Dec 2, 2014 - LR91. Non-tannin PI 506097 guinea. GS 341. Togo. Table S9. A set of 18 sorghum landraces with full-length Tan1 sequence for nucleotide ...
Supporting Information Presence of Tannins in Sorghum Grains Is Conditioned by Different Natural Alleles of Tannin1 Yuye Wu, Xianran Li, Wenwen Xiang, Chengsong Zhu, Zhongwei Lin, Yun Wu, Jiarui Li Satchidanand Pandravada, Dustan D. Ridder, Guihua Bai, Ming L. Wang, Harold N. Trick, Scott R. Bean, Mitchell R. Tuinstra, Tesfaye T. Tesso, Jianming Yu
Fig. S1. QTL mapping results from the Tx430/ShanQuiRui population with tannin content measured quantitatively with the vanillin-HCl test. The chromosome 2 and 4 QTL are consistent with the mapping results with the tannin presence scored with the bleach test (Table S1). The chromosome 1 QTL is present only when tannin content is used in the analysis.
Fig. S2. Consensus linkage map of chromosome 2 and 4 regions across three mapping populations.
Fig. S3. Predicted protein structure of different Tan1 alleles. (A) Protein structure of the function allele Tan1 (ShanQuiRed). (B) Frame shift in tan1-b (Tx623) results in the disruption of the protein structure after Thr at 306-aa. (C) Frame shift in tan1-a (Tx430) results in the disruption of the protein structure after Gly at 139-aa. The 3-D structure was modeled by SwissModel Automatic Modeling Mode on SWISS-MODEL server. The structure was displayed by Jmol 12.2.14. Reference: Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modeling. Bioinformatics 22,195-201. Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
Fig. S4. Sequence variations across sorghum tan1-a and tan1-b alleles, and seven Arabidopsis TTG1 mutants. The truncation of the C-terminal of the amino acid sequence is the common feature of the non-functional alleles in both species. Accordingly, the complementation experiment of transforming the ttg1-1 mutant (minimum truncation in C-terminal) with the 35STan1-ORF construct (complete amino acid sequence) was carried out. The hexagon represents the stop codon and the truncation point of the amino acid sequence.
ATG
N‐terminal
WD‐40 repeats
C‐terminal TAA
ttg1-1 ttg1-15 ttg1-16 ttg1-17 ttg1-18 ttg1-19 ttg1-20 tan1-a tan1-b
NS Deletion Insertion ^
Fig. S5. Gene expression of Tan1 and other genes associated with anthocyanin and proanthocyanidin pathways by RT-PCR. (A) Expression of the Tan1 gene in different sorghum tissues of the tannin line, ShanQuiRed (S), and the non-tannin line, Tx430 (T). (B) Schematic pathway of the proanthocyanidin pathway in Arabidopsis. (C) Expression of other genes in the tannin pathway between the tannin (S) or non-tannin (T) lines. Tissue for seed coat 1 was harvested at 15 days after pollination and seed coat 2 at 30 days after pollination.
Fig. S6. Phylogenetic analysis of SbiTAN1 and its orthologs across 23 plant species. Only the orthologs with the highest similarity scores within each species was selected for the neighborjoining tree.
Fig. S7. The conservation of the predicted amino acid sequences of SbiTAN1 and its orthologs across 23 plant species. Bar chart under the amino acid position indicates the level of conservation across the species. The positions of four WD-40 repeat domains are marked with brackets and triangles. The general level of conservation is much higher at the WD-40 repeat domains and the C-terminal than the N-terminal.
Fig. S8. Sliding-window analysis of θw at the Tan1 locus in wild sorghums, landraces, and cultivars. Values at the Adh1 locus, a neutral gene, are included for comparison. The full-length Tan1 genomic sequence was obtained for this analysis. The θw values approach zero in the Tan1 coding region in landraces (18 accessions) and cultivars (87 accessions), but remains at 0.010 in the set (18 accessions) of wild, weedy sorghums, and sorghum relatives. A 400-bp window with a 50-bp step was used.
