Additional file 5: Table S3.

Co-expression analysis of ARF genes. (XLSX 74 kb

Additional file 4: Table S2.

Components analysis in the amino acid of middle regions of 14 PsARF proteins. (XLSX 14 kb

Additional file 6: Table S4.

Function and GO annotation of co-expression genes correlated with ARFs. + means the correlation of co-expressed genes with corresponding ARF, and – means no correlation of co-expressed genes with corresponding ARF. (XLSX 198 kb

Additional file 1: Table S1. of Identification of AUXIN RESPONSE FACTOR gene family from Prunus sibirica and its expression analysis during mesocarp and kernel development

Primer sequences used for real-time PCR. (DOCX 19 kb

Additional file 3: Figure S2.

Amino acid sequence alignments of 14 conserved motifs. (TIF 219 kb

Selection of Reference Genes for Gene Expression Studies in Siberian Apricot (<i>Prunus sibirica</i> L.) Germplasm Using Quantitative Real-Time PCR

<div><p>Quantitative real time reverse transcription polymerase chain reaction has been applied in a vast range of studies of gene expression analysis. However, real-time PCR data must be normalized with one or more reference genes. In this study, eleven putative consistently expressed genes (<i>ACT</i>, <i>TUA</i>, <i>TUB</i>, <i>CYP</i>, <i>DNAj</i>, <i>ELFA</i>, <i>F-box27</i>, <i>RPL12</i>, <i>GAPDH</i>, <i>UBC</i> and <i>UBQ</i>) in nine Siberian Apricot Germplasms (including much variability) were evaluated for their potential as references for the normalization of gene expression by NormFinder and geNorm programs. From our studies, <i>ACT</i>, <i>UBC</i>, <i>CYP</i>, <i>UBQ</i> and <i>RPL12</i> as suitable for normalization were identified by geNorm, while <i>UBC</i> and <i>CYP</i> as the best pair by NormFinder. Moreover, <i>UBC</i> was selected as the most stably expressed gene by both algorithms in different Siberian Apricot seed samples. We also detected that a set of three genes (<i>ACT</i>, <i>CYP</i> and <i>UBC</i>) by geNorm as control for normalization could lead to accurate results. Furthermore, the expression levels of oleosin gene were analyzed to validate the suitability of the selected reference genes. These obtained experimental results could make an important contribution to normalize real-time PCR data for gene expression analysis in Siberian Apricot Germplasm.</p></div

Performance of the amplification primers.

<p>Amplicons obtained by real-time PCR using cDNA (up) and gDNA (down) as template and electrophoresis using agarose gel (1.5%). The amplification primers from left to right are <i>ACT</i>, <i>TUA</i>, <i>TUB</i>, <i>CYP</i>, <i>DNAj</i>, <i>ELFA</i>, <i>F-box27</i>, <i>RPL12</i>, <i>GAPDH</i>, <i>UBC</i> and <i>UBQ</i>.</p

The data of material location, meteorological data and edaphic condition.

<p><b>*</b>All of the trees are full bearing period.</p

Description of Siberian Apricot candidate reference genes.

a<p>A<i>CT</i>, <i>TUA</i>, <i>TUB</i>, <i>CYP</i>, <i>DNAj</i>, <i>ELFA</i> and <i>UBQ</i> were ESTs based on the other species reference gene sequence determined via BLASTN.</p>b<p>The prediction of exon, the previous digits indicated the site of primer forward and the back correspond to primer reverse. N/F meaning no intron or limited ESTs could not conjecture the intron.</p

geNorm analysis of candidate reference genes in Siberian Apricot Germplasms.

<p>A: all reference genes. B: <i>TUB</i> and <i>UBQ</i> excluded from analysis. C: <i>TUB</i> excluded from analysis. D: <i>UBQ</i> excluded from analysis.</p