PDS) genes from wheat and tobacco, separately. For gene editing experiments, tobacco lines expressing Cas9 were infiltrated with a WDIV-based vector carrying gRNA targeting the PDS gene. RESULTS: About 80 to 90% of plants inoculated with infectious clones of WDIV alone or WDIV together with AYLCB showed mild symptoms, whereas some plants showed more prominent symptoms. WDIV and AYLCB were detected in the systemically infected leaves of all the plant species. Furthermore, the inoculation of the WDIV vector carrying PDS fragments induced silencing of the PDS gene in both wheat and tobacco plants. We also observed high-efficiency genome editing in the Cas9-expressing tobacco plants that were inoculated with WDIV vector-carrying gRNA. CONCLUSION: Detection of WDIV in naturally infected wheat, barley, and sugarcane in the field and its ability to systemically infect wheat, oat, barley, corn, soybean, and tobacco under laboratory conditions, provides compelling evidence that WDIV is the first geminivirus identified with the capability of infecting both monocot and dicot plant species. The wide host range of WDIV can be exploited for developing a single vector system for high-throughput genome editing in many plant species.
ABSTRACT
The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.
ABSTRACT
Barley leaf rust, caused by Puccinia hordei, is an important disease of barley worldwide. The pathogen can develop new races that overcome resistance genes, emphasizing the need for monitoring its virulence. This study characterized 519 P. hordei isolates collected in the United States from the 1989 to 2000 and 2010 to 2020 survey periods on 15 Rph (Reaction to Puccinia hordei) genes. We analyzed linearized infection type data to detect virulence patterns across the United States and in five geographical regions: Pacific/West (PW), Southwest (SW), Midwest (MW), Northeast (NE), and Southeast (SE). Over 32 years, we observed high mean infection scores for Rph1.a, Rph4.d, and Rph8.h; intermediate scores for Rph2.b, Rph9.i, Rph10.o, Rph11.p, and Rph13.x; and low scores for Rph3.c, Rph5.e, Rph5.f, Rph7.g, Rph9.z, Rph14.ab, and Rph15.ad. Virulence for Rph2.b, Rph3.c, Rph5.e, Rph9.z, Rph10.o, Rph11.p, and Rph13.x significantly differed between the two survey periods. From 1989 to 2020, regional patterns of virulence were found for Rph5.e, Rph5.f, Rph7.g, and Rph14.ab, while regionalities of virulence for Rph3.c, Rph9.i, Rph9.z were only observed in the 2010 to 2020 survey period. Virulence associations were also detected in the P. hordei population. Notably, isolates that were virulent to Rph5.e and Rph6.f were more likely to be avirulent to Rph7.g and Rph13.x, and vice versa. In decreasing order of effectiveness, Rph15.ad, Rph5.e, Rph3.c, Rph9.z, Rph7.g, Rph5.f, and Rph14.ab were the most effective Rph genes in the United States from 1989 to 2020. Pyramiding Rph15.ad with other widely effective Rph and adult plant resistance genes may provide long-lasting resistance against P. hordei.
Subject(s)
Basidiomycota , Hordeum , United States , Chromosome Mapping , Hordeum/genetics , Disease Resistance/genetics , Virulence , Basidiomycota/genetics , Plant Diseases/geneticsABSTRACT
To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
Subject(s)
Basidiomycota , Disease Resistance , Disease Resistance/genetics , Plant Diseases/genetics , Plant Breeding , Genes, Plant , Basidiomycota/geneticsABSTRACT
Bacterial leaf streak (BLS), caused chiefly by the pathogen Xanthomonas translucens pv. translucens, is becoming an increasingly important foliar disease of barley in the Upper Midwest. The deployment of resistant cultivars is the most economical and practical method of control. To identify sources of BLS resistance, we evaluated two panels of breeding lines from the University of Minnesota (UMN) and Anheuser-Busch InBev (ABI) barley improvement programs for reaction to strain CIX95 in the field at St. Paul and Crookston, MN, in 2020 and 2021. The percentage of resistant lines in the UMN and ABI panels with mid-season maturity was 1.8% (6 of 333 lines) and 5.2% (13 of 251 lines), respectively. Both panels were genotyped with the barley 50K iSelect SNP array, and then a genome-wide association study was performed. A single, highly significant association was identified for BLS resistance on chromosome 6H in the UMN panel. This association was also identified in the ABI panel. Seven other significant associations were detected in the ABI panel: two each on chromosomes 1H, 2H, and 3H and one on chromosome 5H. Of the eight associations identified in the panels, five were novel. The discovery of resistance in elite breeding lines will hasten the time needed to develop and release a BLS-resistant cultivar.