Table S1. Intitial QTL mapping results with the recombinant inbred line population of Tx430/ShanQuiRed using a combination of AFLP and SSR markers. R2 Total R2 Chromosome QTL Flanking markers LOD Effect SBI-02 Qsqr.t-2 Txa2724, Txa2018 4.8 0.186 0.17 SBI-04 Qsqr.t-4 PgMf244, Txa60 5.8 0.221 0.19 Interaction 3.2 0.158 0.16 0.52
Table S2. Annotated sorghum genes, within the chromosome 4 consensus QTL region, homologous to known genes in the anthocyanin and proanthocyanidin biosynthetic pathways. Marker Locus Location Homologs Functional annotation CT1 Sb04g037630.1 67224600..67226599 Arabidopsis TT12 Similar to MATE efflux protein-like CT2 Sb04g030570.1 60538583..60543582 Vitis vinifera (grape) Phenylcoumaran benzylic ether leucoanthocyanidin reductase PT1 reductase LAR1 CT5 Sb04g031710.1 61642693..61644692 Arabidopsis LEC2 and Similar to RAV-like B3 domain DNA FUS3 genes binding protein-like CT7 Sb04g031730.1 61663774..61668774 Arabidopsis TTG1 Similar to Anthocyanin biosynthetic gene regulator PAC1
Table S3. The set of 24 sorghum accessions for initial candidate gene sequencing. Accessions Phenotype Tan1 Original country Germplasm type Ajabsido Tannin Tan1 Sudan Cultivar P898012 Tannin Tan1 United States Cultivar SC1103 Tannin Tan1 Nigeria Sorghum conversion line SC1108 Tannin Tan1 India Sorghum conversion line SC1345 Tannin Tan1 Mali Sorghum conversion line ShanQuiRed Tannin Tan1 China Cultivar 00MN7645 Non-tannin tan1-a United States Inbred line SC22 Non-tannin tan1-a Ethiopia Sorghum conversion line SC329 Non-tannin tan1-a NA Sorghum conversion line SC35 Non-tannin tan1-a Ethiopia Sorghum conversion line TX2737 Non-tannin tan1-a United States Inbred line Tx430 Non-tannin tan1-a United States Inbred line Tx436 Non-tannin tan1-a United States Inbred line Macia Non-tannin tan1-b South Africa Cultivar Malisor 84-7 Non-tannin tan1-b Mali Cultivar Tx623 Non-tannin tan1-b United States Inbred line B.QL41 Non-tannin Tan1 Australia Inbred line MR732 Non-tannin Tan1 Niger Cultivar SC971 Non-tannin Tan1 United States Sorghum conversion line SC265 Non-tannin Tan1 West Volta Sorghum conversion line SC283 Non-tannin Tan1 Tanzania Sorghum conversion line Segaolane Non-tannin Tan1 Southern Africa Cultivar Tx2752 Non-tannin Tan1 United States Inbred line Tx631 Non-tannin Tan1 United States Inbred line Note: NA, not available
Table S4. Nucleotide polymorphisms identified In Tan1 gene. ID Position* Location Nucleotide polymorphism 1 -1189 Promoter AGTGA> 2 -1178 Promoter C>T 3 -1133 Promoter T> 4 -1082 Promoter G>A 5 -1050 Promoter A>T 6 -1044 Promoter G>A 7 -917 Promoter T>C 8 -906 Promoter C>T 9 -874 Promoter G>A 10 -803 Promoter C>G 11 -492 Promoter G>A 12 -481 Promoter A>G 13 -377 Promoter C>T 14 -333 Promoter GTTTT>15 -321 Promoter G>T 16 -309 Promoter A>G 17 -228 Promoter C>T 18 -207 Promoter A>G 19 -205 Promoter G>T 20 -165 Promoter G>C 21 -149 Promoter A>G 22 -144 Promoter C>A 23 -92 Promoter T>C 24 580 Exon G> 25 798 Exon G>T 26 923 Exon - > CGGGCAGCGG Note: *, Transcription starting site (TSS) as "0".
