Comparative Analysis of the Transcriptomes of Persisting and Abscised Fruitlets: Insights into Plant Hormone and Carbohydrate Metabolism Regulated Self-Thinning of Pecan Fruitlets during the Early Stage

Abstract

Pecan is one of the most popular nut species in the world. The fruit drop rate of the pecan ‘Pawnee’ is more than 57%, with four fruit drop stages, which is very serious. In this study, we conducted transcriptomic profiling of persisting and abscised fruitlets in early fruit development by RNA-seq. A total of 11,976 differentially expressed genes (DEGs) were identified, 3012 upregulated and 8964 downregulated, in a comparison of abscised vs. persisting fruitlets at 35 days after anthesis (DAA). Our transcriptomic data suggest that gene subsets encoding elements involving the biosynthesis, metabolism, perception, signal transduction, and crosstalk of the plant hormones abscisic acid (ABA), auxin, cytokinin, ethylene, and gibberellin (GA) and plant growth regulators jasmonates, salicylic acid, and brassinosteroids were differentially expressed. In addition, the majority of transcriptionally activated genes involved in hormone signaling (except for ethylene and salicylic acid signaling) were downregulated in abscised fruitlets. The differential expression of transcripts coding for enzymes involved in sucrose, glucose, trehalose, starch, galactose, and galactinol metabolism shows that sucrose, galactinol, and glucose synthesis and starch content were reduced as starch biosynthesis was blocked, and retrogradation and degradation intensified. These results suggest that the abscised pecan fruitlets stopped growing and developing for some time before dropping, further indicating that their sugar supply was reduced or stopped. The transcriptome characterization described in this paper contributes to unravelling the molecular mechanisms and pathways involved in the physiological abscission of pecan fruits.

Transcriptome Analysis Reveals a Comprehensive Virus Resistance Response Mechanism in Pecan Infected by a Novel Badnavirus Pecan Virus

“…Total RNA extraction, mRNA enrichment, and cDNA library conduction construction were performed according to the report of Zhang et al [ 94 ]. Briefly, Total RNA was extracted from the leaves of infected with PMV and healthy plants using a Trizol reagent kit (Invitrogen, Carlsbad, CA, USA).…”

“…Ten key DEGs were selected for qRT-PCR analysis to validate the Illumina RNA-seq results. RNA was isolated from leaves according to the report of Zhang et al [ 94 ]. First-strand cDNA synthesis was performed using the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Dalian, China) according to the manufacturer’s protocol.…”