Additional file 1 of Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice

Additional file 1:Table S1. Example of DAS-ELISA results on O. glaberrima accessions. DAS-ELISA were performed on the systemic leaves of individual plants harvested 15 days after inoculation as described in [50]. OD is the optical density at 405 nm; ODcor represents OD minus the mean of negative (buffer) controls. Samples were considered positive when ODcor are superior to 0,1. Tog5681 and Tog7291 were included as resistant controls; CG14 and Og82 as susceptible ones. This table presents data acquired in a single experiment, on a subset of 8 plants per accession, on all the accessions identified as resistant in this study, except Og423. Table S2. ID, phenotype and genotype of accessions characterized for RYMV resistance. Resistance to RYMV was evaluated after mechanical inoculation of the BF1 isolate in this study or in previous studies [12, 13]. Alleles on resistance genes or candidates refer to the results presented in the Additional file 1: Table S3, Table S4, Table S5 or in previous studies [12]. Table S3. Genotype on the RYMV1 resistance gene. Only positions where polymorphisms were detected in the O. glaberrima collection analyzed in Cubry et al. [21] were included. Nucleotide positions refer to the IRGSP1.0 reference sequence of the O. sativa Nipponbare accession [51] that was used as mapping reference. The effect of the mutations are based on the ORGLA04G0147000.1 gene model established on the O. glaberrima CG14 accession [1]. Mutations are described according to the nomenclature proposed by Den Dunnen et al. [55], except that synonymous mutations and mutations occurring in an intron are denoted “syn” and “intron”, respectively. Different variants at the protein level were considered as different alleles. Names for resistance alleles were previously attributed by Albar et al. [14] and Thiemele et al. [12], but an additional protein variant observed in susceptible accessions was given the name “Rymv1–1-Og2”, and for greater clarity the allele named “Rymv1–1-Og” in [12] was referred to as “Rymv1–1-Og1”. Table S4. Genotype on the CPR5–1 gene, candidate for RYMV2. Only positions were polymorphisms were detected in the O. glaberrima collection analyzed in Cubry et al. [21] were included. Nucleotide positions referred to the IRGSP1.0 reference sequence of the O. sativa Nipponbare accession [51] that was used as mapping reference. The effects of the mutations are based on the ORGLA01G0359000.1 gene model established on the O. glaberrima CG14 accession [1]. Mutations are described according to the nomenclature proposed by Den Dunnen et al. [55], except that synonymous mutations and mutations occurring in an intron are noted “syn” and “intron”, respectively. Different variants at the protein level were considered as different alleles. The allele names were chosen to distinguish protein variants associated or not with RYMV resistance. Table S5. Genotype on the NLRRYMV3 gene, candidate for RYMV3. Only positions were polymorphisms were detected in to the O. glaberrima collection analyzed in Cubry et al. [21] were included. Nucleotide positions refer to the IRGSP1.0 reference sequence of the O. sativa Nipponbare accession [51] that was used as mapping reference. The effects of the mutations are based on the ORGLA11G0175800.1 gene model established on the O. glaberrima CG14 accession [1]. Mutations are described according to the nomenclature proposed by Den Dunnen et al. [55], except that synonymous mutations and mutations occurring in an intron are noted “syn” and “intron”, respectively. Different variants at the protein level were considered as different alleles. The allele names were chosen to distinguish protein variants associated or not with RYMV resistance. Table S6. Diversity on RYMV resistance genes or candidates in accessions from the 3000 Rice Genomes Project [26]. Only non-synonymous SNPs from the base SNPs set are reported here. SNP effects were retrieved from the SNP-Seek database [25] and indels effects were evaluated manually. The effects of mutations on CDS and proteins are based on the Os04g42140.1 and Os01g68970.1 gene models established on the Nipponbare IRGSP1.0 sequence [51], for RYMV1 and CPR5–1, respectively. For NLRRYMV3, the CDS is based on the Os11g43700.1 gene mode, except that the ATG codon was shifted from 180 nucleotides downstream of the original starting codon to best fit the corresponding CDS of the ORGLA11G0175800.1 gene model established on CG14 reference sequence. Effects on the CDS and protein were thus adapted. Frequency refers to the percentage of the alternate variant in the complete set of accessions. Mutations located in the PFAM domains MA3, MIF4G and LRR and in the HMM Panther hit LRR are indicated.