scholarly journals Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria×ananassa)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4976 ◽  
Author(s):  
Panpan Hu ◽  
Gang Li ◽  
Xia Zhao ◽  
Fengli Zhao ◽  
Liangjie Li ◽  
...  

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of fiveubiquitin-conjugating enzymesand 10MADS-box transcription factorswere differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics inFragaria × ananassa.

2018 ◽  
Author(s):  
Panpan Hu ◽  
Gang Li ◽  
Xia Zhao ◽  
Fengli Zhao ◽  
Liangjie Li ◽  
...  

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. Five ubiquitin-conjugating enzymes and ten MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.


2018 ◽  
Author(s):  
Panpan Hu ◽  
Gang Li ◽  
Xia Zhao ◽  
Fengli Zhao ◽  
Liangjie Li ◽  
...  

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. Five ubiquitin-conjugating enzymes and ten MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.


2021 ◽  
pp. 1-15
Author(s):  
Yaqiong Wu ◽  
Chunhong Zhang ◽  
Wenlong Wu ◽  
Weilin Li ◽  
Lianfei Lyu

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.


Plant Science ◽  
2004 ◽  
Vol 166 (6) ◽  
pp. 1451-1459 ◽  
Author(s):  
Badamaranahalli H. Jagadeesh ◽  
Tyakal N. Prabha ◽  
Krishnapura Srinivasan

2021 ◽  
Author(s):  
Julie Graham ◽  
Kay Smith ◽  
Katrin MacKenzie ◽  
Linda Milne ◽  
Nikki Jennings ◽  
...  

Abstract Background The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. This work aimed to expand our knowledge of the genetic control of the ripening process in raspberry by examining a biennial x primocane F1 population to determine if the progeny exhibited both primocane and biennial flowering modes, which if any was dominant, and to identify QTL and genome locations associated with fruit development to understand how developmental control in this population differs from a biennial x biennial F1 population previously studied. Results The progeny from this biennial x primocane population exhibited primocane fruiting completing their lifecycle in a single season and also fruiting on second-year wood not removed in season one. QTL associated with rate of fruit development were identified on both primocane and fruiting canes with both parents impacting. Conclusions Novel QTL associated with the developmental process of primocane fruiting were identified. These in the main, differed from developmental QTL for similar developmental stages on fruiting canes (second year canes) with only one significant overlap on linkage group 6. In general, the process of development on fruiting canes overall differed from that in a biennial x biennial population, with the differences being greatest on linkage groups 3 and 6 suggesting control of development differs in the different fruiting types. Further understanding will be achieved by examining genome regions linked to QTL to allow breeding to meet climate requirements for yield stability.


PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e113211 ◽  
Author(s):  
Xinhong Luan ◽  
Dawei Liu ◽  
Zhongzan Cao ◽  
Lina Luo ◽  
Mei Liu ◽  
...  

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