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.附加文件1：表S1。非洲栽培稻（Oryza glaberrima, O. glaberrima）种质的双抗体夹心酶联免疫吸附试验（DAS-ELISA）结果示例。按照文献[50]所述方法，对接种后15天收获的单株系统叶进行DAS-ELISA检测。光密度（optical density, OD）指405 nm波长下的吸光度；校正光密度（ODcor）为OD值减去阴性（缓冲液）对照的平均值。当ODcor大于0.1时，样本判定为阳性。将Tog5681与Tog7291作为抗病对照，CG14与Og82作为感病对照。本表格呈现单次实验获取的数据，涉及本研究中所有鉴定为抗病的种质（除Og423外），每份种质包含8株单株的亚组样本。 表S2。针对水稻黄花叶病毒（Rice yellow mottle virus, RYMV）抗性进行鉴定的种质的编号、表型与基因型。本研究或既往研究[12,13]通过机械接种BF1分离物，对RYMV抗性进行评估。抗病基因或候选基因的等位基因信息详见附加文件1的表S3、表S4、表S5或既往研究[12]。 表S3。水稻黄花叶病毒1号抗病基因（RYMV1）的基因型。仅纳入Cubry等[21]分析的非洲栽培稻种质集合中检测到多态性的位点。核苷酸位点参照作为作图参考的粳稻日本晴（Oryza sativa Nipponbare）IRGSP1.0参考序列[51]。突变效应基于以非洲栽培稻CG14种质构建的ORGLA04G0147000.1基因模型[1]。突变命名遵循Den Dunnen等[55]提出的命名规范，其中同义突变与内含子区域突变分别标注为"syn"与"intron"。蛋白质水平上的不同变异被视为不同等位基因。抗病等位基因的命名此前由Albar等[14]与Thiemele等[12]确定，但在感病种质中观察到的新增蛋白质变异被命名为"Rymv1–1-Og2"；为提升清晰度，既往研究[12]中命名为"Rymv1–1-Og"的等位基因现更改为"Rymv1–1-Og1"。 表S4。作为RYMV2候选基因的CPR5–1基因的基因型。仅纳入Cubry等[21]分析的非洲栽培稻种质集合中检测到多态性的位点。核苷酸位点参照作为作图参考的粳稻日本晴IRGSP1.0参考序列[51]。突变效应基于以非洲栽培稻CG14种质构建的ORGLA01G0359000.1基因模型[1]。突变命名遵循Den Dunnen等[55]提出的命名规范，其中同义突变与内含子区域突变分别标注为"syn"与"intron"。蛋白质水平上的不同变异被视为不同等位基因。等位基因命名用于区分与RYMV抗性相关或不相关的蛋白质变异。 表S5。作为RYMV3候选基因的NLRRYMV3基因的基因型。仅纳入Cubry等[21]分析的非洲栽培稻种质集合中检测到多态性的位点。核苷酸位点参照作为作图参考的粳稻日本晴IRGSP1.0参考序列[51]。突变效应基于以非洲栽培稻CG14种质构建的ORGLA11G0175800.1基因模型[1]。突变命名遵循Den Dunnen等[55]提出的命名规范，其中同义突变与内含子区域突变分别标注为"syn"与"intron"。蛋白质水平上的不同变异被视为不同等位基因。等位基因命名用于区分与RYMV抗性相关或不相关的蛋白质变异。 表S6。3000份水稻基因组计划（3000 Rice Genomes Project）[26]种质中，RYMV抗病基因或候选基因的多样性。本报告仅呈现基础SNP集合中的非同义单核苷酸多态性（Single Nucleotide Polymorphism, SNP）。SNP效应源自SNP-Seek数据库[25]，插入缺失（insertion-deletion, indel）效应通过人工评估确定。针对RYMV1与CPR5–1基因，其编码区（CDS）与蛋白质的突变效应分别基于以日本晴IRGSP1.0参考序列[51]构建的Os04g42140.1与Os01g68970.1基因模型。对于NLRRYMV3基因，其编码区基于Os11g43700.1基因模型，但起始密码子ATG从原始起始密码子下游180个核苷酸的位置进行偏移，以最佳匹配以CG14参考序列构建的ORGLA11G0175800.1基因模型的对应编码区，因此对编码区与蛋白质的效应进行了适配调整。频率指备选变异在全部种质集合中的占比百分比。标注了位于PFAM结构域MA3、MIF4G、LRR以及HMM Panther预测LRR结构域中的突变。