Resultados de investigación

Table S3. Variance components and broad-sense heritability for the DS scores of U. pisi inoculation experiments., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed

Table S2. Primer sequences used for RT-qPCR analysis., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed

Document S1. Supplemental Figures 1–16 and Supplemental Tables 1–13. Supplemental Table 1. Primers. Supplemental Table 2. Statistics. Supplemental Table 3. DEGs. Supplemental Table 4. DEGs IN versus OUT. Supplemental Table 5. GO IN versus OUT. Supplemental Table 6. Gene list clusters IN. Supplemental Table 7. GO clusters IN PtoAvrRpm1. Supplemental Table 8. GO clusters OUT PtoAvrRpm1. Supplemental Table 9. GO DEGs. Supplemental Table 10 GO cluster IN mock. Supplemental Table 11. GO cluster OUT mock. Supplemental Table 12. Primers. Supplemental Table 13. Quantitative PCR raw data. Document S2. Article plus supplemental information., Peer reviewed

Table S1. Characterization of the grass pea accessions evaluated for the response to U. pisi based on seed color, size, and geographical origin, and respective BLUEs data., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed

This dataset compiles the code for the research article "Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses", currently pubished as a preprint in BioRxiv (DOI:10.1101/2021.10.06.463031). Both the raw and processed transcriptomic data experimentally generated and analysed here in order to identify transcriptional indicators of plant immune cell death are available at GEO (currently under embargo). In addition, supplementary data published with the article, some of which was generated using this code, is available (currently under embargo until manuscript publication) in a linked dataset (https://doi.org/10.34810/data136)., Peer reviewed

Figure S3. Heat map depicting mean log2-fold changes of gene expression levels. Relative gene expression analysis of candidate gene related to U. pisi disease response (A-C) was analyzed in accessions susceptible (PI283574, and PI221467_B) and partially resistant (PI165528, PI283566, and PI577138_A). Relative expression values were normalized to the mean of the non-inoculated control (0 HAI) of the most susceptible accession (PI221467_B). Higher levels of relative gene expression (log2-fold changes > 0) are indicated in red and lower levels (log2-fold changes < 0) are indicated in blue. Small letters represent significant differences (P-value <0.05), among accessions or time-points (0 HAI, 12 HAI, 24 HAI, 48 HAI)., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed

Supplemental information: Document S1. Figures S1–S7 and Table S2. Table S1. JTK_CYCLE analysis and biological process enrichment of rhythmic genes in pistils, related to Figure 4. Document S2. Article plus supplemental information., Peer reviewed

Figure S2. Allele frequency distribution at the DS range scale, of the associated SNPs detected in the GWAS in response to U. pisi. Allele missing data refers to the absence of genotypic data., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed

Figure S1. Quantile-Quantile (QQ) plots of the observed versus expected p-values of the GWAS results related to U. pisi inoculation experiments, using a model accounting for population structure (Eigen), a model accounting for familiar relatedness (Kinship), and a naïve model., Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding., Peer reviewed

Supplementary Figure 1 | Analysis of differential splicing events under individual and simultaneous deficiency of copper and iron. Venn diagrams for multiple comparisons among differentially splicing events per treatment according to an absolute fold-change of at least 2 in pair-wise comparisons (adjusted-p-value ≤ 0.05, two-way ANOVA with post hoc Tukey’s test)., Supplementary Figure 2 | Primary analysis of intron retention in transcripts involved in tryptophan and asparagine biosynthesis under single and simultaneous copper and iron deficiency. The average of read counts per exon or intron bins for the selected genes under standard conditions (Cont) and single and double copper and iron deficiencies (–Cu, –Fe, and –Cu–Fe) was calculated using the ASpli package. Bars represent the percentage of reads detected in intronic bins over the total reads in the whole genic region (introns plus exons bins)., Peer reviewed