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Table 1 Putative and confirmed root-to-shoot transmission of PTGS (rtp) mutations identified by Can-Seq and complementation tests

From: Can-Seq: a PCR and DNA sequencing strategy for identifying new alleles of known and candidate genes

Candidate gene

Homozygous candidate mutation

rtp mutant

Putative rtp mutation

Causative rtp mutation

Mutant crossed to

AGO1

P204S

EMS#193

Yes

n.d.

EMS#152

G277E

EMS#97

Yes

n.d.

EMS#152

D769N

EMS#101

Yes

n.d.

EMS#152

Intron 5 donor splice variant

EMS#152

Yes

Yes

EMS#193, EMS#97, EMS#101

AGO9

M261I

EMS#155

Yes

n.d.

EMS#140

G853R

EMS#140

Yes

n.d.

EMS#155

DCL2a

W796*a

EMS#193a

Yes

Yes

EMS#149, dcl2 (Kas-1)

A1098Va

EMS#149a

Yes

Yes

EMS#193, dcl2 (Kas-1)

HASTY

R544H

EMS#193

Yes

n.d.

EMS#155

G1083S

EMS#155

Yes

n.d.

EMS#193

JMJ14

Q183*

EMS#38

Yes

n.d.

EMS#90

G331E

EMS#148

Yes

n.d.

EMS#90

Intron 2 acceptor splice variant

EMS#90

Yes

Yes

EMS#38, EMS#148

NRPD1A

S222F

EMS#193

Yes

n.d.

EMS#144

R1174*

EMS#144

Yes

n.d.

EMS#193

NRPD1Ba

A513Ta

EMS#149a

Inconclusive

n.d.

EMS#193

R1174*a

EMS#193a

Inconclusive

n.d.

EMS#149

RDR6b

G19Eb

EMS#157b

No

n.d.

EMS#153

W227*

EMS#153

(rtp2-5)c

Yes

Yes

EMS#19, EMS#94, EMS#146, EMS#159, EMS#157, sde1-1

W685*c

EMS#19 (rtp2-2)c

Yes

Yes

EMS#153, sde1-1

W764*

EMS#94

Yes

n.d.

EMS#153

P1073Lb

EMS#146b

No

n.d.

EMS#153

R828Kc

EMS#159

(rtp2-6)c

Yes

Yes

EMS#153, sde1-1

R376*c

EMS#11 (rtp2-1)c

Yes

n.d.

sde1-1

  1. Multiple independent candidate mutations were identified in all of the genes listed in the table, and complementation tests were used to identify putative and confirmed rtp causative mutations. We classified a candidate mutation as putative when an rtp phenotype was observed in the F1 progeny of a cross between a mutant and one other independent mutant carrying a homozygous mutation in the same candidate gene. On the other hand, we classified a candidate mutation as causative when an rtp phenotype was observed in the F1 progeny of a cross between a mutant and at least two other independent rtp mutants carrying a homozygous mutation in the same candidate gene. Based on the complementation tests shown in the table, most of the candidate mutations identified by Can-Seq were classified as at least putative rtp mutations. Furthermore, all seven candidate mutations that were tested by crossing to at least two other independent rtp mutants carrying mutations in the same candidate gene were confirmed to be causative rtp mutations. The two dcl2 mutants in the Table were crossed to each other and also to the naturally occurring dcl2 mutant in ecotype Kas-1, and in all cases, the F1 phenotype was mutant [11]. At least three F1 progeny plants were characterized for each combination of crosses. n.d., not determined
  2. aBoth EMS#193 and EMS#149 carried causative mutations in DCL2 [11] and additional mutations in NRPD1B (also see Additional file 4: Table S4)
  3. bThe causative mutations in EMS#157 and EMS#146 did not map to the RDR6 missense mutations (also see Additional file 4: Table S4)
  4. crdr6 alleles described in Taochy et al. [11]