In order to screen out the most stable reference genes in tomatoes under powdery mildew (PM) stress and study the expression of related genes in the interaction between tomato and PM more accurately, this study will provide a calibration basis for the expression of related functional genes. In this study, the expression stabilities of eight tomato candidate reference genes of EF1α, L33, Act, Ubi, GAPDH, UK, CAC and TIP41 in susceptible tomato and resistant tomatoes under PM stress were ranked using four different computation programs, including geNorm, Normfinder, BestKeeper and the comparative ∆CT method. Then RefFinder was used to analyze the ranking results of four kinds of software comprehensively. Finally, the selected reference genes were validated by the target gene SlMLO1. The results of geNorm showed that the normalization of qRT-PCR using two reference genes could meet the requirements. The comprehensive analysis of RefFinder showed that the most stable reference genes were Act and EF1α for both tomato varieties. The combination of Act and GAPDH was most stable in susceptible tomato ‘MM’. The combination of Act and EF1α was most stable in resistant tomato ‘62579′. Generally, the Act was the most stable reference gene in the two tomato varieties under PM stress. This study will lay a foundation for the related functional gene expression research in tomatoes under PM stress.

In order to compare and analyze the chloroplast (cp) genomes of tomato germplasms and understand their phylogenetic relationships, the cp genomes of 29 tomato germplasms were sequenced and analyzed in this study. The results showed highly conserved characteristics in structure, number of gene and intron, inverted repeat regions, and repeat sequences among the 29 cp genomes. Moreover, single-nucleotide polymorphism (SNP) loci with high polymorphism located at 17 fragments were selected as candidate SNP markers for future studies. In the phylogenetic tree, the cp genomes of tomatoes were clustered into two major clades, and the genetic relationship between S. pimpinellifolium and S. lycopersicum was very close. In addition, only rps15 showed the highest average KA/KS ratio in the analysis of adaptive evolution, which was strongly positively selected. It may be very important for the study of adaptive evolution and breeding of tomato. In general, this study provides valuable information for further study of phylogenetic relationships, evolution, germplasm identification, and molecular marker-assisted selection breeding of tomato.

Powdery mildew is a serious problem in tomato production; therefore, the PM-resistant tomato inbred line, ‘63187’, and the susceptible tomato variety, ‘Moneymaker (MM)’, were used as experimental materials for the combined analysis of transcriptome and widely targeted metabolome on tomato leaves at 0 h post inoculation (hpi), 12 hpi, and 48 hpi. The results indicated that 276 genes were expressed in all treatments, and the K-means cluster analysis showed that these genes were divided into eight classes in ‘63187’ and ten classes in ‘MM’. KEGG enrichment showed that amino acid metabolism, signal transduction, energy metabolism, and other secondary metabolites biosynthesis pathways were significantly enriched. Interestingly, the analysis of WRKY family transcription factors (TFs) showed that the expression of four TFs in ‘63187’ increased with no obvious change in ‘MM’; and the expression of one TF in ‘MM’ increased with no obvious change in ‘63187’. The combined analysis revealed that both phenylpropanoid biosynthesis and flavonoid biosynthesis pathways were enriched in ‘63187’ and ‘MM’. In ‘63187’, six metabolites involved in this pathway were downregulated, and four genes were highly expressed, while in ‘MM’, three metabolites were upregulated, four metabolites were downregulated, and ten genes were highly expressed. These metabolites and genes might be candidates for PM resistance or susceptibility in subsequent studies. These results provide favorable molecular information for the study of the different resistances of tomatoes to PM, and they provide a basis for the breeding of tomato varieties resistant to PM.