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Comparative transcript profiling reveals the mechanism of female sterility associated with seedless Ponkan mandarin (Citrus reticulata Blanco).

Seedlessness is a highly desirable trait in citrus varieties. Sterility is the key determination for seedlessness formation. However, the molecular basis for female sterility in seedless mandarin remains unclear. Thus, a seedless Ponkan mandarin (Citrus reticulata Blanco 'Lipeng No.2'), considered the bud mutation of normal seedy Ponkan, was collected to identify candidate genes involved in seedless variation. Suppression subtractive hybridization (SSH) screened 1091 uniESTs related to seedy and seedless Ponkan (727 singlets and 364 contigs), which mainly governed catalytic activity, transferase activity, and oxygen binding. By using RNA-Seq technology, 106 differentially expressed genes (DEGs) were captured, of which 74 were up-regulated and 32 were down-regulated. Gene Ontology and pathway analysis showed that six DEGs were enriched in the biosynthesis of secondary metabolite, whereas five DEGs were enriched in the signaling of plant hormones. The combined results of SSH and RNA-Seq indicated the importance of amino acid metabolism in seedless Ponkan. Our findings revealed that the mechanism of seedless Ponkan generation may be related to gene regulation, signal cascade, and hormone levels. This study provided a solid foundation for functional gene identification in seedless Ponkan and a good reference for relevant research on molecular mechanisms of female sterility in Ponkan mandarin.