Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties.

Qionghou Li,Xin Qiao,Yuxin Zhang,Luting Jia,Shaoling Zhang

doi:10.3390/ijms22179622

Qionghou Li, Xin Qiao + Show 3 more

Open Access

https://doi.org/10.3390/ijms22179622

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Abstract

Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears.

Highlights

Fruit acidity is an essential component of the organoleptic quality of fruits
Several enzymes are involved in the tricarboxylic acid (TCA) cycle, including phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), NADP-malic enzyme (NADP-ME), aconitase (ACO), NAD-dependent isocitrate dehydrogenase (NAD-IDH), and succinate dehydrogenase (SDH), among others
Through quantitative trait locus (QTL) mapping for fruit acidity, some candidate genes that encode organic acid metabolism- and proton transport–related genes were identified in Cucumis melo [15]

Summary

Introduction

Fruit acidity is an essential component of the organoleptic quality of fruits. In general, malic acid (MA) is the predominant organic acid in pear fruit, followed by citric acid (CA) and oxalic acid (OA) [1]. In apple (Malus domestica), three genes encoding NAD-dependent malate dehydrogenase (cyMDH), phosphoenolpyruvate carboxylase (PEPC), and cytosolic NADP–dependent malic enzyme (ME) were first cloned and their roles in malate accumulation were verified [4,5]. The PH, ALMT, ALMT-like, PH-like, and V-type ATPase (V-ATPase) genes contribute to organic acid accumulation in orange (Citrus sinensis), apple and pear [11,12,13]. Bulked segregant analysis (BSA) and quantitative trait locus (QTL) analyses were used to map the genes associated with fruit acidity. Through QTL mapping for fruit acidity, some candidate genes that encode organic acid metabolism- and proton transport–related genes were identified in Cucumis melo [15]. Compared with BSA or QTL mapping, transcriptome sequencing can provide candidate gene information for the identification of target traits at a lower cost. With the rapid development of clustering algorithms, RNA-seq data-based gene co-expression network analysis has become an effective way to investigate agronomic trait-related genes and their regulatory networks [17,18,19,20]

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