The file contains supplementary tables arranged in separate sheets, from A to G.
(A) Complete Information for the teff samples used in this study. For each accession, the table reports the name of the accession at the germplasm repository (Name), the ID used in this study, the species, the type of materials (Status), the pedigree if known, the source of the accession, research center (Center) and release year if available (EBI, Ethiopian Biodiversity Institute; DZARC, Debre Zeit Agricultural Research Center; AARC, Adet Agricultural Research Center; HARC, Holleta Agricultural Research Center; BARC, Bako Agricultural Research Center; MARC, Melkassa Agricultural Research Center; SARC, Sirinka Agricultural Research Center). For accessions deriving from landraces, the table also reports the corresponding agroecological zone and the region name at three levels (Region_1, Region_2, and Region_3), the longitude, and the latitude. The table then reports the genetic cluster assigned by the analyses, the altitude, and the historical bioclim variables. Finally, BLUP values for phenotypes are farmer traits are reported. When specific by location, the trait code is attached to either Akaki or Adet. When specific by gender, M (men) or W (women) is attached. DH, days to heading; DM, days to maturity; PH, plant height; PL, panicle length; PBPM, number of primary branches per main shoot panicle; TT, total tillers; CLF, first culm length; CDF, first culm diameter; PW, panicle weight; PY, panicle yield; GY, grain yield; BY, biomass yield; HI, harvest index; GFP, grain filling period; GFR, grain filling rate; BPR, biomass production rate; OA, overall appreciation; PA, panicle appreciation. (B) Haplotype blocks for SNPs used in this study. For each SNP, the table reports the SNP name, the chromosome, and the position. If any, the table reports the corresponding haplotype block with start and stop position and number of SNPs in the block. (C) Variance components from BLUP model calculation on agronomic traits and farmer traits. The table reports solution, standard error, z ratio, and percent variance explained for each component of the model for each trait. Trait codes as in Supplemenary File 1A. Factor codes as follows: ID, genotype; REP, replication within the field; LOCATION, field location; F_TYPE, gender; interactions between factors are indicated as in F_TYPE:LOCATION, for example gender by location. (D) Main effects of and interactions between location, genetic cluster, and, in the case of PVS traits, gender, regarding teff traits. Phentoype codes as in (A). Values in the table are p values for a two- (metric traits) and three-way ANOVA (PVS traits). Significant effects are highlighted in bold. (E) Genome-wide association results. For each SNP-trait combination, the table reports the trait name, the SNP name, its chromosome, and position. The reference (REF) and alternative (ALT) allele are reported for each SNP. For each association, the table reports the effect, the standard error (SE), the corresponding p value (pvalue), and multiple-test correction with a q value (qvalue). The number of PC covariates used in the GWAS scan is reported in column n_PC. DH, days to heading; DM, days to maturity; PH, plant height; PL, panicle length; PBPM, number of primary branches per main shoot panicle; TT, total tillers; CLF, first culm length; CDF, first culm diameter; PW, panicle weight; PY, panicle yield; GY, grain yield; BY, biomass yield; HI, harvest index; GFP, grain filling period; GFR, grain filling rate; BPR, biomass production rate; OA, overall appreciation; PA, panicle appreciation. Bio2: mean diurnal temperature range; Bio3: Isothermality; Bio4: Temp. Seasonality; Bio9: Mean Temp. of Driest Quarter; Bio13: Precipitation of Wettest Month; Bio14: Precipitation of Driest Month; Bio15: Precipitation Seasonality; Bio18: Precipitation of Warmest Quarter; Bio19: Precipitation of Coldest Quarter. PC1_bio: first bioclimatic principal component; PC2_bio: second bioclimatic principal component; PC3_bio: third bioclimatic principal component. (F) Candidate genes mining for significant associations. The table reports genes in LD blocks with at least one significant association. Each row reports the Eragrostis tef gene ID (Et_gene), with chromosome, start position, end position, and DNA strand (positive + or negative −). When present, the table reports the closest homolog gene in Arabidopsis (id_At) with the percentual identity in the alignment (perc_identity_At), the E value reported by the BLASTP, the percentual query coverage in the target gene (perc_query_coverage_per_subject_At). The same information is reported for Zea mays (Zm) hits. The table reports the name of the LD block and the number of quantitative trait loci (QTN) in that block. (G) SNPs with adaptation potential. For each marker, the table reports the chromosome, position, Fst values, and gradient forest model fit (GF r2).