Identification of early fruit development reference genes in plum.

Area of Science:

• Plant molecular biology
• Genomics
• Fruit development research

Background:

• Accurate gene expression normalization is crucial for understanding fruit development.
• Previously identified reference genes in Prunus showed high variability in endocarp tissue.
• RNAseq data mining offers a potential source for novel reference gene discovery.

Purpose of the Study:

• Identify and validate stable reference genes for early fruit and stone development in plum (Prunus domestica).
• Evaluate the expression stability of candidate genes across different fruit tissues and developmental stages.
• Assess the universality of potential reference genes in other Rosaceae species like peach and apple.

Main Methods:

• Bioinformatic analysis of existing plum RNAseq data to identify candidate reference genes with low expression variation.
• Experimental validation of nine candidate genes across plum fruit developmental stages using quantitative PCR.
• Utilized RefFinder to determine the expression stability of candidate genes.
• Cross-species validation of top candidate genes using RNAseq data from peach and apple.

Main Results:

• Expression of previously identified reference genes varied significantly in plum endocarp tissue.
• Nine candidate genes with less than 2-fold variation were selected for validation.
• Imidazole glycerol-phosphate dehydratase (IPGD), histone acetyltransferase (HAM1), and sorting nexin 1 (SNX1) were identified as the most stable plum reference genes.
• Sorting nexin 1 (SNX1) demonstrated universal expression patterns across plum, peach, and apple at various developmental stages and tissue types.

Conclusions:

• Existing RNAseq data can effectively identify stable reference genes for specific experimental contexts.
• IPGD, HAM1, and SNX1 are suitable reference genes for plum fruit development studies.
• SNX1 is a highly promising universal reference gene for gene expression studies within the Rosaceae family.