Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing.
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ABSTRACT:
SUBMITTER: Klymiuk V
PROVIDER: S-EPMC9386016 | biostudies-literature | 2022 Aug
REPOSITORIES: biostudies-literature
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Discovery of stripe rust resistance with incomplete dominance in wild emmer wheat using bulked segregant analysis sequencing.
Klymiuk Valentyna V Chawla Harmeet Singh HS Wiebe Krystalee K Ens Jennifer J Fatiukha Andrii A Govta Liubov L Fahima Tzion T Pozniak Curtis J CJ
Communications biology 20220817 1
Durable crop disease resistance is an essential component of global food security. Continuous pathogen evolution leads to a breakdown of resistance and there is a pressing need to characterize new resistance genes for use in plant breeding. Here we identified an accession of wild emmer wheat (Triticum turgidum ssp. dicoccoides), PI 487260, that is highly resistant to multiple stripe rust isolates. Genetic analysis revealed resistance was conferred by a single, incompletely dominant gene designat ...[more]
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Project description:IntroductionContinuous identification and application of novel resistance genes against stripe rust are of great importance for wheat breeding. Wild emmer wheat, Triticum dicoccoides, has adapted to a broad range of environments and is a valuable genetic resource that harbors important beneficial traits, including resistance to stripe rust caused by Puccinia striiformis f. sp. tritici (Pst). However, there has been a lack of systematic exploration of genes against Pst races in wild emmer wheat.MethodsGenome-wide transcriptome profiles were conducted on two wild emmer wheat genotypes with different levels of resistance to (Pst (DR3 exhibiting moderate (Pst resistance, and D7 displaying high (Pst resistance). qRT-PCR was performed to verify findings by RNA-seq.ResultsA higher number of DEGs were identified in the moderately (Pst-resistant genotype, while the highly (Pst-resistant genotype exhibited a greater enrichment of pathways. Nonetheless, there were consistent patterns in the enrichment of pathways between the two genotypes at the same time of inoculation. At 24 hpi, a majority of pathways such as the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, phenylalanine metabolism, and alpha-Linolenic acid metabolism exhibited significant enrichment in both genotypes. At 72 hpi, the biosynthesis of secondary metabolites and circadian rhythm-plant pathways were notably and consistently enriched in both genotypes. The majority of (WRKY, MADs , and AP2-ERF families were found to be involved in the initial stage of response to Pst invasion (24 hpi), while the MYB, NAC, TCP, and b-ZIP families played a role in defense during the later stage of Pst infection (72 hpi).DiscussionIn this present study, we identified numerous crucial genes, transcription factors, and pathways associated with the response and regulation of wild emmer wheat to Pst infection. Our findings offer valuable information for understanding the function of crucial Pst-responsive genes, and will deepen the understanding of the complex resistance mechanisms against Pst in wheat.
| S-EPMC10791934 | biostudies-literature
Project description:Key messageSNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.
| S-EPMC5641275 | biostudies-literature
Project description:Many disease resistance genes that have been transferred from wild relatives to cultivated wheat have played a significant role in wheat production worldwide. Ae. umbellulata is one of the species within the genus Aegilops that have been successfully used as sources of resistance genes to leaf rust, stem rust and powdery mildew. The objectives of the current work was to validate the map position of a major QTL that confers resistance to the stem rust pathogen races Ug99 (TTKSK) and TTTTF with an independent bi-parental mapping population and to refine the QTL region with a bulk segregant analysis approach. Two F2 bi-parental mapping populations were developed from stem rust resistant Ae. umbellulata accessions (PI 298905 and PI 5422375) and stem rust susceptible accessions (PI 542369 and PI 554395). Firstly, one of the two populations was used to map the chromosome location of the resistance gene. Later on, the 2nd population was used to validate the chromosome location in combination with a bulk segregant analysis approach. For the bulk segregant analysis, RNA was extracted from a bulk of leaf tissues of 12 homozygous resistant F3 families, and a separate bulk of 11 susceptible homozygous F3 families derived from the PI 5422375 and PI 554395 cross. The RNA samples of the two bulks and the two parents were sequenced for SNPs identification. Stem rust resistance QTL was validated on chromosome 2U of Ae. umbellulata in the same region in both populations. With bulk segregant analysis, the QTL position was delimited within 3.2 Mbp. Although there were a large number of genes in the orthologous region of the detected QTL on chromosome 2D of Ae. tauschii, we detected only two Ae. umbellulata NLR genes which can be considered as a potential candidate genes.
