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Background  Mature fruit cracking during the normal season in African Pride (AP) atemoya is a major problem in postharvest storage. Our current understanding of the molecular mechanism underlying fruit cracking is limited. The aim of this study was to unravel the role starch degradation and cell wall polysaccharide metabolism in fruit ripening and cracking after harvest through transcriptome analysis.    Results  Transcriptome analysis of AP atemoya pericarp from cracking fruits of ethylene treatments and controls was performed. KEGG pathway analysis revealed that the starch and sucrose metabolism pathway was significantly enriched, and approximately 39 DEGs could be functionally annotated, which included starch, cellulose, pectin, and other sugar metabolism-related genes. Starch, protopectin, and soluble pectin contents among the different cracking stages after ethylene treatment and the controls were monitored. The results revealed that ethylene accelerated starch degradation, inhibited protopectin synthesis, and enhanced the soluble pectin content, compared to the control, which coincides with the phenotype of ethylene-induced fruit cracking. Key genes implicated in the starch, pectin, and cellulose degradation were further investigated using RT-qPCR analysis. The results revealed that alpha-amylase 1 ( AMY1 ), alpha-amylase 3 ( AMY3 ), beta-amylase 1 ( BAM1 ), beta-amylase 3 ( BAM3 ), beta-amylase 9 ( BAM9) , pullulanase ( PUL) , and glycogen debranching enzyme ( glgX ), were the major genes involved in starch degradation.  AMY1 ,  BAM3 ,  BAM9 ,  PUL , and  glgX  all were upregulated and had higher expression levels with ethylene treatment compared to the controls, suggesting that ethylene treatment may be responsible for accelerating starch degradation. The expression profile of alpha-1,4-galacturonosyltransferase ( GAUT ) and granule-bound starch synthase ( GBSS ) coincided with protopectin content changes and could involve protopectin synthesis. Pectinesterase ( PE ), polygalacturonase ( PG ), and pectate lyase ( PEL ) all involved in pectin degradation;  PE  was significantly upregulated by ethylene and was the key enzyme implicated pectin degradation.    Conclusion  Both KEGG pathway enrichment analysis of DEGs and material content analysis confirmed that starch decomposition into soluble sugars and cell wall polysaccharides metabolism are closely related to the ripening and cracking of AP atemoya. A link between gene up- or downregulation during different cracking stages of atemoya fruits and how their expression affects starch and pectin contents were established by RT-qPCR analysis.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1756-4) contains supplementary material, which is available to authorized users.

Transcriptome analysis of atemoya pericarp elucidates the role of polysaccharide metabolism in fruit ripening and cracking after harvest