Download Figure S1. Map-based cloning of Tu. (a) Tu was mapped to a 7.3cM

Figure S1. Map-based cloning of Tu.
(a) Tu was mapped to a 7.3cM genetic region between molecular markers SSR16203
and C_SC933 on Chr. 5 (Zhang et al., 2010).
(b) Based on the F2 population (2808 individuals) from the cross S52 and S06, Tu was
mapped between the molecular markers SSR42 and SNP18, and was co-segregant
with the marker S-CR68. The rectangular splice lines represent the Scaffold number
in
the
Cucumber
Genome
Database
(http://cucumber.vcru.wisc.edu/wenglab/gy14-9930/index.htm); the names of
cucumber lines whose genome sequences have been published shown in brackets on
the left hand side.
(b-c) The numerical value in anchor brackets represents the sequence location starting
at the first nucleotide of the positive primers designed using the nucleotide sequence
between SSR16203 and C_SC933 (Data S1). The numerical value on the right hand
side represents the number of remaining exchange plants, and × represents an
exchange event.
(d)
Referring
to
the
Cucumber
Genome
Database
(http://cucumber.genomics.org.cn/page/cucumber/mapview.jsp?dbKey=Cucumber&re
fId=5) revelaed that the 41.6kb physical region contains two candidate genes:
Csa016922 encoding phosphoenolpyruvate carboxykinase homolog, and Csa016861
encoding a C2H2-type zinc finger protein.
Figure S2. Analysis of the difference between two candidate genes in the 41.6kb
physical region.
(a) The differences in two candidate genes’ alleles. Primers P1 and C1 were designed
using the promoter of genes Csa016922 and Csa016861, respectively. Primers P2 and
C2 were respectively designed using the coding region of genes Csa016922 and
Csa016861, respectively.
(b) PCR results using the primers C3-F/R. M: Markers (DL10000).
(c) S52 and S06 sequence differences at the Tu/tu locus.
Figure S3. Analysis of Tu amino acid sequence .
The sequence of 213 amino acids encoded by the CDS region of Tu was compared
with other C2H2 ZFPs (XP_002283623.1, XP_003614563.1, XP_003532346.1,
NP_177003.1 and NP_176873.1 from NCBI database). The black line indicates the
location of the plant-specific conserved sequence QALGGH in all C2H2 ZFPs.
Figure S4. Morphological observations in the fruits of S06, mutant gl, F1 and F2
plants.
(a) Fruit of line S06 had no tubercules and exhibited small, fine fruit trichomes
(spines).
(b) Fruit of mutant line gl exhibited a glabrous and tubercule-free trait.
(c-d) Fruits of F1 (S06 × gl) (c) and F1 (gl × S06) (d) exhibited the Wty fruit trait.
(e-h) Morphological observations of fruits of genotype Gl_Tu_ (e), genotype Gl_tutu
(f), mutant gl genotype glglTu_ (g), and double mutant genotype glgltutu (h) in F2 (gl
× S06) and F2 (S06 × gl) populations. Scale bars: (a-h) = 1cm.
Abbreviations: Gl, trichome gene; gl, glabrous gene; Tu, tubercule gene; tu,
tubercule-free gene.
1
Figure S5. Phylogenetic analysis of Tu. The phylogenetic tree was constructed using
the cucumber Tu protein sequence (marked with an asterisk), the melon homolog
(MELO3C005347), and sequences of 15 close homologs from the NCBI database.
The accession ID and names of 17 homologs are as follows:
XP_006344147.1, Solanum tuberosum; AFK47742.1, Lotus japonicus;
XP_004300974.1, Fragaria vesca; NP_001148305.1, Zea mays; XP_002457427.1,
Sorghum bicolor; NP_001172162.1, Oryza sativa; BAK05966.1, Hordeum vulgare;
XP_004238917.1, Solanum lycopersicum; XP_002527000.1, Ricinus communis;
XP_003536676.1, Glycine max; XP_003614563.1, Medicago truncatula;
AEE34586.1 (ZFP6), Arabidopsis lyrata; AEE28584.1 (ZFP5), Arabidopsis lyrata;
XP_002283623.1, Vitis vinifera; ABR18213.1 (as the outgroup), Picea glauca
(Gymnospermae).
Figure S6. Analysis of the CDS regions of Tu homologs. Comparison of cucumber
Tu nucleotide (a) and amino acid (b) sequences with the melon homolog. The red
arrow indicates the single amino acid difference between the protein sequences.
Table S1. Segregation analysis of the Wty/nWty fruit trait in the F1, F2, and BC1
progenies of different crosses.
S52 and S94 are Wty fruit lines; S06 and SB are nWty fruit lines; Mutant gl is a
glabrous and tubercule-free fruit line. ＊: the population used for fine mapping of Tu;
△: the populations verified by Tu; ○: the populations used for relationship analysis
between Tu and the glabrous fruit gene gl. aχ2 (0.05, 1) =3.84.
Abbreviations: S, spring; A, autumn; Wty, warty; nWty, non-warty.
Table S2. 94 Wty/nWty cucumber lines tested with the dominant markers TY-1
and TY-2 for the Tu/tu locus.
Primers TY-1 and TY-2 are shown in Table S4;
Abbreviations: Wty, warty; nWty, non-warty; W, Wty fruit line; S, nWty fruit line; A,
existence of Tu; B, absence of Tu.
Table S3. Up-regulated genes for transgenic fruit warts at 2 DBF.
Table S4. Primers used in this study.
Data S1. Nucleotide sequences between markers SSR16203 and C_SC933 on
chromosome 5 in cucumber.
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