There were 567 methylated genome loci used for mapping QTSs of two tobacco leaf traits (chromium content and total sugar content)

with 60 phenotypes obtained from harvested leaves at three positions and different time points for three varieties grown in two locations. The QTS module in QTXNetwork was applied for mapping significant QTSs by setting two varieties and three locations selleck inhibitor as six treatments for detecting treatment-specific genetic effects. The QTT/P/M module in QTXNetwork was applied to screen for significant RNA transcripts and to predict their genetic effects. A total of 2894 mRNA transcripts and 802 miRNA transcripts were used for QTT mapping. Similarly, QTP Small molecule library and QTM were applied to search significant proteins and metabolites. The concentration of 14 amino acids was measured for QTP mapping and 35 metabolites for QTM mapping accordingly. For QTS, QTP and QTM search, a total of 60 observations in six treatments were collected. The raw data of expression of RNAs, proteins and metabolites were transformed by standardization (y − μ) / σ for association

mapping. There were a total of nine QTX loci (three for QTSs, four for QTTs, one for QTP, and one for QTM) that were detected as controlling chromium content in tobacco leaves (Table 1, Fig. 1 and Fig. 2). Three treatment-specific epistatic Casein kinase 1 effects were identified between two QTSs with no individual effects. Large treatment-specific additive effects were found for QTSs, QTTs and QTP. In the

case of QTS, there were three methylated SNP loci (DArT markers) detected with significant additive (q), additive × treatment interaction (qe), and epistasis × treatment interaction effect (qqe) ( Table 1). Phm1376 had a very significant additive effect (− log10P = 10.05) and high heritability (hq2 = 20.29%). The total additive × environment interaction had higher heritability (hqqe2 = 30.09%). For the three varieties tested, treatment interaction effects of Phm1376 were negative in Guiding, but positive in Xingyi. It was suggested that Phm1376 could decrease chromium content in Guiding for all three varieties. Phm1053 and Phm1471 had epistasis × treatment interaction in the Xingyi with negative qqe effect only for cultivar Zunyan 6. It was indicated that the loci could have opposite impact on chromium content in tobacco leaves of a set of cultivars in different environments or various cultivars in the same environment.