| S-EPMC6754143 | biostudies-literature
Project description:Autophagy-related 8 (ATG8) protein has been reported to be involved in plant's innate immune response, but it is not clear whether such genes play a similar role in cereal crops against obligate biotrophic fungal pathogens. Here, we reported an ATG8 gene from wheat (Triticum aestivum), designated TaATG8j. This gene has three copies located in chromosomes 2AS, 2BS, and 2DS. The transcriptions of all three copies were upregulated in plants of the wheat cultivar Suwon 11, inoculated with an avirulent race (CYR23) of Puccinia striiformis f. sp. tritici (Pst), the causal fungal pathogen of stripe rust. The transient expression of TaATG8j in Nicotiana benthamiana showed that TaATG8j proteins were distributed throughout the cytoplasm, but mainly in the nucleus and plasma membrane. The overexpression of TaATG8j in N. benthamiana slightly delayed the cell death caused by the mouse apoptotic protein BAX (BCL2-associated X protein). However, the expression of TaATG8j in yeast (Schizosaccharomyces pombe) induced cell death. The virus-induced gene silencing of all TaATG8j copies rendered Suwon 11 susceptible to the avirulent Pst race CYR23, accompanied by an increased fungal biomass and a decreased necrotic area per infection site. These results indicate that TaATG8j contributes to wheat resistance against stripe rust fungus by regulating cell death, providing information for the understanding of the mechanisms of wheat resistance to the stripe rust pathogen.
| S-EPMC6032272 | biostudies-literature
Project description:Next generation sequencing (NGS) technologies are providing new ways to accelerate fine-mapping and gene isolation in many species. To date, the majority of these efforts have focused on diploid organisms with readily available whole genome sequence information. In this study, as a proof of concept, we tested the use of NGS for SNP discovery in tetraploid wheat lines differing for the previously cloned grain protein content (GPC) gene GPC-B1. Bulked segregant analysis (BSA) was used to define a subset of putative SNPs within the candidate gene region, which were then used to fine-map GPC-B1.We used Illumina paired end technology to sequence mRNA (RNAseq) from near isogenic lines differing across a ~30-cM interval including the GPC-B1 locus. After discriminating for SNPs between the two homoeologous wheat genomes and additional quality filtering, we identified inter-varietal SNPs in wheat unigenes between the parental lines. The relative frequency of these SNPs was examined by RNAseq in two bulked samples made up of homozygous recombinant lines differing for their GPC phenotype. SNPs that were enriched at least 3-fold in the corresponding pool (6.5% of all SNPs) were further evaluated. Marker assays were designed for a subset of the enriched SNPs and mapped using DNA from individuals of each bulk. Thirty nine new SNP markers, corresponding to 67% of the validated SNPs, mapped across a 12.2-cM interval including GPC-B1. This translated to 1 SNP marker per 0.31 cM defining the GPC-B1 gene to within 13-18 genes in syntenic cereal genomes and to a 0.4 cM interval in wheat.This study exemplifies the use of RNAseq for SNP discovery in polyploid species and supports the use of BSA as an effective way to target SNPs to specific genetic intervals to fine-map genes in unsequenced genomes.