Table S5. Sorghum genes related to the anthocyanin and proanthocyanidin biosynthetic pathways for gene expression analysis. Gene Location Homologs Forward primer Reverse primer GAATGTGACGGCAGTGATCT SbCHS Sb05g020220 Arabidopsis At5g13930, CGAATCACCAAGAGTGAGCA Maize C2 GAGATCGGAGGCAACTTCAT CTCGCAGAGGTGCTTGTTCT SbCHI Sb01g003330 Maize chi AGACAGAGAGCAGGCCACAT ACCTTCTGGTCCATGTCCAC SbF3H Sb06g031790 Arabidopsis tt6, Maize fht1 TGGACTTCGAGTCCCAAGA GGGTGCTCGAAGAGGAAGAT SbDFR Chromosome 4, Maize A1 CAA75998 40750044076074 CGCGGCGATAGTGAATTAGT TGCAGCAGGTGGAAGAGGTA SbANS Sb04g000260 Maize A2 CAA39022 TGGAGAAGAACTCCCACCTC AGACGGTGACGAGGCTGAT SbLAR Sb06g029590 Maize Loc100282500 AGTGAGCTGATGCTGACTGG TGTAACTCGGGTGACTGCTG SbTT8 Sb02g006390 Maize in1 ACAAGATCAACCGCCAGGT ATCGAGGGGATGGAAGAAGT SbTT16 Sb07g026200.1 Arabidopsis tt16 GGGTGCCAACTTCACCTACA CATTGATGACCGGCAGGTAG SbTT10 Sb04g027860 Arabidopsis tt10
Table S6. Tan1 allele distribution across the diverse association panel. Accessions Phenotype Tan1 allel Origin Ajabsido Tannin Sudan Tan1 El Mota Tannin Niger Tan1 HEGARI Tannin NA Tan1 San Chi San Tannin China Tan1 SC103 Tannin South Africa Tan1 SC1057 Tannin Uganda Tan1 SC1074 Tannin Nigeria Tan1 SC1108 Tannin NA Tan1 SC115 Tannin Uganda Tan1 SC118 Tannin Sudan Tan1 SC1203 Tannin Brazil Tan1 SC1205 Tannin NA Tan1 SC121 Tannin South Africa Tan1 SC1246 Tannin Chad Tan1 SC1319 Tannin Ethiopia Tan1 SC1328 Tannin Sudan Tan1 SC1329 Tannin NA Tan1 SC1330 Tannin Sudan Tan1 SC1345 Tannin Mali Tan1 SC135 Tannin Ethiopia Tan1 SC1356 Tannin Sudan Tan1 SC141 Tannin NA Tan1 SC145 Tannin Ethiopia Tan1 SC146 Tannin NA Tan1 SC1471 Tannin Sudan Tan1 SC15 Tannin Ethiopia Tan1 SC155 Tannin Ethiopia Tan1 SC175 Tannin Ethiopia Tan1 SC223 Tannin Nigeria Tan1 SC224 Tannin Ethiopia Tan1 SC305 Tannin Chad Tan1 SC309 Tannin Sudan Tan1 SC319 Tannin Uganda Tan1 SC322 Tannin Tanzania Tan1 SC323 Tannin Sudan Tan1 SC325 Tannin United States Tan1 SC328 Tannin Uganda Tan1 SC331 Tannin NA Tan1 SC336 Tannin NA Tan1 SC405 Tannin NA Tan1 SC420 Tannin Sudan Tan1 SC423 Tannin Sudan Tan1 SC424 Tannin Japan Tan1 SC502 Tannin Sudan Tan1 SC504 Tannin NA Tan1 SC53 Tannin Sudan Tan1 SC557 Tannin Mosambique Tan1 SC558 Tannin Zaire Tan1 SC56 Tannin Sudan Tan1 SC57 Tannin Sudan Tan1
Germplasm type Cultivar Cultivar Cultivar Cultivar Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line
Table S6. Tan1 allele distribution across the diverse association panel. Accessions Phenotype Tan1 allel Origin SC59 Tannin Sudan Tan1 SC6 Tannin Ethiopia Tan1 SC60 Tannin Sudan Tan1 SC605 Tannin Kenya Tan1 SC623 Tannin Congo Tan1 SC624 Tannin India Tan1 SC627 Tannin South Africa Tan1 SC637 Tannin Uganda Tan1 SC639 Tannin India Tan1 SC64 Tannin Sudan Tan1 SC645 Tannin Uganda Tan1 SC648 Tannin South Africa Tan1 SC655 Tannin South Africa Tan1 SC67 Tannin Sudan Tan1 SC672 Tannin Zimbabwe Tan1 SC695 Tannin Tanzania Tan1 SC701 Tannin Sudan Tan1 SC704 Tannin Japan Tan1 SC708 Tannin Uganda Tan1 SC725 Tannin Japan Tan1 SC760 Tannin Sudan Tan1 SC782 Tannin India Tan1 SC790 Tannin NA Tan1 SC84 Tannin Uganda Tan1 SC937 Tannin United States Tan1 SC941 Tannin United States Tan1 SC942 Tannin United States Tan1 SC947 Tannin NA Tan1 SC949 Tannin NA Tan1 SC968 Tannin Zimbabwe Tan1 SC970 Tannin Uganda Tan1 SC991 Tannin Uganda Tan1 Shan Qui Red Tannin China Tan1 Sorghum Virgatum Tannin NA Tan1 (SN142)SA386 REDBINE60 Non-tannin NA Tan1 (SN147)SA7078 COMBINE 7078 Non-tannin United States Tan1 (SN149)SA7000 CAPROCK Non-tannin United States Tan1 B.OK11 Non-tannin United States Tan1 B.QL41 Non-tannin Austrilia Tan1 Dorado Non-tannin NA Tan1 MR732 Non-tannin Niger Tan1 P9517 Non-tannin United States Tan1 SC170 Non-tannin Ethiopia Tan1 SC173 Non-tannin NA Tan1 SC241 Non-tannin NA Tan1 SC261 Non-tannin NA Tan1 SC265 Non-tannin West Volta Tan1
