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Article|14 Feb 2023|OPEN
Multiple-model GWAS identifies optimal allelic combinations of quantitative trait loci for malic acid in tomato
Wenxian Gai1 , Fan Yang3 , Liangdan Yuan1 , Saeed ul Haq3,4 , Yaru Wang1 , Ying Wang1 , Lele Shang1 , Fangman Li1 , Pingfei Ge1 , Haiqiang Dong1 , Jinbao Tao1 , Fei Wang1 and Xingyu Zhang1 , Yuyang Zhang,1,2 ,
1National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
2Hubei Hongshan Laboratory, Wuhan 430070, China
3College of Horticulture, Northwest A&F University, Yangling 712100, China
4Department of Horticulture, The University of Agriculture Peshawar, Peshawar 25130, Pakistan
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad021 (2023)
Views: 281

Received: 15 Oct 2022
Accepted: 10 Feb 2023
Published online: 14 Feb 2023


Malic acid (MA) is an important flavor acid in fruits and acts as a mediator in a series of metabolic pathways. It is important to understand the factors affecting MA metabolism for fruit flavor improvement and to understand MA-mediated biological processes. However, the metabolic accumulation of MA is controlled by complex heredity and environmental factors, making it difficult to predict and regulate the metabolism of MA. In this study, we carried out a genome-wide association study (GWAS) on MA using eight milestone models with two-environment repeats. A series of associated SNP variations were identified from the GWAS, and 15 high-confidence annotated genes were further predicted based on linkage disequilibrium and lead SNPs. The transcriptome data of candidate genes were explored within different tomato organs as well as various fruit tissues, and suggested specific expression patterns in fruit pericarp. Based on the genetic parameters of population differentiation and SNP distribution, tomato MA content has been more influenced by domestication sweeps and less affected by improvement sweeps in the long-term history of tomato breeding. In addition, genotype × environment interaction might contribute to the difference in domestication phenotypic data under different environments. This study provides new genetic insights into how tomato changed its MA content during breeding and makes available function-based markers for breeding by marker-assisted selection.