| S-EPMC3296661 | biostudies-literature
Project description:BackgroundDeveloping wheat cultivars with durable resistance to powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is crucial for sustainable agriculture. The wheat genotype MYC exhibited high resistance to the Bgt isolate E09 at the seedling stage. Genetic analysis identified a recessive gene, temporarily named PmMYC, responsible for this resistance. Understanding the molecular mechanisms underlying this resistance is essential for advancing breeding programs.ResultsBulked Segregant RNA-Seq revealed numerous alternative splicing events generated following Bgt infection, suggesting powdery mildew may disrupt alternative splicing and affect immune responses. Gene Ontology (GO) analysis indicated significant enrichment of differentially expressed genes in "response to stimuli" and "immune system processes", implying their roles in disease defense. BSR-Seq analysis identified two high-confidence candidate regions for PmMYC on chromosome 2B, spanning 40,451,950 - 102,426,703 bp and 421,707,046-449,840,516 bp. Within these intervals, 740 genes were identified, with nonsynonymous mutations in 46 genes in the parents and bulks. Real-time PCR showed distinct expression profiles in four genes in resistant MYC compared to susceptible Yannong 21. KEGG and COG analyses of differentially expressed genes in candidate intervals revealed enrichment in immune processes related to plant-pathogen interactions, confirming that PmMYC initiated a broad immune response to prevent Bgt invasion.ConclusionThe study identified key genetic intervals and genes involved in the resistance of wheat genotype MYC to Bgt. The identified genes, particularly those with altered expression profiles, could serve as valuable targets for breeding programs aimed at developing wheat cultivars with durable resistance to powdery mildew. These findings enhanced our understanding of plant-pathogen interactions and provided a foundation for future genetic and functional studies.
| S-EPMC11552326 | biostudies-literature
Project description:Puccinia striiformis f. sp. tritici is an obligate biotrophic fungus that causes destructive stripe rust disease in wheat. During infection, Pst secretes virulence effectors via a specific infection structure-the haustorium-inside host cells to disturb host immunity and promote fungal colonization and expansion. Hence, the identification and functional analyses of Pst effectors are of great significance in deciphering the Pst pathogenicity mechanism. Here, we identified one candidate Pst effector Pst_9302 that could suppress Bax-triggered cell death in Nicotiana benthamiana. qRT-PCR analyses showed that the transcript levels of Pst_9302 were highly increased during the early infection stages of Pst. The transient expression of Pst_9302 in wheat via the type-three secretion system (T3SS) significantly inhibited the callose deposition induced by Pseudomonas syringae EtHAn. During wheat-Pst interaction, Pst_9302 overexpression suppressed reactive oxygen species (ROS) accumulation and cell death caused by the avirulent Pst race CYR23. The host-induced gene silencing (HIGS) of Pst_9302 resulted in decreased Pst pathogenicity with reduced infection area. The results suggest that Pst_9302 plays a virulence role in suppressing plant immunity and promoting Pst pathogenicity. Moreover, wheat voltage-dependent anion channel 1 protein (TaVDAC1) was identified as candidate Pst_9302-interacting proteins by yeast two-hybrid (Y2H) screening. Pull-down assays using the His-Pst_9302 and GST-TaVDAC1 protein verified their interactions. These results suggest that Pst_9302 may modulate wheat TaVDAC1 to regulate plant immunity.
| S-EPMC10780974 | biostudies-literature
Project description:Stripe rust caused by the fungus Puccinia striiformis f.sp. tritici (Pst) is a major constraint to wheat production worldwide. The molecular events that underlie Pst pathogenicity are largely unknown. Like all rusts, Pst creates a specialized cellular structure within host cells called the haustorium to obtain nutrients from wheat, and to secrete pathogenicity factors called effector proteins. We purified Pst haustoria and used next-generation sequencing platforms to assemble the haustorial transcriptome as well as the transcriptome of germinated spores. 12,282 transcripts were assembled from 454-pyrosequencing data and used as reference for digital gene expression analysis to compare the germinated uredinospores and haustoria transcriptomes based on Illumina RNAseq data. More than 400 genes encoding secreted proteins which constitute candidate effectors were identified from the haustorial transcriptome, with two thirds of these up-regulated in this tissue compared to germinated spores. RT-PCR analysis confirmed the expression patterns of 94 effector candidates. The analysis also revealed that spores rely mainly on stored energy reserves for growth and development, while haustoria take up host nutrients for massive energy production for biosynthetic pathways and the ultimate production of spores. Together, these studies substantially increase our knowledge of potential Pst effectors and provide new insights into the pathogenic strategies of this important organism.