Germplasm type Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Cultivar Wild sorghum Cultivar Cultivar Cultivar Inbred line Inbred line Cultivar Cultivar Inbred line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line
Table S6. Tan1 allele distribution across the diverse association panel. Accessions Phenotype Tan1 allel Origin SC283 Non-tannin Tanzania Tan1 SC295 Non-tannin Nigeria Tan1 SC299 Non-tannin Nigeria Tan1 SC303 Non-tannin Nigeria Tan1 SC317 Non-tannin India Tan1 SC413 Non-tannin Nigeria Tan1 SC418 Non-tannin Tanzania Tan1 SC449 Non-tannin India Tan1 SC465 Non-tannin Arabia Tan1 SC532 Non-tannin West Volta Tan1 SC553 Non-tannin NA Tan1 SC625 Non-tannin Japan Tan1 SC663 Non-tannin United States Tan1 SC671 Non-tannin Kenya Tan1 SC673 Non-tannin Zimbabwe Tan1 SC679 Non-tannin NA Tan1 SC755 Non-tannin NA Tan1 SC79 Non-tannin Kenya Tan1 SC91 Non-tannin Zimbabwe Tan1 SC971 Non-tannin United States Tan1 Segaolane Non-tannin Tan1 Southern Africa SRN39 Non-tannin NA Tan1 TAM2566 Non-tannin United States Tan1 TAM428 Non-tannin United States Tan1 Tx2783 Non-tannin United States Tan1 Tx2917 Non-tannin United States Tan1 Tx378 Non-tannin United States Tan1 Tx615 Non-tannin United States Tan1 Tx641 Non-tannin United States Tan1 00MN7645 Non-tannin United States tan1-a Day Non-tannin United States tan1-a KS19 Non-tannin United States tan1-a SC132 Non-tannin NA tan1-a SC192 Non-tannin India tan1-a SC199 Non-tannin India tan1-a SC206 Non-tannin India tan1-a SC209 Non-tannin India tan1-a SC21 Non-tannin Ethiopia tan1-a SC214 Non-tannin India tan1-a SC22 Non-tannin Ethiopia tan1-a SC23 Non-tannin Ethiopia tan1-a SC240 Non-tannin India tan1-a SC25 Non-tannin Ethiopia tan1-a SC33 Non-tannin Ethiopia tan1-a SC334 Non-tannin Sudan tan1-a SC38 Non-tannin Ethiopia tan1-a SC382 Non-tannin Nigeria tan1-a SC414 Non-tannin Sudan tan1-a SC480 Non-tannin India tan1-a
Germplasm type Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Cultivar Cultivar inbreed lines inbreed lines inbreed lines inbreed lines Inbred line Inbred line Inbred line Inbred line Inbred line Inbred line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line
Table S6. Tan1 allele distribution across the diverse association panel. Accessions Phenotype Tan1 allel Origin SC489 Non-tannin India tan1-a SC498 Non-tannin India tan1-a SC500 Non-tannin India tan1-a SC51 Non-tannin Sudan tan1-a SURENO Non-tannin Central America tan1-a TX2536 Non-tannin United States tan1-a TX2737 Non-tannin United States tan1-a Tx2741 Non-tannin United States tan1-a Tx430 Non-tannin United States tan1-a Tx436 Non-tannin United States tan1-a Tx437 Non-tannin United States tan1-a Tx642 Non-tannin United States tan1-a Macia Non-tannin South Africa tan1-b Malisor 84-7 Non-tannin Mali tan1-b Tx623 Non-tannin United States tan1-b Note: NA, not available.
