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




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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. durumAe. tauschii W79843

no

yes

synthetic T. dicoccoidesAe. 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).



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