Subject(s)
Hordeum , Hordeum/genetics , Hordeum/microbiology , Genome-Wide Association Study , Plant Diseases/microbiology , Plant Breeding , Chromosome MappingABSTRACT
Bacterial leaf streak (BLS) is a sporadic yet damaging disease of cereals that is growing in importance across the Upper Midwest production region. In barley (Hordeum vulgare ssp. vulgare), this disease is caused primarily by the bacterium Xanthomonas translucens pv. translucens. Accessions resistant to BLS have been reported in past studies, but few have been rigorously validated in the field. To identify accessions carrying diverse resistance alleles to BLS, a largescale germplasm screening study was undertaken against strain CIX95 of X. translucens pv. translucens in St. Paul and Crookston, Minnesota, in 2020 and 2021. The germplasm screened was diverse and included adapted breeding lines from two improvement programs, two landrace panels (one global and one from Ethiopia/Eritrea), introgression lines from wild barley (H. vulgare ssp. spontaneum) in the genetic background of barley cultivar 'Rasmusson', and an assemblage of accessions previously reported to carry BLS resistance. Of the 2,094 accessions evaluated in this study, 32 (1.5%) exhibited a consistently high level of resistance across locations and years and had heading dates similar to standard cultivars grown in the region. Accessions resistant to BLS were identified from all germplasm panels tested, providing genetically diverse sources for barley improvement programs focused on breeding for resistance to this important bacterial disease.
Subject(s)
Bacterial Infections , Hordeum , Hordeum/genetics , Hordeum/microbiology , Plant Breeding , Minnesota , EthiopiaABSTRACT
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici Eriks. & E. Henn, is the most devastating fungal disease of bread wheat. Here, a wheat-rye multiple disomic substitution line, SLU126 4R (4D), 5R (5D), and 6R (7D), possessing resistance against 25 races of P. striiformis f. sp. tritici, was used and crossed with Chinese Spring ph1b to induce homeologous recombination to produce introgressions with a reduced rye chromosome segment. Seedling assays confirmed that the stripe rust resistance from SLU126 was retained over multiple generations. Through genotyping-by-sequencing (GBS) platforms and aligning the putative GBS-single-nucleotide polymorphism (SNPs) to the full-length annotated rye nucleotide-binding leucine-rich repeat (NLR) genes in the parental lines (CS ph1b, SLU126, CSA, and SLU820), we identified the physical position of 26, 13, and 9 NLR genes on chromosomes 6R, 4R, and 5R, respectively. The physical positions of 25 NLR genes on chromosome 6R were identified from 568,460,437 bp to 879,958,268 bp in the 6RL chromosome segment. Based on these NLR positions on the 6RL chromosome segment, the three linked SNPs (868,123,650 to 873,285,112 bp) were validated through kompetitive allele-specific PCR (KASP) assays in SLU126 and resistance plants in the family 29-N3-5. Using these KASP markers, we identified a small piece of the rye translocation (i.e., as a possible 6DS.6DL.6RL.6DL) containing the stripe resistance gene, temporary designated YrSLU, within the 6RL segment. This new stripe rust resistance gene provides an additional asset for wheat improvement to mitigate yield losses caused by stripe rust.
Subject(s)
Basidiomycota , Triticum , Triticum/genetics , Triticum/microbiology , Chromosomes, Plant/genetics , Disease Resistance/genetics , Basidiomycota/genetics , Alleles , Translocation, Genetic , PucciniaABSTRACT
Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.
