Integrative transcriptome and proteome analyses provide new insights into different stages of Akebia trifoliata fruit cracking during ripening

Abstract

Background: Akebia trifoliata (Thunb.) Koidz may have applications as a new potential source of biofuels owing to its high seed count, seed oil content, and in-field yields. However, the pericarp of A. trifoliata cracks longitudinally during fruit ripening, which increases the incidence of pests and diseases and can lead to fruit decay and deterioration, resulting in significant losses in yield. Few studies have evaluated the mechanisms underlying A. trifoliata fruit cracking. Results: In this study, by observing the cell wall structure of the pericarp, we found that the cell wall became thinner and looser and showed substantial breakdown in the pericarp of cracking fruit compared with that in non-cracking fruit. Moreover, integrative analyses of transcriptome and proteome profiles at different stages of fruit ripening demonstrated changes in the expression of various genes and proteins after cracking. Furthermore, the mRNA levels of 20 differentially expressed genes were analyzed, and parallel reaction monitoring analysis of 20 differentially expressed proteins involved in cell wall metabolism was conducted. Among the molecular targets, pectate lyases and pectinesterase, which are involved in pentose and glucuronate interconversion, and β-galactosidase 2, which is involved in galactose metabolism, were significantly upregulated in cracking fruits than in non-cracking fruits. This suggested that they might play crucial roles in A. trifoliata fruit cracking. Conclusions: Our findings provided new insights into potential genes influencing the fruit cracking trait in A. trifoliata and established a basis for further research on the breeding of cracking-resistant varieties to increase seed yields for biorefineries.

Comparative Analysis of Akebia trifoliata Fruit Softening at Different Flesh Ripening Stages Using Tandem Mass Tag Technology

“…Fruit ripening leads to the development of soft and edible fruit, which is one of the most important changes that determine fruit quality and improve palatability ( 25 ). However, only two recent study has reported the use of transcriptome sequencing for A. trifoliata fruit ( 14 , 17 ), and the limited genetic research has impeded an understanding of the genetic basis for its postharvest quality control, consumer acceptance, and breeding for cultivar improvement. Proteomic-based technologies have been extensively applied to analyze many aspects of fruit development; large-scale protein profiling and proteomic analysis provide more direct information on fruit softening at the protein level ( 9 , 26 , 27 ).…”

“…8” fruit at different development stages (UR, HR, and FR) were analyzed using RT-qPCR to evaluate the expression profiles of selected DAPs. Total RNA was extracted according to the method previously described by Niu et al ( 14 ), and the cDNA synthesis was performed with the Hiscript qRT SuperMix (Vazyme, Biotech). The primers of an internal control gene ( EF- α) and candidate genes were designed with Primer 5.0 ( Supplementary Table 1 ), and the reaction was carried out using SYBR Green PCR master mix (Aidlab Biotechnologies, Co., Ltd) in a Bio-Rad CFX96 PCR system (Bio-Rad, Richmond, CA, USA).…”

“…The average temperature is 26 • C/17 • C, maximum 29 • C/18 • C and minimum 19 • C/16 • C in early October and an average rainfall of 72.3 mm in October. The pericarp of A. trifoliata cracks longitudinally along the ventral suture with fruit ripening (14). The fruit is hard, the flesh is white, and the pericarp ventral suture is closed when the fruit is immature (UR, Figure 1A).…”

“…Various proteins/genes involved in cell wall modifications in fruit softening during ripening have been studied in several fruit, such as the banana ( 9 ), apple ( 11 ), and strawberry ( 12 ). For example, polygalacturonase (PG), pectin esterase (PE), pectin methylesterase, and pectate lyase (PL) are considered the main hydrolases involved in pectin solubilization and depolymerization during fruit ripening ( 13 , 14 ). Xyloglucan endo-transglucosylase/hydrolase (XTH) and expansin (EXP) are the main hydrolases involved in remodeling or modification of hemicellulose ( 15 ).…”

“…However, the process of fruit ripening is a complicated and the mechanism underlying this process in fleshy fruit remains unclear, which has hindered an understanding of fruit softening and the increase in the postharvest shelf life of the fruit. Moreover, only the expression patterns of several genes from transcriptome data have been investigated during fruit ripening ( 14 , 17 ). The lack of genetic data has greatly limited extensive and intensive research on this fruit crop.…”