| S-EPMC3694141 | biostudies-literature
Project description:The actin cytoskeleton participates in numerous cellular processes, including less-characterized processes, such as nuclear organization, chromatin remodeling, transcription, and signal transduction. As a key regulator of actin cytoskeletal dynamics, the actin related protein 2/3 complex (Arp2/3 complex) controls multiple developmental processes in a variety of tissues and cell types. To date, the role of the Arp2/3 complex in plant disease resistance signaling is largely unknown. Herein, we identified and characterized wheat ARPC3, TaARPC3, which encodes the C3 subunit of the Arp2/3 complex. Expression of TaARPC3 in the arc18 mutant of Saccharomyces cerevisiae Δarc18 resulted in complementation of stress-induced phenotypes in S. cerevisiae, as well as restore wild-type cell shape malformations. TaARPC3 was found predominantly to be localized in the nucleus and cytoplasm when expressed transiently in wheat protoplast. TaARPC3 was significantly induced in response to avirulent race of Puccinia striiformis f. sp. tritici (Pst). Knock-down of TaARPC3 by virus-induced gene silencing resulted in a reduction of resistance against Pst through a specific reduction in actin cytoskeletal organization. Interestingly, this reduction was found to coincide with a block in reactive oxygen species (ROS) accumulation, the hypersensitive response (HR), an increase in TaCAT1 mRNA accumulation, and the growth of Pst. Taken together, these findings suggest that TaARPC3 is a key subunit of the Arp2/3 complex which is required for wheat resistance against Pst, a process that is associated with the regulation of the actin cytoskeleton.
| S-EPMC5513970 | biostudies-literature
Project description:BackgroundStripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63 from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection.ResultsYR63 exhibits resistance to a broad spectrum of Pst races from Australia, Africa, Asia, Europe, Middle East and South America. It was mapped to the short arm of chromosome 7B, between two single nucleotide polymorphic (SNP) markers sunCS_YR63 and sunCS_67, positioned at 0.8 and 3.7 Mb, respectively, in the Chinese Spring genome assembly v2.1. We characterised YR63 locus using an integrated approach engaging targeted genotyping-by-sequencing (tGBS), mutagenesis, resistance gene enrichment and sequencing (MutRenSeq), RNA sequencing (RNASeq) and comparative genomic analysis with tetraploid (Zavitan and Svevo) and hexaploid (Chinese Spring) wheat genome references and 10+ hexaploid wheat genomes. YR63 is positioned at a hot spot enriched with multiple nucleotide-binding and leucine rich repeat (NLR) and kinase domain encoding genes, known widely for defence against pests and diseases in plants and animals. Detection of YR63 within these gene clusters is not possible through short-read sequencing due to high homology between members. However, using the sequence of a NLR member we were successful in detecting a closely linked SNP marker for YR63 and validated on a panel of Australian bread wheat, durum and triticale cultivars.ConclusionsThis study highlights YR63 as a valuable source for resistance against Pst in Australia and elsewhere. The closely linked SNP marker will facilitate rapid introgression of YR63 into elite cultivars through marker-assisted selection. The bottleneck of this study reinforces the necessity for a long-read sequencing such as PacBio or Oxford Nanopore based techniques for accurate detection of the underlying resistance gene when it is part of a large gene cluster.
| S-EPMC10680240 | biostudies-literature