ABSTRACT
Genetic manipulation of whole-plant transpiration rate (TR) response to increasing atmospheric vapor pressure deficit (VPD) is a promising approach for crop adaptation to various drought regimes under current and future climates. Genotypes with a non-linear TR response to VPD are expected to achieve yield gains under terminal drought, thanks to a water conservation strategy, while those with a linear response exhibit a consumptive strategy that is more adequate for well-watered or transient-drought environments. In wheat, previous efforts indicated that TR has a genetic basis under naturally fluctuating conditions, but because TR is responsive to variation in temperature, photosynthetically active radiation, and evaporative demand, the genetic basis of its response VPD per se has never been isolated. To address this, we developed a controlled-environment gravimetric phenotyping approach where we imposed VPD regimes independent from other confounding environmental variables. We screened three nested association mapping populations totaling 150 lines, three times over a 3-year period. The resulting dataset, based on phenotyping nearly 1400 plants, enabled constructing 63-point response curves for each genotype, which were subjected to a genome-wide association study. The analysis revealed a hotspot for TR response to VPD on chromosome 5A, with SNPs explaining up to 17% of the phenotypic variance. The key SNPs were found in haploblocks that are enriched in membrane-associated genes, consistent with the hypothesized physiological determinants of the trait. These results indicate a promising potential for identifying new alleles and designing next-gen wheat cultivars that are better adapted to current and future drought regimes.
Subject(s)
Genome-Wide Association Study , Triticum , Vapor Pressure , Triticum/genetics , Plant Leaves/physiology , Plant Transpiration/geneticsABSTRACT
The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.
Subject(s)
Hordeum , Chromosomes , Domestication , Hordeum/genetics , Linkage Disequilibrium/geneticsABSTRACT
Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
Subject(s)
Basidiomycota , Puccinia , Avena/genetics , Avena/microbiology , Basidiomycota/genetics , Chromosomes , Edible Grain/genetics , Genomics , Plant Diseases/microbiologyABSTRACT
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.
Subject(s)
Aegilops , Basidiomycota , Aegilops/genetics , Basidiomycota/genetics , Disease Resistance/genetics , Genes, Plant/genetics , Plant Breeding , Plant Diseases/genetics , Triticum/geneticsABSTRACT
Precise segmentation of wheat spikes from a complex background is necessary for obtaining image-based phenotypic information of wheat traits such as yield estimation and spike morphology. A new instance segmentation method based on a Hybrid Task Cascade model was proposed to solve the wheat spike detection problem with improved detection results. In this study, wheat images were collected from fields where the environment varied both spatially and temporally. Res2Net50 was adopted as a backbone network, combined with multi-scale training, deformable convolutional networks, and Generic ROI Extractor for rich feature learning. The proposed methods were trained and validated, and the average precision (AP) obtained for the bounding box and mask was 0.904 and 0.907, respectively, and the accuracy for wheat spike counting was 99.29%. Comprehensive empirical analyses revealed that our method (Wheat-Net) performed well on challenging field-based datasets with mixed qualities, particularly those with various backgrounds and wheat spike adjacence/occlusion. These results provide evidence for dense wheat spike detection capabilities with masking, which is useful for not only wheat yield estimation but also spike morphology assessments.
ABSTRACT
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.
Subject(s)
Aegilops , Aegilops/genetics , Bread , Genomics , Metagenomics , Plant Breeding , Triticum/geneticsABSTRACT
Crop losses caused by plant pathogens are a primary threat to stable food production. Stripe rust (Puccinia striiformis) is a fungal pathogen of cereal crops that causes significant, persistent yield loss. Stripe rust exhibits host species specificity, with lineages that have adapted to infect wheat and barley. While wheat stripe rust and barley stripe rust are commonly restricted to their corresponding hosts, the genes underlying this host specificity remain unknown. Here, we show that three resistance genes, Rps6, Rps7, and Rps8, contribute to immunity in barley to wheat stripe rust. Rps7 cosegregates with barley powdery mildew resistance at the Mla locus. Using transgenic complementation of different Mla alleles, we confirm allele-specific recognition of wheat stripe rust by Mla. Our results show that major resistance genes contribute to the host species specificity of wheat stripe rust on barley and that a shared genetic architecture underlies resistance to the adapted pathogen barley powdery mildew and non-adapted pathogen wheat stripe rust.
