Fig. 6: SVs associated with gene expression and functional impact on fruit ripening and softening of European pears.
a, Manhattan plot displaying the SVs at exon or promoter regions significantly associated with gene expression. Sugar- and acid-related genes were marked in red and ethylene biosynthesis genes were marked in purple. b, The expression of PyACS1 in Asian (n = 62), European (n = 38) and interspecific hybrid (n = 10) pears. The ‘n’ means the number of accessions (center line as median, box limits as first and third quartiles and whiskers as 1.5× the IQR). c, PyACS1 expression pattern of DS and MRB at eight fruit stages. d, Phenotype of WT tomato fruit and tomato transformants overexpressing PyACS1 (OE-PyACS1). e–g, Breaker stage (nWT = 10, nOE-PyACS1 = 10), ethylene production (nWT = 8, nOE-PyACS1 = 12) and firmness (nWT = 12, nOE-PyACS1 = 12) in the WT and OE-PyACS1 tomato fruit (center line as median, box limits as first and third quartiles and whiskers as 1.5× the IQR). The nWT and nOE-PyACS1 refer to the numbers of fruit samples used for WT and OE-PyACS1. h, A 286-bp insertion sequence identified at the promoter region of PyACS1 in MRB. i, PCR-based screen showing the absence (right) or presence (left) of the insertion sequence in the upstream of PyACS1 in European (I–V represent ‘Max Red Bartlett’, ‘Red comice’, ‘Spalding’, ‘Charneus’ and ‘Anjou’, respectively) and Asian (VI–X represent ‘Dangshansuli’, ‘Cuiguan’, ‘Cuiyu’, ‘Yunhong No. 1’ and ‘Yali’, respectively) pears. j, The insertion appearance frequency in Asian, European and interspecific hybrid pears. k, TE assays showing significant differences in promoter activities for PyACS1proMRB and PyACS1proDS. The data are presented as mean ± s.e.m. l, Relative activity levels of luciferase of three truncated promoters (830 bp, 1,221 bp and 2,000 bp) of PyACS1proMRB. The data are presented as mean ± s.e.m. m, EMSA showing that PybHLH94 binds directly to the G-box and E-box within the insertion sequence at the promoter region of PyACS1. Hot-P and Mut-P represent biotin-labeled WT and mutation probes, respectively; competitor-P represents the unlabeled WT sequence. In b, e–g and k–l, P values were computed from two-sided Student’s t-tests. The numbers of biologically independent samples used in k–l is 3. The full scans of all the gels are included in Source data.
