The core regulatory network of the abscisic acid pathway in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress

Abstract

BackgroundAbscisic acid (ABA) signaling plays a crucial role in developmental and environmental adaptation processes of plants. However, the PYL-PP2C-SnRK2 families that function as the core components of ABA signaling are not well understood in banana.ResultsIn the present study, 24 PYL, 87 PP2C, and 11 SnRK2 genes were identified from banana, which was further supported by evolutionary relationships, conserved motif and gene structure analyses. The comprehensive transcriptomic analyses showed that banana PYL-PP2C-SnRK2 genes are involved in tissue development, fruit development and ripening, and response to abiotic stress in two cultivated varieties. Moreover, comparative expression analyses of PYL-PP2C-SnRK2 genes between BaXi Jiao (BX) and Fen Jiao (FJ) revealed that PYL-PP2C-SnRK2-mediated ABA signaling might positively regulate banana fruit ripening and tolerance to cold, salt, and osmotic stresses. Finally, interaction networks and co-expression assays demonstrated that the core components of ABA signaling were more active in FJ than in BX in response to abiotic stress, further supporting the crucial role of the genes in tolerance to abiotic stress in banana.ConclusionsThis study provides new insights into the complicated transcriptional control of PYL-PP2C-SnRK2 genes, improves the understanding of PYL-PP2C-SnRK2-mediated ABA signaling in the regulation of fruit development, ripening, and response to abiotic stress, and identifies some candidate genes for genetic improvement of banana.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-1093-4) contains supplementary material, which is available to authorized users.

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

“…The suppressed expression of SlMBP8 , a MADS-box gene, promotes carotenoid and ETH biosynthesis and induces the expressions of cell wall metabolism genes, which ultimately accelerate tomato fruit ripening ( Yin et al, 2017 ). The MADS-box genes of MaMADS24 and MaMADS49 regulate the fruit development and ripening process by interacting with MaMADS proteins themselves and ETH signal transduction, biosynthesis-related proteins, starch biosynthesis proteins, and metabolism-related proteins ( Liu et al, 2013 ; Hu et al, 2017 ). The PrupeSEP1 gene, a subfamily of MADS-box transcription factors, regulates fruit ripening and softening by exhibiting similar expression patterns of cell wall modification-related genes and N-glycan processing genes in melting flesh peach ( Li et al, 2017a ).…”

“…The functions of the ubiquitin mediated proteolysis pathway in the regulation of fruit ripening have been studied in banana, tomato, papaya, and barbarum, and these studies confirm the regulatory role of the ubiquitin proteasome in the fruit ripening process ( Liu et al, 2013 ; Wang et al, 2014 ; Bi et al, 2015 ; Zeng et al, 2015 ). Research on the regulatory mechanism of fruit ripening indicates that MADS-box transcription factors have a pivotal effect on fruit ripening by regulating carotenoid synthesis, the ETH signaling pathway, cell wall metabolism, flavonoid and lignin biosynthesis, and cuticle development in apple, banana, tomato, and peach ( Youssef et al, 2012 ; Ireland et al, 2013 ; Liu et al, 2013 ; Feng et al, 2016 ; Garceau, Batson & Pan, 2017 ; Yin et al, 2017 ; Hu et al, 2017 ).…”

Early Cold-Induced Peroxidases and Aquaporins Are Associated With High Cold Tolerance in Dajiao (Musa spp. ‘Dajiao’)

“…In the past decade, a few genetic studies mainly on MAPK cascades-ICE1-CBF pathway and ABA signaling have been reported. Recently, comprehensive transcriptomic analyses have shown that banana PYL-PP2C-SnRK2 genes, the core components of ABA signaling, are involved in response to cold stress ( Hu et al, 2017b ) and MaMEKK1-MaMKK2 genes are activated by cold stress in cold-resistant banana ( Wang et al, 2017 ). The rapid activation and selective induction of ICE1 and MYBS3 cold tolerance pathways in Dajiao may be one of the main reasons that Dajiao has higher cold resistance than Cavendish ( Yang et al, 2015 ).…”

Genome-wide analysis of PYL-PP2C-SnRK2s family in Camellia sinensis

“…Highthroughput next generation sequencing showed that PYL, PP2C, and SRK2E respond to drought stress in Gossypium spp [53]. In banana, the PYL-PP2C-SnRK2 gene family regulated its tolerance to abiotic stress, such as salt and drought stress conditions [54]. In this work, transcriptome data from C. sinensis treated with PEG and NaCl were obtained from the NCBI-SRA database and analyzed.…”