Germplasm type Sorghum conversion line Sorghum conversion line Sorghum conversion line Sorghum conversion line Cultivar Inbred line Inbred line Inbred line Inbred line Inbred line Inbred line Inbred line Cultivar Cultivar Inbred line
Table S7. Tan1 homologs across 23 plant species for phylogenetics anlaysis. Species Orthologs Protein Locus or GenBank size (aa) accession Monocot Brachypodium BdiWD40-1 351 Bradi3g51820 distachyon Hordeum vulgare HvuWD40-1 356 BAK06996.1 Oryza sativa OsWD40-1 355 LOC_Os02g45810 Setaria italica SitWD40-1 359 scaffold_1:34663907..34665 185 Sorghum bicolor SbiTAN1 353 Zea mays ZmaPAC1 353 GRMZM2G058292 Eudicot Arabidopsis lyrata Arabidopsis thaliana Brassica rapa Carica papaya Citrus clementina Cucumis sativus Eucalyptus grandis Glycine max Lotus japonicus Manihot esculenta Medicago truncatula Nicotiana tabacum Petunia x hybridagi Populus trichocarpa Prunus persica Solanum tuberosum Vitis vinifera
AlyWD40-1 AtTTG1 BraWD40-1 CpaWD40-1 CclWD40-1 CsaWD40-1 EgrWD40-1 GmaWD40-1 LjaWD40-1 MesWD40-1 MtrWD40 NtaWD40-1 PhyAN11 PtrWD40-1 PpeWD40-1 StuAN11 VviWDR1
341 341 337 343 337 333 341 336 349 342 342 342 337 340 342 342 336
489315 AT5G24520 ADK11704.1 evm.TU.supercontig_3.159 clementine0.9_015140m.g Cucsa.397650 Egrandis_v1_0.018423m.g Glyma06g14180 BAH28880.1 cassava4.1_011123m.g Medtr3g122570 ACN87316.1 AAC18914.1 POPTR_0012s00640 ppa008187m.g AEF01097.1 ABF66625.2
Genome version
Aligned WD40 consensus 1 (aa)
Bd21
147-289
MSU6 v2.1
147-289 147-289 147-289
Phytozome 7 RefGen_2
147-289 147-289
v1.0 TAIR10 Phytozome 7 Phytozome 7 Phytozome 7 Phytozome 7 Glyma1 Cassava4 Mt3.0 v2.2 peach v1.0 -
108-289 92-289 147-289 117-289 106-289 147-289 102-189 108-289 92-289 92-289 92-289 92-289 92-289 142-289 100-289 92-289 92-289
Table S8. A set of 18 wild, weedy sorghum, and sorghum relatives with with full-length Tan1 sequence for nucleotide diversity analysis. Sequence ID Accession Phenotype Species Origin W1 PI 185574 Tannin Sorghum bicolor subsp. verticilliflorum South Africa W2 PI 213901 Tannin Sorghum bicolor subsp. verticilliflorum Zimbabwe W3 PI 302112 Tannin Sorghum bicolor subsp. verticilliflorum Zimbabwe W4 PI 302116 Tannin Sorghum bicolor subsp. verticilliflorum Australia W5 PI 365024 Tannin Sorghum bicolor subsp. verticilliflorum South Africa W14 PI 302224 Tannin Sorghum bicolor nothosubsp. drummondii United States W17 Grif 16331 Non-tannin Sorghum bicolor nothosubsp. drummondii Sudan W18 Grif 16345 Tannin Sorghum sp. POACEAE Unknown W22 PI 330287 Non-tannin Sorghum sp. POACEAE Ethiopia W10 PI 300121 Tannin Sorghum sp. POACEAE South Africa W20 Grif 16353 Tannin Sorghum halepense (L.) Pers. POACEAE United States W21 Grif 16312 Tannin Sorghum halepense (L.) Pers. POACEAE Unknown W6 PI 209217 Tannin Sorghum halepense (L.) Pers. POACEAE South Africa W7 PI 198999 Tannin Sorghum plumosum (R. Br.) P. Beauv. POACEAE Australia W9 PI 536008 Tannin Sorghum purpureosericeum (Hochst. ex A. Rich.) Cameroon Asch. & Schweinf. POACEAE W11 PI 202411 Tannin Sorghum × almum Parodi POACEAE Argentina W12 PI 208702 Tannin Sorghum × almum Parodi POACEAE Algeria W8 PI 653737 Tannin Sorghum propinquum (Kunth) Hitchc. POACEAE Note: Sorghum × almum Parodi POACEAE equivalent to Sorghum bicolor × Sorghum halepense