Subject(s)
Hordeum/immunology , Host Specificity , Plant Immunity , Plant Proteins/immunology , Adaptation, Physiological , Alleles , Crops, Agricultural/genetics , Edible Grain , Plant Breeding , Plant Diseases/immunology , Puccinia , Receptors, Immunologic , Ribosomal Proteins , TriticumABSTRACT
KEY MESSAGE: Fine mapping of barley 6H pericentromeric region identified FHB QTL with opposite effects, and high grain protein content was associated with increased FHB severity. Resistance to Fusarium head blight (FHB), kernel discoloration (KD), deoxynivalenol (DON) accumulation and grain protein content (GPC) are important traits for breeding malting barley varieties. Previous work mapped a Chevron-derived FHB QTL to the pericentromeric region of 6H, coinciding with QTL for KD resistance and GPC. The Chevron allele reduced FHB and KD, but unfavorably increased GPC. To determine whether the correlations are caused by linkage or pleiotropy, a fine mapping approach was used to dissect the QTL underlying these quality and disease traits. Two populations, referred to as Gen10 and Gen10/Lacey, derived from a recombinant near-isogenic line (rNIL) were developed. Recombinants were phenotyped for FHB, KD, DON, GPC and other agronomic traits. Three FHB, two DON and two KD QTLs were identified. One of the three FHB QTLs, one DON QTL and one KD QTL were coincident with the GPC QTL, which contains the Hv-NAM1 locus affecting grain protein accumulation. The Chevron allele at the GPC QTL increased GPC and FHB and decreased DON and KD. The other two FHB QTL and the other DON and KD QTL were identified in the regions flanking the Hv-NAM1 locus, and the Chevron alleles decreased FHB, DON and KD. Our results suggested that the QTL associated with FHB, KD, DON and GPC in the pericentromeric region of 6H was controlled by both pleiotropy and tightly linked loci. The rNILs identified in this study with low FHB severity and moderate GPC may be used for breeding malting barley cultivars.
Subject(s)
Disease Resistance/genetics , Fusarium/pathogenicity , Grain Proteins/analysis , Hordeum/genetics , Plant Diseases/genetics , Alleles , Chromosome Mapping , Chromosomes, Plant/genetics , Genetic Pleiotropy , Genotype , Phenotype , Plant Diseases/microbiology , Quantitative Trait LociABSTRACT
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.
ABSTRACT
Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness.
Subject(s)
Basidiomycota/genetics , Disease Resistance/genetics , Plant Diseases/genetics , Triticum/genetics , Basidiomycota/pathogenicity , Chromosome Mapping , Plant Breeding , Plant Diseases/microbiology , Transgenes/genetics , Triticum/microbiology , Virulence/geneticsABSTRACT
Leaf rust, caused by Puccinia hordei, is a devastating fungal disease affecting barley (Hordeum vulgare subsp. vulgare) production globally. Despite the effectiveness of genetic resistance, the deployment of single genes often compromises durability due to the emergence of virulent P. hordei races, prompting the search for new sources of resistance. Here we report on the cloning of Rph15, a resistance gene derived from barley's wild progenitor H. vulgare subsp. spontaneum. We demonstrate using introgression mapping, mutation and complementation that the Rph15 gene from the near-isogenic line (NIL) Bowman + Rph15 (referred to as BW719) encodes a coiled-coil nucleotide-binding leucine-rich repeat (NLR) protein with an integrated Zinc finger BED (ZF-BED) domain. A predicted KASP marker was developed and validated across a collection of Australian cultivars and a series of introgression lines in the Bowman background known to carry the Rph15 resistance. Rph16 from HS-680, another wild barley derived leaf rust resistance gene, was previously mapped to the same genomic region on chromosome 2H and was assumed to be allelic with Rph15 based on genetic studies. Both sequence analysis, race specificity and the identification of a knockout mutant in the HS-680 background suggest that Rph15- and Rph16-mediated resistances are in fact the same and not allelic as previously thought. The cloning of Rph15 now permits efficient gene deployment and the production of resistance gene cassettes for sustained leaf rust control.