Scald resistance in hybrid rye (Secale cereale): genomic prediction and GWAS

Rye (Secale cereale L.) is an important cereal crop used for food, beverages, and feed, especially in North-Eastern Europe. While rye is generally more tolerant to biotic and abiotic stresses than other cereals, it still can be infected by several diseases, including scald caused by Rhynchosporium secalis. The aims of this study were to investigate the genetic architecture of scald resistance, to identify genetic markers associated with scald resistance, which could be used in breeding of hybrid rye and to develop a model for genomic prediction for scald resistance. Four datasets with records of scald resistance on a population of 251 hybrid winter rye lines grown in 2 years and at 3 locations were used for this study. Four genomic models were used to obtain variance components and heritabilities of scald resistance. All genomic models included additive genetic effects of the parental components of the hybrids and three of the models included additive-by-additive epistasis and/or dominance effects. All models showed moderate to high broad sense heritabilities in the range of 0.31 (SE 0.05) to 0.76 (0.02). The model without non-additive genetic effects and the model with dominance effects had moderate narrow sense heritabilities ranging from 0.24 (0.06) to 0.55 (0.08). None of the models detected significant non-additive genomic variances, likely due to a limited data size. A genome wide association study was conducted to identify markers associated with scald resistance in hybrid winter rye. In three datasets, the study identified a total of twelve markers as being significantly associated with scald resistance. Only one marker was associated with a major quantitative trait locus (QTL) influencing scald resistance. This marker explained 11-12% of the phenotypic variance in two locations. Evidence of genotype-by-environment interactions was found for scald resistance between one location and the other two locations, which suggested that scald resistance was influenced by different QTLs in different environments. Based on the results of the genomic prediction models and GWAS, scald resistance seems to be a quantitative trait controlled by many minor QTL and one major QTL, and to be influenced by genotype-by-environment interactions

Macroscopic and Microscopic Phenotyping Using Diverse Yellow Rust Races Increased the Resolution of Seedling and Adult Plant Resistance in Wheat Breeding Lines

We characterized yellow rust (YR) resistance in sixteen winter wheat breeding lines using three different pathogen races and macroscopic and microscopic phenotyping in lab and greenhouse. Three rust races were used on seedlings and two races on fifth and flag leaf growth stages. The wheat lines were previously characterized to possess none or different quantitative trait loci for YR resistance in field trials. At the seedling stage, twelve lines showed race-specific seedling resistance whereas four lines gave strong seedling resistance to all three races. Seven of eight lines with QTL.1B showed strong seedling resistance against the two races also used at fifth and flag leaves. Microscopic phenotyping of line NOS50906215 (QTL.1B) showed small fungal colonies stopped within 3 dpi associated with extensive hypersensitive response (HR). The lines NOS51014910 and NOS51014911 (QTL.3D alone) showed strong adult plant resistance (APR) from the fifth leaf stage. The lines NOS70140801 and NOS70140808 (QTL.3D + 7B) showed strong APR to one race but partial resistance to the other race at all growth stages. Microscopic phenotyping of line NOS70140801 (QTL.3D + 7B) showed more fungal growth and less HR against the race revealing strong APR compared to the one revealing partial resistance. Line NOS51010312 (QTL.7B alone) showed strong APR response against both races whereas line NOS51010313 (QTL.7B) was susceptible. A partial APR response was observed on line NOS51005019 (no QTLs reported). In conclusion, the approach of combining macroscopic and microscopic phenotyping and diverse pathogen races facilitates the identification of multiple and diverse seedling and adult plant resistance responses to yellow rust in wheat

Macroscopic and Microscopic Phenotyping Using Diverse Yellow Rust Races Increased the Resolution of Seedling and Adult Plant Resistance in Wheat Breeding Lines

We characterized yellow rust (YR) resistance in sixteen winter wheat breeding lines using three different pathogen races and macroscopic and microscopic phenotyping in lab and greenhouse. Three rust races were used on seedlings and two races on fifth and flag leaf growth stages. The wheat lines were previously characterized to possess none or different quantitative trait loci for YR resistance in field trials. At the seedling stage, twelve lines showed race-specific seedling resistance whereas four lines gave strong seedling resistance to all three races. Seven of eight lines with QTL.1B showed strong seedling resistance against the two races also used at fifth and flag leaves. Microscopic phenotyping of line NOS50906215 (QTL.1B) showed small fungal colonies stopped within 3 dpi associated with extensive hypersensitive response (HR). The lines NOS51014910 and NOS51014911 (QTL.3D alone) showed strong adult plant resistance (APR) from the fifth leaf stage. The lines NOS70140801 and NOS70140808 (QTL.3D + 7B) showed strong APR to one race but partial resistance to the other race at all growth stages. Microscopic phenotyping of line NOS70140801 (QTL.3D + 7B) showed more fungal growth and less HR against the race revealing strong APR compared to the one revealing partial resistance. Line NOS51010312 (QTL.7B alone) showed strong APR response against both races whereas line NOS51010313 (QTL.7B) was susceptible. A partial APR response was observed on line NOS51005019 (no QTLs reported). In conclusion, the approach of combining macroscopic and microscopic phenotyping and diverse pathogen races facilitates the identification of multiple and diverse seedling and adult plant resistance responses to yellow rust in wheat

Rapid emergency response to yellow rust epidemics caused by newly introduced lineages of Puccinia striiformis f. sp. tritici in Argentina

Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat worldwide. In 2017, YR emerged in Argentina and spread quickly into three million hectares, causing damage at levels only seen during the severe epidemics during the late 1930s. This widespread occurrence coincided with reports of newly introduced exotic races into the country. Therefore, little was known about actual impact of the disease on yield, reaction of commercial wheat cultivars, efficacy and best timing for fungicide applications. This study addressed these fundamental questions to provide a quick response to the re-emergence of YR in Argentina. Thirty wheat cultivars (short and long cycle) were evaluated for their response to a PstS13 lineage of Puccinia striiformis f.sp. tritici. The efficacy of one or two fungicide applications for controlling YR was also assessed. Disease severity reached about 50% in the untreated plots at early crop growth stages. Disease and yield data analyses showed that one fungicide application provided effective YR control, but two applications further secured a significant relative increase in yield. Grain yield was negatively correlated with disease severity, and losses reached up to 4,700 kg/ha in the untreated control plots for several varieties. We provide new and important information on the control of and potential yield losses by a new exotic race of Puccinia striiformis f.sp. tritici introduced to South America.EEA RafaelaFil: Carmona, Marcelo Anibal. Universidad de Buenos Aires. Facultad de Agronomía. Cátedra de Fitopatología; ArgentinaFil: Sautua, Francisco José. Universidad de Buenos Aires. Facultad de Agronomía. Cátedra de Fitopatología; ArgentinaFil: Pérez-Hernández, Oscar. University of Central Missouri. Department of Biology and Agriculture; Estados UnidosFil: Grosso, Carlos. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; ArgentinaFil: Vettorello, Lucas. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; ArgentinaFil: Milanesio, Barbarina. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; ArgentinaFil: Corvi, Eduardo. Kelymar SA (Santa Fé); ArgentinaFil: Almada, Gustavo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela. Agencia De Extensión Rural Carlos Pellegrini; ArgentinaFil: Hovmøller, Mogens Støvring. Aarhus University. Department of Agroecology; Dinamarc

Distinct life histories impact dikaryotic genome evolution in the rust fungus Puccinia striiformis causing stripe rust in wheat

Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.This work was supported by an Australian Research Council DECRA (DE150101897) and Future Fellowship (FT180100024) to B.S

Data from: Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici

Understanding the mode of temporal maintenance of plant pathogens is an important domain of microbial ecology research. Due to the inconspicuous nature of microbes, their temporal maintenance cannot be studied directly through tracking individuals and their progeny. Here, we suggest a series of population genetic analyses on molecular marker variation in temporally-spaced samples to infer about the relative contribution of sexual reproduction, off-season survival and migration in the temporal maintenance of pathogen populations. We used the proposed approach to investigate the temporal maintenance of wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (PST), in the Himalayan region of Pakistan. Multilocus microsatellite genotyping of PST isolates revealed high genotypic diversity and recombinant population structure across all locations, confirming the existence of sexual reproduction in this region. The genotypes were assigned to four genetic groups, revealing a clear differentiation between zones with and without Berberis spp., the alternate host of PST, with an additional subdivision within the Berberis zone. The lack of any differentiation between samples across two sampling years, and the very few re-sampling of multilocus genotypes over-years at a given location was consistent with limited over-year clonal survival, and a limited genetic drift. The off-season over-summering population in the Berberis zone, likely to be maintained locally, served as a source of migrants contributing to the temporal maintenance in the non-Berberis zone. Our study hence demonstrated the contribution of both sexual recombination and off-season over-summering survival to the temporal maintenance of the pathogen. These new insights into the population biology of PST highlight the general usefulness of the analytical approach proposed

Not Available

Not AvailableStripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.Not Availabl

Table_2_Scald resistance in hybrid rye (Secale cereale): genomic prediction and GWAS.docx

Rye (Secale cereale L.) is an important cereal crop used for food, beverages, and feed, especially in North-Eastern Europe. While rye is generally more tolerant to biotic and abiotic stresses than other cereals, it still can be infected by several diseases, including scald caused by Rhynchosporium secalis. The aims of this study were to investigate the genetic architecture of scald resistance, to identify genetic markers associated with scald resistance, which could be used in breeding of hybrid rye and to develop a model for genomic prediction for scald resistance. Four datasets with records of scald resistance on a population of 251 hybrid winter rye lines grown in 2 years and at 3 locations were used for this study. Four genomic models were used to obtain variance components and heritabilities of scald resistance. All genomic models included additive genetic effects of the parental components of the hybrids and three of the models included additive-by-additive epistasis and/or dominance effects. All models showed moderate to high broad sense heritabilities in the range of 0.31 (SE 0.05) to 0.76 (0.02). The model without non-additive genetic effects and the model with dominance effects had moderate narrow sense heritabilities ranging from 0.24 (0.06) to 0.55 (0.08). None of the models detected significant non-additive genomic variances, likely due to a limited data size. A genome wide association study was conducted to identify markers associated with scald resistance in hybrid winter rye. In three datasets, the study identified a total of twelve markers as being significantly associated with scald resistance. Only one marker was associated with a major quantitative trait locus (QTL) influencing scald resistance. This marker explained 11-12% of the phenotypic variance in two locations. Evidence of genotype-by-environment interactions was found for scald resistance between one location and the other two locations, which suggested that scald resistance was influenced by different QTLs in different environments. Based on the results of the genomic prediction models and GWAS, scald resistance seems to be a quantitative trait controlled by many minor QTL and one major QTL, and to be influenced by genotype-by-environment interactions.</p