Table S9. A set of 18 sorghum landraces with full-length Tan1 sequence for nucleotide diversity analysis. Sequence ID Phenotype Accession Race Identifier Origin LR01 Tannin NSL 51233 bicolor 65I 1995 Malawi LR03 Tannin NSL 51365 guinea IS 6272 India LR17 Tannin NSL 87666 caudatum 74L 11921 Central African Rep LR19 Tannin NSL 92371 bicolor HD-043 Swaziland LR29 Tannin PI 221720 caudatum Row 86 Central African Rep LR32 Tannin PI 267354 bicolor NSL 51249 Uganda LR66 Tannin PI 527129 bicolor AMM 1196 Zimbabwe LR05 Non-tannin NSL 54236 guinea 66I 3139 Nigeria LR13 Non-tannin NSL 82459 bicolor Purdue No 50840 Cameroon LR14 Non-tannin NSL 83707 guinea Purdue No 49506 Cameroon LR16 Non-tannin NSL 87088 durra 74I 10917 India LR46 Non-tannin NSL 56174 kafir 66I 5133 Ethiopia LR57 Non-tannin PI 537079 caudatum Farfara Niger LR64 Non-tannin PI 527132 kafir AMM 1221 Zimbabwe LR77 Non-tannin PI 526678 guinea AMM 225 Zimbabwe LR78 Non-tannin PI 526671 guinea AMM 208 Zimbabwe LR79 Non-tannin PI 526650 kafir AMM 164 Zimbabwe LR91 Non-tannin PI 506097 guinea GS 341 Togo
Table S10. A set of 86 sorghum cultivars and breeding lines with full-length Tan1 sequence for nucleotide diversity analysis Sequence ID Accessions Phenotype Original country Germplasm type C81 Ajabsido Tannin Sudan Cultivar C74 P898012 Tannin United States Cultivar C6 SC1019 Tannin Ethiopia Sorghum conversion line C11 SC1056 Tannin Sudan Sorghum conversion line C12 SC1057 Tannin Uganda Sorghum conversion line C14 SC1074 Tannin Nigeria Sorghum conversion line C17 SC1079 Tannin Sudan Sorghum conversion line C82 SC1103 Tannin Nigeria Sorghum conversion line C22 SC1154 Tannin Ethiopia Sorghum conversion line C25 SC1203 Tannin Brazil Sorghum conversion line C26 SC1205 Tannin NA Sorghum conversion line C29 SC1214 Tannin Burkina Faso Sorghum conversion line C31 SC1218 Tannin Sudan Sorghum conversion line C32 SC1246 Tannin Chad Sorghum conversion line C36 SC1319 Tannin Ethiopia Sorghum conversion line C38 SC1328 Tannin Sudan Sorghum conversion line C39 SC1329 Tannin NA Sorghum conversion line C40 SC1330 Tannin Sudan Sorghum conversion line C78 SC1345 Tannin Mali Sorghum conversion line C42 SC1356 Tannin Sudan Sorghum conversion line C53 SC141 Tannin NA Sorghum conversion line C48 SC1451 Tannin Malawi Sorghum conversion line C55 SC146 Tannin NA Sorghum conversion line C49 SC1471 Tannin Sudan Sorghum conversion line C52 SC1494 Tannin Sudan Sorghum conversion line C59 SC330 Tannin NA Sorghum conversion line Sorghum conversion line C60 SC336 Tannin NA C65 SC405 Tannin NA Sorghum conversion line C69 SC504 Tannin NA Sorghum conversion line C1 SC987 Tannin Ethiopia Sorghum conversion line C2 SC991 Tannin Uganda Sorghum conversion line C57 SU629 Tannin NA Sorghum conversion line C80 Macia Non-tannin South Africa Cultivar C84 OOMN7645 Non-tannin United States Inbred line C4 SC1014 Non-tannin Ethiopia Sorghum conversion line C5 SC1017 Non-tannin Ethiopia Sorghum conversion line C7 SC1033 Non-tannin Ethiopia Sorghum conversion line C8 SC1038 Non-tannin Ethiopia Sorghum conversion line C9 SC1047 Non-tannin Ethiopia Sorghum conversion line C10 SC1055 Non-tannin Sudan Sorghum conversion line C13 SC1070 Non-tannin Nigeria Sorghum conversion line C15 SC1076 Non-tannin Nigeria Sorghum conversion line C16 SC1077 Non-tannin Nigeria Sorghum conversion line C18 SC1080 Non-tannin South Africa Sorghum conversion line C19 SC1085 Non-tannin India Sorghum conversion line C20 SC1104 Non-tannin Uganda Sorghum conversion line C21 SC1124 Non-tannin Nigeria Sorghum conversion line C23 SC1155 Non-tannin Ethiopia Sorghum conversion line C24 SC1158 Non-tannin Ethiopia Sorghum conversion line
