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All PCRs were performed in 12-well strip tubes, in a 96-well MJ thermocycler with heated lid assembly, using specified primers and conditions (Table S1, S2).
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The PCR amplification and HRMA were then performed using the methylation specified primers (MS-HRM-F, MS-HRM-R, Table 1).
Reverse transcriptase was carried out with specified primer pairs using the OneStep RT-PCR Kit (Qiagen) and quantified using SYBR Green (Invitrogen, Carlsbad, CA) and the DNA Engine Opticon Continuous Fluorescence Detection System (CMJ Research).
Additional file 2: Specify primers used in expression analysis of selected genes.
For transmission analysis, seedlings were harvested after 12 days and genotyped using primers specified in Supplementary file 1.
To construct RIVET reporters, putative promoters of interest were PCR amplified using primers specified in Table S2 using genomic DNA of S. enterica sv Typhimurium 14028 as a template.
For the generation of a Col PEG2::PEG2 construct, At1g49290 including 1.5 kb of upstream secuence was amplified by PCR using primers specified in Supplementary file 1.
DNase-treated total RNA was reverse-transcribed into cDNA using random primers and SuperTranscript™ III Reverse Transcriptase (Invitrogen), as specified by the manufacturer.
DNase-treated total RNA from each LCL was reverse-transcribed into cDNA using random primers and SuperTranscript™ III Reverse Transcriptase (Invitrogen), as specified by the manufacturer.
PCR amplification of exon 17 of the ATP1A3 gene was performed using primers and conditions specified previously [ 11], and the mutation was confirmed by Sanger sequencing.
The chloroplast encoded trnG UCC) intron (trnG) was amplified, sequenced and aligned using primers and conditions as specified in Pedersen and Newton [22].
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