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Background  Our previous study finds that male sterility in  Salvia miltiorrhiza  could result in stunted growth and reduced biomass, but their molecular mechanisms have not yet been revealed. In this article, we investigate the underlying mechanism of male sterility and its impact on plant growth and metabolic yield by using physiological analysis and mRNA sequencing (RNA-Seq).    Results  In this study, transcriptomic and physiological analysis were performed to identify the mechanism of male sterility in mutants and its impact on plant growth and metabolic yield. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, it is found that the pathways are mainly enriched in processes including organ development, primary metabolic process and secondary metabolic process. Physiological analysis show that the chloroplast structure of male sterile mutants of  S. miltiorrhiza  is abnormally developed, which could result in decrease in leaf gas exchange ( A ,  E  and  g  s ), chlorophyll fluorescence (F v , F m  and F v /F m ), and the chlorophyll content. Expression level of 7 differentially expressed genes involved in photosynthesis-related pathways is downregulated in male sterile lines of  S. miltiorrhiza , which could explain the corresponding phenotypic changes in chlorophyll fluorescence, chlorophyll content and leaf gas exchange. Transcriptomic analysis establishes the role of disproportionating enzyme 1 ( DPE1 ) as catalyzing the degradation of starch, and the role of sucrose synthase 3 ( SUS3 ) and cytosolic invertase 2 ( CINV2 ) as catalyzing the degradation of sucrose in the  S. miltiorrhiza  mutants. The results also confirm that phenylalanine ammonialyase ( PAL)  is involved in the biosynthesis of rosmarinic acid and salvianolic acid B, and flavone synthase ( FLS)  is an important enzyme catalyzing steps of flavonoid biosynthesis.    Conclusions  Our results from the physiological and transcriptome analysis reveal underlying mechanism of plant growth and metabolic yield in male sterile mutants, and provide insight into the crop yield of  S. miltiorrhiza .

bmc genomics

Physiological and transcriptome analysis reveal molecular mechanism in Salvia miltiorrhiza leaves of near-isogenic male fertile lines and male sterile lines