Table S10. A set of 86 sorghum cultivars and breeding lines with full-length Tan1 sequence for nucleotide diversity analysis Sequence ID Accessions Phenotype Original country Germplasm type C27 SC1211 Non-tannin Guatemala Sorghum conversion line C28 SC1212 Non-tannin Venezuela Sorghum conversion line C30 SC1215 Non-tannin NA Sorghum conversion line C33 SC1251 Non-tannin Sudan Sorghum conversion line C34 SC1271 Non-tannin Ethiopia Sorghum conversion line C35 SC1277 Non-tannin Ethiopia Sorghum conversion line C37 SC1320 Non-tannin Ethiopia Sorghum conversion line C41 SC1337 Non-tannin Mali Sorghum conversion line C43 SC1416 Non-tannin Niger Sorghum conversion line C54 SC142 Non-tannin NA Sorghum conversion line C44 SC1424 Non-tannin Mali Sorghum conversion line C45 SC1429 Non-tannin Zimbabwe Sorghum conversion line C46 SC1439 Non-tannin Gambia Sorghum conversion line C47 SC1440 Non-tannin NA Sorghum conversion line C50 SC1484 Non-tannin Somalia Sorghum conversion line C51 SC1489 Non-tannin Somalia Sorghum conversion line C56 SC202 Non-tannin NA Sorghum conversion line C73 SC265 Non-tannin West Volta Sorghum conversion line C75 SC283 Non-tannin Tanzania Sorghum conversion line C58 SC284 Non-tannin NA Sorghum conversion line C61 SC337 Non-tannin NA Sorghum conversion line C62 SC346 Non-tannin NA Sorghum conversion line C63 SC348 Non-tannin NA Sorghum conversion line C83 SC35 Non-tannin Ethiopia Sorghum conversion line C64 SC367 Non-tannin NA Sorghum conversion line C66 SC452 Non-tannin NA Sorghum conversion line Sorghum conversion line C67 SC477 Non-tannin NA C68 SC499 Non-tannin NA Sorghum conversion line C70 SC520 Non-tannin NA Sorghum conversion line C71 SC575 Non-tannin NA Sorghum conversion line C79 SC971 Non-tannin United States Sorghum conversion line C3 SC998 Non-tannin NA Sorghum conversion line C76 Segaolane Non-tannin Southern Africa Cultivar C77 Tx2752 Non-tannin United States Inbred line C85 Tx430 Non-tannin United States Inbred line C72 Tx623 Non-tannin United States Inbred line C86 Tx631 Non-tannin United States Inbred line Note: NA, not available
Table S11. Sequence diversity at the Tan1 locus in wild sorghums, landraces, and cultivars. The full-length Tan1 genome sequence was obtained for 18 landraces, 86 cultivars, and18 accessions of wild, weedy sorghums, and sorghum relatives. Parameter Tan1 Adh1 -1293 – 1167 nt 1-750 nt -1293 – -93 nt -692 – -93 nt -92 – 518 nt 519 – 1167 nt (whole length) Wild sorghum π 0.0130 0.0090 0.0093 0.0057 0.0093 0.0088 θw 0.0179 0.0114 0.0100 0.0100 0.0122 0.0096 Tajima’s D -0.4810 -1.5533 -1.7073 -2.2150** -1.9887* Landrace π θw
0.0094 0.0110
0.0087 0.0073
0.0054 0.0058
Cultivar π 0.0240 0.0109 0.0042 θw 0.0162 0.0106 0.0046 Note: Transcription starting site (TSS) as "0"; *, P
