Supplementary materials intron loss in the chalcone-flavanone isomerase gene of rye

SUPPLEMENTARY MATERIALS Intron loss in the chalcone-flavanone isomerase gene of rye Khlestkina E.K.*, Shoeva O.Y. Table S1. Triticeae accessions employed and the outcome of PCR analysis for intron loss Species Sample name/No/Var. Intron 2 loss Intron 3 loss Aegilops bicornis (Forssk.) Jaub. et Spach. TB054 no yes Aegilops caudata L. 67801 no yes Aegilops cylindrica Host. k-1852 no yes Aegilops longissima Schweinf. et Muschl. TL034 no yes TL044 no yes TL054 no yes Aegilops searsii Feldman et Kislev ex Hammer TE014 no yes TE124 no yes TE164 no yes TE204 no yes Aegilops sharonensis Eig TH014 no yes TH034 no yes Aegilops speltoides Tausch. TS014 no yes TS054 no yes TS474 no yes Aegilops tauschii Coss. AE 4543 no yes AE 16023 no yes Aegilops triuncialis L. Ganchi1 no yes Nurabad1 no yes Aegilops uniaristata Vis. 69331 no yes Agropyron cristatum (L.) Gaertn. Yarovoe1 no yes 29311 no yes Agropyron glaucum (Desf. ex DC.) Roem. & Schult. 0041 no yes Elymus dahuricus Turcz. ex Griseb. 22471 no yes Elymus sibiricus L. 22161 no yes Elytrigia repens (L.) Desv. ex Nevski 40031 no yes Hordeum vulgare L. Acha1 no yes Biom1 no yes Bowman3 no yes Vorsinsky1 no yes Leumys arenarius (L.) Hochst. 0091 no yes Phalaris arundinacea L. 393721 no yes Phalaris arundinacea L. Tomsk1 no yes Psathyrostachys Nevski 22501 no yes Table S1. Continuation Species Sample name/No/Var. Intron 2 loss Intron 3 loss Secale cereale L. Onokhoiskaya1 yes yes P873 yes yes P1053 yes yes Imperial3 yes yes Triticum aestivum L. Chinese Spring3 no yes Novosibirskaya 671 no yes Saratovskaya 291 no yes synthetic T. durumAe. tauschii W79843 no yes synthetic T. dicoccoides Ae. tauschii 6x3 no yes Triticum compactum Host k-221802 no yes Triticum dicoccoides (Körn. ex Aschers. et Graebn.) Schweinf. 67771 no yes 67961 no yes 68011 no yes 68171 no yes Triticum dicoccum (Schrank) Schübl. 69571 no yes 74771 no yes Triticum durum Desf. Svetlana1 no yes k-164772 no yes TRI 27193 no yes TRI 157443 no yes Triticum militinae Zhuk. et Migusch. -1 no yes Triticum persicum Vav. k-133832 no yes Triticum spelta L. k-536602 no yes Triticum timopheevii Zhuk. var. typica1 no yes 385551 no yes Triticum urartu Thum. ex Gandil TRI 114993 no yes TRI 174123 no yes TRI 171203 no yes non Triticeae control Beckmannia eruciformis (Steud.) Fernald 224081 no no Beckmannia eruciformis (Steud.) Fern. 30051 no no 1 Collection of the Institute of Cytology and Genetics (Novosibirsk, Russia). 2 Collection of the Vavilov Research Institute for Plant Industry (St. Petersburg, Russia) 3 Collection of the Leibniz Institute of Plant Genetics and Crop Plant Research (Gatersleben, Germany) 4 Collection of the Weizmann Institute of Science (Rehovot, Israel). Table S2. Triticeae intergenera lines and their parents employed and the outcome of PCR analysis for the presence of the rye Chi gene as marker of rye genome/chromosome 5R. * - chromosome substitution lines (Adonina et al. 2011), ** - chromosome addition lines, *** - ditelosomic chromosome addition lines (Driscoll and Sears, 1971). Name Genome composition (haploid) The presence of the rye-specific PCR-fragment Secale cereale Selenga r7 yes x Triticosecale 131/731 w14+r7 yes x Triticosecale 131/745 w14+r7 yes x Triticosecale 131/749 w14+r7 yes x Triticosecale 131/797 w14+r7 yes x Triticosecale (Aegilops umbellulata) 1R(1U)* w14+r6+u1 yes x Triticosecale (Aegilops umbellulata) 2R(2U)* w14+r6+u1 yes Triticum aestivum Chinese Spring (CS) w21 no Secale cereale Imperial r7 yes CS + Imperial 1R** w21+r1 no CS + Imperial 2R** w21+r1 no CS + Imperial 3R** w21+r1 no CS + Imperial 4R** w21+r1 no CS + Imperial 5R** w21+r1 yes CS + Imperial 5RS*** w21+r1ditelo no CS + Imperial 5RL*** w21+r1 ditelo yes CS + Imperial 6R** w21+r1 no CS + Imperial 7R** w21+r1 no Fig. S1. Multiple alignment of the Chi nucleotide sequences in different rye cultivars. Primers are indicated with arrows. Fig. S2. PCR assay of a part of the mapping population P87/P105 (lines 1-13) and parental lines P87 (line 14) and P105 (line 15) with primer pair Chi_1F/2R (Table 1) separated in 5% HR agarose gel. Fig. S3. Multiple alignment of the deduced polypeptide sequences encoded by Сhi in different rye cultivars. Residues associated with the substrate binding cleft are shown in green, those with the active site hydrogen bond network in pink, and other conserved residues in blue (following Jez et al. 2000). Fig. S4. The 3D structure of CHI in Medicago sativa L. (Jez et al. 2000) and in rye cultivars (determined in the current study). The open-faced β-sandwich fold structure was revealed in M. sativa by crystallography (Jez et al. 2000).