Uncovering co-expression gene network modules regulating fruit acidity in diverse apples

Area of Science:

• Plant genetics and molecular biology
• Fruit quality and biochemistry
• Agricultural science

Background:

• Fruit acidity, primarily determined by malic acid, is a key factor in apple quality.
• The Malic acid (Ma) locus, with Ma1 as a strong candidate gene, largely controls this trait.
• This study investigates the gene network governing fruit acidity, with Ma1 as a central component.

Purpose of the Study:

• To identify the gene network controlling fruit acidity in apples.
• To elucidate the mechanisms through which this network operates.
• To understand the role of the Ma1 gene within this network.

Main Methods:

• RNA sequencing (RNA-seq) of apple fruit transcriptomes from accessions with contrasting acidity.
• Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene modules correlated with malate content.
• Lemon-Tree algorithms to identify potential regulator genes.

Main Results:

• 1301 fruit acidity-associated genes were identified, including 18 most significant acidity genes (MSAGs).
• A WGCNA module (Turquoise) containing Ma1 showed the highest correlation (0.79) with malate content, comprising 336 genes.
• 12 intramodular hub genes and 12 regulator genes were identified, some overlapping with MSAGs and hub genes, including LLR receptor kinase and EIN3-like transcription factor.

Conclusions:

• The study identified key genes (MSAGs, hub genes, regulators) and processes (photosynthesis) within the Ma1-containing WGCNA module.
• This Ma1-mediated gene network provides crucial insights into the genetic control of acidity in mature apple fruit.
• The findings contribute to understanding the molecular basis of apple fruit quality.