Transcriptomic analysis of flowers in an apple petalless mutant and its parents

Apple petals are required for insect pollination, and the number of petals is an important commercial trait for ornamental apples. Owing to the relatively small number of apple mutants, the molecular mechanism underlying flower organ development in apple remains unclear. A petalless apple mutant was discovered from hybrid seedlings of ‘Wanbai’ crabapple × ‘Huayue’. Transcriptome analysis of the petalless mutant and its two parents was conducted. A total of 5,118 differentially expressed genes (DEGs) were identified between flowers from ‘Wanbai’ crabapple and the petalless mutant (WBvsH), whereas 6,886 DEGs were identified between flowers from ‘Huayue’ and the petalless mutant (HYvsH). A total of 1,718 and 1,640 DEGs were co-upregulated and co-downregulated respectively, in the WBvsH and HYvsH comparison groups. KEGG analysis revealed that these co-upregulated DEGs were significantly enriched in plant hormone signal transduction, circadian rhythm-plant, and photosynthesis pathways, and these co-downregulated DEGs were significantly enriched in the biosynthesis of amino acids, carbon metabolism, and glycolysis/gluconeogenesis pathways. Among these coregulated DEGs, compared with those in WB and HY, the expression of four organ identity class A genes, MdTOEL1 , MdTOEL2 , MdFUL2 , and MdFUL1 , and one organ identity class C gene, MdSTKL , were upregulated in H; the expression of three organ identity class B genes, MdAP3L1 , MdAP3L2 , and MdAP3L3 , were downregulated in H; and the expression of the organ identity class E gene MdSEPL3 was upregulated, but the expression of MdSEPL1 and MdSEPL2 were downregulated. Yeast two-hybrid and split-luciferase complementation assays revealed that the class E protein MdSEPL1 promoted interactions between any two class B proteins; however, no interactions were detected between B proteins. This study provides comprehensive analysis of the gene expression in flowers of the two parents and the petalless mutant offspring to understand the mechanism of the formation of the petalless phenotype. In apple mutant, genes involved in auxin signaling pathway were activated and genes involved in primary metabolism pathways were inhibited. 3 floral organ identity-related AP3 orthologues were downregulated in apple mutant, suggesting that these genes may be candidate genes responsible for petal phenotype.